From 04072faea7c2fe9fd241c6d4c5b85c764d46de75 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Mon, 18 Mar 2024 15:16:00 +0100
Subject: [PATCH 001/530] Generate reports per lane, group and rundir

---
 conf/modules.config       |  20 ++++++-
 main.nf                   |   5 +-
 workflows/seqinspector.nf | 120 ++++++++++++++++++++++++++++++++++----
 3 files changed, 133 insertions(+), 12 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index e3ea8fa6..296ca786 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -35,7 +35,25 @@ process {
         publishDir = [
             path: { "${params.outdir}/multiqc" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: {
+                filename -> 
+                    switch (filename) {
+                        case 'versions.yml':
+                            null
+                            break
+                        case ~/L\d+_multiqc_(report\.html|plots|data)/:
+                            "lanes/L${(filename =~ /L(\d+)_multiqc_(report\.html|plots|data)/)[0][1]}/${filename}"
+                            break
+                        case ~/G-.+_multiqc_(report\.html|plots|data)/:
+                            "groups/G-${(filename =~ /G-(.+)_multiqc_(report\.html|plots|data)/)[0][1]}/${filename}"
+                            break
+                        case ~/D-.+_multiqc_(report\.html|plots|data)/:
+                            "rundirs/D-${(filename =~ /D-(.+)_multiqc_(report\.html|plots|data)/)[0][1]}/${filename}"
+                            break
+                        default:
+                            filename
+                    }
+            }
         ]
     }
 
diff --git a/main.nf b/main.nf
index 1e9c2ede..58afd1fe 100644
--- a/main.nf
+++ b/main.nf
@@ -58,7 +58,10 @@ workflow NFCORE_SEQINSPECTOR {
     )
 
     emit:
-    multiqc_report = SEQINSPECTOR.out.multiqc_report // channel: /path/to/multiqc_report.html
+    global_report = SEQINSPECTOR.out.global_report // channel: /path/to/multiqc_report.html
+    lane_reports = SEQINSPECTOR.out.lane_reports // channel: /path/to/multiqc_report.html
+    group_report = SEQINSPECTOR.out.group_reports // channel: /path/to/multiqc_report.html
+    rundir_report = SEQINSPECTOR.out.rundir_reports // channel: /path/to/multiqc_report.html
 
 }
 /*
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 9ae3384b..b6fd3bc4 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -5,7 +5,10 @@
 */
 
 include { FASTQC                 } from '../modules/nf-core/fastqc/main'
-include { MULTIQC                } from '../modules/nf-core/multiqc/main'
+include { MULTIQC } from '../modules/nf-core/multiqc/main'
+include { MULTIQC as MULTIQC_PER_LANE } from '../modules/nf-core/multiqc/main'
+include { MULTIQC as MULTIQC_PER_GROUP } from '../modules/nf-core/multiqc/main'
+include { MULTIQC as MULTIQC_PER_RUNDIR } from '../modules/nf-core/multiqc/main'
 include { paramsSummaryMap       } from 'plugin/nf-validation'
 include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
@@ -26,6 +29,8 @@ workflow SEQINSPECTOR {
 
     ch_versions = Channel.empty()
     ch_multiqc_files = Channel.empty()
+    ch_multiqc_extra_files = Channel.empty()
+    ch_multiqc_reports = Channel.empty()
 
     //
     // MODULE: Run FastQC
@@ -33,7 +38,7 @@ workflow SEQINSPECTOR {
     FASTQC (
         ch_samplesheet
     )
-    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]})
+    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip)
     ch_versions = ch_versions.mix(FASTQC.out.versions.first())
 
     //
@@ -46,26 +51,121 @@ workflow SEQINSPECTOR {
     //
     // MODULE: MultiQC
     //
-    ch_multiqc_config                     = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-    ch_multiqc_custom_config              = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
+    ch_multiqc_config              = params.multiqc_config ? 
+        Channel.fromPath(params.multiqc_config, checkIfExists: true) :
+        Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
     ch_multiqc_logo                       = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
     summary_params                        = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
     ch_workflow_summary                   = Channel.value(paramsSummaryMultiqc(summary_params))
     ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
     ch_methods_description                = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
-    ch_multiqc_files                      = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
-    ch_multiqc_files                      = ch_multiqc_files.mix(ch_collated_versions)
-    ch_multiqc_files                      = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false))
+    ch_multiqc_extra_files                      = ch_multiqc_extra_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+    ch_multiqc_extra_files                      = ch_multiqc_extra_files.mix(ch_collated_versions)
+    ch_multiqc_extra_files                      = ch_multiqc_extra_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false))
 
     MULTIQC (
-        ch_multiqc_files.collect(),
+        ch_multiqc_files
+            .map { meta, file -> file }
+            .mix(ch_multiqc_extra_files)
+            .collect(),
         ch_multiqc_config.toList(),
-        ch_multiqc_custom_config.toList(),
+        Channel.empty().toList(),
+        ch_multiqc_logo.toList()
+    )
+
+    multiqc_extra_files = ch_multiqc_extra_files.toList()
+
+    // Generate reports by lane
+    lane_mqc_files = ch_multiqc_files
+        .map { meta, sample -> [ "L${meta.lane}", meta, sample ] }
+        .groupTuple()
+        .tap { mqc_by_lane }
+        .collectFile{
+            lane, meta, samples -> [
+                "${lane}_multiqc_extra_config.yml",
+                "output_fn_name: \"${lane}_multiqc_report.html\"\ndata_dir_name: \"${lane}_multiqc_data\"\nplots_dir_name: \"${lane}_multiqc_plots\""
+            ]
+        }
+        .map { file -> def fileparts = file.name.split("_")
+             [ fileparts[0], file ] 
+        }
+        .join(mqc_by_lane)
+        .multiMap { lane, config, meta , samples_per_lane ->
+            samples_per_lane: samples_per_lane
+            config: config
+        }
+
+    MULTIQC_PER_LANE(
+        lane_mqc_files.samples_per_lane
+            .map { samples -> samples + multiqc_extra_files.value },
+        ch_multiqc_config.toList(),
+        lane_mqc_files.config,
+        ch_multiqc_logo.toList()
+    )
+
+    // Generate reports by group
+    group_mqc_files = ch_multiqc_files
+        .filter { meta, sample -> meta.group }
+        .map { meta, sample -> [ "G-${meta.group}", meta, sample ] }
+        .groupTuple()
+        .tap { mqc_by_group }
+        .collectFile{
+            group, meta, samples -> [
+                "${group}_multiqc_extra_config.yml",
+                "output_fn_name: \"${group}_multiqc_report.html\"\ndata_dir_name: \"${group}_multiqc_data\"\nplots_dir_name: \"${group}_multiqc_plots\""
+            ]
+        }
+        .map { file -> def fileparts = file.name.split("_")
+             [ fileparts[0], file ] 
+        }
+        .join(mqc_by_group)
+        .multiMap { group, config, meta , samples_per_group ->
+            samples_per_group: samples_per_group
+            config: config
+        }
+
+    MULTIQC_PER_GROUP(
+        group_mqc_files.samples_per_group
+            .map { samples -> samples + multiqc_extra_files.value },
+        ch_multiqc_config.toList(),
+        group_mqc_files.config,
+        ch_multiqc_logo.toList()
+    )
+
+    // Generate reports by rundir
+    rundir_mqc_files = ch_multiqc_files
+        .filter { meta, sample -> meta.rundir }
+        .map { meta, sample -> [ "D-${meta.rundir.name}", meta, sample ] }
+        .groupTuple()
+        .tap { mqc_by_rundir }
+        .collectFile{
+            rundir, meta, samples -> [
+                "${rundir}_multiqc_extra_config.yml",
+                "output_fn_name: \"${rundir}_multiqc_report.html\"\ndata_dir_name: \"${rundir}_multiqc_data\"\nplots_dir_name: \"${rundir}_multiqc_plots\""
+            ]
+        }
+        .map { file -> def fileparts = file.name.split("_")
+             [ fileparts[0], file ] 
+        }
+        .join(mqc_by_rundir)
+        .multiMap { rundir, config, meta , samples_per_rundir ->
+            samples_per_rundir: samples_per_rundir
+            config: config
+        }
+
+    MULTIQC_PER_RUNDIR(
+        rundir_mqc_files.samples_per_rundir
+            .map { samples -> samples + multiqc_extra_files.value },
+        ch_multiqc_config.toList(),
+        rundir_mqc_files.config,
         ch_multiqc_logo.toList()
     )
 
     emit:
-    multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
+    global_report = MULTIQC.out.report.toList()             // channel: /path/to/multiqc_report.html
+    lane_reports = MULTIQC_PER_LANE.out.report.toList() // channel: [ /path/to/multiqc_report.html ]
+    group_reports = MULTIQC_PER_GROUP.out.report.toList() // channel: [ /path/to/multiqc_report.html ]
+    rundir_reports = MULTIQC_PER_RUNDIR.out.report.toList() // channel: [ /path/to/multiqc_report.html ]
     versions       = ch_versions                 // channel: [ path(versions.yml) ]
 }
 

From 36976bc769dae4dde31b93a058ab4d539e242196 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Thu, 28 Mar 2024 16:21:45 +0100
Subject: [PATCH 002/530] Improve formatting

---
 conf/modules.config       |  2 +-
 main.nf                   |  6 ++--
 workflows/seqinspector.nf | 71 +++++++++++++++++++++++++--------------
 3 files changed, 50 insertions(+), 29 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 296ca786..8b7a9c69 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -52,7 +52,7 @@ process {
                             break
                         default:
                             filename
-                    }
+                }
             }
         ]
     }
diff --git a/main.nf b/main.nf
index 58afd1fe..1ee043e9 100644
--- a/main.nf
+++ b/main.nf
@@ -58,9 +58,9 @@ workflow NFCORE_SEQINSPECTOR {
     )
 
     emit:
-    global_report = SEQINSPECTOR.out.global_report // channel: /path/to/multiqc_report.html
-    lane_reports = SEQINSPECTOR.out.lane_reports // channel: /path/to/multiqc_report.html
-    group_report = SEQINSPECTOR.out.group_reports // channel: /path/to/multiqc_report.html
+    global_report = SEQINSPECTOR.out.global_report  // channel: /path/to/multiqc_report.html
+    lane_reports = SEQINSPECTOR.out.lane_reports    // channel: /path/to/multiqc_report.html
+    group_report = SEQINSPECTOR.out.group_reports   // channel: /path/to/multiqc_report.html
     rundir_report = SEQINSPECTOR.out.rundir_reports // channel: /path/to/multiqc_report.html
 
 }
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index b6fd3bc4..f0a269a0 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -4,15 +4,17 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { FASTQC                 } from '../modules/nf-core/fastqc/main'
-include { MULTIQC } from '../modules/nf-core/multiqc/main'
-include { MULTIQC as MULTIQC_PER_LANE } from '../modules/nf-core/multiqc/main'
-include { MULTIQC as MULTIQC_PER_GROUP } from '../modules/nf-core/multiqc/main'
+include { FASTQC                        } from '../modules/nf-core/fastqc/main'
+
+include { MULTIQC                       } from '../modules/nf-core/multiqc/main'
+include { MULTIQC as MULTIQC_PER_LANE   } from '../modules/nf-core/multiqc/main'
+include { MULTIQC as MULTIQC_PER_GROUP  } from '../modules/nf-core/multiqc/main'
 include { MULTIQC as MULTIQC_PER_RUNDIR } from '../modules/nf-core/multiqc/main'
-include { paramsSummaryMap       } from 'plugin/nf-validation'
-include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline'
+
+include { paramsSummaryMap              } from 'plugin/nf-validation'
+include { paramsSummaryMultiqc          } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { softwareVersionsToYAML        } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { methodsDescriptionText        } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -27,10 +29,10 @@ workflow SEQINSPECTOR {
 
     main:
 
-    ch_versions = Channel.empty()
-    ch_multiqc_files = Channel.empty()
+    ch_versions            = Channel.empty()
+    ch_multiqc_files       = Channel.empty()
     ch_multiqc_extra_files = Channel.empty()
-    ch_multiqc_reports = Channel.empty()
+    ch_multiqc_reports     = Channel.empty()
 
     //
     // MODULE: Run FastQC
@@ -45,23 +47,42 @@ workflow SEQINSPECTOR {
     // Collate and save software versions
     //
     softwareVersionsToYAML(ch_versions)
-        .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true)
-        .set { ch_collated_versions }
+        .collectFile(
+            storeDir: "${params.outdir}/pipeline_info",
+            name: 'nf_core_pipeline_software_mqc_versions.yml',
+            sort: true,
+            newLine: true
+        ).set { ch_collated_versions }
 
     //
     // MODULE: MultiQC
     //
-    ch_multiqc_config              = params.multiqc_config ? 
+    ch_multiqc_config = params.multiqc_config ?
         Channel.fromPath(params.multiqc_config, checkIfExists: true) :
         Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-    ch_multiqc_logo                       = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
-    summary_params                        = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
-    ch_workflow_summary                   = Channel.value(paramsSummaryMultiqc(summary_params))
-    ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
-    ch_methods_description                = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
-    ch_multiqc_extra_files                      = ch_multiqc_extra_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
-    ch_multiqc_extra_files                      = ch_multiqc_extra_files.mix(ch_collated_versions)
-    ch_multiqc_extra_files                      = ch_multiqc_extra_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false))
+    ch_multiqc_logo   = params.multiqc_logo ?
+        Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
+        Channel.empty()
+
+    summary_params                        = paramsSummaryMap(
+        workflow, parameters_schema: "nextflow_schema.json")
+    ch_workflow_summary                   = Channel.value(
+        paramsSummaryMultiqc(summary_params))
+    ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
+        file(params.multiqc_methods_description, checkIfExists: true) :
+        file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
+    ch_methods_description                = Channel.value(
+        methodsDescriptionText(ch_multiqc_custom_methods_description))
+
+    ch_multiqc_extra_files = ch_multiqc_extra_files.mix(
+        ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+    ch_multiqc_extra_files = ch_multiqc_extra_files.mix(ch_collated_versions)
+    ch_multiqc_extra_files = ch_multiqc_extra_files.mix(
+        ch_methods_description.collectFile(
+            name: 'methods_description_mqc.yaml',
+            sort: false
+        )
+    )
 
     MULTIQC (
         ch_multiqc_files
@@ -163,10 +184,10 @@ workflow SEQINSPECTOR {
 
     emit:
     global_report = MULTIQC.out.report.toList()             // channel: /path/to/multiqc_report.html
-    lane_reports = MULTIQC_PER_LANE.out.report.toList() // channel: [ /path/to/multiqc_report.html ]
-    group_reports = MULTIQC_PER_GROUP.out.report.toList() // channel: [ /path/to/multiqc_report.html ]
+    lane_reports = MULTIQC_PER_LANE.out.report.toList()     // channel: [ /path/to/multiqc_report.html ]
+    group_reports = MULTIQC_PER_GROUP.out.report.toList()   // channel: [ /path/to/multiqc_report.html ]
     rundir_reports = MULTIQC_PER_RUNDIR.out.report.toList() // channel: [ /path/to/multiqc_report.html ]
-    versions       = ch_versions                 // channel: [ path(versions.yml) ]
+    versions       = ch_versions                            // channel: [ path(versions.yml) ]
 }
 
 /*

From be329eee36a9f3170ddd869a94e38ce2ecaf6f67 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Thu, 28 Mar 2024 16:56:51 +0100
Subject: [PATCH 003/530] Improve output sorting

---
 conf/modules.config | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 8b7a9c69..3b2fc025 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -42,13 +42,25 @@ process {
                             null
                             break
                         case ~/L\d+_multiqc_(report\.html|plots|data)/:
-                            "lanes/L${(filename =~ /L(\d+)_multiqc_(report\.html|plots|data)/)[0][1]}/${filename}"
+                            def lane = (filename =~ /L(\d+)_multiqc_(report\.html|plots|data)/)[0][1]
+                            def new_filename = filename.replaceFirst(
+                                "(?<prefix>.*)L${lane}_(?<suffix>multiqc_(report\\.html|plots|data).*)",
+                                '${prefix}${suffix}')
+                            "lanes/L${lane}/${new_filename}"
                             break
                         case ~/G-.+_multiqc_(report\.html|plots|data)/:
-                            "groups/G-${(filename =~ /G-(.+)_multiqc_(report\.html|plots|data)/)[0][1]}/${filename}"
+                            def group = (filename =~ /G-(.+)_multiqc_(report\.html|plots|data)/)[0][1]
+                            def new_filename = filename.replaceFirst(
+                                "(?<prefix>.*)G-${group}_(?<suffix>multiqc_(report\\.html|plots|data).*)",
+                                '${prefix}${suffix}')
+                            "groups/${group}/${new_filename}"
                             break
                         case ~/D-.+_multiqc_(report\.html|plots|data)/:
-                            "rundirs/D-${(filename =~ /D-(.+)_multiqc_(report\.html|plots|data)/)[0][1]}/${filename}"
+                            def rundir = (filename =~ /D-(.+)_multiqc_(report\.html|plots|data)/)[0][1]
+                            def new_filename = filename.replaceFirst(
+                                "(?<prefix>.*)D-${rundir}_(?<suffix>multiqc_(report\\.html|plots|data).*)",
+                                '${prefix}${suffix}')
+                            "rundirs/${rundir}/${new_filename}"
                             break
                         default:
                             filename

From 82eafbe0b63b2914f2841e3c7b82a3265074cff9 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Mon, 8 Apr 2024 14:11:47 +0200
Subject: [PATCH 004/530] Use `group` instead of `project`

---
 assets/schema_input.json                                      | 4 ++--
 subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/assets/schema_input.json b/assets/schema_input.json
index 9fb321b5..1648944f 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -19,11 +19,11 @@
                 "errorMessage": "Lane ID must be a number",
                 "meta": ["lane"]
             },
-            "project": {
+            "group": {
                 "type": "string",
                 "pattern": "^\\S+$",
                 "errorMessage": "Project ID cannot contain spaces",
-                "meta": ["project"]
+                "meta": ["group"]
             },
             "fastq_1": {
                 "type": "string",
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index cdbb6400..e1f8e4de 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -84,7 +84,7 @@ workflow PIPELINE_INITIALISATION {
         .fromSamplesheet("input") // Validates samplesheet against $projectDir/assets/schema_input.json. Path to validation schema is defined by $projectDir/nextflow_schema.json
         .map {
             meta, fastq_1, fastq_2 ->
-                def id_string = "${meta.sample}_${meta.project ?: "ungrouped"}_${meta.lane}"
+                def id_string = "${meta.sample}_${meta.group ?: "ungrouped"}_${meta.lane}"
                 def updated_meta = meta + [ id: id_string ]
                 if (!fastq_2) {
                     return [ updated_meta.id, updated_meta + [ single_end:true ], [ fastq_1 ] ]

From 72f47025d53427730302c62beb30f6f8bc32c1c2 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Mon, 8 Apr 2024 14:21:59 +0200
Subject: [PATCH 005/530] Fix output channel

---
 main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index 1ee043e9..9de4f94e 100644
--- a/main.nf
+++ b/main.nf
@@ -104,7 +104,7 @@ workflow {
         params.outdir,
         params.monochrome_logs,
         params.hook_url,
-        NFCORE_SEQINSPECTOR.out.multiqc_report
+        NFCORE_SEQINSPECTOR.out.global_report,
     )
 }
 

From 1846607816f276fdbf3a03dbd9e02af828c98693 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Mon, 8 Apr 2024 14:22:17 +0200
Subject: [PATCH 006/530] Fix linting

---
 conf/modules.config                                         | 2 +-
 .../local/utils_nfcore_seqinspector_pipeline/main.nf        | 1 -
 workflows/seqinspector.nf                                   | 6 +++---
 3 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 3b2fc025..44a35137 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -36,7 +36,7 @@ process {
             path: { "${params.outdir}/multiqc" },
             mode: params.publish_dir_mode,
             saveAs: {
-                filename -> 
+                filename ->
                     switch (filename) {
                         case 'versions.yml':
                             null
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index e1f8e4de..9001400e 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -101,7 +101,6 @@ workflow PIPELINE_INITIALISATION {
         //     meta, fastqs ->
         //         return [ meta, fastqs.flatten() ]
         // }
-        .view()
         .set { ch_samplesheet }
 
     emit:
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index f0a269a0..815bc40f 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -108,7 +108,7 @@ workflow SEQINSPECTOR {
             ]
         }
         .map { file -> def fileparts = file.name.split("_")
-             [ fileparts[0], file ] 
+            [ fileparts[0], file ]
         }
         .join(mqc_by_lane)
         .multiMap { lane, config, meta , samples_per_lane ->
@@ -137,7 +137,7 @@ workflow SEQINSPECTOR {
             ]
         }
         .map { file -> def fileparts = file.name.split("_")
-             [ fileparts[0], file ] 
+            [ fileparts[0], file ]
         }
         .join(mqc_by_group)
         .multiMap { group, config, meta , samples_per_group ->
@@ -166,7 +166,7 @@ workflow SEQINSPECTOR {
             ]
         }
         .map { file -> def fileparts = file.name.split("_")
-             [ fileparts[0], file ] 
+            [ fileparts[0], file ]
         }
         .join(mqc_by_rundir)
         .multiMap { rundir, config, meta , samples_per_rundir ->

From 9cf987c7a6868af900802b3dbfdd26fba5094bc0 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Mon, 8 Apr 2024 15:48:41 +0200
Subject: [PATCH 007/530] Give credits back to NGI

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 5e2bc4ca..abe0d4ef 100644
--- a/README.md
+++ b/README.md
@@ -80,11 +80,11 @@ For more details about the output files and reports, please refer to the
 
 ## Credits
 
-nf-core/seqinspector was originally written by Adrien Coulier.
+nf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/).
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 
-<!-- TODO nf-core: If applicable, make list of people who have also contributed -->
+- [@mahesh-panchal](https://github.com/mahesh-panchal)
 
 ## Contributions and Support
 

From b24a280854941adf2d6fd5e67f4fb7b717d77fd5 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 9 Apr 2024 09:26:32 +0200
Subject: [PATCH 008/530] Fix file names

---
 conf/modules.config       | 18 +++++++++---------
 workflows/seqinspector.nf | 24 ++++++++++++++++++------
 2 files changed, 27 insertions(+), 15 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 44a35137..b2e48f3d 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -41,24 +41,24 @@ process {
                         case 'versions.yml':
                             null
                             break
-                        case ~/L\d+_multiqc_(report\.html|plots|data)/:
-                            def lane = (filename =~ /L(\d+)_multiqc_(report\.html|plots|data)/)[0][1]
+                        case ~/\[LANE:\d+\]_multiqc_(report\.html|plots|data)/:
+                            def lane = (filename =~ /\[LANE:(\d+)\]_multiqc_(report\.html|plots|data)/)[0][1]
                             def new_filename = filename.replaceFirst(
-                                "(?<prefix>.*)L${lane}_(?<suffix>multiqc_(report\\.html|plots|data).*)",
+                                "(?<prefix>.*)\\[LANE:${lane}\\]_(?<suffix>multiqc_(report\\.html|plots|data).*)",
                                 '${prefix}${suffix}')
                             "lanes/L${lane}/${new_filename}"
                             break
-                        case ~/G-.+_multiqc_(report\.html|plots|data)/:
-                            def group = (filename =~ /G-(.+)_multiqc_(report\.html|plots|data)/)[0][1]
+                        case ~/\[GROUP:.+\]_multiqc_(report\.html|plots|data)/:
+                            def group = (filename =~ /\[GROUP:(.+)\]_multiqc_(report\.html|plots|data)/)[0][1]
                             def new_filename = filename.replaceFirst(
-                                "(?<prefix>.*)G-${group}_(?<suffix>multiqc_(report\\.html|plots|data).*)",
+                                "(?<prefix>.*)\\[GROUP:${group}\\]_(?<suffix>multiqc_(report\\.html|plots|data).*)",
                                 '${prefix}${suffix}')
                             "groups/${group}/${new_filename}"
                             break
-                        case ~/D-.+_multiqc_(report\.html|plots|data)/:
-                            def rundir = (filename =~ /D-(.+)_multiqc_(report\.html|plots|data)/)[0][1]
+                        case ~/\[RUNDIR:.+\]_multiqc_(report\.html|plots|data)/:
+                            def rundir = (filename =~ /\[RUNDIR:(.+)\]_multiqc_(report\.html|plots|data)/)[0][1]
                             def new_filename = filename.replaceFirst(
-                                "(?<prefix>.*)D-${rundir}_(?<suffix>multiqc_(report\\.html|plots|data).*)",
+                                "(?<prefix>.*)\\[RUNDIR:${rundir}\\]_(?<suffix>multiqc_(report\\.html|plots|data).*)",
                                 '${prefix}${suffix}')
                             "rundirs/${rundir}/${new_filename}"
                             break
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 815bc40f..2acafc3f 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -98,13 +98,17 @@ workflow SEQINSPECTOR {
 
     // Generate reports by lane
     lane_mqc_files = ch_multiqc_files
-        .map { meta, sample -> [ "L${meta.lane}", meta, sample ] }
+        .map { meta, sample -> [ "[LANE:${meta.lane}]", meta, sample ] }
         .groupTuple()
         .tap { mqc_by_lane }
         .collectFile{
             lane, meta, samples -> [
                 "${lane}_multiqc_extra_config.yml",
-                "output_fn_name: \"${lane}_multiqc_report.html\"\ndata_dir_name: \"${lane}_multiqc_data\"\nplots_dir_name: \"${lane}_multiqc_plots\""
+                """
+                    |output_fn_name: \"${lane}_multiqc_report.html\"
+                    |data_dir_name:  \"${lane}_multiqc_data\"
+                    |plots_dir_name: \"${lane}_multiqc_plots\"
+                """.stripMargin()
             ]
         }
         .map { file -> def fileparts = file.name.split("_")
@@ -127,13 +131,17 @@ workflow SEQINSPECTOR {
     // Generate reports by group
     group_mqc_files = ch_multiqc_files
         .filter { meta, sample -> meta.group }
-        .map { meta, sample -> [ "G-${meta.group}", meta, sample ] }
+        .map { meta, sample -> [ "[GROUP:${meta.group}]", meta, sample ] }
         .groupTuple()
         .tap { mqc_by_group }
         .collectFile{
             group, meta, samples -> [
                 "${group}_multiqc_extra_config.yml",
-                "output_fn_name: \"${group}_multiqc_report.html\"\ndata_dir_name: \"${group}_multiqc_data\"\nplots_dir_name: \"${group}_multiqc_plots\""
+                """
+                    |output_fn_name: \"${group}_multiqc_report.html\"
+                    |data_dir_name:  \"${group}_multiqc_data\"
+                    |plots_dir_name: \"${group}_multiqc_plots\"
+                """.stripMargin()
             ]
         }
         .map { file -> def fileparts = file.name.split("_")
@@ -156,13 +164,17 @@ workflow SEQINSPECTOR {
     // Generate reports by rundir
     rundir_mqc_files = ch_multiqc_files
         .filter { meta, sample -> meta.rundir }
-        .map { meta, sample -> [ "D-${meta.rundir.name}", meta, sample ] }
+        .map { meta, sample -> [ "[RUNDIR:${meta.rundir.name}]", meta, sample ] }
         .groupTuple()
         .tap { mqc_by_rundir }
         .collectFile{
             rundir, meta, samples -> [
                 "${rundir}_multiqc_extra_config.yml",
-                "output_fn_name: \"${rundir}_multiqc_report.html\"\ndata_dir_name: \"${rundir}_multiqc_data\"\nplots_dir_name: \"${rundir}_multiqc_plots\""
+                """
+                    |output_fn_name: \"${rundir}_multiqc_report.html\"
+                    |data_dir_name:  \"${rundir}_multiqc_data\"
+                    |plots_dir_name: \"${rundir}_multiqc_plots\"
+                """.stripMargin()
             ]
         }
         .map { file -> def fileparts = file.name.split("_")

From a0ce8a3b5b338eacb2b3abec49f85ff0ad7648e1 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Fri, 3 May 2024 09:50:42 +0200
Subject: [PATCH 009/530] Set up tests

---
 .gitignore                           |  1 +
 nf-test.config                       |  8 ++++++++
 tests/main.nf.test                   | 20 +++++++++++++++++++
 tests/nextflow.config                |  5 +++++
 tests/workflows/seqinspector.nf.test | 30 ++++++++++++++++++++++++++++
 5 files changed, 64 insertions(+)
 create mode 100644 nf-test.config
 create mode 100644 tests/main.nf.test
 create mode 100644 tests/nextflow.config
 create mode 100644 tests/workflows/seqinspector.nf.test

diff --git a/.gitignore b/.gitignore
index 5124c9ac..089a4079 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,3 +6,4 @@ results/
 testing/
 testing*
 *.pyc
+.nf-test
diff --git a/nf-test.config b/nf-test.config
new file mode 100644
index 00000000..6969c085
--- /dev/null
+++ b/nf-test.config
@@ -0,0 +1,8 @@
+config {
+
+    testsDir "tests"
+    workDir ".nf-test"
+    configFile "tests/nextflow.config"
+    profile "test,docker"
+
+}
diff --git a/tests/main.nf.test b/tests/main.nf.test
new file mode 100644
index 00000000..72498b5b
--- /dev/null
+++ b/tests/main.nf.test
@@ -0,0 +1,20 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir = "tests/results"
+            }
+        }
+
+        then {
+            assert workflow.success
+        }
+
+    }
+
+}
diff --git a/tests/nextflow.config b/tests/nextflow.config
new file mode 100644
index 00000000..c19b1ad0
--- /dev/null
+++ b/tests/nextflow.config
@@ -0,0 +1,5 @@
+/*
+========================================================================================
+    Nextflow config file for running tests
+========================================================================================
+*/
diff --git a/tests/workflows/seqinspector.nf.test b/tests/workflows/seqinspector.nf.test
new file mode 100644
index 00000000..bbb529dd
--- /dev/null
+++ b/tests/workflows/seqinspector.nf.test
@@ -0,0 +1,30 @@
+nextflow_workflow {
+
+    name "Test Workflow SEQINSPECTOR"
+    script "workflows/seqinspector.nf"
+    workflow "SEQINSPECTOR"
+
+    test("Should run without failures pipeline") {
+
+        when {
+            params {
+                // define parameters here. Example:
+                // outdir = "tests/results"
+            }
+            workflow {
+                """
+                // define inputs of the workflow here. Example:
+                // input[0] = file("https://raw.githubusercontent.com/nf-core/test-datasets/e47966b63444ec0fcdef23bfc410eeca22535ac7/testdata/MiSeq/samplesheet.csv")
+                input[0] = file("assets/samplesheet.csv")
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert snapshot(workflow.out).match()
+        }
+
+    }
+
+}

From 1aaf73b41733f6d91c0d617ad4d30a05f099b880 Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Fri, 3 May 2024 12:18:42 +0200
Subject: [PATCH 010/530] point test conf upstream

---
 conf/test.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/test.config b/conf/test.config
index 38e9ee32..2c26a9c1 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -22,7 +22,7 @@ params {
     // Input data
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input  = 'https://raw.githubusercontent.com/KarNair/test-datasets/seqinspector/testdata/MiSeq/samplesheet.csv'
+    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/seqinspector/testdata/MiSeq/samplesheet.csv'
 
     // Genome references
     genome = 'R64-1-1'

From 0c38819be827c7c320af4210b94c9f835a2a3f88 Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Fri, 3 May 2024 13:05:47 +0200
Subject: [PATCH 011/530] project -> group

---
 assets/samplesheet.csv | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
index fbe5de2d..fef3b4e6 100644
--- a/assets/samplesheet.csv
+++ b/assets/samplesheet.csv
@@ -1,3 +1,3 @@
-sample,lane,project,fastq_1,fastq_2,rundir
+sample,lane,group,fastq_1,fastq_2,rundir
 SAMPLE_PAIRED_END,1,P001,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz,/path/to/rundir
 SAMPLE_SINGLE_END,2,P002,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir

From f842ad0ff6ce7cb3eba1e386cd91d6ed0e1c0b07 Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Fri, 3 May 2024 13:06:48 +0200
Subject: [PATCH 012/530] project -> group

---
 assets/schema_input.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/assets/schema_input.json b/assets/schema_input.json
index 1648944f..7115bfab 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -22,7 +22,7 @@
             "group": {
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "Project ID cannot contain spaces",
+                "errorMessage": "Group ID cannot contain spaces",
                 "meta": ["group"]
             },
             "fastq_1": {

From 2ffc86726fe4b89b4ae52251c360d8f5b0f02a5a Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Fri, 3 May 2024 13:53:31 +0200
Subject: [PATCH 013/530] make lane non-compulsory

---
 assets/schema_input.json  | 2 +-
 workflows/seqinspector.nf | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/assets/schema_input.json b/assets/schema_input.json
index 7115bfab..c9800d5d 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -47,7 +47,7 @@
                 "meta": ["rundir"]
             }
         },
-        "required": ["sample", "lane", "fastq_1"],
+        "required": ["sample", "fastq_1"],
         "dependentRequired": {
             "fastq_2": ["fastq_1"]
         }
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 2acafc3f..018e079d 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -98,6 +98,7 @@ workflow SEQINSPECTOR {
 
     // Generate reports by lane
     lane_mqc_files = ch_multiqc_files
+        .filter { meta, sample -> meta.lane }
         .map { meta, sample -> [ "[LANE:${meta.lane}]", meta, sample ] }
         .groupTuple()
         .tap { mqc_by_lane }

From 978836605ea655b9a6b9aa72add50bb059a59a6c Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Fri, 3 May 2024 15:59:10 +0200
Subject: [PATCH 014/530] remove unused file

---
 assets/samplesheet.csv | 3 ---
 1 file changed, 3 deletions(-)
 delete mode 100644 assets/samplesheet.csv

diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
deleted file mode 100644
index fef3b4e6..00000000
--- a/assets/samplesheet.csv
+++ /dev/null
@@ -1,3 +0,0 @@
-sample,lane,group,fastq_1,fastq_2,rundir
-SAMPLE_PAIRED_END,1,P001,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz,/path/to/rundir
-SAMPLE_SINGLE_END,2,P002,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir

From b0c02e3803a31d28c6bbb85a60306bbd9ba15168 Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Fri, 3 May 2024 16:38:52 +0200
Subject: [PATCH 015/530] revamp nf-test, run once for each sequencing platform

---
 tests/MiSeq.main.nf.test             | 23 +++++++++++++++++++++
 tests/NovaSeq6000.main.nf.test       | 23 +++++++++++++++++++++
 tests/PromethION.main.nf.test        | 23 +++++++++++++++++++++
 tests/main.nf.test                   | 20 -------------------
 tests/nextflow.config                | 11 ++++++++++
 tests/workflows/seqinspector.nf.test | 30 ----------------------------
 6 files changed, 80 insertions(+), 50 deletions(-)
 create mode 100644 tests/MiSeq.main.nf.test
 create mode 100644 tests/NovaSeq6000.main.nf.test
 create mode 100644 tests/PromethION.main.nf.test
 delete mode 100644 tests/main.nf.test
 delete mode 100644 tests/workflows/seqinspector.nf.test

diff --git a/tests/MiSeq.main.nf.test b/tests/MiSeq.main.nf.test
new file mode 100644
index 00000000..0246a75b
--- /dev/null
+++ b/tests/MiSeq.main.nf.test
@@ -0,0 +1,23 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf on MiSeq data"
+    script "../main.nf"
+    tag "seqinspector"
+    tag "PIPELINE"
+
+    test("MiSeq data test") {
+
+        when {
+            params {
+                outdir = "tests/results/MiSeq"
+                input  = "https://raw.githubusercontent.com/nf-core/test-datasets/seqinspector/testdata/MiSeq/samplesheet.csv"
+            }
+        }
+
+        then {
+            assert workflow.success
+        }
+
+    }
+
+}
diff --git a/tests/NovaSeq6000.main.nf.test b/tests/NovaSeq6000.main.nf.test
new file mode 100644
index 00000000..7c410e57
--- /dev/null
+++ b/tests/NovaSeq6000.main.nf.test
@@ -0,0 +1,23 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf on NovaSeq6000 data"
+    script "../main.nf"
+    tag "seqinspector"
+    tag "PIPELINE"
+
+    test("NovaSeq6000 data test") {
+
+        when {
+            params {
+                outdir = "tests/results/NovaSeq6000"
+                input  = "https://raw.githubusercontent.com/nf-core/test-datasets/seqinspector/testdata/NovaSeq6000/samplesheet.csv"
+            }
+        }
+
+        then {
+            assert workflow.success
+        }
+
+    }
+
+}
diff --git a/tests/PromethION.main.nf.test b/tests/PromethION.main.nf.test
new file mode 100644
index 00000000..9987c953
--- /dev/null
+++ b/tests/PromethION.main.nf.test
@@ -0,0 +1,23 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf on PromethION data"
+    script "../main.nf"
+    tag "seqinspector"
+    tag "PIPELINE"
+
+    test("PromethION data test") {
+
+        when {
+            params {
+                outdir = "tests/results/PromethION"
+                input  = "https://raw.githubusercontent.com/nf-core/test-datasets/seqinspector/testdata/PromethION/samplesheet.csv"
+            }
+        }
+
+        then {
+            assert workflow.success
+        }
+
+    }
+
+}
diff --git a/tests/main.nf.test b/tests/main.nf.test
deleted file mode 100644
index 72498b5b..00000000
--- a/tests/main.nf.test
+++ /dev/null
@@ -1,20 +0,0 @@
-nextflow_pipeline {
-
-    name "Test Workflow main.nf"
-    script "main.nf"
-
-    test("Should run without failures") {
-
-        when {
-            params {
-                outdir = "tests/results"
-            }
-        }
-
-        then {
-            assert workflow.success
-        }
-
-    }
-
-}
diff --git a/tests/nextflow.config b/tests/nextflow.config
index c19b1ad0..422545be 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -3,3 +3,14 @@
     Nextflow config file for running tests
 ========================================================================================
 */
+
+params {
+    config_profile_name        = 'nf-test profile'
+    config_profile_description = 'Configuration profile to use for nf-test.'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = '3.GB'
+    max_time   = '2.h'
+
+}
diff --git a/tests/workflows/seqinspector.nf.test b/tests/workflows/seqinspector.nf.test
deleted file mode 100644
index bbb529dd..00000000
--- a/tests/workflows/seqinspector.nf.test
+++ /dev/null
@@ -1,30 +0,0 @@
-nextflow_workflow {
-
-    name "Test Workflow SEQINSPECTOR"
-    script "workflows/seqinspector.nf"
-    workflow "SEQINSPECTOR"
-
-    test("Should run without failures pipeline") {
-
-        when {
-            params {
-                // define parameters here. Example:
-                // outdir = "tests/results"
-            }
-            workflow {
-                """
-                // define inputs of the workflow here. Example:
-                // input[0] = file("https://raw.githubusercontent.com/nf-core/test-datasets/e47966b63444ec0fcdef23bfc410eeca22535ac7/testdata/MiSeq/samplesheet.csv")
-                input[0] = file("assets/samplesheet.csv")
-                """
-            }
-        }
-
-        then {
-            assert workflow.success
-            assert snapshot(workflow.out).match()
-        }
-
-    }
-
-}

From f60e951516b500dc42c7773219ffe3d2c1d6f526 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Mon, 6 May 2024 15:54:05 +0200
Subject: [PATCH 016/530] Update modules and subworkflows

---
 modules.json                                       | 4 ++--
 modules/nf-core/fastqc/main.nf                     | 6 ++++++
 subworkflows/nf-core/utils_nfcore_pipeline/main.nf | 8 +++++++-
 3 files changed, 15 insertions(+), 3 deletions(-)

diff --git a/modules.json b/modules.json
index ebbc5dc2..87fe816c 100644
--- a/modules.json
+++ b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c",
+                        "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
@@ -26,7 +26,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfvalidation_plugin": {
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 9e19a74c..d79f1c86 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -25,6 +25,11 @@ process FASTQC {
     def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
     def rename_to = old_new_pairs*.join(' ').join(' ')
     def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
+
+    def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB')
+    // FastQC memory value allowed range (100 - 10000)
+    def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
+
     """
     printf "%s %s\\n" $rename_to | while read old_name new_name; do
         [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
@@ -33,6 +38,7 @@ process FASTQC {
     fastqc \\
         $args \\
         --threads $task.cpus \\
+        --memory $fastqc_memory \\
         $renamed_files
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index a8b55d6f..14558c39 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -65,9 +65,15 @@ def checkProfileProvided(nextflow_cli_args) {
 // Citation string for pipeline
 //
 def workflowCitation() {
+    def temp_doi_ref = ""
+    String[] manifest_doi = workflow.manifest.doi.tokenize(",")
+    // Using a loop to handle multiple DOIs
+    // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
+    // Removing ` ` since the manifest.doi is a string and not a proper list
+    for (String doi_ref: manifest_doi) temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
     return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
         "* The pipeline\n" +
-        "  ${workflow.manifest.doi}\n\n" +
+        temp_doi_ref + "\n" +
         "* The nf-core framework\n" +
         "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
         "* Software dependencies\n" +

From 16e36206b726ba21ec9803caac2f3b305bcfb19f Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 7 May 2024 16:45:09 +0200
Subject: [PATCH 017/530] Fix multiqc extra files

Issue with the previous implementation was that sometimes
MULTIQC_PER_LANE would execute before the extra files were collected
into `ch_multiqc_extra_files`, causing `null` to be added to the list of
files passed to multiqc.
---
 workflows/seqinspector.nf | 35 +++++++++++++++++++++++++++--------
 1 file changed, 27 insertions(+), 8 deletions(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 018e079d..65343a8b 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -94,11 +94,17 @@ workflow SEQINSPECTOR {
         ch_multiqc_logo.toList()
     )
 
-    multiqc_extra_files = ch_multiqc_extra_files.toList()
-
     // Generate reports by lane
+    multiqc_extra_files_per_lane = ch_multiqc_files
+        .filter { meta, sample -> meta.lane }
+        .map { meta, sample -> meta.lane }
+        .unique()
+        .map { lane -> [lane:lane] }
+        .cross(ch_multiqc_extra_files)
+
     lane_mqc_files = ch_multiqc_files
         .filter { meta, sample -> meta.lane }
+        .mix(multiqc_extra_files_per_lane)
         .map { meta, sample -> [ "[LANE:${meta.lane}]", meta, sample ] }
         .groupTuple()
         .tap { mqc_by_lane }
@@ -122,16 +128,23 @@ workflow SEQINSPECTOR {
         }
 
     MULTIQC_PER_LANE(
-        lane_mqc_files.samples_per_lane
-            .map { samples -> samples + multiqc_extra_files.value },
+        lane_mqc_files.samples_per_lane,
         ch_multiqc_config.toList(),
         lane_mqc_files.config,
         ch_multiqc_logo.toList()
     )
 
     // Generate reports by group
+    multiqc_extra_files_per_group = ch_multiqc_files
+        .filter { meta, sample -> meta.group }
+        .map { meta, sample -> meta.group }
+        .unique()
+        .map { group -> [group:group] }
+        .cross(ch_multiqc_extra_files)
+
     group_mqc_files = ch_multiqc_files
         .filter { meta, sample -> meta.group }
+        .mix(multiqc_extra_files_per_group)
         .map { meta, sample -> [ "[GROUP:${meta.group}]", meta, sample ] }
         .groupTuple()
         .tap { mqc_by_group }
@@ -155,16 +168,23 @@ workflow SEQINSPECTOR {
         }
 
     MULTIQC_PER_GROUP(
-        group_mqc_files.samples_per_group
-            .map { samples -> samples + multiqc_extra_files.value },
+        group_mqc_files.samples_per_group,
         ch_multiqc_config.toList(),
         group_mqc_files.config,
         ch_multiqc_logo.toList()
     )
 
     // Generate reports by rundir
+    multiqc_extra_files_per_rundir = ch_multiqc_files
+        .filter { meta, sample -> meta.rundir }
+        .map { meta, sample -> meta.rundir }
+        .unique()
+        .map { rundir -> [rundir:rundir] }
+        .cross(ch_multiqc_extra_files)
+
     rundir_mqc_files = ch_multiqc_files
         .filter { meta, sample -> meta.rundir }
+        .mix(multiqc_extra_files_per_rundir)
         .map { meta, sample -> [ "[RUNDIR:${meta.rundir.name}]", meta, sample ] }
         .groupTuple()
         .tap { mqc_by_rundir }
@@ -188,8 +208,7 @@ workflow SEQINSPECTOR {
         }
 
     MULTIQC_PER_RUNDIR(
-        rundir_mqc_files.samples_per_rundir
-            .map { samples -> samples + multiqc_extra_files.value },
+        rundir_mqc_files.samples_per_rundir,
         ch_multiqc_config.toList(),
         rundir_mqc_files.config,
         ch_multiqc_logo.toList()

From 93c66a40091d6228c28a965af19f0aa64dfe9f0d Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Wed, 8 May 2024 14:01:12 +0000
Subject: [PATCH 018/530] Template update for nf-core/tools version 2.14.0

---
 .editorconfig                                 |   6 +-
 .github/PULL_REQUEST_TEMPLATE.md              |   2 +-
 .github/workflows/awsfulltest.yml             |  10 +-
 .github/workflows/awstest.yml                 |  12 +-
 .github/workflows/ci.yml                      |   4 +-
 .github/workflows/download_pipeline.yml       |  22 ++-
 .github/workflows/fix-linting.yml             |   6 +-
 .github/workflows/linting.yml                 |  18 +-
 .github/workflows/linting_comment.yml         |   2 +-
 .github/workflows/release-announcements.yml   |   6 +-
 .nf-core.yml                                  |   1 +
 .pre-commit-config.yaml                       |   3 +
 README.md                                     |   2 +-
 conf/base.config                              |   3 -
 conf/modules.config                           |   8 -
 conf/test.config                              |   2 +-
 conf/test_full.config                         |   2 +-
 docs/usage.md                                 |   2 +
 modules.json                                  |   4 +-
 modules/nf-core/fastqc/main.nf                |   6 +
 nextflow.config                               | 176 +++++++++---------
 nextflow_schema.json                          |   7 +
 pyproject.toml                                |  15 --
 .../main.nf                                   |  16 +-
 .../nf-core/utils_nfcore_pipeline/main.nf     |   8 +-
 workflows/seqinspector.nf                     |  46 +++--
 26 files changed, 220 insertions(+), 169 deletions(-)
 delete mode 100644 pyproject.toml

diff --git a/.editorconfig b/.editorconfig
index dd9ffa53..72dda289 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -28,10 +28,6 @@ indent_style = unset
 [/assets/email*]
 indent_size = unset
 
-# ignore Readme
-[README.md]
-indent_style = unset
-
-# ignore python
+# ignore python and markdown
 [*.{py,md}]
 indent_style = unset
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 5d27c53a..6de151f7 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/seqi
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/seqinspector/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/seqinspector _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 1b153a69..9278410e 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -8,12 +8,12 @@ on:
     types: [published]
   workflow_dispatch:
 jobs:
-  run-tower:
+  run-platform:
     name: Run AWS full tests
     if: github.repository == 'nf-core/seqinspector'
     runs-on: ubuntu-latest
     steps:
-      - name: Launch workflow via tower
+      - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
@@ -33,7 +33,7 @@ jobs:
 
       - uses: actions/upload-artifact@v4
         with:
-          name: Tower debug log file
+          name: Seqera Platform debug log file
           path: |
-            tower_action_*.log
-            tower_action_*.json
+            seqera_platform_action_*.log
+            seqera_platform_action_*.json
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index 6def58c8..eef6f2c3 100644
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@@ -5,13 +5,13 @@ name: nf-core AWS test
 on:
   workflow_dispatch:
 jobs:
-  run-tower:
+  run-platform:
     name: Run AWS tests
     if: github.repository == 'nf-core/seqinspector'
     runs-on: ubuntu-latest
     steps:
-      # Launch workflow using Tower CLI tool action
-      - name: Launch workflow via tower
+      # Launch workflow using Seqera Platform CLI tool action
+      - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
@@ -27,7 +27,7 @@ jobs:
 
       - uses: actions/upload-artifact@v4
         with:
-          name: Tower debug log file
+          name: Seqera Platform debug log file
           path: |
-            tower_action_*.log
-            tower_action_*.json
+            seqera_platform_action_*.log
+            seqera_platform_action_*.json
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 7a2be9af..59c94105 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -28,10 +28,10 @@ jobs:
           - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 08622fd5..2d20d644 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -14,6 +14,8 @@ on:
   pull_request:
     types:
       - opened
+      - edited
+      - synchronize
     branches:
       - master
   pull_request_target:
@@ -28,11 +30,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
       - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
         with:
@@ -65,8 +70,17 @@ jobs:
       - name: Inspect download
         run: tree ./${{ env.REPOTITLE_LOWERCASE }}
 
-      - name: Run the downloaded pipeline
+      - name: Run the downloaded pipeline (stub)
+        id: stub_run_pipeline
+        continue-on-error: true
         env:
           NXF_SINGULARITY_CACHEDIR: ./
           NXF_SINGULARITY_HOME_MOUNT: true
         run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
+      - name: Run the downloaded pipeline (stub run not supported)
+        id: run_pipeline
+        if: ${{ job.steps.stub_run_pipeline.status == failure() }}
+        env:
+          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_HOME_MOUNT: true
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 45e06861..1984e17d 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,9 +32,9 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 073e1876..a3fb2541 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -14,12 +14,12 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
           cache: "pip"
 
       - name: Install pre-commit
@@ -32,14 +32,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
 
       - name: Install dependencies
@@ -60,7 +60,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index b706875f..40acc23f 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
+        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
         with:
           workflow: linting.yml
           workflow_conclusion: completed
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index d468aeaa..03ecfcf7 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -12,7 +12,7 @@ jobs:
       - name: get topics and convert to hashtags
         id: get_topics
         run: |
-          curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' >> $GITHUB_OUTPUT
+          echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')"  >> $GITHUB_OUTPUT
 
       - uses: rzr/fediverse-action@master
         with:
@@ -25,13 +25,13 @@ jobs:
 
             Please see the changelog: ${{ github.event.release.html_url }}
 
-            ${{ steps.get_topics.outputs.GITHUB_OUTPUT }} #nfcore #openscience #nextflow #bioinformatics
+            ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
 
   send-tweet:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.10"
       - name: Install dependencies
diff --git a/.nf-core.yml b/.nf-core.yml
index 3805dc81..d6daa403 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1 +1,2 @@
 repository_type: pipeline
+nf_core_version: "2.14.0"
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index af57081f..4dc0f1dc 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -3,6 +3,9 @@ repos:
     rev: "v3.1.0"
     hooks:
       - id: prettier
+        additional_dependencies:
+          - prettier@3.2.5
+
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
     rev: "2.7.3"
     hooks:
diff --git a/README.md b/README.md
index 5e2bc4ca..bfb53fee 100644
--- a/README.md
+++ b/README.md
@@ -13,7 +13,7 @@
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
-[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/seqinspector)
+[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)
 
 [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
 
diff --git a/conf/base.config b/conf/base.config
index 8d7dffc6..aab50f93 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -59,7 +59,4 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
-    withName:CUSTOM_DUMPSOFTWAREVERSIONS {
-        cache = false
-    }
 }
diff --git a/conf/modules.config b/conf/modules.config
index e3ea8fa6..d203d2b6 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -22,14 +22,6 @@ process {
         ext.args = '--quiet'
     }
 
-    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
-        publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
-            pattern: '*_versions.yml'
-        ]
-    }
-
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
diff --git a/conf/test.config b/conf/test.config
index fbbffdd6..6a7b9846 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -22,7 +22,7 @@ params {
     // Input data
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
+    input  = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
 
     // Genome references
     genome = 'R64-1-1'
diff --git a/conf/test_full.config b/conf/test_full.config
index 6fbea31a..53b22883 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -17,7 +17,7 @@ params {
     // Input data for full size test
     // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
+    input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
 
     // Genome references
     genome = 'R64-1-1'
diff --git a/docs/usage.md b/docs/usage.md
index f926de73..ec180e49 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -156,6 +156,8 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
   - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
 - `apptainer`
   - A generic configuration profile to be used with [Apptainer](https://apptainer.org/)
+- `wave`
+  - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later).
 - `conda`
   - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer.
 
diff --git a/modules.json b/modules.json
index ebbc5dc2..87fe816c 100644
--- a/modules.json
+++ b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c",
+                        "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
@@ -26,7 +26,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfvalidation_plugin": {
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 9e19a74c..d79f1c86 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -25,6 +25,11 @@ process FASTQC {
     def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
     def rename_to = old_new_pairs*.join(' ').join(' ')
     def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
+
+    def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB')
+    // FastQC memory value allowed range (100 - 10000)
+    def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
+
     """
     printf "%s %s\\n" $rename_to | while read old_name new_name; do
         [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
@@ -33,6 +38,7 @@ process FASTQC {
     fastqc \\
         $args \\
         --threads $task.cpus \\
+        --memory $fastqc_memory \\
         $renamed_files
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/nextflow.config b/nextflow.config
index 776814f7..a73f66ba 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -16,7 +16,8 @@ params {
     genome                     = null
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
     igenomes_ignore            = false
-    fasta                      = null// MultiQC options
+
+    // MultiQC options
     multiqc_config             = null
     multiqc_title              = null
     multiqc_logo               = null
@@ -24,15 +25,16 @@ params {
     multiqc_methods_description = null
 
     // Boilerplate options
-    outdir                     = null
-    publish_dir_mode           = 'copy'
-    email                      = null
-    email_on_fail              = null
-    plaintext_email            = false
-    monochrome_logs            = false
-    hook_url                   = null
-    help                       = false
-    version                    = false
+    outdir                       = null
+    publish_dir_mode             = 'copy'
+    email                        = null
+    email_on_fail                = null
+    plaintext_email              = false
+    monochrome_logs              = false
+    hook_url                     = null
+    help                         = false
+    version                      = false
+    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
 
     // Config options
     config_profile_name        = null
@@ -68,103 +70,109 @@ try {
 }
 
 // Load nf-core/seqinspector custom profiles from different institutions.
-// Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs!
-// try {
-//   includeConfig "${params.custom_config_base}/pipeline/seqinspector.config"
-// } catch (Exception e) {
-//   System.err.println("WARNING: Could not load nf-core/config/seqinspector profiles: ${params.custom_config_base}/pipeline/seqinspector.config")
-// }
+try {
+    includeConfig "${params.custom_config_base}/pipeline/seqinspector.config"
+} catch (Exception e) {
+    System.err.println("WARNING: Could not load nf-core/config/seqinspector profiles: ${params.custom_config_base}/pipeline/seqinspector.config")
+}
 profiles {
     debug {
-        dumpHashes             = true
-        process.beforeScript   = 'echo $HOSTNAME'
-        cleanup                = false
+        dumpHashes              = true
+        process.beforeScript    = 'echo $HOSTNAME'
+        cleanup                 = false
         nextflow.enable.configProcessNamesValidation = true
     }
     conda {
-        conda.enabled          = true
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        channels               = ['conda-forge', 'bioconda', 'defaults']
-        apptainer.enabled      = false
+        conda.enabled           = true
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        conda.channels          = ['conda-forge', 'bioconda', 'defaults']
+        apptainer.enabled       = false
     }
     mamba {
-        conda.enabled          = true
-        conda.useMamba         = true
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
+        conda.enabled           = true
+        conda.useMamba          = true
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
     }
     docker {
-        docker.enabled         = true
-        conda.enabled          = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
-        docker.runOptions      = '-u $(id -u):$(id -g)'
+        docker.enabled          = true
+        conda.enabled           = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
+        docker.runOptions       = '-u $(id -u):$(id -g)'
     }
     arm {
-        docker.runOptions      = '-u $(id -u):$(id -g) --platform=linux/amd64'
+        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
     }
     singularity {
-        singularity.enabled    = true
-        singularity.autoMounts = true
-        conda.enabled          = false
-        docker.enabled         = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
+        singularity.enabled     = true
+        singularity.autoMounts  = true
+        conda.enabled           = false
+        docker.enabled          = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
     }
     podman {
-        podman.enabled         = true
-        conda.enabled          = false
-        docker.enabled         = false
-        singularity.enabled    = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
+        podman.enabled          = true
+        conda.enabled           = false
+        docker.enabled          = false
+        singularity.enabled     = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
     }
     shifter {
-        shifter.enabled        = true
-        conda.enabled          = false
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
+        shifter.enabled         = true
+        conda.enabled           = false
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
     }
     charliecloud {
-        charliecloud.enabled   = true
-        conda.enabled          = false
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        apptainer.enabled      = false
+        charliecloud.enabled    = true
+        conda.enabled           = false
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        apptainer.enabled       = false
     }
     apptainer {
-        apptainer.enabled      = true
-        apptainer.autoMounts   = true
-        conda.enabled          = false
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
+        apptainer.enabled       = true
+        apptainer.autoMounts    = true
+        conda.enabled           = false
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+    }
+    wave {
+        apptainer.ociAutoPull   = true
+        singularity.ociAutoPull = true
+        wave.enabled            = true
+        wave.freeze             = true
+        wave.strategy           = 'conda,container'
     }
     gitpod {
-        executor.name          = 'local'
-        executor.cpus          = 4
-        executor.memory        = 8.GB
+        executor.name           = 'local'
+        executor.cpus           = 4
+        executor.memory         = 8.GB
     }
     test      { includeConfig 'conf/test.config'      }
     test_full { includeConfig 'conf/test_full.config' }
diff --git a/nextflow_schema.json b/nextflow_schema.json
index ec323b90..36308a0d 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -265,6 +265,13 @@
                     "description": "Validation of parameters in lenient more.",
                     "hidden": true,
                     "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
+                },
+                "pipelines_testdata_base_path": {
+                    "type": "string",
+                    "fa_icon": "far fa-check-circle",
+                    "description": "Base URL or local path to location of pipeline test dataset files",
+                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
+                    "hidden": true
                 }
             }
         }
diff --git a/pyproject.toml b/pyproject.toml
deleted file mode 100644
index 56110621..00000000
--- a/pyproject.toml
+++ /dev/null
@@ -1,15 +0,0 @@
-# Config file for Python. Mostly used to configure linting of bin/*.py with Ruff.
-# Should be kept the same as nf-core/tools to avoid fighting with template synchronisation.
-[tool.ruff]
-line-length = 120
-target-version = "py38"
-cache-dir = "~/.cache/ruff"
-
-[tool.ruff.lint]
-select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"]
-
-[tool.ruff.lint.isort]
-known-first-party = ["nf_core"]
-
-[tool.ruff.lint.per-file-ignores]
-"__init__.py" = ["E402", "F401"]
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index 56b144f3..87281414 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -140,6 +140,10 @@ workflow PIPELINE_COMPLETION {
             imNotification(summary_params, hook_url)
         }
     }
+
+    workflow.onError {
+        log.error "Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting"
+    }
 }
 
 /*
@@ -230,8 +234,16 @@ def methodsDescriptionText(mqc_methods_yaml) {
     meta["manifest_map"] = workflow.manifest.toMap()
 
     // Pipeline DOI
-    meta["doi_text"] = meta.manifest_map.doi ? "(doi: <a href=\'https://doi.org/${meta.manifest_map.doi}\'>${meta.manifest_map.doi}</a>)" : ""
-    meta["nodoi_text"] = meta.manifest_map.doi ? "": "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
+    if (meta.manifest_map.doi) {
+        // Using a loop to handle multiple DOIs
+        // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
+        // Removing ` ` since the manifest.doi is a string and not a proper list
+        def temp_doi_ref = ""
+        String[] manifest_doi = meta.manifest_map.doi.tokenize(",")
+        for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: <a href=\'https://doi.org/${doi_ref.replace("https://doi.org/", "").replace(" ", "")}\'>${doi_ref.replace("https://doi.org/", "").replace(" ", "")}</a>), "
+        meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2)
+    } else meta["doi_text"] = ""
+    meta["nodoi_text"] = meta.manifest_map.doi ? "" : "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
 
     // Tool references
     meta["tool_citations"] = ""
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index a8b55d6f..14558c39 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -65,9 +65,15 @@ def checkProfileProvided(nextflow_cli_args) {
 // Citation string for pipeline
 //
 def workflowCitation() {
+    def temp_doi_ref = ""
+    String[] manifest_doi = workflow.manifest.doi.tokenize(",")
+    // Using a loop to handle multiple DOIs
+    // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
+    // Removing ` ` since the manifest.doi is a string and not a proper list
+    for (String doi_ref: manifest_doi) temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
     return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
         "* The pipeline\n" +
-        "  ${workflow.manifest.doi}\n\n" +
+        temp_doi_ref + "\n" +
         "* The nf-core framework\n" +
         "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
         "* Software dependencies\n" +
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 9ae3384b..cf7a85c4 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -40,22 +40,44 @@ workflow SEQINSPECTOR {
     // Collate and save software versions
     //
     softwareVersionsToYAML(ch_versions)
-        .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true)
-        .set { ch_collated_versions }
+        .collectFile(
+            storeDir: "${params.outdir}/pipeline_info",
+            name: 'nf_core_pipeline_software_mqc_versions.yml',
+            sort: true,
+            newLine: true
+        ).set { ch_collated_versions }
 
     //
     // MODULE: MultiQC
     //
-    ch_multiqc_config                     = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-    ch_multiqc_custom_config              = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
-    ch_multiqc_logo                       = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
-    summary_params                        = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
-    ch_workflow_summary                   = Channel.value(paramsSummaryMultiqc(summary_params))
-    ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
-    ch_methods_description                = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
-    ch_multiqc_files                      = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
-    ch_multiqc_files                      = ch_multiqc_files.mix(ch_collated_versions)
-    ch_multiqc_files                      = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false))
+    ch_multiqc_config        = Channel.fromPath(
+        "$projectDir/assets/multiqc_config.yml", checkIfExists: true)
+    ch_multiqc_custom_config = params.multiqc_config ?
+        Channel.fromPath(params.multiqc_config, checkIfExists: true) :
+        Channel.empty()
+    ch_multiqc_logo          = params.multiqc_logo ?
+        Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
+        Channel.empty()
+
+    summary_params      = paramsSummaryMap(
+        workflow, parameters_schema: "nextflow_schema.json")
+    ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
+
+    ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
+        file(params.multiqc_methods_description, checkIfExists: true) :
+        file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
+    ch_methods_description                = Channel.value(
+        methodsDescriptionText(ch_multiqc_custom_methods_description))
+
+    ch_multiqc_files = ch_multiqc_files.mix(
+        ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+    ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
+    ch_multiqc_files = ch_multiqc_files.mix(
+        ch_methods_description.collectFile(
+            name: 'methods_description_mqc.yaml',
+            sort: true
+        )
+    )
 
     MULTIQC (
         ch_multiqc_files.collect(),

From 88ca813165306088552d29cbf9ae4e93ae46a912 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Thu, 9 May 2024 11:43:27 +0000
Subject: [PATCH 019/530] Template update for nf-core/tools version 2.14.1

---
 .github/workflows/linting.yml | 1 -
 .nf-core.yml                  | 2 +-
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index a3fb2541..1fcafe88 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -20,7 +20,6 @@ jobs:
         uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.12"
-          cache: "pip"
 
       - name: Install pre-commit
         run: pip install pre-commit
diff --git a/.nf-core.yml b/.nf-core.yml
index d6daa403..e0b85a77 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,2 +1,2 @@
 repository_type: pipeline
-nf_core_version: "2.14.0"
+nf_core_version: "2.14.1"

From 6525874499c0dde7ae8ef4532294f30717c93454 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 14 May 2024 10:29:17 +0200
Subject: [PATCH 020/530] Add test snapshots

---
 tests/MiSeq.main.nf.test            | 25 +++++++++++++++---
 tests/MiSeq.main.nf.test.snap       | 19 ++++++++++++++
 tests/NovaSeq6000.main.nf.test      | 40 ++++++++++++++++++++++++++---
 tests/NovaSeq6000.main.nf.test.snap | 31 ++++++++++++++++++++++
 tests/PromethION.main.nf.test       | 20 ++++++++++++---
 tests/PromethION.main.nf.test.snap  | 15 +++++++++++
 workflows/seqinspector.nf           | 18 +++++--------
 7 files changed, 144 insertions(+), 24 deletions(-)
 create mode 100644 tests/MiSeq.main.nf.test.snap
 create mode 100644 tests/NovaSeq6000.main.nf.test.snap
 create mode 100644 tests/PromethION.main.nf.test.snap

diff --git a/tests/MiSeq.main.nf.test b/tests/MiSeq.main.nf.test
index 0246a75b..1e72de95 100644
--- a/tests/MiSeq.main.nf.test
+++ b/tests/MiSeq.main.nf.test
@@ -9,15 +9,32 @@ nextflow_pipeline {
 
         when {
             params {
-                outdir = "tests/results/MiSeq"
+                outdir = "$outputDir"
                 input  = "https://raw.githubusercontent.com/nf-core/test-datasets/seqinspector/testdata/MiSeq/samplesheet.csv"
             }
         }
 
         then {
-            assert workflow.success
-        }
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_software_versions.txt"),
 
-    }
+                    path("$outputDir/multiqc/groups/P001/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/groups/P001/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/groups/P001/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/groups/P001/multiqc_data/multiqc_software_versions.txt"),
 
+                    path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/multiqc_data/multiqc_software_versions.txt"),
+                    ).match()
+                }
+            )
+        }
+    }
 }
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
new file mode 100644
index 00000000..e222b515
--- /dev/null
+++ b/tests/MiSeq.main.nf.test.snap
@@ -0,0 +1,19 @@
+{
+    "MiSeq data test": {
+        "content": [
+            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_fastqc.txt:md5,692b8aed0614ed1655f2c1cbea1ba312",
+            "multiqc_general_stats.txt:md5,630167d67d3f92408cd1a04422c7196f",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_fastqc.txt:md5,692b8aed0614ed1655f2c1cbea1ba312",
+            "multiqc_general_stats.txt:md5,630167d67d3f92408cd1a04422c7196f",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_fastqc.txt:md5,692b8aed0614ed1655f2c1cbea1ba312",
+            "multiqc_general_stats.txt:md5,630167d67d3f92408cd1a04422c7196f",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
+        ],
+        "timestamp": "2024-05-08T16:29:33.284003"
+    }
+}
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test b/tests/NovaSeq6000.main.nf.test
index 7c410e57..f5de9aa3 100644
--- a/tests/NovaSeq6000.main.nf.test
+++ b/tests/NovaSeq6000.main.nf.test
@@ -9,15 +9,47 @@ nextflow_pipeline {
 
         when {
             params {
-                outdir = "tests/results/NovaSeq6000"
+                outdir = "$outputDir"
                 input  = "https://raw.githubusercontent.com/nf-core/test-datasets/seqinspector/testdata/NovaSeq6000/samplesheet.csv"
             }
         }
 
         then {
-            assert workflow.success
-        }
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_software_versions.txt"),
 
-    }
+                    path("$outputDir/multiqc/groups/S1/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/groups/S1/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/groups/S1/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/groups/S1/multiqc_data/multiqc_software_versions.txt"),
+
+                    path("$outputDir/multiqc/groups/S2/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/groups/S2/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/groups/S2/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/groups/S2/multiqc_data/multiqc_software_versions.txt"),
+
+                    path("$outputDir/multiqc/groups/S3/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/groups/S3/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/groups/S3/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/groups/S3/multiqc_data/multiqc_software_versions.txt"),
 
+                    path("$outputDir/multiqc/groups/S4/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/groups/S4/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/groups/S4/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/groups/S4/multiqc_data/multiqc_software_versions.txt"),
+
+                    path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/multiqc_data/multiqc_software_versions.txt"),
+                    ).match()
+                },
+            )
+        }
+    }
 }
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
new file mode 100644
index 00000000..a406b891
--- /dev/null
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -0,0 +1,31 @@
+{
+    "NovaSeq6000 data test": {
+        "content": [
+            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_fastqc.txt:md5,5ba3f4f4ec6026a5f5d55418384dcd3e",
+            "multiqc_general_stats.txt:md5,123cd6b64c9c15607405bcdd45a843d4",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_fastqc.txt:md5,9b4fd8a6d6e8a9acabecd592f633472e",
+            "multiqc_general_stats.txt:md5,8237b88ceb018d3cb1edcea62d10f4a2",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_fastqc.txt:md5,9246a5b6b7b0410c79049fc3dbd08e92",
+            "multiqc_general_stats.txt:md5,44328403f423c6f5ac9ee0a8a01e6725",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_fastqc.txt:md5,84820276fae52d4d492831280ae6207c",
+            "multiqc_general_stats.txt:md5,dd07799e5e4b9d389f9de49a852c3363",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_fastqc.txt:md5,59ae05d89453da6f57010ffb6466f902",
+            "multiqc_general_stats.txt:md5,e4629691992bfe639c01a84b90563334",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_fastqc.txt:md5,5ba3f4f4ec6026a5f5d55418384dcd3e",
+            "multiqc_general_stats.txt:md5,123cd6b64c9c15607405bcdd45a843d4",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
+        ],
+        "timestamp": "2024-05-14T10:17:35.440827"
+    }
+}
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test b/tests/PromethION.main.nf.test
index 9987c953..de2beb35 100644
--- a/tests/PromethION.main.nf.test
+++ b/tests/PromethION.main.nf.test
@@ -9,15 +9,27 @@ nextflow_pipeline {
 
         when {
             params {
-                outdir = "tests/results/PromethION"
+                outdir = "$outputDir"
                 input  = "https://raw.githubusercontent.com/nf-core/test-datasets/seqinspector/testdata/PromethION/samplesheet.csv"
             }
         }
 
         then {
-            assert workflow.success
-        }
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    path("$outputDir/multiqc/groups/r10p41_e8p2_human_runs_jkw/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/groups/r10p41_e8p2_human_runs_jkw/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/groups/r10p41_e8p2_human_runs_jkw/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/groups/r10p41_e8p2_human_runs_jkw/multiqc_data/multiqc_software_versions.txt"),
 
+                    path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/multiqc_data/multiqc_software_versions.txt"),
+                    ).match()
+                },
+            )
+        }
     }
-
 }
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
new file mode 100644
index 00000000..24e52bd1
--- /dev/null
+++ b/tests/PromethION.main.nf.test.snap
@@ -0,0 +1,15 @@
+{
+    "PromethION data test": {
+        "content": [
+            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_fastqc.txt:md5,333360ff12007d64f2bf7673b0658bed",
+            "multiqc_general_stats.txt:md5,b1999255f9a502618d59be2f2e93bad2",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_fastqc.txt:md5,333360ff12007d64f2bf7673b0658bed",
+            "multiqc_general_stats.txt:md5,b1999255f9a502618d59be2f2e93bad2",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
+        ],
+        "timestamp": "2024-05-08T17:17:23.151259"
+    }
+}
\ No newline at end of file
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 65343a8b..3e2a08dc 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -100,7 +100,7 @@ workflow SEQINSPECTOR {
         .map { meta, sample -> meta.lane }
         .unique()
         .map { lane -> [lane:lane] }
-        .cross(ch_multiqc_extra_files)
+        .combine(ch_multiqc_extra_files)
 
     lane_mqc_files = ch_multiqc_files
         .filter { meta, sample -> meta.lane }
@@ -118,9 +118,7 @@ workflow SEQINSPECTOR {
                 """.stripMargin()
             ]
         }
-        .map { file -> def fileparts = file.name.split("_")
-            [ fileparts[0], file ]
-        }
+        .map { file -> [ (file =~ /(\[LANE:.+\])/)[0][1], file ] }
         .join(mqc_by_lane)
         .multiMap { lane, config, meta , samples_per_lane ->
             samples_per_lane: samples_per_lane
@@ -140,7 +138,7 @@ workflow SEQINSPECTOR {
         .map { meta, sample -> meta.group }
         .unique()
         .map { group -> [group:group] }
-        .cross(ch_multiqc_extra_files)
+        .combine(ch_multiqc_extra_files)
 
     group_mqc_files = ch_multiqc_files
         .filter { meta, sample -> meta.group }
@@ -158,9 +156,7 @@ workflow SEQINSPECTOR {
                 """.stripMargin()
             ]
         }
-        .map { file -> def fileparts = file.name.split("_")
-            [ fileparts[0], file ]
-        }
+        .map { file -> [ (file =~ /(\[GROUP:.+\])/)[0][1], file ] }
         .join(mqc_by_group)
         .multiMap { group, config, meta , samples_per_group ->
             samples_per_group: samples_per_group
@@ -180,7 +176,7 @@ workflow SEQINSPECTOR {
         .map { meta, sample -> meta.rundir }
         .unique()
         .map { rundir -> [rundir:rundir] }
-        .cross(ch_multiqc_extra_files)
+        .combine(ch_multiqc_extra_files)
 
     rundir_mqc_files = ch_multiqc_files
         .filter { meta, sample -> meta.rundir }
@@ -198,9 +194,7 @@ workflow SEQINSPECTOR {
                 """.stripMargin()
             ]
         }
-        .map { file -> def fileparts = file.name.split("_")
-            [ fileparts[0], file ]
-        }
+        .map { file -> [ (file =~ /(\[RUNDIR:.+\])/)[0][1], file ] }
         .join(mqc_by_rundir)
         .multiMap { rundir, config, meta , samples_per_rundir ->
             samples_per_rundir: samples_per_rundir

From ca41c810dfd9384f89391d6aaf8bd521da18f9de Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 14 May 2024 11:08:13 +0200
Subject: [PATCH 021/530] Remove unused module configuration

---
 conf/base.config    | 3 ---
 conf/modules.config | 8 --------
 2 files changed, 11 deletions(-)

diff --git a/conf/base.config b/conf/base.config
index 8d7dffc6..aab50f93 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -59,7 +59,4 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
-    withName:CUSTOM_DUMPSOFTWAREVERSIONS {
-        cache = false
-    }
 }
diff --git a/conf/modules.config b/conf/modules.config
index b2e48f3d..da3d2ca2 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -22,14 +22,6 @@ process {
         ext.args = '--quiet'
     }
 
-    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
-        publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
-            pattern: '*_versions.yml'
-        ]
-    }
-
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [

From fd40f7be7532363bdc02a285d38e99001771719c Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 14 May 2024 11:16:41 +0200
Subject: [PATCH 022/530] Update usage docs and restore example samplesheet

---
 assets/samplesheet.csv |  3 +++
 docs/usage.md          | 36 ++++++++++++------------------------
 2 files changed, 15 insertions(+), 24 deletions(-)
 create mode 100644 assets/samplesheet.csv

diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
new file mode 100644
index 00000000..fef3b4e6
--- /dev/null
+++ b/assets/samplesheet.csv
@@ -0,0 +1,3 @@
+sample,lane,group,fastq_1,fastq_2,rundir
+SAMPLE_PAIRED_END,1,P001,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz,/path/to/rundir
+SAMPLE_SINGLE_END,2,P002,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir
diff --git a/docs/usage.md b/docs/usage.md
index f926de73..df2be203 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -16,39 +16,27 @@ You will need to create a samplesheet with information about the samples you wou
 --input '[path to samplesheet file]'
 ```
 
-### Multiple runs of the same sample
-
-The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes:
-
-```csv title="samplesheet.csv"
-sample,fastq_1,fastq_2
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
-CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz
-CONTROL_REP1,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz
-```
-
 ### Full samplesheet
 
-The pipeline will auto-detect whether a sample is single- or paired-end using the information provided in the samplesheet. The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 3 columns to match those defined in the table below.
-
-A final samplesheet file consisting of both single- and paired-end data may look something like the one below. This is for 6 samples, where `TREATMENT_REP3` has been sequenced twice.
-
 ```csv title="samplesheet.csv"
-sample,fastq_1,fastq_2
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
-CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz
-CONTROL_REP3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz
-TREATMENT_REP1,AEG588A4_S4_L003_R1_001.fastq.gz,
-TREATMENT_REP2,AEG588A5_S5_L003_R1_001.fastq.gz,
-TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz,
-TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz,
+sample,lane,group,fastq_1,fastq_2,rundir
+CONTROL_REP1,1,,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX
+CONTROL_REP2,1,,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX
+CONTROL_REP3,1,,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX
+TREATMENT_REP1,2,GROUP1,AEG588A4_S4_L003_R1_001.fastq.gz,,200624_A00834_0183_BHMTFYDRXX
+TREATMENT_REP2,2,GROUP1,AEG588A5_S5_L003_R1_001.fastq.gz,,200624_A00834_0183_BHMTFYDRXX
+TREATMENT_REP3,2,GROUP2,AEG588A6_S6_L003_R1_001.fastq.gz,,200624_A00834_0183_BHMTFYDRXX
+TREATMENT_REP3,2,GROUP2,AEG588A6_S6_L004_R1_001.fastq.gz,,200624_A00834_0183_BHMTFYDRXX
 ```
 
 | Column    | Description                                                                                                                                                                            |
 | --------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | `sample`  | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). |
+| `lane`    | Lane where the sample was processed on an Illumina instrument (optional).                                                                                                              |
+| `group`   | Group the sample belongs too, useful when several groups are pooled together (optional).                                                                                               |
+| `rundir`  | Path to the runfolder containing extra information about the sequencing run (optional) .                                                                                               |
 | `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                             |
-| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                             |
+| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz" (optional).                                                  |
 
 An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
 

From a7dfd886aacaeb2f8be255c4252d750c372817de Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 14 May 2024 12:09:51 +0200
Subject: [PATCH 023/530] Update output docs

---
 docs/output.md | 27 +++++++++++++++++++++++++--
 1 file changed, 25 insertions(+), 2 deletions(-)

diff --git a/docs/output.md b/docs/output.md
index 77e4cc1c..f83e1fa0 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -6,8 +6,6 @@ This document describes the output produced by the pipeline. Most of the plots a
 
 The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory.
 
-<!-- TODO nf-core: Write this documentation describing your workflow's output -->
-
 ## Pipeline overview
 
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
@@ -48,6 +46,31 @@ The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They m
   - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
   - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
   - `multiqc_plots/`: directory containing static images from the report in various formats.
+  - `lanes/` [1]
+    - `L1/`
+      - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
+      - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
+      - `multiqc_plots/`: directory containing static images from the report in various formats.
+    - `L2/`
+      - ...
+  - `groups/` [1]
+    - `GROUPNAME1/`
+      - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
+      - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
+      - `multiqc_plots/`: directory containing static images from the report in various formats.
+    - `GROUPNAME2/`
+      - ...
+  - `rundir/` [1]
+    - `RUNDIR1/`
+      - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
+      - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
+      - `multiqc_plots/`: directory containing static images from the report in various formats.
+    - `RUNDIR2/`
+      - ...
+
+
+[1] These files will only be generated if `lane`, `group` or `rundir` were specified for some samples.
+
 
 </details>
 

From 2b1eeb43b88159fec6033a564729fd2698454c9b Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 14 May 2024 12:16:38 +0200
Subject: [PATCH 024/530] Update changelog

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 58a53ef4..6430addb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,8 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 
 ### `Added`
 
+- [#13](https://github.com/nf-core/seqinspector/pull/13) Generate reports per run, per project and per lane.
+
 ### `Fixed`
 
 ### `Dependencies`

From 61648ccc1ac0c2aae3dec422eafd0ec225f54d6a Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 14 May 2024 12:20:34 +0200
Subject: [PATCH 025/530] Update samplesheet in readme file

---
 README.md | 11 ++---------
 1 file changed, 2 insertions(+), 9 deletions(-)

diff --git a/README.md b/README.md
index abe0d4ef..edc54ae5 100644
--- a/README.md
+++ b/README.md
@@ -39,26 +39,19 @@
 > [!NOTE]
 > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
 
-<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
-     Explain what rows and columns represent. For instance (please edit as appropriate):
-
 First, prepare a samplesheet with your input data that looks as follows:
 
 `samplesheet.csv`:
 
 ```csv
-sample,fastq_1,fastq_2
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
+sample,lane,group,fastq_1,fastq_2,rundir
+CONTROL_REP1,1,GROUP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX
 ```
 
 Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
 
--->
-
 Now, you can run the pipeline using:
 
-<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
-
 ```bash
 nextflow run nf-core/seqinspector \
    -profile <docker/singularity/.../institute> \

From 74dbadde15348677bf83428f824701ad24890934 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 14 May 2024 12:43:27 +0200
Subject: [PATCH 026/530] Run prettier

---
 docs/output.md | 2 --
 1 file changed, 2 deletions(-)

diff --git a/docs/output.md b/docs/output.md
index f83e1fa0..7af7806c 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -68,10 +68,8 @@ The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They m
     - `RUNDIR2/`
       - ...
 
-
 [1] These files will only be generated if `lane`, `group` or `rundir` were specified for some samples.
 
-
 </details>
 
 [MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.

From 79f99dddc3bb014de0e3221061decd38556a3621 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <89784800+kedhammar@users.noreply.github.com>
Date: Thu, 16 May 2024 16:00:32 +0200
Subject: [PATCH 027/530] Use testdata base path param in
 tests/MiSeq.main.nf.test

Co-authored-by: Matthias Zepper <6963520+MatthiasZepper@users.noreply.github.com>
---
 tests/MiSeq.main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/MiSeq.main.nf.test b/tests/MiSeq.main.nf.test
index 1e72de95..a3dc0a5a 100644
--- a/tests/MiSeq.main.nf.test
+++ b/tests/MiSeq.main.nf.test
@@ -10,7 +10,7 @@ nextflow_pipeline {
         when {
             params {
                 outdir = "$outputDir"
-                input  = "https://raw.githubusercontent.com/nf-core/test-datasets/seqinspector/testdata/MiSeq/samplesheet.csv"
+                input  = params.pipelines_testdata_base_path + "seqinspector/testdata/MiSeq/samplesheet.csv"
             }
         }
 

From f91eace5e050adc0462e17d3c31afca815c73340 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <89784800+kedhammar@users.noreply.github.com>
Date: Thu, 16 May 2024 16:01:00 +0200
Subject: [PATCH 028/530] Use testdata base path param in
 tests/NovaSeq6000.main.nf.test

Co-authored-by: Matthias Zepper <6963520+MatthiasZepper@users.noreply.github.com>
---
 tests/NovaSeq6000.main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/NovaSeq6000.main.nf.test b/tests/NovaSeq6000.main.nf.test
index f5de9aa3..bc687abe 100644
--- a/tests/NovaSeq6000.main.nf.test
+++ b/tests/NovaSeq6000.main.nf.test
@@ -10,7 +10,7 @@ nextflow_pipeline {
         when {
             params {
                 outdir = "$outputDir"
-                input  = "https://raw.githubusercontent.com/nf-core/test-datasets/seqinspector/testdata/NovaSeq6000/samplesheet.csv"
+                input  = params.pipelines_testdata_base_path + "seqinspector/testdata/NovaSeq6000/samplesheet.csv"
             }
         }
 

From d055ce3d64933ad9db9d41ce53b91349857fc6cd Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <89784800+kedhammar@users.noreply.github.com>
Date: Thu, 16 May 2024 16:01:20 +0200
Subject: [PATCH 029/530] Use testdata base path param in
 tests/PromethION.main.nf.test

Co-authored-by: Matthias Zepper <6963520+MatthiasZepper@users.noreply.github.com>
---
 tests/PromethION.main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/PromethION.main.nf.test b/tests/PromethION.main.nf.test
index de2beb35..d1969f3e 100644
--- a/tests/PromethION.main.nf.test
+++ b/tests/PromethION.main.nf.test
@@ -10,7 +10,7 @@ nextflow_pipeline {
         when {
             params {
                 outdir = "$outputDir"
-                input  = "https://raw.githubusercontent.com/nf-core/test-datasets/seqinspector/testdata/PromethION/samplesheet.csv"
+                input  = params.pipelines_testdata_base_path + "seqinspector/testdata/PromethION/samplesheet.csv"
             }
         }
 

From 391fc43d3c292a2c59548c9f75cbc047509cfcb7 Mon Sep 17 00:00:00 2001
From: Matthias Zepper <MatthiasZepper@users.noreply.github.com>
Date: Fri, 17 May 2024 11:38:29 +0200
Subject: [PATCH 030/530] Make the tests work with
 'pipelines_testdata_base_path' parameter.

---
 tests/MiSeq.main.nf.test              | 2 +-
 tests/MiSeq.main.nf.test.config       | 7 +++++++
 tests/NovaSeq6000.main.nf.test        | 2 +-
 tests/NovaSeq6000.main.nf.test.config | 7 +++++++
 tests/PromethION.main.nf.test         | 2 +-
 tests/PromethION.main.nf.test.config  | 7 +++++++
 tests/nextflow.config                 | 5 +++++
 7 files changed, 29 insertions(+), 3 deletions(-)
 create mode 100644 tests/MiSeq.main.nf.test.config
 create mode 100644 tests/NovaSeq6000.main.nf.test.config
 create mode 100644 tests/PromethION.main.nf.test.config

diff --git a/tests/MiSeq.main.nf.test b/tests/MiSeq.main.nf.test
index a3dc0a5a..bfabd954 100644
--- a/tests/MiSeq.main.nf.test
+++ b/tests/MiSeq.main.nf.test
@@ -8,9 +8,9 @@ nextflow_pipeline {
     test("MiSeq data test") {
 
         when {
+            config "./MiSeq.main.nf.test.config"
             params {
                 outdir = "$outputDir"
-                input  = params.pipelines_testdata_base_path + "seqinspector/testdata/MiSeq/samplesheet.csv"
             }
         }
 
diff --git a/tests/MiSeq.main.nf.test.config b/tests/MiSeq.main.nf.test.config
new file mode 100644
index 00000000..073a9774
--- /dev/null
+++ b/tests/MiSeq.main.nf.test.config
@@ -0,0 +1,7 @@
+// Load the basic test config
+includeConfig 'nextflow.config'
+
+// Load the correct samplesheet for that test
+params {
+    input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/MiSeq/samplesheet.csv'
+}
diff --git a/tests/NovaSeq6000.main.nf.test b/tests/NovaSeq6000.main.nf.test
index bc687abe..174e215d 100644
--- a/tests/NovaSeq6000.main.nf.test
+++ b/tests/NovaSeq6000.main.nf.test
@@ -8,9 +8,9 @@ nextflow_pipeline {
     test("NovaSeq6000 data test") {
 
         when {
+            config "./NovaSeq6000.main.nf.test.config"
             params {
                 outdir = "$outputDir"
-                input  = params.pipelines_testdata_base_path + "seqinspector/testdata/NovaSeq6000/samplesheet.csv"
             }
         }
 
diff --git a/tests/NovaSeq6000.main.nf.test.config b/tests/NovaSeq6000.main.nf.test.config
new file mode 100644
index 00000000..cad5edd9
--- /dev/null
+++ b/tests/NovaSeq6000.main.nf.test.config
@@ -0,0 +1,7 @@
+// Load the basic test config
+includeConfig 'nextflow.config'
+
+// Load the correct samplesheet for that test
+params {
+    input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
+}
diff --git a/tests/PromethION.main.nf.test b/tests/PromethION.main.nf.test
index d1969f3e..39284786 100644
--- a/tests/PromethION.main.nf.test
+++ b/tests/PromethION.main.nf.test
@@ -8,9 +8,9 @@ nextflow_pipeline {
     test("PromethION data test") {
 
         when {
+            config "./PromethION.main.nf.test.config"
             params {
                 outdir = "$outputDir"
-                input  = params.pipelines_testdata_base_path + "seqinspector/testdata/PromethION/samplesheet.csv"
             }
         }
 
diff --git a/tests/PromethION.main.nf.test.config b/tests/PromethION.main.nf.test.config
new file mode 100644
index 00000000..e1498a49
--- /dev/null
+++ b/tests/PromethION.main.nf.test.config
@@ -0,0 +1,7 @@
+// Load the basic test config
+includeConfig 'nextflow.config'
+
+// Load the correct samplesheet for that test
+params {
+    input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/PromethION/samplesheet.csv'
+}
diff --git a/tests/nextflow.config b/tests/nextflow.config
index 422545be..8d9ef461 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -13,4 +13,9 @@ params {
     max_memory = '3.GB'
     max_time   = '2.h'
 
+    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
+
+    validationSchemaIgnoreParams = 'genomes,igenomes_base,pipelines_testdata_base_path'
+
+
 }

From 2147a12a1e5000d439ea784e8d337c24cc58bba5 Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Fri, 17 May 2024 13:28:56 +0200
Subject: [PATCH 031/530] update snapshots, add nf-test.log to gitignore

---
 .gitignore                          |  1 +
 tests/MiSeq.main.nf.test.snap       | 12 ++++++++----
 tests/NovaSeq6000.main.nf.test.snap | 18 +++++++++++-------
 tests/PromethION.main.nf.test.snap  | 10 +++++++---
 4 files changed, 27 insertions(+), 14 deletions(-)

diff --git a/.gitignore b/.gitignore
index 089a4079..72277655 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,3 +7,4 @@ testing/
 testing*
 *.pyc
 .nf-test
+.nf-test.log
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index e222b515..96896382 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -4,16 +4,20 @@
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,692b8aed0614ed1655f2c1cbea1ba312",
             "multiqc_general_stats.txt:md5,630167d67d3f92408cd1a04422c7196f",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,692b8aed0614ed1655f2c1cbea1ba312",
             "multiqc_general_stats.txt:md5,630167d67d3f92408cd1a04422c7196f",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,692b8aed0614ed1655f2c1cbea1ba312",
             "multiqc_general_stats.txt:md5,630167d67d3f92408cd1a04422c7196f",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
+            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921"
         ],
-        "timestamp": "2024-05-08T16:29:33.284003"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-17T12:59:21.531493"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index a406b891..cbb75383 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -4,28 +4,32 @@
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,5ba3f4f4ec6026a5f5d55418384dcd3e",
             "multiqc_general_stats.txt:md5,123cd6b64c9c15607405bcdd45a843d4",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,9b4fd8a6d6e8a9acabecd592f633472e",
             "multiqc_general_stats.txt:md5,8237b88ceb018d3cb1edcea62d10f4a2",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,9246a5b6b7b0410c79049fc3dbd08e92",
             "multiqc_general_stats.txt:md5,44328403f423c6f5ac9ee0a8a01e6725",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,84820276fae52d4d492831280ae6207c",
             "multiqc_general_stats.txt:md5,dd07799e5e4b9d389f9de49a852c3363",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,59ae05d89453da6f57010ffb6466f902",
             "multiqc_general_stats.txt:md5,e4629691992bfe639c01a84b90563334",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,5ba3f4f4ec6026a5f5d55418384dcd3e",
             "multiqc_general_stats.txt:md5,123cd6b64c9c15607405bcdd45a843d4",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
+            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921"
         ],
-        "timestamp": "2024-05-14T10:17:35.440827"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-17T13:02:20.874181"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index 24e52bd1..951c5550 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -4,12 +4,16 @@
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,333360ff12007d64f2bf7673b0658bed",
             "multiqc_general_stats.txt:md5,b1999255f9a502618d59be2f2e93bad2",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,333360ff12007d64f2bf7673b0658bed",
             "multiqc_general_stats.txt:md5,b1999255f9a502618d59be2f2e93bad2",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
+            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921"
         ],
-        "timestamp": "2024-05-08T17:17:23.151259"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-17T12:58:02.572837"
     }
 }
\ No newline at end of file

From aa75066cd064883bd7359f5625623f798f0b72c0 Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Fri, 17 May 2024 15:49:01 +0200
Subject: [PATCH 032/530] visualize example run dir corresponsing to
 samplesheet

---
 docs/usage.md | 32 +++++++++++++++++++++-----------
 1 file changed, 21 insertions(+), 11 deletions(-)

diff --git a/docs/usage.md b/docs/usage.md
index 57314973..7a4ec735 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -10,7 +10,7 @@
 
 ## Samplesheet input
 
-You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row as shown in the examples below.
+You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location.
 
 ```bash
 --input '[path to samplesheet file]'
@@ -18,15 +18,25 @@ You will need to create a samplesheet with information about the samples you wou
 
 ### Full samplesheet
 
+The following simple run dir structure...
+
+```
+run_dir
+├── sample1_lane1_group1_r1.fq.gz
+├── sample2_lane1_group1_r1.fq.gz
+├── sample3_lane2_group2_r1.fq.gz
+└── sample4_lane2_group3_r1.fq.gz
+```
+
+...would be represented in the following samplesheet (shown as .tsv for readability)
+
 ```csv title="samplesheet.csv"
-sample,lane,group,fastq_1,fastq_2,rundir
-CONTROL_REP1,1,,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX
-CONTROL_REP2,1,,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX
-CONTROL_REP3,1,,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX
-TREATMENT_REP1,2,GROUP1,AEG588A4_S4_L003_R1_001.fastq.gz,,200624_A00834_0183_BHMTFYDRXX
-TREATMENT_REP2,2,GROUP1,AEG588A5_S5_L003_R1_001.fastq.gz,,200624_A00834_0183_BHMTFYDRXX
-TREATMENT_REP3,2,GROUP2,AEG588A6_S6_L003_R1_001.fastq.gz,,200624_A00834_0183_BHMTFYDRXX
-TREATMENT_REP3,2,GROUP2,AEG588A6_S6_L004_R1_001.fastq.gz,,200624_A00834_0183_BHMTFYDRXX
+sample  lane  group   fastq_1                                       fastq_2 rundir
+sample1 1     group1  path/to/run_dir/sample1_lane1_group1_r1.fq.gz         path/to/run_dir
+sample2 1     group1  path/to/run_dir/sample2_lane1_group1_r1.fq.gz         path/to/run_dir
+sample3 2     group2  path/to/run_dir/sample3_lane2_group2_r1.fq.gz         path/to/run_dir
+sample4 2     group3  path/to/run_dir/sample4_lane2_group3_r1.fq.gz         path/to/run_dir
+
 ```
 
 | Column    | Description                                                                                                                                                                            |
@@ -34,11 +44,11 @@ TREATMENT_REP3,2,GROUP2,AEG588A6_S6_L004_R1_001.fastq.gz,,200624_A00834_0183_BHM
 | `sample`  | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). |
 | `lane`    | Lane where the sample was processed on an Illumina instrument (optional).                                                                                                              |
 | `group`   | Group the sample belongs too, useful when several groups are pooled together (optional).                                                                                               |
-| `rundir`  | Path to the runfolder containing extra information about the sequencing run (optional) .                                                                                               |
 | `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                             |
 | `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz" (optional).                                                  |
+| `rundir`  | Path to the runfolder containing extra information about the sequencing run (optional) .                                                                                               |
 
-An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
+Another [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
 
 ## Running the pipeline
 

From 09f12cc54a91972e9c450542c0e9ccfb462123c9 Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Mon, 20 May 2024 12:41:50 +0200
Subject: [PATCH 033/530] naming fixes

---
 main.nf                   | 4 ++--
 workflows/seqinspector.nf | 9 ++++-----
 2 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/main.nf b/main.nf
index 9de4f94e..fb00bd5d 100644
--- a/main.nf
+++ b/main.nf
@@ -59,8 +59,8 @@ workflow NFCORE_SEQINSPECTOR {
 
     emit:
     global_report = SEQINSPECTOR.out.global_report  // channel: /path/to/multiqc_report.html
-    lane_reports = SEQINSPECTOR.out.lane_reports    // channel: /path/to/multiqc_report.html
-    group_report = SEQINSPECTOR.out.group_reports   // channel: /path/to/multiqc_report.html
+    lane_reports  = SEQINSPECTOR.out.lane_reports   // channel: /path/to/multiqc_report.html
+    group_reports = SEQINSPECTOR.out.group_reports  // channel: /path/to/multiqc_report.html
     rundir_report = SEQINSPECTOR.out.rundir_reports // channel: /path/to/multiqc_report.html
 
 }
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 0eb375dd..50fa481f 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -6,7 +6,7 @@
 
 include { FASTQC                        } from '../modules/nf-core/fastqc/main'
 
-include { MULTIQC                       } from '../modules/nf-core/multiqc/main'
+include { MULTIQC as MULTIQC_GLOBAL     } from '../modules/nf-core/multiqc/main'
 include { MULTIQC as MULTIQC_PER_LANE   } from '../modules/nf-core/multiqc/main'
 include { MULTIQC as MULTIQC_PER_GROUP  } from '../modules/nf-core/multiqc/main'
 include { MULTIQC as MULTIQC_PER_RUNDIR } from '../modules/nf-core/multiqc/main'
@@ -84,7 +84,7 @@ workflow SEQINSPECTOR {
         )
     )
 
-    MULTIQC (
+    MULTIQC_GLOBAL (
         ch_multiqc_files
             .map { meta, file -> file }
             .mix(ch_multiqc_extra_files)
@@ -97,9 +97,8 @@ workflow SEQINSPECTOR {
     // Generate reports by lane
     multiqc_extra_files_per_lane = ch_multiqc_files
         .filter { meta, sample -> meta.lane }
-        .map { meta, sample -> meta.lane }
+        .map { meta, sample -> [lane: meta.lane] }
         .unique()
-        .map { lane -> [lane:lane] }
         .combine(ch_multiqc_extra_files)
 
     lane_mqc_files = ch_multiqc_files
@@ -209,7 +208,7 @@ workflow SEQINSPECTOR {
     )
 
     emit:
-    global_report = MULTIQC.out.report.toList()             // channel: /path/to/multiqc_report.html
+    global_report = MULTIQC_GLOBAL.out.report.toList()      // channel: /path/to/multiqc_report.html
     lane_reports = MULTIQC_PER_LANE.out.report.toList()     // channel: [ /path/to/multiqc_report.html ]
     group_reports = MULTIQC_PER_GROUP.out.report.toList()   // channel: [ /path/to/multiqc_report.html ]
     rundir_reports = MULTIQC_PER_RUNDIR.out.report.toList() // channel: [ /path/to/multiqc_report.html ]

From 3d0be5a1cf662b84c31b0b95881e99a966b53e6f Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Mon, 20 May 2024 12:44:01 +0200
Subject: [PATCH 034/530] nf-core sync

---
 .github/PULL_REQUEST_TEMPLATE.md      |  2 +-
 .github/workflows/linting.yml         | 19 ++++++++++---------
 .github/workflows/linting_comment.yml |  2 +-
 3 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 6de151f7..5d27c53a 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/seqi
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/seqinspector/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/seqinspector _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
+- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 1fcafe88..073e1876 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -14,12 +14,13 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
-      - name: Set up Python 3.12
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - name: Set up Python 3.11
+        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: "3.12"
+          python-version: 3.11
+          cache: "pip"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -31,14 +32,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v2
+        uses: nf-core/setup-nextflow@v1
 
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: "3.12"
+          python-version: "3.11"
           architecture: "x64"
 
       - name: Install dependencies
@@ -59,7 +60,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
+        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 40acc23f..b706875f 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
+        uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
         with:
           workflow: linting.yml
           workflow_conclusion: completed

From 055d7033ab5caaa42eb3102a8ea1dc113a8fc3e2 Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Mon, 20 May 2024 12:44:54 +0200
Subject: [PATCH 035/530] nf-core fixes

---
 .github/PULL_REQUEST_TEMPLATE.md      |  2 +-
 .github/workflows/linting.yml         | 19 +++++++++----------
 .github/workflows/linting_comment.yml |  2 +-
 3 files changed, 11 insertions(+), 12 deletions(-)

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 5d27c53a..6de151f7 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/seqi
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/seqinspector/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/seqinspector _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 073e1876..1fcafe88 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -14,13 +14,12 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
-          cache: "pip"
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -32,14 +31,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
 
       - name: Install dependencies
@@ -60,7 +59,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index b706875f..40acc23f 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
+        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
         with:
           workflow: linting.yml
           workflow_conclusion: completed

From 40691f59717daca640f43e2040a9e86b7eceb6b6 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Thu, 30 May 2024 13:18:36 +0200
Subject: [PATCH 036/530] Improve publishDir logic

---
 conf/modules.config                 | 56 +++++++++++++++++++++++++----
 tests/MiSeq.main.nf.test.snap       | 12 +++----
 tests/NovaSeq6000.main.nf.test.snap | 18 ++++------
 tests/PromethION.main.nf.test.snap  | 10 ++----
 4 files changed, 64 insertions(+), 32 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index da3d2ca2..f7e78457 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -22,11 +22,20 @@ process {
         ext.args = '--quiet'
     }
 
-    withName: 'MULTIQC' {
+    withName: 'MULTIQC_GLOBAL' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
             path: { "${params.outdir}/multiqc" },
             mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: 'MULTIQC_PER_LANE' {
+        ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
+        publishDir = [
+            path: { "${params.outdir}/multiqc/lanes" },
+            mode: params.publish_dir_mode,
             saveAs: {
                 filename ->
                     switch (filename) {
@@ -38,27 +47,62 @@ process {
                             def new_filename = filename.replaceFirst(
                                 "(?<prefix>.*)\\[LANE:${lane}\\]_(?<suffix>multiqc_(report\\.html|plots|data).*)",
                                 '${prefix}${suffix}')
-                            "lanes/L${lane}/${new_filename}"
+                            "L${lane}/${new_filename}"
+                            break
+                        default:
+                            filename
+                    }
+            }
+        ]
+    }
+
+    withName: 'MULTIQC_PER_GROUP' {
+        ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
+        publishDir = [
+            path: { "${params.outdir}/multiqc/groups" },
+            mode: params.publish_dir_mode,
+            saveAs: {
+                filename ->
+                    switch (filename) {
+                        case 'versions.yml':
+                            null
                             break
                         case ~/\[GROUP:.+\]_multiqc_(report\.html|plots|data)/:
                             def group = (filename =~ /\[GROUP:(.+)\]_multiqc_(report\.html|plots|data)/)[0][1]
                             def new_filename = filename.replaceFirst(
                                 "(?<prefix>.*)\\[GROUP:${group}\\]_(?<suffix>multiqc_(report\\.html|plots|data).*)",
                                 '${prefix}${suffix}')
-                            "groups/${group}/${new_filename}"
+                            "${group}/${new_filename}"
+                            break
+                        default:
+                            filename
+                    }
+            }
+        ]
+    }
+
+    withName: 'MULTIQC_PER_RUNDIR' {
+        ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
+        publishDir = [
+            path: { "${params.outdir}/multiqc/rundirss" },
+            mode: params.publish_dir_mode,
+            saveAs: {
+                filename ->
+                    switch (filename) {
+                        case 'versions.yml':
+                            null
                             break
                         case ~/\[RUNDIR:.+\]_multiqc_(report\.html|plots|data)/:
                             def rundir = (filename =~ /\[RUNDIR:(.+)\]_multiqc_(report\.html|plots|data)/)[0][1]
                             def new_filename = filename.replaceFirst(
                                 "(?<prefix>.*)\\[RUNDIR:${rundir}\\]_(?<suffix>multiqc_(report\\.html|plots|data).*)",
                                 '${prefix}${suffix}')
-                            "rundirs/${rundir}/${new_filename}"
+                            "${rundir}/${new_filename}"
                             break
                         default:
                             filename
-                }
+                    }
             }
         ]
     }
-
 }
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 96896382..87c1a561 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -4,20 +4,16 @@
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,692b8aed0614ed1655f2c1cbea1ba312",
             "multiqc_general_stats.txt:md5,630167d67d3f92408cd1a04422c7196f",
-            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,692b8aed0614ed1655f2c1cbea1ba312",
             "multiqc_general_stats.txt:md5,630167d67d3f92408cd1a04422c7196f",
-            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,692b8aed0614ed1655f2c1cbea1ba312",
             "multiqc_general_stats.txt:md5,630167d67d3f92408cd1a04422c7196f",
-            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921"
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
         ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-05-17T12:59:21.531493"
+        "timestamp": "2024-05-30T13:14:20.263485"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index cbb75383..22600251 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -4,32 +4,28 @@
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,5ba3f4f4ec6026a5f5d55418384dcd3e",
             "multiqc_general_stats.txt:md5,123cd6b64c9c15607405bcdd45a843d4",
-            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,9b4fd8a6d6e8a9acabecd592f633472e",
             "multiqc_general_stats.txt:md5,8237b88ceb018d3cb1edcea62d10f4a2",
-            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,9246a5b6b7b0410c79049fc3dbd08e92",
             "multiqc_general_stats.txt:md5,44328403f423c6f5ac9ee0a8a01e6725",
-            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,84820276fae52d4d492831280ae6207c",
             "multiqc_general_stats.txt:md5,dd07799e5e4b9d389f9de49a852c3363",
-            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,59ae05d89453da6f57010ffb6466f902",
             "multiqc_general_stats.txt:md5,e4629691992bfe639c01a84b90563334",
-            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,5ba3f4f4ec6026a5f5d55418384dcd3e",
             "multiqc_general_stats.txt:md5,123cd6b64c9c15607405bcdd45a843d4",
-            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921"
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
         ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-05-17T13:02:20.874181"
+        "timestamp": "2024-05-30T13:13:49.062282"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index 951c5550..0ac213c1 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -4,16 +4,12 @@
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,333360ff12007d64f2bf7673b0658bed",
             "multiqc_general_stats.txt:md5,b1999255f9a502618d59be2f2e93bad2",
-            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,333360ff12007d64f2bf7673b0658bed",
             "multiqc_general_stats.txt:md5,b1999255f9a502618d59be2f2e93bad2",
-            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921"
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
         ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-05-17T12:58:02.572837"
+        "timestamp": "2024-05-30T13:14:40.99246"
     }
 }
\ No newline at end of file

From 97cdfdd9f8b58ebf824c702d204a926c14d72d7d Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 27 Aug 2024 13:17:02 +0200
Subject: [PATCH 037/530] Implement tagging system

---
 README.md                                     |   4 +-
 assets/samplesheet.csv                        |  10 +-
 assets/schema_input.json                      |  16 +--
 conf/modules.config                           |  64 +--------
 docs/output.md                                |  45 +++---
 docs/usage.md                                 |  13 +-
 main.nf                                       |   6 +-
 .../main.nf                                   |   4 +-
 tests/MiSeq.main.nf.test                      |  18 +--
 tests/MiSeq.main.nf.test.snap                 |  14 +-
 tests/NovaSeq6000.main.nf.test                |  53 ++++---
 tests/NovaSeq6000.main.nf.test.snap           |  26 ++--
 tests/PromethION.main.nf.test                 |  13 +-
 tests/PromethION.main.nf.test.snap            |  10 +-
 workflows/seqinspector.nf                     | 131 ++++--------------
 15 files changed, 126 insertions(+), 301 deletions(-)

diff --git a/README.md b/README.md
index 7efdd3e9..31018e7b 100644
--- a/README.md
+++ b/README.md
@@ -44,8 +44,8 @@ First, prepare a samplesheet with your input data that looks as follows:
 `samplesheet.csv`:
 
 ```csv
-sample,lane,group,fastq_1,fastq_2,rundir
-CONTROL_REP1,1,GROUP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX
+sample,fastq_1,fastq_2,rundir,tags
+CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,"patient1"
 ```
 
 Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
index fef3b4e6..00019e58 100644
--- a/assets/samplesheet.csv
+++ b/assets/samplesheet.csv
@@ -1,3 +1,7 @@
-sample,lane,group,fastq_1,fastq_2,rundir
-SAMPLE_PAIRED_END,1,P001,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz,/path/to/rundir
-SAMPLE_SINGLE_END,2,P002,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir
+sample,fastq_1,fastq_2,rundir,tags
+SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz,/path/to/rundir,"paired_sample,cohort1"
+SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A2_S2_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A2_S2_L002_R2_001.fastq.gz,/path/to/rundir,"paired_sample,cohort1"
+SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A3_S3_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A3_S3_L002_R2_001.fastq.gz,/path/to/rundir,"paired_sample,cohort2"
+SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,"patient1"
+SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,"patient2"
+SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,"patient3"
diff --git a/assets/schema_input.json b/assets/schema_input.json
index c9800d5d..62922b79 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -13,18 +13,6 @@
                 "errorMessage": "Sample name must be provided and cannot contain spaces",
                 "meta": ["sample"]
             },
-            "lane": {
-                "type": "integer",
-                "pattern": "^\\d+$",
-                "errorMessage": "Lane ID must be a number",
-                "meta": ["lane"]
-            },
-            "group": {
-                "type": "string",
-                "pattern": "^\\S+$",
-                "errorMessage": "Group ID cannot contain spaces",
-                "meta": ["group"]
-            },
             "fastq_1": {
                 "type": "string",
                 "format": "file-path",
@@ -45,6 +33,10 @@
                 "exists": true,
                 "errorMessage": "Run directory must be a path",
                 "meta": ["rundir"]
+            },
+            "tags": {
+                "type": "string",
+                "meta": ["tags"]
             }
         },
         "required": ["sample", "fastq_1"],
diff --git a/conf/modules.config b/conf/modules.config
index f7e78457..c8838224 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -25,16 +25,16 @@ process {
     withName: 'MULTIQC_GLOBAL' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
-            path: { "${params.outdir}/multiqc" },
+            path: { "${params.outdir}/multiqc/global_report" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
-    withName: 'MULTIQC_PER_LANE' {
+    withName: 'MULTIQC_PER_TAG' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
-            path: { "${params.outdir}/multiqc/lanes" },
+            path: { "${params.outdir}/multiqc/group_reports" },
             mode: params.publish_dir_mode,
             saveAs: {
                 filename ->
@@ -42,62 +42,12 @@ process {
                         case 'versions.yml':
                             null
                             break
-                        case ~/\[LANE:\d+\]_multiqc_(report\.html|plots|data)/:
-                            def lane = (filename =~ /\[LANE:(\d+)\]_multiqc_(report\.html|plots|data)/)[0][1]
+                        case ~/\[TAG:.+\]_multiqc_(report\.html|plots|data)/:
+                            def tag = (filename =~ /\[TAG:(.+)\]_multiqc_(report\.html|plots|data)/)[0][1]
                             def new_filename = filename.replaceFirst(
-                                "(?<prefix>.*)\\[LANE:${lane}\\]_(?<suffix>multiqc_(report\\.html|plots|data).*)",
+                                "(?<prefix>.*)\\[TAG:${tag}\\]_(?<suffix>multiqc_(report\\.html|plots|data).*)",
                                 '${prefix}${suffix}')
-                            "L${lane}/${new_filename}"
-                            break
-                        default:
-                            filename
-                    }
-            }
-        ]
-    }
-
-    withName: 'MULTIQC_PER_GROUP' {
-        ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
-        publishDir = [
-            path: { "${params.outdir}/multiqc/groups" },
-            mode: params.publish_dir_mode,
-            saveAs: {
-                filename ->
-                    switch (filename) {
-                        case 'versions.yml':
-                            null
-                            break
-                        case ~/\[GROUP:.+\]_multiqc_(report\.html|plots|data)/:
-                            def group = (filename =~ /\[GROUP:(.+)\]_multiqc_(report\.html|plots|data)/)[0][1]
-                            def new_filename = filename.replaceFirst(
-                                "(?<prefix>.*)\\[GROUP:${group}\\]_(?<suffix>multiqc_(report\\.html|plots|data).*)",
-                                '${prefix}${suffix}')
-                            "${group}/${new_filename}"
-                            break
-                        default:
-                            filename
-                    }
-            }
-        ]
-    }
-
-    withName: 'MULTIQC_PER_RUNDIR' {
-        ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
-        publishDir = [
-            path: { "${params.outdir}/multiqc/rundirss" },
-            mode: params.publish_dir_mode,
-            saveAs: {
-                filename ->
-                    switch (filename) {
-                        case 'versions.yml':
-                            null
-                            break
-                        case ~/\[RUNDIR:.+\]_multiqc_(report\.html|plots|data)/:
-                            def rundir = (filename =~ /\[RUNDIR:(.+)\]_multiqc_(report\.html|plots|data)/)[0][1]
-                            def new_filename = filename.replaceFirst(
-                                "(?<prefix>.*)\\[RUNDIR:${rundir}\\]_(?<suffix>multiqc_(report\\.html|plots|data).*)",
-                                '${prefix}${suffix}')
-                            "${rundir}/${new_filename}"
+                            "${tag}/${new_filename}"
                             break
                         default:
                             filename
diff --git a/docs/output.md b/docs/output.md
index 7af7806c..15c29ce2 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -39,36 +39,29 @@ The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They m
 
 ### MultiQC
 
+nf-core/seqinspector will generate the following MultiQC reports:
+
+- one global reports including all the samples listed in the samplesheet
+- one group report per unique tag. These reports compile samples that share the same tag.
+
 <details markdown="1">
 <summary>Output files</summary>
 
 - `multiqc/`
-  - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
-  - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
-  - `multiqc_plots/`: directory containing static images from the report in various formats.
-  - `lanes/` [1]
-    - `L1/`
-      - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
-      - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
-      - `multiqc_plots/`: directory containing static images from the report in various formats.
-    - `L2/`
-      - ...
-  - `groups/` [1]
-    - `GROUPNAME1/`
-      - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
-      - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
-      - `multiqc_plots/`: directory containing static images from the report in various formats.
-    - `GROUPNAME2/`
-      - ...
-  - `rundir/` [1]
-    - `RUNDIR1/`
-      - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
-      - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
-      - `multiqc_plots/`: directory containing static images from the report in various formats.
-    - `RUNDIR2/`
-      - ...
-
-[1] These files will only be generated if `lane`, `group` or `rundir` were specified for some samples.
+  - `global_report`
+    - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
+    - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
+    - `multiqc_plots/`: directory containing static images from the report in various formats.
+  - `group_reports`
+    - `tag1/`
+      - `multiqc_report.html`
+      - `multiqc_data/`
+      - `multiqc_plots/`
+    - `tag2/`
+      - `multiqc_report.html`
+      - `multiqc_data/`
+      - `multiqc_plots/`
+    - ...
 
 </details>
 
diff --git a/docs/usage.md b/docs/usage.md
index 7a4ec735..42d596bb 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -31,22 +31,21 @@ run_dir
 ...would be represented in the following samplesheet (shown as .tsv for readability)
 
 ```csv title="samplesheet.csv"
-sample  lane  group   fastq_1                                       fastq_2 rundir
-sample1 1     group1  path/to/run_dir/sample1_lane1_group1_r1.fq.gz         path/to/run_dir
-sample2 1     group1  path/to/run_dir/sample2_lane1_group1_r1.fq.gz         path/to/run_dir
-sample3 2     group2  path/to/run_dir/sample3_lane2_group2_r1.fq.gz         path/to/run_dir
-sample4 2     group3  path/to/run_dir/sample4_lane2_group3_r1.fq.gz         path/to/run_dir
+sample  fastq_1                                       fastq_2 rundir          tags
+sample1 path/to/run_dir/sample1_lane1_group1_r1.fq.gz         path/to/run_dir "cohort1,patient1"
+sample2 path/to/run_dir/sample2_lane1_group1_r1.fq.gz         path/to/run_dir "cohort1,patient2"
+sample3 path/to/run_dir/sample3_lane2_group2_r1.fq.gz         path/to/run_dir "cohort1,patient3"
+sample4 path/to/run_dir/sample4_lane2_group3_r1.fq.gz         path/to/run_dir "control"
 
 ```
 
 | Column    | Description                                                                                                                                                                            |
 | --------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | `sample`  | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). |
-| `lane`    | Lane where the sample was processed on an Illumina instrument (optional).                                                                                                              |
-| `group`   | Group the sample belongs too, useful when several groups are pooled together (optional).                                                                                               |
 | `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                             |
 | `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz" (optional).                                                  |
 | `rundir`  | Path to the runfolder containing extra information about the sequencing run (optional) .                                                                                               |
+| `tags`    | Comma-separated list of tags to group samples in special reports.                                                                                                                      |
 
 Another [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
 
diff --git a/main.nf b/main.nf
index fb00bd5d..a55408ef 100644
--- a/main.nf
+++ b/main.nf
@@ -58,10 +58,8 @@ workflow NFCORE_SEQINSPECTOR {
     )
 
     emit:
-    global_report = SEQINSPECTOR.out.global_report  // channel: /path/to/multiqc_report.html
-    lane_reports  = SEQINSPECTOR.out.lane_reports   // channel: /path/to/multiqc_report.html
-    group_reports = SEQINSPECTOR.out.group_reports  // channel: /path/to/multiqc_report.html
-    rundir_report = SEQINSPECTOR.out.rundir_reports // channel: /path/to/multiqc_report.html
+    global_report   = SEQINSPECTOR.out.global_report    // channel: /path/to/multiqc_report.html
+    grouped_reports = SEQINSPECTOR.out.grouped_reports  // channel: /path/to/multiqc_report.html
 
 }
 /*
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index ea9c9b8a..afcfc68b 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -84,8 +84,8 @@ workflow PIPELINE_INITIALISATION {
         .fromSamplesheet("input") // Validates samplesheet against $projectDir/assets/schema_input.json. Path to validation schema is defined by $projectDir/nextflow_schema.json
         .map {
             meta, fastq_1, fastq_2 ->
-                def id_string = "${meta.sample}_${meta.group ?: "ungrouped"}_${meta.lane}"
-                def updated_meta = meta + [ id: id_string ]
+                def tags = meta.tags ? meta.tags.tokenize(",") : []
+                def updated_meta = meta + [ id:meta.sample, tags:tags ]
                 if (!fastq_2) {
                     return [ updated_meta.id, updated_meta + [ single_end:true ], [ fastq_1 ] ]
                 } else {
diff --git a/tests/MiSeq.main.nf.test b/tests/MiSeq.main.nf.test
index bfabd954..8fbff4a3 100644
--- a/tests/MiSeq.main.nf.test
+++ b/tests/MiSeq.main.nf.test
@@ -18,20 +18,10 @@ nextflow_pipeline {
             assertAll(
                 { assert workflow.success },
                 { assert snapshot(
-                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_software_versions.txt"),
-
-                    path("$outputDir/multiqc/groups/P001/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/groups/P001/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/groups/P001/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/groups/P001/multiqc_data/multiqc_software_versions.txt"),
-
-                    path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/multiqc_data/multiqc_software_versions.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_software_versions.txt"),
                     ).match()
                 }
             )
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 87c1a561..26f0c2a8 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -2,18 +2,10 @@
     "MiSeq data test": {
         "content": [
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,692b8aed0614ed1655f2c1cbea1ba312",
-            "multiqc_general_stats.txt:md5,630167d67d3f92408cd1a04422c7196f",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,692b8aed0614ed1655f2c1cbea1ba312",
-            "multiqc_general_stats.txt:md5,630167d67d3f92408cd1a04422c7196f",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,692b8aed0614ed1655f2c1cbea1ba312",
-            "multiqc_general_stats.txt:md5,630167d67d3f92408cd1a04422c7196f",
+            "multiqc_fastqc.txt:md5,e46e7baa8f57d4cf54d973925b5eadf9",
+            "multiqc_general_stats.txt:md5,a5e626a2e1a3c986092e4f89091cc41c",
             "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
         ],
-        "timestamp": "2024-05-30T13:14:20.263485"
+        "timestamp": "2024-08-26T17:55:16.152573"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test b/tests/NovaSeq6000.main.nf.test
index 174e215d..f93891bf 100644
--- a/tests/NovaSeq6000.main.nf.test
+++ b/tests/NovaSeq6000.main.nf.test
@@ -18,35 +18,30 @@ nextflow_pipeline {
             assertAll(
                 { assert workflow.success },
                 { assert snapshot(
-                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_software_versions.txt"),
-
-                    path("$outputDir/multiqc/groups/S1/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/groups/S1/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/groups/S1/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/groups/S1/multiqc_data/multiqc_software_versions.txt"),
-
-                    path("$outputDir/multiqc/groups/S2/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/groups/S2/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/groups/S2/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/groups/S2/multiqc_data/multiqc_software_versions.txt"),
-
-                    path("$outputDir/multiqc/groups/S3/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/groups/S3/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/groups/S3/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/groups/S3/multiqc_data/multiqc_software_versions.txt"),
-
-                    path("$outputDir/multiqc/groups/S4/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/groups/S4/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/groups/S4/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/groups/S4/multiqc_data/multiqc_software_versions.txt"),
-
-                    path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/multiqc_data/multiqc_software_versions.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_software_versions.txt"),
+
+                    path("$outputDir/multiqc/group_reports/cohort1/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/group_reports/cohort1/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/group_reports/cohort1/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/cohort1/multiqc_data/multiqc_software_versions.txt"),
+
+                    path("$outputDir/multiqc/group_reports/patient1/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/group_reports/patient1/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/group_reports/patient1/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/patient1/multiqc_data/multiqc_software_versions.txt"),
+
+                    path("$outputDir/multiqc/group_reports/patient2/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/group_reports/patient2/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/group_reports/patient2/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/patient2/multiqc_data/multiqc_software_versions.txt"),
+
+                    path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_software_versions.txt"),
                     ).match()
                 },
             )
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index 22600251..f5c4776b 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -2,30 +2,26 @@
     "NovaSeq6000 data test": {
         "content": [
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,5ba3f4f4ec6026a5f5d55418384dcd3e",
-            "multiqc_general_stats.txt:md5,123cd6b64c9c15607405bcdd45a843d4",
+            "multiqc_fastqc.txt:md5,e8ed6dca928396b8873d24e60ea1a133",
+            "multiqc_general_stats.txt:md5,fd9d46c5b441908cd07e5373d116db17",
             "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,9b4fd8a6d6e8a9acabecd592f633472e",
-            "multiqc_general_stats.txt:md5,8237b88ceb018d3cb1edcea62d10f4a2",
+            "multiqc_fastqc.txt:md5,ff9b31c6024f11a8135456e7ea01fc8f",
+            "multiqc_general_stats.txt:md5,f36bd6e27e92c25be076efea411d3a8e",
             "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,9246a5b6b7b0410c79049fc3dbd08e92",
-            "multiqc_general_stats.txt:md5,44328403f423c6f5ac9ee0a8a01e6725",
+            "multiqc_fastqc.txt:md5,62d51280dcd7634f6bed95ffe0d8dab8",
+            "multiqc_general_stats.txt:md5,2012002b6a057be981a97fcc96142a6c",
             "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,84820276fae52d4d492831280ae6207c",
-            "multiqc_general_stats.txt:md5,dd07799e5e4b9d389f9de49a852c3363",
+            "multiqc_fastqc.txt:md5,63749e803a2d5fc7ecc7cd93fa68df1f",
+            "multiqc_general_stats.txt:md5,656931993032400dea3d441b8b61b4d2",
             "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,59ae05d89453da6f57010ffb6466f902",
-            "multiqc_general_stats.txt:md5,e4629691992bfe639c01a84b90563334",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,5ba3f4f4ec6026a5f5d55418384dcd3e",
-            "multiqc_general_stats.txt:md5,123cd6b64c9c15607405bcdd45a843d4",
+            "multiqc_fastqc.txt:md5,91cc62e1b4059bdbe4b88affa43378af",
+            "multiqc_general_stats.txt:md5,6e500f82550e00b07c3e7aa1d46ab9e9",
             "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
         ],
-        "timestamp": "2024-05-30T13:13:49.062282"
+        "timestamp": "2024-08-26T18:03:33.089142"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test b/tests/PromethION.main.nf.test
index 39284786..8fec8b33 100644
--- a/tests/PromethION.main.nf.test
+++ b/tests/PromethION.main.nf.test
@@ -18,15 +18,10 @@ nextflow_pipeline {
             assertAll(
                 { assert workflow.success },
                 { assert snapshot(
-                    path("$outputDir/multiqc/groups/r10p41_e8p2_human_runs_jkw/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/groups/r10p41_e8p2_human_runs_jkw/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/groups/r10p41_e8p2_human_runs_jkw/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/groups/r10p41_e8p2_human_runs_jkw/multiqc_data/multiqc_software_versions.txt"),
-
-                    path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/multiqc_data/multiqc_software_versions.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_software_versions.txt"),
                     ).match()
                 },
             )
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index 0ac213c1..e3b34f23 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -2,14 +2,10 @@
     "PromethION data test": {
         "content": [
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,333360ff12007d64f2bf7673b0658bed",
-            "multiqc_general_stats.txt:md5,b1999255f9a502618d59be2f2e93bad2",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,333360ff12007d64f2bf7673b0658bed",
-            "multiqc_general_stats.txt:md5,b1999255f9a502618d59be2f2e93bad2",
+            "multiqc_fastqc.txt:md5,cecee3cb343c75c80180d3169c6f3ea1",
+            "multiqc_general_stats.txt:md5,e63c25089c4fc10618414ba2254d18c7",
             "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
         ],
-        "timestamp": "2024-05-30T13:14:40.99246"
+        "timestamp": "2024-08-26T17:55:38.755385"
     }
 }
\ No newline at end of file
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 50fa481f..e37df509 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -7,9 +7,7 @@
 include { FASTQC                        } from '../modules/nf-core/fastqc/main'
 
 include { MULTIQC as MULTIQC_GLOBAL     } from '../modules/nf-core/multiqc/main'
-include { MULTIQC as MULTIQC_PER_LANE   } from '../modules/nf-core/multiqc/main'
-include { MULTIQC as MULTIQC_PER_GROUP  } from '../modules/nf-core/multiqc/main'
-include { MULTIQC as MULTIQC_PER_RUNDIR } from '../modules/nf-core/multiqc/main'
+include { MULTIQC as MULTIQC_PER_TAG    } from '../modules/nf-core/multiqc/main'
 
 include { paramsSummaryMap              } from 'plugin/nf-validation'
 include { paramsSummaryMultiqc          } from '../subworkflows/nf-core/utils_nfcore_pipeline'
@@ -94,124 +92,51 @@ workflow SEQINSPECTOR {
         ch_multiqc_logo.toList()
     )
 
-    // Generate reports by lane
-    multiqc_extra_files_per_lane = ch_multiqc_files
-        .filter { meta, sample -> meta.lane }
-        .map { meta, sample -> [lane: meta.lane] }
+    ch_tags = ch_multiqc_files
+        .map { meta, sample -> meta.tags }
+        .flatten()
         .unique()
-        .combine(ch_multiqc_extra_files)
 
-    lane_mqc_files = ch_multiqc_files
-        .filter { meta, sample -> meta.lane }
-        .mix(multiqc_extra_files_per_lane)
-        .map { meta, sample -> [ "[LANE:${meta.lane}]", meta, sample ] }
-        .groupTuple()
-        .tap { mqc_by_lane }
-        .collectFile{
-            lane, meta, samples -> [
-                "${lane}_multiqc_extra_config.yml",
-                """
-                    |output_fn_name: \"${lane}_multiqc_report.html\"
-                    |data_dir_name:  \"${lane}_multiqc_data\"
-                    |plots_dir_name: \"${lane}_multiqc_plots\"
-                """.stripMargin()
-            ]
-        }
-        .map { file -> [ (file =~ /(\[LANE:.+\])/)[0][1], file ] }
-        .join(mqc_by_lane)
-        .multiMap { lane, config, meta , samples_per_lane ->
-            samples_per_lane: samples_per_lane
-            config: config
-        }
-
-    MULTIQC_PER_LANE(
-        lane_mqc_files.samples_per_lane,
-        ch_multiqc_config.toList(),
-        lane_mqc_files.config,
-        ch_multiqc_logo.toList()
-    )
-
-    // Generate reports by group
-    multiqc_extra_files_per_group = ch_multiqc_files
-        .filter { meta, sample -> meta.group }
-        .map { meta, sample -> meta.group }
-        .unique()
-        .map { group -> [group:group] }
-        .combine(ch_multiqc_extra_files)
-
-    group_mqc_files = ch_multiqc_files
-        .filter { meta, sample -> meta.group }
-        .mix(multiqc_extra_files_per_group)
-        .map { meta, sample -> [ "[GROUP:${meta.group}]", meta, sample ] }
-        .groupTuple()
-        .tap { mqc_by_group }
-        .collectFile{
-            group, meta, samples -> [
-                "${group}_multiqc_extra_config.yml",
-                """
-                    |output_fn_name: \"${group}_multiqc_report.html\"
-                    |data_dir_name:  \"${group}_multiqc_data\"
-                    |plots_dir_name: \"${group}_multiqc_plots\"
-                """.stripMargin()
-            ]
-        }
-        .map { file -> [ (file =~ /(\[GROUP:.+\])/)[0][1], file ] }
-        .join(mqc_by_group)
-        .multiMap { group, config, meta , samples_per_group ->
-            samples_per_group: samples_per_group
-            config: config
-        }
-
-    MULTIQC_PER_GROUP(
-        group_mqc_files.samples_per_group,
-        ch_multiqc_config.toList(),
-        group_mqc_files.config,
-        ch_multiqc_logo.toList()
-    )
-
-    // Generate reports by rundir
-    multiqc_extra_files_per_rundir = ch_multiqc_files
-        .filter { meta, sample -> meta.rundir }
-        .map { meta, sample -> meta.rundir }
-        .unique()
-        .map { rundir -> [rundir:rundir] }
+    multiqc_extra_files_per_tag = ch_tags
         .combine(ch_multiqc_extra_files)
 
-    rundir_mqc_files = ch_multiqc_files
-        .filter { meta, sample -> meta.rundir }
-        .mix(multiqc_extra_files_per_rundir)
-        .map { meta, sample -> [ "[RUNDIR:${meta.rundir.name}]", meta, sample ] }
+    // Group samples by tag
+    tagged_mqc_files = ch_tags
+        .combine(ch_multiqc_files)
+        .filter { sample_tag, meta, sample -> sample_tag in meta.tags }
+        .map { sample_tag, meta, sample -> [sample_tag, sample] }
+        .mix(multiqc_extra_files_per_tag)
         .groupTuple()
-        .tap { mqc_by_rundir }
-        .collectFile{
-            rundir, meta, samples -> [
-                "${rundir}_multiqc_extra_config.yml",
+        .tap { mqc_by_tag }
+        .collectFile {
+            sample_tag, samples ->
+            def prefix_tag = "[TAG:${sample_tag}]"
+            [
+                "${prefix_tag}_multiqc_extra_config.yml",
                 """
-                    |output_fn_name: \"${rundir}_multiqc_report.html\"
-                    |data_dir_name:  \"${rundir}_multiqc_data\"
-                    |plots_dir_name: \"${rundir}_multiqc_plots\"
+                    |output_fn_name: \"${prefix_tag}_multiqc_report.html\"
+                    |data_dir_name:  \"${prefix_tag}_multiqc_data\"
+                    |plots_dir_name: \"${prefix_tag}_multiqc_plots\"
                 """.stripMargin()
             ]
         }
-        .map { file -> [ (file =~ /(\[RUNDIR:.+\])/)[0][1], file ] }
-        .join(mqc_by_rundir)
-        .multiMap { rundir, config, meta , samples_per_rundir ->
-            samples_per_rundir: samples_per_rundir
+        .map { file -> [ (file =~ /\[TAG:(.+)\]/)[0][1], file ] }
+        .join(mqc_by_tag)
+        .multiMap { sample_tag, config, samples ->
+            samples_per_tag: samples
             config: config
         }
 
-    MULTIQC_PER_RUNDIR(
-        rundir_mqc_files.samples_per_rundir,
+    MULTIQC_PER_TAG(
+        tagged_mqc_files.samples_per_tag,
         ch_multiqc_config.toList(),
-        rundir_mqc_files.config,
+        tagged_mqc_files.config,
         ch_multiqc_logo.toList()
     )
 
     emit:
     global_report = MULTIQC_GLOBAL.out.report.toList()      // channel: /path/to/multiqc_report.html
-    lane_reports = MULTIQC_PER_LANE.out.report.toList()     // channel: [ /path/to/multiqc_report.html ]
-    group_reports = MULTIQC_PER_GROUP.out.report.toList()   // channel: [ /path/to/multiqc_report.html ]
-    rundir_reports = MULTIQC_PER_RUNDIR.out.report.toList() // channel: [ /path/to/multiqc_report.html ]
+    grouped_reports = MULTIQC_PER_TAG.out.report.toList()   // channel: [ /path/to/multiqc_report.html ]
     versions       = ch_versions                            // channel: [ path(versions.yml) ]
 }
 

From 81d79a15d2a6b14d88a3c9b8ea2dcab0829c2405 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 27 Aug 2024 15:08:20 +0200
Subject: [PATCH 038/530] Update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6430addb..3aa5bacc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 
 ### `Added`
 
+- [#20](https://github.com/nf-core/seqinspector/pull/20) Use tags to generate group reports
 - [#13](https://github.com/nf-core/seqinspector/pull/13) Generate reports per run, per project and per lane.
 
 ### `Fixed`

From aee596e51b8fc5d5f23b422144a7f2176a260ce0 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <89784800+kedhammar@users.noreply.github.com>
Date: Tue, 27 Aug 2024 15:52:46 +0200
Subject: [PATCH 039/530] Try adding regex assertion and error for samplesheet
 tags

---
 assets/schema_input.json | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/assets/schema_input.json b/assets/schema_input.json
index 62922b79..bde27fa7 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -36,6 +36,8 @@
             },
             "tags": {
                 "type": "string",
+                "pattern": "^\\\"([A-Za-z0-9_-]+,\\ ?)*([A-Za-z0-9_-]+)\\\"$",
+                "errorMessage": "Tags must consist of numbers, letters, underscores or dashes and must be provided as a comma-separated list flanked by a pair of double-quotes, e.g. \"patient_01, lane1, pos-CTRL_2\"."
                 "meta": ["tags"]
             }
         },

From 9b1c7074a27a12b387202cef9cca7012cf0a9a88 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <89784800+kedhammar@users.noreply.github.com>
Date: Tue, 27 Aug 2024 15:55:26 +0200
Subject: [PATCH 040/530] Add missing comma

---
 assets/schema_input.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/assets/schema_input.json b/assets/schema_input.json
index bde27fa7..d4a6dc70 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -37,7 +37,7 @@
             "tags": {
                 "type": "string",
                 "pattern": "^\\\"([A-Za-z0-9_-]+,\\ ?)*([A-Za-z0-9_-]+)\\\"$",
-                "errorMessage": "Tags must consist of numbers, letters, underscores or dashes and must be provided as a comma-separated list flanked by a pair of double-quotes, e.g. \"patient_01, lane1, pos-CTRL_2\"."
+                "errorMessage": "Tags must consist of numbers, letters, underscores or dashes and must be provided as a comma-separated list flanked by a pair of double-quotes, e.g. \"patient_01, lane1, pos-CTRL_2\".",
                 "meta": ["tags"]
             }
         },

From 830aa46601aa46329362776e0569f2a4323c27df Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 3 Sep 2024 10:35:51 +0200
Subject: [PATCH 041/530] Change example tags to more neutral ones

---
 README.md     | 2 +-
 docs/usage.md | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 31018e7b..679b6f1c 100644
--- a/README.md
+++ b/README.md
@@ -45,7 +45,7 @@ First, prepare a samplesheet with your input data that looks as follows:
 
 ```csv
 sample,fastq_1,fastq_2,rundir,tags
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,"patient1"
+CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,"group1"
 ```
 
 Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
diff --git a/docs/usage.md b/docs/usage.md
index 42d596bb..621c7c0a 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -32,9 +32,9 @@ run_dir
 
 ```csv title="samplesheet.csv"
 sample  fastq_1                                       fastq_2 rundir          tags
-sample1 path/to/run_dir/sample1_lane1_group1_r1.fq.gz         path/to/run_dir "cohort1,patient1"
-sample2 path/to/run_dir/sample2_lane1_group1_r1.fq.gz         path/to/run_dir "cohort1,patient2"
-sample3 path/to/run_dir/sample3_lane2_group2_r1.fq.gz         path/to/run_dir "cohort1,patient3"
+sample1 path/to/run_dir/sample1_lane1_group1_r1.fq.gz         path/to/run_dir "project1,group1"
+sample2 path/to/run_dir/sample2_lane1_group1_r1.fq.gz         path/to/run_dir "project1,group1"
+sample3 path/to/run_dir/sample3_lane2_group2_r1.fq.gz         path/to/run_dir "project1,group2"
 sample4 path/to/run_dir/sample4_lane2_group3_r1.fq.gz         path/to/run_dir "control"
 
 ```

From 8b59f0b31f654f8e49203a6e29794833a70d4a2d Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 3 Sep 2024 12:36:42 +0200
Subject: [PATCH 042/530] Check for tag collisions

---
 .../utils_nfcore_seqinspector_pipeline/main.nf     | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index afcfc68b..bb875af6 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -103,6 +103,20 @@ workflow PIPELINE_INITIALISATION {
         // }
         .set { ch_samplesheet }
 
+    ch_samplesheet
+        .map {
+            meta, fastqs -> meta.tags
+        }
+        .flatten()
+        .unique()
+        .map { tag_name -> [tag_name.toLowerCase(), tag_name] }
+        .groupTuple()
+        .map {
+            tag_lowercase, tags ->
+                assert tags.size() == 1 :
+                "Tag name collision: " + tags.join(", ")
+        }
+
     emit:
     samplesheet = ch_samplesheet
     versions    = ch_versions

From 4b54f546fcde02aa28521cbdff224b0b7e31658f Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 3 Sep 2024 12:58:50 +0200
Subject: [PATCH 043/530] Use columns to separate tags

---
 README.md                                     |  2 +-
 assets/samplesheet.csv                        | 12 ++++----
 assets/schema_input.json                      |  4 +--
 docs/usage.md                                 | 10 +++----
 .../main.nf                                   |  2 +-
 tests/NovaSeq6000.main.nf.test                | 28 +++++++++----------
 6 files changed, 29 insertions(+), 29 deletions(-)

diff --git a/README.md b/README.md
index 679b6f1c..d7cd233f 100644
--- a/README.md
+++ b/README.md
@@ -45,7 +45,7 @@ First, prepare a samplesheet with your input data that looks as follows:
 
 ```csv
 sample,fastq_1,fastq_2,rundir,tags
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,"group1"
+CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,group1
 ```
 
 Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
index 00019e58..ba2542dd 100644
--- a/assets/samplesheet.csv
+++ b/assets/samplesheet.csv
@@ -1,7 +1,7 @@
 sample,fastq_1,fastq_2,rundir,tags
-SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz,/path/to/rundir,"paired_sample,cohort1"
-SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A2_S2_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A2_S2_L002_R2_001.fastq.gz,/path/to/rundir,"paired_sample,cohort1"
-SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A3_S3_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A3_S3_L002_R2_001.fastq.gz,/path/to/rundir,"paired_sample,cohort2"
-SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,"patient1"
-SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,"patient2"
-SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,"patient3"
+SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz,/path/to/rundir,paired_sample:lane1
+SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A2_S2_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A2_S2_L002_R2_001.fastq.gz,/path/to/rundir,paired_sample:lane1
+SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A3_S3_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A3_S3_L002_R2_001.fastq.gz,/path/to/rundir,paired_sample:lane2
+SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,group1
+SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,group2
+SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,group3
diff --git a/assets/schema_input.json b/assets/schema_input.json
index d4a6dc70..3569ae2f 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -36,8 +36,8 @@
             },
             "tags": {
                 "type": "string",
-                "pattern": "^\\\"([A-Za-z0-9_-]+,\\ ?)*([A-Za-z0-9_-]+)\\\"$",
-                "errorMessage": "Tags must consist of numbers, letters, underscores or dashes and must be provided as a comma-separated list flanked by a pair of double-quotes, e.g. \"patient_01, lane1, pos-CTRL_2\".",
+                "pattern": "^([A-Za-z0-9_-]+:)*([A-Za-z0-9_-]+)$",
+                "errorMessage": "Tags must consist of numbers, letters, underscores or dashes and must be provided as a column-separated list, e.g. group_01:lane1:pos-CTRL_2.",
                 "meta": ["tags"]
             }
         },
diff --git a/docs/usage.md b/docs/usage.md
index 621c7c0a..38a039c4 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -32,10 +32,10 @@ run_dir
 
 ```csv title="samplesheet.csv"
 sample  fastq_1                                       fastq_2 rundir          tags
-sample1 path/to/run_dir/sample1_lane1_group1_r1.fq.gz         path/to/run_dir "project1,group1"
-sample2 path/to/run_dir/sample2_lane1_group1_r1.fq.gz         path/to/run_dir "project1,group1"
-sample3 path/to/run_dir/sample3_lane2_group2_r1.fq.gz         path/to/run_dir "project1,group2"
-sample4 path/to/run_dir/sample4_lane2_group3_r1.fq.gz         path/to/run_dir "control"
+sample1 path/to/run_dir/sample1_lane1_group1_r1.fq.gz         path/to/run_dir project1:group1
+sample2 path/to/run_dir/sample2_lane1_group1_r1.fq.gz         path/to/run_dir project1:group1
+sample3 path/to/run_dir/sample3_lane2_group2_r1.fq.gz         path/to/run_dir project1:group2
+sample4 path/to/run_dir/sample4_lane2_group3_r1.fq.gz         path/to/run_dir control
 
 ```
 
@@ -45,7 +45,7 @@ sample4 path/to/run_dir/sample4_lane2_group3_r1.fq.gz         path/to/run_dir "c
 | `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                             |
 | `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz" (optional).                                                  |
 | `rundir`  | Path to the runfolder containing extra information about the sequencing run (optional) .                                                                                               |
-| `tags`    | Comma-separated list of tags to group samples in special reports.                                                                                                                      |
+| `tags`    | Column-separated list of tags to group samples in special reports.                                                                                                                     |
 
 Another [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
 
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index bb875af6..eec4d09c 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -84,7 +84,7 @@ workflow PIPELINE_INITIALISATION {
         .fromSamplesheet("input") // Validates samplesheet against $projectDir/assets/schema_input.json. Path to validation schema is defined by $projectDir/nextflow_schema.json
         .map {
             meta, fastq_1, fastq_2 ->
-                def tags = meta.tags ? meta.tags.tokenize(",") : []
+                def tags = meta.tags ? meta.tags.tokenize(":") : []
                 def updated_meta = meta + [ id:meta.sample, tags:tags ]
                 if (!fastq_2) {
                     return [ updated_meta.id, updated_meta + [ single_end:true ], [ fastq_1 ] ]
diff --git a/tests/NovaSeq6000.main.nf.test b/tests/NovaSeq6000.main.nf.test
index f93891bf..d050399e 100644
--- a/tests/NovaSeq6000.main.nf.test
+++ b/tests/NovaSeq6000.main.nf.test
@@ -23,20 +23,20 @@ nextflow_pipeline {
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_software_versions.txt"),
 
-                    path("$outputDir/multiqc/group_reports/cohort1/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/group_reports/cohort1/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/group_reports/cohort1/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/group_reports/cohort1/multiqc_data/multiqc_software_versions.txt"),
-
-                    path("$outputDir/multiqc/group_reports/patient1/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/group_reports/patient1/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/group_reports/patient1/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/group_reports/patient1/multiqc_data/multiqc_software_versions.txt"),
-
-                    path("$outputDir/multiqc/group_reports/patient2/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/group_reports/patient2/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/group_reports/patient2/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/group_reports/patient2/multiqc_data/multiqc_software_versions.txt"),
+                    path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_software_versions.txt"),
+
+                    path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt"),
+
+                    path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_software_versions.txt"),
 
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt"),

From 97f848a166c44996e75b7f92e3758a543d61cb33 Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Tue, 3 Sep 2024 13:55:23 +0200
Subject: [PATCH 044/530] switch to colon-separated tags

---
 README.md                                            |  2 +-
 assets/samplesheet.csv                               | 12 ++++++------
 assets/schema_input.json                             |  4 ++--
 docs/usage.md                                        | 12 ++++++------
 .../local/utils_nfcore_seqinspector_pipeline/main.nf |  2 +-
 5 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/README.md b/README.md
index 31018e7b..acba2cec 100644
--- a/README.md
+++ b/README.md
@@ -45,7 +45,7 @@ First, prepare a samplesheet with your input data that looks as follows:
 
 ```csv
 sample,fastq_1,fastq_2,rundir,tags
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,"patient1"
+CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2
 ```
 
 Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
index 00019e58..de5f1a68 100644
--- a/assets/samplesheet.csv
+++ b/assets/samplesheet.csv
@@ -1,7 +1,7 @@
 sample,fastq_1,fastq_2,rundir,tags
-SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz,/path/to/rundir,"paired_sample,cohort1"
-SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A2_S2_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A2_S2_L002_R2_001.fastq.gz,/path/to/rundir,"paired_sample,cohort1"
-SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A3_S3_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A3_S3_L002_R2_001.fastq.gz,/path/to/rundir,"paired_sample,cohort2"
-SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,"patient1"
-SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,"patient2"
-SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,"patient3"
+SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz,/path/to/rundir,paired_sample:cohort1
+SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A2_S2_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A2_S2_L002_R2_001.fastq.gz,/path/to/rundir,paired_sample:cohort1
+SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A3_S3_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A3_S3_L002_R2_001.fastq.gz,/path/to/rundir,paired_sample:cohort2
+SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,patient1
+SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,patient2
+SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,patient3
diff --git a/assets/schema_input.json b/assets/schema_input.json
index d4a6dc70..18941557 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -36,8 +36,8 @@
             },
             "tags": {
                 "type": "string",
-                "pattern": "^\\\"([A-Za-z0-9_-]+,\\ ?)*([A-Za-z0-9_-]+)\\\"$",
-                "errorMessage": "Tags must consist of numbers, letters, underscores or dashes and must be provided as a comma-separated list flanked by a pair of double-quotes, e.g. \"patient_01, lane1, pos-CTRL_2\".",
+                "pattern": "^([a-z0-9_-]+:)*([a-z0-9_-]+)$",
+                "errorMessage": "Tags must be separated by colons and only consist of lowercase letters, numbers, underscores and hyphens.",
                 "meta": ["tags"]
             }
         },
diff --git a/docs/usage.md b/docs/usage.md
index 42d596bb..e2da41de 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -32,10 +32,10 @@ run_dir
 
 ```csv title="samplesheet.csv"
 sample  fastq_1                                       fastq_2 rundir          tags
-sample1 path/to/run_dir/sample1_lane1_group1_r1.fq.gz         path/to/run_dir "cohort1,patient1"
-sample2 path/to/run_dir/sample2_lane1_group1_r1.fq.gz         path/to/run_dir "cohort1,patient2"
-sample3 path/to/run_dir/sample3_lane2_group2_r1.fq.gz         path/to/run_dir "cohort1,patient3"
-sample4 path/to/run_dir/sample4_lane2_group3_r1.fq.gz         path/to/run_dir "control"
+sample1 path/to/run_dir/sample1_lane1_group1_r1.fq.gz         path/to/run_dir cohort1:patient1
+sample2 path/to/run_dir/sample2_lane1_group1_r1.fq.gz         path/to/run_dir cohort1:patient2
+sample3 path/to/run_dir/sample3_lane2_group2_r1.fq.gz         path/to/run_dir cohort1:patient3
+sample4 path/to/run_dir/sample4_lane2_group3_r1.fq.gz         path/to/run_dir control
 
 ```
 
@@ -44,8 +44,8 @@ sample4 path/to/run_dir/sample4_lane2_group3_r1.fq.gz         path/to/run_dir "c
 | `sample`  | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). |
 | `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                             |
 | `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz" (optional).                                                  |
-| `rundir`  | Path to the runfolder containing extra information about the sequencing run (optional) .                                                                                               |
-| `tags`    | Comma-separated list of tags to group samples in special reports.                                                                                                                      |
+| `rundir`  | Path to the runfolder containing extra information about the sequencing run (optional).                                                                                               |
+| `tags`    | Colon-separated list of tags to group samples in special reports.                                                                                                                      |
 
 Another [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
 
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index afcfc68b..0ebfdd0a 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -84,7 +84,7 @@ workflow PIPELINE_INITIALISATION {
         .fromSamplesheet("input") // Validates samplesheet against $projectDir/assets/schema_input.json. Path to validation schema is defined by $projectDir/nextflow_schema.json
         .map {
             meta, fastq_1, fastq_2 ->
-                def tags = meta.tags ? meta.tags.tokenize(",") : []
+                def tags = meta.tags ? meta.tags.tokenize(":") : []
                 def updated_meta = meta + [ id:meta.sample, tags:tags ]
                 if (!fastq_2) {
                     return [ updated_meta.id, updated_meta + [ single_end:true ], [ fastq_1 ] ]

From cd4c0e6f410b0ecdb9ef1ad9f5cc58cf55488ccb Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Tue, 3 Sep 2024 13:55:30 +0200
Subject: [PATCH 045/530] use testdata with tags

---
 conf/test.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/test.config b/conf/test.config
index 658e75f3..c458ad0f 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -22,7 +22,7 @@ params {
     // Input data
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/MiSeq/samplesheet.csv'
+    input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
 
     // Genome references
     genome = 'R64-1-1'

From 519ee5e5afab01ae87c36492bc500fd34b7efeb4 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 3 Sep 2024 14:10:16 +0200
Subject: [PATCH 046/530] Make ids unique

---
 .../local/utils_nfcore_seqinspector_pipeline/main.nf | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index eec4d09c..632acb38 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -87,9 +87,17 @@ workflow PIPELINE_INITIALISATION {
                 def tags = meta.tags ? meta.tags.tokenize(":") : []
                 def updated_meta = meta + [ id:meta.sample, tags:tags ]
                 if (!fastq_2) {
-                    return [ updated_meta.id, updated_meta + [ single_end:true ], [ fastq_1 ] ]
+                    return [
+                        updated_meta.id + fastq_1.toString().replaceAll('/', '_'),
+                        updated_meta + [ single_end:true ],
+                        [ fastq_1 ]
+                    ]
                 } else {
-                    return [ updated_meta.id, updated_meta + [ single_end:false ], [ fastq_1, fastq_2 ] ]
+                    return [
+                        updated_meta.id + fastq_1.toString().replaceAll('/', '_') + '_' + fastq_2.toString().replaceAll('/', '_'),
+                        updated_meta + [ single_end:false ],
+                        [ fastq_1, fastq_2 ]
+                    ]
                 }
         }
         .groupTuple()

From 5e7a81da13b2f2ca7d27aac8dd2cafd9c39dd596 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Tue, 3 Sep 2024 12:26:11 +0000
Subject: [PATCH 047/530] bump multiqc to prevent gitpod crashing, populate the
 new process inputs w. empty channels

---
 modules.json                                  |  2 +-
 modules/nf-core/multiqc/environment.yml       |  2 +-
 modules/nf-core/multiqc/main.nf               | 14 ++++++++++---
 modules/nf-core/multiqc/meta.yml              | 13 ++++++++++++
 modules/nf-core/multiqc/tests/main.nf.test    |  8 ++++++++
 .../nf-core/multiqc/tests/main.nf.test.snap   | 20 +++++++++----------
 modules/nf-core/multiqc/tests/nextflow.config |  5 +++++
 workflows/seqinspector.nf                     |  8 ++++++--
 8 files changed, 55 insertions(+), 17 deletions(-)
 create mode 100644 modules/nf-core/multiqc/tests/nextflow.config

diff --git a/modules.json b/modules.json
index 87fe816c..70f3486c 100644
--- a/modules.json
+++ b/modules.json
@@ -12,7 +12,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
+                        "git_sha": "19ca321db5d8bd48923262c2eca6422359633491",
                         "installed_by": ["modules"]
                     }
                 }
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index ca39fb67..a31464c9 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::multiqc=1.21
+  - bioconda::multiqc=1.24.1
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 47ac352f..ceaec139 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,14 +3,16 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.21--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.24.1--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.24.1--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
     path(multiqc_config)
     path(extra_multiqc_config)
     path(multiqc_logo)
+    path(replace_names)
+    path(sample_names)
 
     output:
     path "*multiqc_report.html", emit: report
@@ -23,16 +25,22 @@ process MULTIQC {
 
     script:
     def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : ''
     def config = multiqc_config ? "--config $multiqc_config" : ''
     def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
-    def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : ''
+    def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : ''
+    def replace = replace_names ? "--replace-names ${replace_names}" : ''
+    def samples = sample_names ? "--sample-names ${sample_names}" : ''
     """
     multiqc \\
         --force \\
         $args \\
         $config \\
+        $prefix \\
         $extra_config \\
         $logo \\
+        $replace \\
+        $samples \\
         .
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index 45a9bc35..382c08cb 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -29,6 +29,19 @@ input:
       type: file
       description: Optional logo file for MultiQC
       pattern: "*.{png}"
+  - replace_names:
+      type: file
+      description: |
+        Optional two-column sample renaming file. First column a set of
+        patterns, second column a set of corresponding replacements. Passed via
+        MultiQC's `--replace-names` option.
+      pattern: "*.{tsv}"
+  - sample_names:
+      type: file
+      description: |
+        Optional TSV file with headers, passed to the MultiQC --sample_names
+        argument.
+      pattern: "*.{tsv}"
 output:
   - report:
       type: file
diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test
index f1c4242e..33316a7d 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test
+++ b/modules/nf-core/multiqc/tests/main.nf.test
@@ -8,6 +8,8 @@ nextflow_process {
     tag "modules_nfcore"
     tag "multiqc"
 
+    config "./nextflow.config"
+
     test("sarscov2 single-end [fastqc]") {
 
         when {
@@ -17,6 +19,8 @@ nextflow_process {
                 input[1] = []
                 input[2] = []
                 input[3] = []
+                input[4] = []
+                input[5] = []
                 """
             }
         }
@@ -41,6 +45,8 @@ nextflow_process {
                 input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true))
                 input[2] = []
                 input[3] = []
+                input[4] = []
+                input[5] = []
                 """
             }
         }
@@ -66,6 +72,8 @@ nextflow_process {
                 input[1] = []
                 input[2] = []
                 input[3] = []
+                input[4] = []
+                input[5] = []
                 """
             }
         }
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index bfebd802..83fa080c 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d"
+                "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-02-29T08:48:55.657331"
+        "timestamp": "2024-07-10T12:41:34.562023"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d"
+                "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-02-29T08:49:49.071937"
+        "timestamp": "2024-07-10T11:27:11.933869532"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d"
+                "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-02-29T08:49:25.457567"
+        "timestamp": "2024-07-10T11:26:56.709849369"
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config
new file mode 100644
index 00000000..c537a6a3
--- /dev/null
+++ b/modules/nf-core/multiqc/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'MULTIQC' {
+        ext.prefix = null
+    }
+}
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index e37df509..1ba00c62 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -89,7 +89,9 @@ workflow SEQINSPECTOR {
             .collect(),
         ch_multiqc_config.toList(),
         Channel.empty().toList(),
-        ch_multiqc_logo.toList()
+        ch_multiqc_logo.toList(),
+        Channel.empty().toList(),
+        Channel.empty().toList()
     )
 
     ch_tags = ch_multiqc_files
@@ -131,7 +133,9 @@ workflow SEQINSPECTOR {
         tagged_mqc_files.samples_per_tag,
         ch_multiqc_config.toList(),
         tagged_mqc_files.config,
-        ch_multiqc_logo.toList()
+        ch_multiqc_logo.toList(),
+        Channel.empty().toList(),
+        Channel.empty().toList()
     )
 
     emit:

From a6a7b351059364f79275c15997e06d9f6e3387a3 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 3 Sep 2024 16:36:59 +0200
Subject: [PATCH 048/530] Allow for uppercase letters

---
 assets/schema_input.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/assets/schema_input.json b/assets/schema_input.json
index 18941557..f2440839 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -36,7 +36,7 @@
             },
             "tags": {
                 "type": "string",
-                "pattern": "^([a-z0-9_-]+:)*([a-z0-9_-]+)$",
+                "pattern": "^([A-Za-z0-9_-]+:)*([A-Za-z0-9_-]+)$",
                 "errorMessage": "Tags must be separated by colons and only consist of lowercase letters, numbers, underscores and hyphens.",
                 "meta": ["tags"]
             }

From fe757ebca7caff802ab5e8b877718aa74f44bdbd Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 10 Sep 2024 08:54:03 +0200
Subject: [PATCH 049/530] Use samplesheet row in id

Co-authored-by: Matthias Zepper <MatthiasZepper@users.noreply.github.com>
---
 .../local/utils_nfcore_seqinspector_pipeline/main.nf   | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index 632acb38..3c63037b 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -82,19 +82,21 @@ workflow PIPELINE_INITIALISATION {
     //
     Channel
         .fromSamplesheet("input") // Validates samplesheet against $projectDir/assets/schema_input.json. Path to validation schema is defined by $projectDir/nextflow_schema.json
+        .toList()
+        .flatMap { it.withIndex().collect {  entry, idx -> entry + "${idx+1}" } }
         .map {
-            meta, fastq_1, fastq_2 ->
+            meta, fastq_1, fastq_2, idx ->
                 def tags = meta.tags ? meta.tags.tokenize(":") : []
-                def updated_meta = meta + [ id:meta.sample, tags:tags ]
+                def updated_meta = meta + [ id:"${meta.sample}_${idx}", tags:tags ]
                 if (!fastq_2) {
                     return [
-                        updated_meta.id + fastq_1.toString().replaceAll('/', '_'),
+                        updated_meta.id,
                         updated_meta + [ single_end:true ],
                         [ fastq_1 ]
                     ]
                 } else {
                     return [
-                        updated_meta.id + fastq_1.toString().replaceAll('/', '_') + '_' + fastq_2.toString().replaceAll('/', '_'),
+                        updated_meta.id,
                         updated_meta + [ single_end:false ],
                         [ fastq_1, fastq_2 ]
                     ]

From 0122993e9217787fbe65ee2d136da8c537e7d351 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 10 Sep 2024 09:03:50 +0200
Subject: [PATCH 050/530] Update snapshots

---
 tests/MiSeq.main.nf.test.snap       | 12 ++++++----
 tests/NovaSeq6000.main.nf.test.snap | 36 ++++++++++++++++-------------
 tests/PromethION.main.nf.test.snap  | 12 ++++++----
 3 files changed, 36 insertions(+), 24 deletions(-)

diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 26f0c2a8..9dacaf8a 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -2,10 +2,14 @@
     "MiSeq data test": {
         "content": [
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,e46e7baa8f57d4cf54d973925b5eadf9",
-            "multiqc_general_stats.txt:md5,a5e626a2e1a3c986092e4f89091cc41c",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
+            "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
+            "multiqc_general_stats.txt:md5,962713a1473a318f2cb29bb5290c4c8e",
+            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5"
         ],
-        "timestamp": "2024-08-26T17:55:16.152573"
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-10T08:57:05.870194"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index f5c4776b..3f27e5a2 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -2,26 +2,30 @@
     "NovaSeq6000 data test": {
         "content": [
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,e8ed6dca928396b8873d24e60ea1a133",
-            "multiqc_general_stats.txt:md5,fd9d46c5b441908cd07e5373d116db17",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d",
+            "multiqc_general_stats.txt:md5,d521de54d1e659bf7892105f7d23d4db",
+            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,ff9b31c6024f11a8135456e7ea01fc8f",
-            "multiqc_general_stats.txt:md5,f36bd6e27e92c25be076efea411d3a8e",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
+            "multiqc_general_stats.txt:md5,d52544eb1a505c889a2f9117cf94a5fa",
+            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,62d51280dcd7634f6bed95ffe0d8dab8",
-            "multiqc_general_stats.txt:md5,2012002b6a057be981a97fcc96142a6c",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
+            "multiqc_general_stats.txt:md5,5b1190093085ef073d4bd5818c9cde79",
+            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,63749e803a2d5fc7ecc7cd93fa68df1f",
-            "multiqc_general_stats.txt:md5,656931993032400dea3d441b8b61b4d2",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
+            "multiqc_general_stats.txt:md5,79c1090dd8a97912893f8491641b9dc9",
+            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,91cc62e1b4059bdbe4b88affa43378af",
-            "multiqc_general_stats.txt:md5,6e500f82550e00b07c3e7aa1d46ab9e9",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
+            "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
+            "multiqc_general_stats.txt:md5,41611bd5ab9e79425c466bf976b03bdc",
+            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5"
         ],
-        "timestamp": "2024-08-26T18:03:33.089142"
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-10T08:58:26.732622"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index e3b34f23..fb8cda25 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -2,10 +2,14 @@
     "PromethION data test": {
         "content": [
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,cecee3cb343c75c80180d3169c6f3ea1",
-            "multiqc_general_stats.txt:md5,e63c25089c4fc10618414ba2254d18c7",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
+            "multiqc_fastqc.txt:md5,35984961f25a0d4e7352cab4d5650178",
+            "multiqc_general_stats.txt:md5,1465b0b1959e3864b28ecc2340df351b",
+            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5"
         ],
-        "timestamp": "2024-08-26T17:55:38.755385"
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-10T08:58:57.180636"
     }
 }
\ No newline at end of file

From f530e314af225eb3d5fa61fd31a59e3861bae1d6 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Tue, 8 Oct 2024 12:33:12 +0000
Subject: [PATCH 051/530] Template update for nf-core/tools version 3.0.0

---
 .editorconfig                                 |   4 +
 .github/CONTRIBUTING.md                       |  10 +-
 .github/PULL_REQUEST_TEMPLATE.md              |   2 +-
 .github/workflows/awsfulltest.yml             |  23 +-
 .github/workflows/ci.yml                      |  17 +-
 .github/workflows/download_pipeline.yml       |  53 ++-
 .github/workflows/linting.yml                 |  23 +-
 .github/workflows/linting_comment.yml         |   2 +-
 .github/workflows/release-announcements.yml   |   2 +-
 .../workflows/template_version_comment.yml    |  43 ++
 .gitpod.yml                                   |   7 +-
 .nf-core.yml                                  |  16 +-
 .pre-commit-config.yaml                       |   2 +-
 .prettierignore                               |   1 +
 CITATIONS.md                                  |   4 +-
 README.md                                     |   5 +-
 assets/schema_input.json                      |   2 +-
 conf/base.config                              |  34 +-
 conf/igenomes_ignored.config                  |   9 +
 conf/modules.config                           |   1 -
 conf/test.config                              |  13 +-
 docs/images/mqc_fastqc_adapter.png            | Bin 23458 -> 0 bytes
 docs/images/mqc_fastqc_counts.png             | Bin 33918 -> 0 bytes
 docs/images/mqc_fastqc_quality.png            | Bin 55769 -> 0 bytes
 docs/output.md                                |  11 +-
 docs/usage.md                                 |  12 +-
 main.nf                                       |  10 +-
 modules.json                                  |  12 +-
 modules/nf-core/fastqc/environment.yml        |   2 -
 modules/nf-core/fastqc/main.nf                |   5 +-
 modules/nf-core/fastqc/meta.yml               |  57 +--
 modules/nf-core/fastqc/tests/main.nf.test     | 225 ++++++++---
 .../nf-core/fastqc/tests/main.nf.test.snap    | 370 ++++++++++++++++--
 modules/nf-core/multiqc/environment.yml       |   4 +-
 modules/nf-core/multiqc/main.nf               |  14 +-
 modules/nf-core/multiqc/meta.yml              |  78 ++--
 modules/nf-core/multiqc/tests/main.nf.test    |   8 +
 .../nf-core/multiqc/tests/main.nf.test.snap   |  20 +-
 modules/nf-core/multiqc/tests/nextflow.config |   5 +
 nextflow.config                               | 146 ++++---
 nextflow_schema.json                          |  85 +---
 .../main.nf                                   |  56 +--
 .../nf-core/utils_nextflow_pipeline/main.nf   |  24 +-
 .../tests/nextflow.config                     |   2 +-
 .../nf-core/utils_nfcore_pipeline/main.nf     |  45 ++-
 .../nf-core/utils_nfschema_plugin/main.nf     |  46 +++
 .../nf-core/utils_nfschema_plugin/meta.yml    |  35 ++
 .../utils_nfschema_plugin/tests/main.nf.test  | 117 ++++++
 .../tests/nextflow.config                     |   8 +
 .../tests/nextflow_schema.json                |   8 +-
 .../nf-core/utils_nfvalidation_plugin/main.nf |  62 ---
 .../utils_nfvalidation_plugin/meta.yml        |  44 ---
 .../tests/main.nf.test                        | 200 ----------
 .../utils_nfvalidation_plugin/tests/tags.yml  |   2 -
 workflows/seqinspector.nf                     |  23 +-
 55 files changed, 1203 insertions(+), 806 deletions(-)
 create mode 100644 .github/workflows/template_version_comment.yml
 create mode 100644 conf/igenomes_ignored.config
 delete mode 100755 docs/images/mqc_fastqc_adapter.png
 delete mode 100755 docs/images/mqc_fastqc_counts.png
 delete mode 100755 docs/images/mqc_fastqc_quality.png
 create mode 100644 modules/nf-core/multiqc/tests/nextflow.config
 create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/main.nf
 create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/meta.yml
 create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
 create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
 rename subworkflows/nf-core/{utils_nfvalidation_plugin => utils_nfschema_plugin}/tests/nextflow_schema.json (95%)
 delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
 delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
 delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
 delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml

diff --git a/.editorconfig b/.editorconfig
index 72dda289..e1058815 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -11,6 +11,7 @@ indent_style = space
 [*.{md,yml,yaml,html,css,scss,js}]
 indent_size = 2
 
+
 # These files are edited and tested upstream in nf-core/modules
 [/modules/nf-core/**]
 charset = unset
@@ -25,9 +26,12 @@ insert_final_newline = unset
 trim_trailing_whitespace = unset
 indent_style = unset
 
+
+
 [/assets/email*]
 indent_size = unset
 
+
 # ignore python and markdown
 [*.{py,md}]
 indent_style = unset
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index ee3dfbd0..78893ac8 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -19,7 +19,7 @@ If you'd like to write some code for nf-core/seqinspector, the standard workflow
 1. Check that there isn't already an issue about your idea in the [nf-core/seqinspector issues](https://github.com/nf-core/seqinspector/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
 2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/seqinspector repository](https://github.com/nf-core/seqinspector) to your GitHub account
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
-4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
+4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
 
 If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).
@@ -40,7 +40,7 @@ There are typically two types of tests that run:
 ### Lint tests
 
 `nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to.
-To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command.
+To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint <pipeline-directory>` command.
 
 If any failures or warnings are encountered, please follow the listed URL for more documentation.
 
@@ -75,7 +75,7 @@ If you wish to contribute a new step, please use the following coding standards:
 2. Write the process block (see below).
 3. Define the output channel if needed (see below).
 4. Add any new parameters to `nextflow.config` with a default (see below).
-5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool).
+5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool).
 6. Add sanity checks and validation for all relevant parameters.
 7. Perform local tests to validate that the new code works as expected.
 8. If applicable, add a new test command in `.github/workflow/ci.yml`.
@@ -86,7 +86,7 @@ If you wish to contribute a new step, please use the following coding standards:
 
 Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
 
-Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
+Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`.
 
 ### Default processes resource requirements
 
@@ -103,7 +103,7 @@ Please use the following naming schemes, to make it easy to understand what is g
 
 ### Nextflow version bumping
 
-If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]`
+If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]`
 
 ### Images and figures
 
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 6de151f7..9dcf6a33 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -17,7 +17,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/seqi
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/seqinspector/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/seqinspector _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
-- [ ] Make sure your code lints (`nf-core lint`).
+- [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 9278410e..c9462a57 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -1,18 +1,33 @@
 name: nf-core AWS full size tests
-# This workflow is triggered on published releases.
+# This workflow is triggered on PRs opened against the master branch.
 # It can be additionally triggered manually with GitHub actions workflow dispatch button.
 # It runs the -profile 'test_full' on AWS batch
 
 on:
-  release:
-    types: [published]
+  pull_request:
+    branches:
+      - master
   workflow_dispatch:
+  pull_request_review:
+    types: [submitted]
+
 jobs:
   run-platform:
     name: Run AWS full tests
-    if: github.repository == 'nf-core/seqinspector'
+    if: github.repository == 'nf-core/seqinspector' && github.event.review.state == 'approved'
     runs-on: ubuntu-latest
     steps:
+      - uses: octokit/request-action@v2.x
+        id: check_approvals
+        with:
+          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.review.number }}/reviews
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - id: test_variables
+        run: |
+          JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
+          CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
+          test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         # TODO nf-core: You can customise AWS full pipeline tests as required
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 59c94105..5666673f 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -7,6 +7,7 @@ on:
   pull_request:
   release:
     types: [published]
+  workflow_dispatch:
 
 env:
   NXF_ANSI_LOG: false
@@ -24,7 +25,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "23.04.0"
+          - "24.04.2"
           - "latest-everything"
     steps:
       - name: Check out pipeline code
@@ -38,9 +39,21 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - name: Run pipeline with test data
+      - name: Run pipeline with test data (docker)
         # TODO nf-core: You can customise CI pipeline run tests as required
         # For example: adding multiple test runs with different parameters
         # Remember that you can parallelise this by using strategy.matrix
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+
+      - name: Run pipeline with test data (singularity)
+        # TODO nf-core: You can customise CI pipeline run tests as required
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test,singularity --outdir ./results
+        if: "${{ github.base_ref == 'master' }}"
+
+      - name: Run pipeline with test data (conda)
+        # TODO nf-core: You can customise CI pipeline run tests as required
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test,conda --outdir ./results
+        if: "${{ github.base_ref == 'master' }}"
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 2d20d644..713dc3e7 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -1,4 +1,4 @@
-name: Test successful pipeline download with 'nf-core download'
+name: Test successful pipeline download with 'nf-core pipelines download'
 
 # Run the workflow when:
 #  - dispatched manually
@@ -8,7 +8,7 @@ on:
   workflow_dispatch:
     inputs:
       testbranch:
-        description: "The specific branch you wish to utilize for the test execution of nf-core download."
+        description: "The specific branch you wish to utilize for the test execution of nf-core pipelines download."
         required: true
         default: "dev"
   pull_request:
@@ -39,9 +39,11 @@ jobs:
         with:
           python-version: "3.12"
           architecture: "x64"
-      - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
+
+      - name: Setup Apptainer
+        uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0
         with:
-          singularity-version: 3.8.3
+          apptainer-version: 1.3.4
 
       - name: Install dependencies
         run: |
@@ -54,33 +56,64 @@ jobs:
           echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
           echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}
 
+      - name: Make a cache directory for the container images
+        run: |
+          mkdir -p ./singularity_container_images
+
       - name: Download the pipeline
         env:
-          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
         run: |
-          nf-core download ${{ env.REPO_LOWERCASE }} \
+          nf-core pipelines download ${{ env.REPO_LOWERCASE }} \
           --revision ${{ env.REPO_BRANCH }} \
           --outdir ./${{ env.REPOTITLE_LOWERCASE }} \
           --compress "none" \
           --container-system 'singularity' \
-          --container-library "quay.io" -l "docker.io" -l "ghcr.io" \
+          --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \
           --container-cache-utilisation 'amend' \
-          --download-configuration
+          --download-configuration 'yes'
 
       - name: Inspect download
         run: tree ./${{ env.REPOTITLE_LOWERCASE }}
 
+      - name: Count the downloaded number of container images
+        id: count_initial
+        run: |
+          image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
+          echo "Initial container image count: $image_count"
+          echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV}
+
       - name: Run the downloaded pipeline (stub)
         id: stub_run_pipeline
         continue-on-error: true
         env:
-          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
         run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
       - name: Run the downloaded pipeline (stub run not supported)
         id: run_pipeline
         if: ${{ job.steps.stub_run_pipeline.status == failure() }}
         env:
-          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
         run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
+
+      - name: Count the downloaded number of container images
+        id: count_afterwards
+        run: |
+          image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
+          echo "Post-pipeline run container image count: $image_count"
+          echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV}
+
+      - name: Compare container image counts
+        run: |
+          if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then
+            initial_count=${{ env.IMAGE_COUNT_INITIAL }}
+            final_count=${{ env.IMAGE_COUNT_AFTER }}
+            difference=$((final_count - initial_count))
+            echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!"
+            tree ./singularity_container_images
+            exit 1
+          else
+            echo "The pipeline can be downloaded successfully!"
+          fi
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 1fcafe88..b882838a 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -1,6 +1,6 @@
 name: nf-core linting
 # This workflow is triggered on pushes and PRs to the repository.
-# It runs the `nf-core lint` and markdown lint tests to ensure
+# It runs the `nf-core pipelines lint` and markdown lint tests to ensure
 # that the code meets the nf-core guidelines.
 on:
   push:
@@ -41,17 +41,32 @@ jobs:
           python-version: "3.12"
           architecture: "x64"
 
+      - name: read .nf-core.yml
+        uses: pietrobolcato/action-read-yaml@1.0.0
+        id: read_yml
+        with:
+          config: ${{ github.workspace }}/.nf-core.yaml
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install nf-core
+          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
+
+      - name: Run nf-core pipelines lint
+        if: ${{ github.base_ref != 'master' }}
+        env:
+          GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
+        run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
-      - name: Run nf-core lint
+      - name: Run nf-core pipelines lint --release
+        if: ${{ github.base_ref == 'master' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
-        run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
+        run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
       - name: Save PR number
         if: ${{ always() }}
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 40acc23f..42e519bf 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
+        uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6
         with:
           workflow: linting.yml
           workflow_conclusion: completed
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index 03ecfcf7..c6ba35df 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -12,7 +12,7 @@ jobs:
       - name: get topics and convert to hashtags
         id: get_topics
         run: |
-          echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')"  >> $GITHUB_OUTPUT
+          echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT
 
       - uses: rzr/fediverse-action@master
         with:
diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml
new file mode 100644
index 00000000..9dea41f0
--- /dev/null
+++ b/.github/workflows/template_version_comment.yml
@@ -0,0 +1,43 @@
+name: nf-core template version comment
+# This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version.
+# It posts a comment to the PR, even if it comes from a fork.
+
+on: pull_request_target
+
+jobs:
+  template_version:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+
+      - name: Read template version from .nf-core.yml
+        uses: pietrobolcato/action-read-yaml@1.0.0
+        id: read_yml
+        with:
+          config: ${{ github.workspace }}/.nf-core.yml
+
+      - name: Install nf-core
+        run: |
+          python -m pip install --upgrade pip
+          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
+
+      - name: Check nf-core outdated
+        id: nf_core_outdated
+        run: pip list --outdated | grep nf-core
+
+      - name: Post nf-core template version comment
+        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
+        if: |
+          ${{ steps.nf_core_outdated.outputs.stdout }} =~ 'nf-core'
+        with:
+          repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
+          allow-repeats: false
+          message: |
+            ## :warning: Newer version of the nf-core template is available.
+
+            Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}.
+            Please update your pipeline to the latest version.
+
+            For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).
+          #
diff --git a/.gitpod.yml b/.gitpod.yml
index 105a1821..46118637 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -4,17 +4,14 @@ tasks:
     command: |
       pre-commit install --install-hooks
       nextflow self-update
-  - name: unset JAVA_TOOL_OPTIONS
-    command: |
-      unset JAVA_TOOL_OPTIONS
 
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
-    - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
+    #- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
     - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
     - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
     - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
-    # - nextflow.nextflow                    # Nextflow syntax highlighting
+    - nextflow.nextflow # Nextflow syntax highlighting
     - oderwat.indent-rainbow # Highlight indentation level
     - streetsidesoftware.code-spell-checker # Spelling checker for source code
     - charliermarsh.ruff # Code linter Ruff
diff --git a/.nf-core.yml b/.nf-core.yml
index e0b85a77..ca26523b 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,2 +1,16 @@
+bump_version: null
+lint: null
+nf_core_version: 3.0.0
+org_path: null
 repository_type: pipeline
-nf_core_version: "2.14.1"
+template:
+  author: Adrien Coulier
+  description: Pipeline to QC your sequences
+  force: false
+  is_nfcore: true
+  name: seqinspector
+  org: nf-core
+  outdir: .
+  skip_features: null
+  version: 1.0dev
+update: null
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 4dc0f1dc..9e9f0e1c 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,7 +7,7 @@ repos:
           - prettier@3.2.5
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "2.7.3"
+    rev: "3.0.3"
     hooks:
       - id: editorconfig-checker
         alias: ec
diff --git a/.prettierignore b/.prettierignore
index 437d763d..610e5069 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -1,3 +1,4 @@
+
 email_template.html
 adaptivecard.json
 slackreport.json
diff --git a/CITATIONS.md b/CITATIONS.md
index a5854252..ecbfb16e 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -12,11 +12,11 @@
 
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
-  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
+> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
 
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
-  > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
+> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
 ## Software packaging/containerisation tools
 
diff --git a/README.md b/README.md
index bfb53fee..2b5e2c85 100644
--- a/README.md
+++ b/README.md
@@ -9,7 +9,7 @@
 [![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
@@ -67,8 +67,7 @@ nextflow run nf-core/seqinspector \
 ```
 
 > [!WARNING]
-> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
-> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
+> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).
 
 For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).
 
diff --git a/assets/schema_input.json b/assets/schema_input.json
index 338d3557..d7d48374 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -1,5 +1,5 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/seqinspector/master/assets/schema_input.json",
     "title": "nf-core/seqinspector pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",
diff --git a/conf/base.config b/conf/base.config
index aab50f93..b8e828de 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -11,9 +11,9 @@
 process {
 
     // TODO nf-core: Check the defaults for all processes
-    cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
-    memory = { check_max( 6.GB * task.attempt, 'memory' ) }
-    time   = { check_max( 4.h  * task.attempt, 'time'   ) }
+    cpus   = { 1      * task.attempt }
+    memory = { 6.GB   * task.attempt }
+    time   = { 4.h    * task.attempt }
 
     errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
     maxRetries    = 1
@@ -27,30 +27,30 @@ process {
     // TODO nf-core: Customise requirements for specific processes.
     // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
     withLabel:process_single {
-        cpus   = { check_max( 1                  , 'cpus'    ) }
-        memory = { check_max( 6.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
+        cpus   = { 1                   }
+        memory = { 6.GB * task.attempt }
+        time   = { 4.h  * task.attempt }
     }
     withLabel:process_low {
-        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
+        cpus   = { 2     * task.attempt }
+        memory = { 12.GB * task.attempt }
+        time   = { 4.h   * task.attempt }
     }
     withLabel:process_medium {
-        cpus   = { check_max( 6     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 36.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
+        cpus   = { 6     * task.attempt }
+        memory = { 36.GB * task.attempt }
+        time   = { 8.h   * task.attempt }
     }
     withLabel:process_high {
-        cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
-        memory = { check_max( 72.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 16.h  * task.attempt, 'time'    ) }
+        cpus   = { 12    * task.attempt }
+        memory = { 72.GB * task.attempt }
+        time   = { 16.h  * task.attempt }
     }
     withLabel:process_long {
-        time   = { check_max( 20.h  * task.attempt, 'time'    ) }
+        time   = { 20.h  * task.attempt }
     }
     withLabel:process_high_memory {
-        memory = { check_max( 200.GB * task.attempt, 'memory' ) }
+        memory = { 200.GB * task.attempt }
     }
     withLabel:error_ignore {
         errorStrategy = 'ignore'
diff --git a/conf/igenomes_ignored.config b/conf/igenomes_ignored.config
new file mode 100644
index 00000000..b4034d82
--- /dev/null
+++ b/conf/igenomes_ignored.config
@@ -0,0 +1,9 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for iGenomes paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Empty genomes dictionary to use when igenomes is ignored.
+----------------------------------------------------------------------------------------
+*/
+
+params.genomes = [:]
diff --git a/conf/modules.config b/conf/modules.config
index d203d2b6..d266a387 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -21,7 +21,6 @@ process {
     withName: FASTQC {
         ext.args = '--quiet'
     }
-
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
diff --git a/conf/test.config b/conf/test.config
index 6a7b9846..1838ae52 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -10,15 +10,18 @@
 ----------------------------------------------------------------------------------------
 */
 
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+}
+
 params {
     config_profile_name        = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
     // Input data
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
diff --git a/docs/images/mqc_fastqc_adapter.png b/docs/images/mqc_fastqc_adapter.png
deleted file mode 100755
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GIT binary patch
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diff --git a/docs/output.md b/docs/output.md
index 77e4cc1c..9184bd0a 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -14,6 +14,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 - [FastQC](#fastqc) - Raw read QC
 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
+
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
 ### FastQC
@@ -29,16 +30,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
 
-![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png)
-
-![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png)
-
-![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png)
-
-:::note
-The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
-:::
-
 ### MultiQC
 
 <details markdown="1">
diff --git a/docs/usage.md b/docs/usage.md
index ec180e49..bbc141ef 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -85,9 +85,9 @@ The above pipeline run specified with a params file in yaml format:
 nextflow run nf-core/seqinspector -profile docker -params-file params.yaml
 ```
 
-with `params.yaml` containing:
+with:
 
-```yaml
+```yaml title="params.yaml"
 input: './samplesheet.csv'
 outdir: './results/'
 genome: 'GRCh37'
@@ -199,14 +199,6 @@ See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config
 
 If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs).
 
-## Azure Resource Requests
-
-To be used with the `azurebatch` profile by specifying the `-profile azurebatch`.
-We recommend providing a compute `params.vm_type` of `Standard_D16_v3` VMs by default but these options can be changed if required.
-
-Note that the choice of VM size depends on your quota and the overall workload during the analysis.
-For a thorough list, please refer the [Azure Sizes for virtual machines in Azure](https://docs.microsoft.com/en-us/azure/virtual-machines/sizes).
-
 ## Running in the background
 
 Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished.
diff --git a/main.nf b/main.nf
index 2e9b1e37..df5d2162 100644
--- a/main.nf
+++ b/main.nf
@@ -9,8 +9,6 @@
 ----------------------------------------------------------------------------------------
 */
 
-nextflow.enable.dsl = 2
-
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
@@ -20,7 +18,6 @@ nextflow.enable.dsl = 2
 include { SEQINSPECTOR  } from './workflows/seqinspector'
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
-
 include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
 
 /*
@@ -56,10 +53,8 @@ workflow NFCORE_SEQINSPECTOR {
     SEQINSPECTOR (
         samplesheet
     )
-
     emit:
     multiqc_report = SEQINSPECTOR.out.multiqc_report // channel: /path/to/multiqc_report.html
-
 }
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -70,27 +65,24 @@ workflow NFCORE_SEQINSPECTOR {
 workflow {
 
     main:
-
     //
     // SUBWORKFLOW: Run initialisation tasks
     //
     PIPELINE_INITIALISATION (
         params.version,
-        params.help,
         params.validate_params,
         params.monochrome_logs,
         args,
         params.outdir,
         params.input
     )
-
+    
     //
     // WORKFLOW: Run main workflow
     //
     NFCORE_SEQINSPECTOR (
         PIPELINE_INITIALISATION.out.samplesheet
     )
-
     //
     // SUBWORKFLOW: Run completion tasks
     //
diff --git a/modules.json b/modules.json
index 87fe816c..0ab8a797 100644
--- a/modules.json
+++ b/modules.json
@@ -7,12 +7,12 @@
                 "nf-core": {
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     }
                 }
@@ -21,17 +21,17 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
+                        "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab",
                         "installed_by": ["subworkflows"]
                     },
-                    "utils_nfvalidation_plugin": {
+                    "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml
index 1787b38a..691d4c76 100644
--- a/modules/nf-core/fastqc/environment.yml
+++ b/modules/nf-core/fastqc/environment.yml
@@ -1,7 +1,5 @@
-name: fastqc
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::fastqc=0.12.1
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index d79f1c86..d8989f48 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -26,7 +26,10 @@ process FASTQC {
     def rename_to = old_new_pairs*.join(' ').join(' ')
     def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
 
-    def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB')
+    // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory)
+    // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222
+    // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label
+    def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus
     // FastQC memory value allowed range (100 - 10000)
     def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
 
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
index ee5507e0..4827da7a 100644
--- a/modules/nf-core/fastqc/meta.yml
+++ b/modules/nf-core/fastqc/meta.yml
@@ -16,35 +16,44 @@ tools:
       homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
       documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
       licence: ["GPL-2.0-only"]
+      identifier: biotools:fastqc
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: |
-        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-        respectively.
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: file
+        description: |
+          List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+          respectively.
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - html:
-      type: file
-      description: FastQC report
-      pattern: "*_{fastqc.html}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.html":
+          type: file
+          description: FastQC report
+          pattern: "*_{fastqc.html}"
   - zip:
-      type: file
-      description: FastQC report archive
-      pattern: "*_{fastqc.zip}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.zip":
+          type: file
+          description: FastQC report archive
+          pattern: "*_{fastqc.zip}"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@drpatelh"
   - "@grst"
diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test
index 70edae4d..e9d79a07 100644
--- a/modules/nf-core/fastqc/tests/main.nf.test
+++ b/modules/nf-core/fastqc/tests/main.nf.test
@@ -23,17 +23,14 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it.
-            // looks like this: <div id="header_filename">Mon 2 Oct 2023<br/>test.gz</div>
-            // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039
-
-            { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
-            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
-            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_single") }
+                { assert process.success },
+                // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it.
+                // looks like this: <div id="header_filename">Mon 2 Oct 2023<br/>test.gz</div>
+                // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039
+                { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+                { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -54,16 +51,14 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
-            { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
-            { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
-            { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
-            { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-            { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_paired") }
+                { assert process.success },
+                { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
+                { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
+                { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
+                { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
+                { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -83,13 +78,11 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
-            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
-            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") }
+                { assert process.success },
+                { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+                { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -109,13 +102,11 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
-            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
-            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_bam") }
+                { assert process.success },
+                { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+                { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -138,22 +129,20 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
-            { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
-            { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" },
-            { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" },
-            { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
-            { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
-            { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" },
-            { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" },
-            { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-            { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-            { assert path(process.out.html[0][1][2]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-            { assert path(process.out.html[0][1][3]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_multiple") }
+                { assert process.success },
+                { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
+                { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
+                { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" },
+                { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" },
+                { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
+                { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
+                { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" },
+                { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" },
+                { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert path(process.out.html[0][1][2]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert path(process.out.html[0][1][3]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -173,21 +162,18 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" },
-            { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" },
-            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") }
+                { assert process.success },
+                { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" },
+                { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" },
+                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
 
     test("sarscov2 single-end [fastq] - stub") {
 
-        options "-stub"
-
+    options "-stub"
         when {
             process {
                 """
@@ -201,12 +187,123 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-            { assert snapshot(process.out.html.collect { file(it[1]).getName() } +
-                                process.out.zip.collect { file(it[1]).getName() } +
-                                process.out.versions ).match("fastqc_stub") }
+                { assert process.success },
+                { assert snapshot(process.out).match() }
             )
         }
     }
 
+    test("sarscov2 paired-end [fastq] - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 interleaved [fastq] - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true)
+                ])
+            """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 paired-end [bam] - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 multiple [fastq] - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 custom_prefix - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'mysample', single_end:true ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
 }
diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap
index 86f7c311..d5db3092 100644
--- a/modules/nf-core/fastqc/tests/main.nf.test.snap
+++ b/modules/nf-core/fastqc/tests/main.nf.test.snap
@@ -1,88 +1,392 @@
 {
-    "fastqc_versions_interleaved": {
+    "sarscov2 custom_prefix": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:40:07.293713"
+        "timestamp": "2024-07-22T11:02:16.374038"
     },
-    "fastqc_stub": {
+    "sarscov2 single-end [fastq] - stub": {
         "content": [
-            [
-                "test.html",
-                "test.zip",
-                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-            ]
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:24.993809"
+    },
+    "sarscov2 custom_prefix - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:31:01.425198"
+        "timestamp": "2024-07-22T11:03:10.93942"
     },
-    "fastqc_versions_multiple": {
+    "sarscov2 interleaved [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:40:55.797907"
+        "timestamp": "2024-07-22T11:01:42.355718"
     },
-    "fastqc_versions_bam": {
+    "sarscov2 paired-end [bam]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:40:26.795862"
+        "timestamp": "2024-07-22T11:01:53.276274"
     },
-    "fastqc_versions_single": {
+    "sarscov2 multiple [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:39:27.043675"
+        "timestamp": "2024-07-22T11:02:05.527626"
     },
-    "fastqc_versions_paired": {
+    "sarscov2 paired-end [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:01:31.188871"
+    },
+    "sarscov2 paired-end [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:34.273566"
+    },
+    "sarscov2 multiple [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:39:47.584191"
+        "timestamp": "2024-07-22T11:03:02.304411"
     },
-    "fastqc_versions_custom_prefix": {
+    "sarscov2 single-end [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:01:19.095607"
+    },
+    "sarscov2 interleaved [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:44.640184"
+    },
+    "sarscov2 paired-end [bam] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:41:14.576531"
+        "timestamp": "2024-07-22T11:02:53.550742"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index ca39fb67..f1cd99b0 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -1,7 +1,5 @@
-name: multiqc
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::multiqc=1.21
+  - bioconda::multiqc=1.24.1
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 47ac352f..b9ccebdb 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,14 +3,16 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.21--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.25--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.25--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
     path(multiqc_config)
     path(extra_multiqc_config)
     path(multiqc_logo)
+    path(replace_names)
+    path(sample_names)
 
     output:
     path "*multiqc_report.html", emit: report
@@ -23,16 +25,22 @@ process MULTIQC {
 
     script:
     def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : ''
     def config = multiqc_config ? "--config $multiqc_config" : ''
     def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
-    def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : ''
+    def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : ''
+    def replace = replace_names ? "--replace-names ${replace_names}" : ''
+    def samples = sample_names ? "--sample-names ${sample_names}" : ''
     """
     multiqc \\
         --force \\
         $args \\
         $config \\
+        $prefix \\
         $extra_config \\
         $logo \\
+        $replace \\
+        $samples \\
         .
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index 45a9bc35..b16c1879 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -1,5 +1,6 @@
 name: multiqc
-description: Aggregate results from bioinformatics analyses across many samples into a single report
+description: Aggregate results from bioinformatics analyses across many samples into
+  a single report
 keywords:
   - QC
   - bioinformatics tools
@@ -12,40 +13,59 @@ tools:
       homepage: https://multiqc.info/
       documentation: https://multiqc.info/docs/
       licence: ["GPL-3.0-or-later"]
+      identifier: biotools:multiqc
 input:
-  - multiqc_files:
-      type: file
-      description: |
-        List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
-  - multiqc_config:
-      type: file
-      description: Optional config yml for MultiQC
-      pattern: "*.{yml,yaml}"
-  - extra_multiqc_config:
-      type: file
-      description: Second optional config yml for MultiQC. Will override common sections in multiqc_config.
-      pattern: "*.{yml,yaml}"
-  - multiqc_logo:
-      type: file
-      description: Optional logo file for MultiQC
-      pattern: "*.{png}"
+  - - multiqc_files:
+        type: file
+        description: |
+          List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
+  - - multiqc_config:
+        type: file
+        description: Optional config yml for MultiQC
+        pattern: "*.{yml,yaml}"
+  - - extra_multiqc_config:
+        type: file
+        description: Second optional config yml for MultiQC. Will override common sections
+          in multiqc_config.
+        pattern: "*.{yml,yaml}"
+  - - multiqc_logo:
+        type: file
+        description: Optional logo file for MultiQC
+        pattern: "*.{png}"
+  - - replace_names:
+        type: file
+        description: |
+          Optional two-column sample renaming file. First column a set of
+          patterns, second column a set of corresponding replacements. Passed via
+          MultiQC's `--replace-names` option.
+        pattern: "*.{tsv}"
+  - - sample_names:
+        type: file
+        description: |
+          Optional TSV file with headers, passed to the MultiQC --sample_names
+          argument.
+        pattern: "*.{tsv}"
 output:
   - report:
-      type: file
-      description: MultiQC report file
-      pattern: "multiqc_report.html"
+      - "*multiqc_report.html":
+          type: file
+          description: MultiQC report file
+          pattern: "multiqc_report.html"
   - data:
-      type: directory
-      description: MultiQC data dir
-      pattern: "multiqc_data"
+      - "*_data":
+          type: directory
+          description: MultiQC data dir
+          pattern: "multiqc_data"
   - plots:
-      type: file
-      description: Plots created by MultiQC
-      pattern: "*_data"
+      - "*_plots":
+          type: file
+          description: Plots created by MultiQC
+          pattern: "*_data"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@abhi18av"
   - "@bunop"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test
index f1c4242e..33316a7d 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test
+++ b/modules/nf-core/multiqc/tests/main.nf.test
@@ -8,6 +8,8 @@ nextflow_process {
     tag "modules_nfcore"
     tag "multiqc"
 
+    config "./nextflow.config"
+
     test("sarscov2 single-end [fastqc]") {
 
         when {
@@ -17,6 +19,8 @@ nextflow_process {
                 input[1] = []
                 input[2] = []
                 input[3] = []
+                input[4] = []
+                input[5] = []
                 """
             }
         }
@@ -41,6 +45,8 @@ nextflow_process {
                 input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true))
                 input[2] = []
                 input[3] = []
+                input[4] = []
+                input[5] = []
                 """
             }
         }
@@ -66,6 +72,8 @@ nextflow_process {
                 input[1] = []
                 input[2] = []
                 input[3] = []
+                input[4] = []
+                input[5] = []
                 """
             }
         }
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index bfebd802..b779e469 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d"
+                "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-02-29T08:48:55.657331"
+        "timestamp": "2024-07-10T12:41:34.562023"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d"
+                "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-02-29T08:49:49.071937"
+        "timestamp": "2024-07-10T11:27:11.933869532"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d"
+                "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-02-29T08:49:25.457567"
+        "timestamp": "2024-07-10T11:26:56.709849369"
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config
new file mode 100644
index 00000000..c537a6a3
--- /dev/null
+++ b/modules/nf-core/multiqc/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'MULTIQC' {
+        ext.prefix = null
+    }
+}
diff --git a/nextflow.config b/nextflow.config
index a73f66ba..90df1661 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -16,7 +16,6 @@ params {
     genome                     = null
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
     igenomes_ignore            = false
-
     // MultiQC options
     multiqc_config             = null
     multiqc_title              = null
@@ -33,48 +32,26 @@ params {
     monochrome_logs              = false
     hook_url                     = null
     help                         = false
+    help_full                    = false
+    show_hidden                  = false
     version                      = false
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
-
     // Config options
     config_profile_name        = null
     config_profile_description = null
+
     custom_config_version      = 'master'
     custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
     config_profile_contact     = null
     config_profile_url         = null
-
-    // Max resource options
-    // Defaults only, expecting to be overwritten
-    max_memory                 = '128.GB'
-    max_cpus                   = 16
-    max_time                   = '240.h'
-
     // Schema validation default options
-    validationFailUnrecognisedParams = false
-    validationLenientMode            = false
-    validationSchemaIgnoreParams     = 'genomes,igenomes_base'
-    validationShowHiddenParams       = false
-    validate_params                  = true
-
+    validate_params            = true
+    
 }
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
 
-// Load nf-core custom profiles from different Institutions
-try {
-    includeConfig "${params.custom_config_base}/nfcore_custom.config"
-} catch (Exception e) {
-    System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
-}
-
-// Load nf-core/seqinspector custom profiles from different institutions.
-try {
-    includeConfig "${params.custom_config_base}/pipeline/seqinspector.config"
-} catch (Exception e) {
-    System.err.println("WARNING: Could not load nf-core/config/seqinspector profiles: ${params.custom_config_base}/pipeline/seqinspector.config")
-}
 profiles {
     debug {
         dumpHashes              = true
@@ -89,7 +66,7 @@ profiles {
         podman.enabled          = false
         shifter.enabled         = false
         charliecloud.enabled    = false
-        conda.channels          = ['conda-forge', 'bioconda', 'defaults']
+        conda.channels          = ['conda-forge', 'bioconda']
         apptainer.enabled       = false
     }
     mamba {
@@ -178,25 +155,23 @@ profiles {
     test_full { includeConfig 'conf/test_full.config' }
 }
 
-// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
-// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
-// Set to your registry if you have a mirror of containers
-apptainer.registry   = 'quay.io'
-docker.registry      = 'quay.io'
-podman.registry      = 'quay.io'
-singularity.registry = 'quay.io'
+// Load nf-core custom profiles from different Institutions
+includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
 
-// Nextflow plugins
-plugins {
-    id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet
-}
+// Load nf-core/seqinspector custom profiles from different institutions.
+// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
+// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/seqinspector.config" : "/dev/null"
+// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
+// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
+// Set to your registry if you have a mirror of containers
+apptainer.registry    = 'quay.io'
+docker.registry       = 'quay.io'
+podman.registry       = 'quay.io'
+singularity.registry  = 'quay.io'
+charliecloud.registry = 'quay.io'
 
 // Load igenomes.config if required
-if (!params.igenomes_ignore) {
-    includeConfig 'conf/igenomes.config'
-} else {
-    params.genomes = [:]
-}
+includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container
 // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
 // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
@@ -208,8 +183,15 @@ env {
     JULIA_DEPOT_PATH = "/usr/local/share/julia"
 }
 
-// Capture exit codes from upstream processes when piping
-process.shell = ['/bin/bash', '-euo', 'pipefail']
+// Set bash options
+process.shell = """\
+bash
+
+set -e # Exit if a tool returns a non-zero status/exit code
+set -u # Treat unset variables and parameters as an error
+set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
+set -C # No clobber - prevent output redirection from overwriting files.
+"""
 
 // Disable process selector warnings by default. Use debug profile to enable warnings.
 nextflow.enable.configProcessNamesValidation = false
@@ -238,43 +220,47 @@ manifest {
     homePage        = 'https://github.com/nf-core/seqinspector'
     description     = """Pipeline to QC your sequences"""
     mainScript      = 'main.nf'
-    nextflowVersion = '!>=23.04.0'
+    nextflowVersion = '!>=24.04.2'
     version         = '1.0dev'
     doi             = ''
 }
 
-// Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'
+// Nextflow plugins
+plugins {
+    id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+}
+
+validation {
+    defaultIgnoreParams = ["genomes"]
+    help {
+        enabled = true
+        command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
+        fullParameter = "help_full"
+        showHiddenParameter = "show_hidden"
+        beforeText = """
+-\033[2m----------------------------------------------------\033[0m-
+                                        \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
+\033[0;34m        ___     __   __   __   ___     \033[0;32m/,-._.--~\'\033[0m
+\033[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \033[0;33m}  {\033[0m
+\033[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \033[0;32m\\`-._,-`-,\033[0m
+                                        \033[0;32m`._,._,\'\033[0m
+\033[0;35m  ${manifest.name} ${manifest.version}\033[0m
+-\033[2m----------------------------------------------------\033[0m-
+"""
+        afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "  https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
+* The nf-core framework
+  https://doi.org/10.1038/s41587-020-0439-x
 
-// Function to ensure that resource requirements don't go beyond
-// a maximum limit
-def check_max(obj, type) {
-    if (type == 'memory') {
-        try {
-            if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
-                return params.max_memory as nextflow.util.MemoryUnit
-            else
-                return obj
-        } catch (all) {
-            println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
-            return obj
-        }
-    } else if (type == 'time') {
-        try {
-            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
-                return params.max_time as nextflow.util.Duration
-            else
-                return obj
-        } catch (all) {
-            println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
-            return obj
-        }
-    } else if (type == 'cpus') {
-        try {
-            return Math.min( obj, params.max_cpus as int )
-        } catch (all) {
-            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
-            return obj
-        }
+* Software dependencies
+  https://github.com/${manifest.name}/blob/master/CITATIONS.md
+"""
+    }
+    summary {
+        beforeText = validation.help.beforeText
+        afterText = validation.help.afterText
     }
 }
+
+// Load modules.config for DSL2 module specific options
+includeConfig 'conf/modules.config'
+
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 36308a0d..88fd607b 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -1,10 +1,10 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/seqinspector/master/nextflow_schema.json",
     "title": "nf-core/seqinspector pipeline parameters",
     "description": "Pipeline to QC your sequences",
     "type": "object",
-    "definitions": {
+    "$defs": {
         "input_output_options": {
             "title": "Input/output options",
             "type": "object",
@@ -71,6 +71,14 @@
                     "fa_icon": "fas fa-ban",
                     "hidden": true,
                     "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`."
+                },
+                "igenomes_base": {
+                    "type": "string",
+                    "format": "directory-path",
+                    "description": "The base path to the igenomes reference files",
+                    "fa_icon": "fas fa-ban",
+                    "hidden": true,
+                    "default": "s3://ngi-igenomes/igenomes/"
                 }
             }
         },
@@ -122,41 +130,6 @@
                 }
             }
         },
-        "max_job_request_options": {
-            "title": "Max job request options",
-            "type": "object",
-            "fa_icon": "fab fa-acquisitions-incorporated",
-            "description": "Set the top limit for requested resources for any single job.",
-            "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.",
-            "properties": {
-                "max_cpus": {
-                    "type": "integer",
-                    "description": "Maximum number of CPUs that can be requested for any single job.",
-                    "default": 16,
-                    "fa_icon": "fas fa-microchip",
-                    "hidden": true,
-                    "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`"
-                },
-                "max_memory": {
-                    "type": "string",
-                    "description": "Maximum amount of memory that can be requested for any single job.",
-                    "default": "128.GB",
-                    "fa_icon": "fas fa-memory",
-                    "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
-                    "hidden": true,
-                    "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`"
-                },
-                "max_time": {
-                    "type": "string",
-                    "description": "Maximum amount of time that can be requested for any single job.",
-                    "default": "240.h",
-                    "fa_icon": "far fa-clock",
-                    "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$",
-                    "hidden": true,
-                    "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`"
-                }
-            }
-        },
         "generic_options": {
             "title": "Generic options",
             "type": "object",
@@ -164,12 +137,6 @@
             "description": "Less common options for the pipeline, typically set in a config file.",
             "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
             "properties": {
-                "help": {
-                    "type": "boolean",
-                    "description": "Display help text.",
-                    "fa_icon": "fas fa-question-circle",
-                    "hidden": true
-                },
                 "version": {
                     "type": "boolean",
                     "description": "Display version and exit.",
@@ -245,27 +212,6 @@
                     "fa_icon": "fas fa-check-square",
                     "hidden": true
                 },
-                "validationShowHiddenParams": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-eye-slash",
-                    "description": "Show all params when using `--help`",
-                    "hidden": true,
-                    "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
-                },
-                "validationFailUnrecognisedParams": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-check-circle",
-                    "description": "Validation of parameters fails when an unrecognised parameter is found.",
-                    "hidden": true,
-                    "help_text": "By default, when an unrecognised parameter is found, it returns a warinig."
-                },
-                "validationLenientMode": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-check-circle",
-                    "description": "Validation of parameters in lenient more.",
-                    "hidden": true,
-                    "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
-                },
                 "pipelines_testdata_base_path": {
                     "type": "string",
                     "fa_icon": "far fa-check-circle",
@@ -278,19 +224,16 @@
     },
     "allOf": [
         {
-            "$ref": "#/definitions/input_output_options"
-        },
-        {
-            "$ref": "#/definitions/reference_genome_options"
+            "$ref": "#/$defs/input_output_options"
         },
         {
-            "$ref": "#/definitions/institutional_config_options"
+            "$ref": "#/$defs/reference_genome_options"
         },
         {
-            "$ref": "#/definitions/max_job_request_options"
+            "$ref": "#/$defs/institutional_config_options"
         },
         {
-            "$ref": "#/definitions/generic_options"
+            "$ref": "#/$defs/generic_options"
         }
     ]
 }
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index 87281414..2571a5f5 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -8,17 +8,14 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin'
-include { paramsSummaryMap          } from 'plugin/nf-validation'
-include { fromSamplesheet           } from 'plugin/nf-validation'
-include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
+include { UTILS_NFSCHEMA_PLUGIN     } from '../../nf-core/utils_nfschema_plugin'
+include { paramsSummaryMap          } from 'plugin/nf-schema'
+include { samplesheetToList         } from 'plugin/nf-schema'
 include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
 include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
-include { dashedLine                } from '../../nf-core/utils_nfcore_pipeline'
-include { nfCoreLogo                } from '../../nf-core/utils_nfcore_pipeline'
 include { imNotification            } from '../../nf-core/utils_nfcore_pipeline'
 include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
-include { workflowCitation          } from '../../nf-core/utils_nfcore_pipeline'
+include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
 
 /*
 ========================================================================================
@@ -30,7 +27,6 @@ workflow PIPELINE_INITIALISATION {
 
     take:
     version           // boolean: Display version and exit
-    help              // boolean: Display help text
     validate_params   // boolean: Boolean whether to validate parameters against the schema at runtime
     monochrome_logs   // boolean: Do not use coloured log outputs
     nextflow_cli_args //   array: List of positional nextflow CLI args
@@ -51,20 +47,16 @@ workflow PIPELINE_INITIALISATION {
         workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1
     )
 
+    
     //
     // Validate parameters and generate parameter summary to stdout
     //
-    pre_help_text = nfCoreLogo(monochrome_logs)
-    post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs)
-    def String workflow_command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
-    UTILS_NFVALIDATION_PLUGIN (
-        help,
-        workflow_command,
-        pre_help_text,
-        post_help_text,
+    UTILS_NFSCHEMA_PLUGIN (
+        workflow,
         validate_params,
-        "nextflow_schema.json"
+        null
     )
+    
 
     //
     // Check config provided to the pipeline
@@ -80,8 +72,9 @@ workflow PIPELINE_INITIALISATION {
     //
     // Create channel from input file provided through params.input
     //
+
     Channel
-        .fromSamplesheet("input")
+        .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
         .map {
             meta, fastq_1, fastq_2 ->
                 if (!fastq_2) {
@@ -91,8 +84,8 @@ workflow PIPELINE_INITIALISATION {
                 }
         }
         .groupTuple()
-        .map {
-            validateInputSamplesheet(it)
+        .map { samplesheet ->
+            validateInputSamplesheet(samplesheet)
         }
         .map {
             meta, fastqs ->
@@ -117,13 +110,13 @@ workflow PIPELINE_COMPLETION {
     email           //  string: email address
     email_on_fail   //  string: email address sent on pipeline failure
     plaintext_email // boolean: Send plain-text email instead of HTML
+    
     outdir          //    path: Path to output directory where results will be published
     monochrome_logs // boolean: Disable ANSI colour codes in log output
     hook_url        //  string: hook URL for notifications
     multiqc_report  //  string: Path to MultiQC report
 
     main:
-
     summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
 
     //
@@ -131,11 +124,18 @@ workflow PIPELINE_COMPLETION {
     //
     workflow.onComplete {
         if (email || email_on_fail) {
-            completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList())
+            completionEmail(
+                summary_params,
+                email,
+                email_on_fail,
+                plaintext_email,
+                outdir,
+                monochrome_logs,
+                multiqc_report.toList()
+            )
         }
 
         completionSummary(monochrome_logs)
-
         if (hook_url) {
             imNotification(summary_params, hook_url)
         }
@@ -165,7 +165,7 @@ def validateInputSamplesheet(input) {
     def (metas, fastqs) = input[1..2]
 
     // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end
-    def endedness_ok = metas.collect{ it.single_end }.unique().size == 1
+    def endedness_ok = metas.collect{ meta -> meta.single_end }.unique().size == 1
     if (!endedness_ok) {
         error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}")
     }
@@ -197,7 +197,6 @@ def genomeExistsError() {
         error(error_string)
     }
 }
-
 //
 // Generate methods description for MultiQC
 //
@@ -239,8 +238,10 @@ def methodsDescriptionText(mqc_methods_yaml) {
         // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
         // Removing ` ` since the manifest.doi is a string and not a proper list
         def temp_doi_ref = ""
-        String[] manifest_doi = meta.manifest_map.doi.tokenize(",")
-        for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: <a href=\'https://doi.org/${doi_ref.replace("https://doi.org/", "").replace(" ", "")}\'>${doi_ref.replace("https://doi.org/", "").replace(" ", "")}</a>), "
+        def manifest_doi = meta.manifest_map.doi.tokenize(",")
+        manifest_doi.each { doi_ref ->
+            temp_doi_ref += "(doi: <a href=\'https://doi.org/${doi_ref.replace("https://doi.org/", "").replace(" ", "")}\'>${doi_ref.replace("https://doi.org/", "").replace(" ", "")}</a>), "
+        }
         meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2)
     } else meta["doi_text"] = ""
     meta["nodoi_text"] = meta.manifest_map.doi ? "" : "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
@@ -261,3 +262,4 @@ def methodsDescriptionText(mqc_methods_yaml) {
 
     return description_html.toString()
 }
+
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index ac31f28f..28e32b20 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -2,10 +2,6 @@
 // Subworkflow with functionality that may be useful for any Nextflow pipeline
 //
 
-import org.yaml.snakeyaml.Yaml
-import groovy.json.JsonOutput
-import nextflow.extension.FilesEx
-
 /*
 ========================================================================================
     SUBWORKFLOW DEFINITION
@@ -58,7 +54,7 @@ workflow UTILS_NEXTFLOW_PIPELINE {
 // Generate version string
 //
 def getWorkflowVersion() {
-    String version_string = ""
+    def version_string = "" as String
     if (workflow.manifest.version) {
         def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
         version_string += "${prefix_v}${workflow.manifest.version}"
@@ -79,10 +75,10 @@ def dumpParametersToJSON(outdir) {
     def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
     def filename   = "params_${timestamp}.json"
     def temp_pf    = new File(workflow.launchDir.toString(), ".${filename}")
-    def jsonStr    = JsonOutput.toJson(params)
-    temp_pf.text   = JsonOutput.prettyPrint(jsonStr)
+    def jsonStr    = groovy.json.JsonOutput.toJson(params)
+    temp_pf.text   = groovy.json.JsonOutput.prettyPrint(jsonStr)
 
-    FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
+    nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
     temp_pf.delete()
 }
 
@@ -90,7 +86,7 @@ def dumpParametersToJSON(outdir) {
 // When running with -profile conda, warn if channels have not been set-up appropriately
 //
 def checkCondaChannels() {
-    Yaml parser = new Yaml()
+    def parser = new org.yaml.snakeyaml.Yaml()
     def channels = []
     try {
         def config = parser.load("conda config --show channels".execute().text)
@@ -102,14 +98,16 @@ def checkCondaChannels() {
 
     // Check that all channels are present
     // This channel list is ordered by required channel priority.
-    def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
+    def required_channels_in_order = ['conda-forge', 'bioconda']
     def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
 
     // Check that they are in the right order
     def channel_priority_violation = false
-    def n = required_channels_in_order.size()
-    for (int i = 0; i < n - 1; i++) {
-        channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1]))
+
+    required_channels_in_order.eachWithIndex { channel, index ->
+        if (index < required_channels_in_order.size() - 1) {
+            channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index+1]))
+        }
     }
 
     if (channels_missing | channel_priority_violation) {
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
index d0a926bf..a09572e5 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
@@ -3,7 +3,7 @@ manifest {
     author          = """nf-core"""
     homePage        = 'https://127.0.0.1'
     description     = """Dummy pipeline"""
-    nextflowVersion  = '!>=23.04.0'
+    nextflowVersion = '!>=23.04.0'
     version         = '9.9.9'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index 14558c39..cbd8495b 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -2,9 +2,6 @@
 // Subworkflow with utility functions specific to the nf-core pipeline template
 //
 
-import org.yaml.snakeyaml.Yaml
-import nextflow.extension.FilesEx
-
 /*
 ========================================================================================
     SUBWORKFLOW DEFINITION
@@ -34,7 +31,7 @@ workflow UTILS_NFCORE_PIPELINE {
 //  Warn if a -profile or Nextflow config has not been provided to run the pipeline
 //
 def checkConfigProvided() {
-    valid_config = true
+    def valid_config = true as Boolean
     if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
         log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
             "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
@@ -66,11 +63,13 @@ def checkProfileProvided(nextflow_cli_args) {
 //
 def workflowCitation() {
     def temp_doi_ref = ""
-    String[] manifest_doi = workflow.manifest.doi.tokenize(",")
+    def manifest_doi = workflow.manifest.doi.tokenize(",")
     // Using a loop to handle multiple DOIs
     // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
     // Removing ` ` since the manifest.doi is a string and not a proper list
-    for (String doi_ref: manifest_doi) temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
+    manifest_doi.each { doi_ref ->
+        temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
+    }
     return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
         "* The pipeline\n" +
         temp_doi_ref + "\n" +
@@ -84,7 +83,7 @@ def workflowCitation() {
 // Generate workflow version string
 //
 def getWorkflowVersion() {
-    String version_string = ""
+    def version_string = "" as String
     if (workflow.manifest.version) {
         def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
         version_string += "${prefix_v}${workflow.manifest.version}"
@@ -102,8 +101,8 @@ def getWorkflowVersion() {
 // Get software versions for pipeline
 //
 def processVersionsFromYAML(yaml_file) {
-    Yaml yaml = new Yaml()
-    versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
+    def yaml = new org.yaml.snakeyaml.Yaml()
+    def versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
     return yaml.dumpAsMap(versions).trim()
 }
 
@@ -124,7 +123,7 @@ def workflowVersionToYAML() {
 def softwareVersionsToYAML(ch_versions) {
     return ch_versions
                 .unique()
-                .map { processVersionsFromYAML(it) }
+                .map { version -> processVersionsFromYAML(version) }
                 .unique()
                 .mix(Channel.of(workflowVersionToYAML()))
 }
@@ -134,19 +133,19 @@ def softwareVersionsToYAML(ch_versions) {
 //
 def paramsSummaryMultiqc(summary_params) {
     def summary_section = ''
-    for (group in summary_params.keySet()) {
+    summary_params.keySet().each { group ->
         def group_params = summary_params.get(group)  // This gets the parameters of that particular group
         if (group_params) {
             summary_section += "    <p style=\"font-size:110%\"><b>$group</b></p>\n"
             summary_section += "    <dl class=\"dl-horizontal\">\n"
-            for (param in group_params.keySet()) {
+            group_params.keySet().sort().each { param ->
                 summary_section += "        <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
             }
             summary_section += "    </dl>\n"
         }
     }
 
-    String yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n"
+    def yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" as String
     yaml_file_text        += "description: ' - this information is collected when the pipeline is started.'\n"
     yaml_file_text        += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
     yaml_file_text        += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
@@ -161,7 +160,7 @@ def paramsSummaryMultiqc(summary_params) {
 // nf-core logo
 //
 def nfCoreLogo(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     String.format(
         """\n
         ${dashedLine(monochrome_logs)}
@@ -180,7 +179,7 @@ def nfCoreLogo(monochrome_logs=true) {
 // Return dashed line
 //
 def dashedLine(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     return "-${colors.dim}----------------------------------------------------${colors.reset}-"
 }
 
@@ -188,7 +187,7 @@ def dashedLine(monochrome_logs=true) {
 // ANSII colours used for terminal logging
 //
 def logColours(monochrome_logs=true) {
-    Map colorcodes = [:]
+    def colorcodes = [:] as Map
 
     // Reset / Meta
     colorcodes['reset']      = monochrome_logs ? '' : "\033[0m"
@@ -287,7 +286,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     }
 
     def summary = [:]
-    for (group in summary_params.keySet()) {
+    summary_params.keySet().sort().each { group ->
         summary << summary_params[group]
     }
 
@@ -344,10 +343,10 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     def sendmail_html          = sendmail_template.toString()
 
     // Send the HTML e-mail
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     if (email_address) {
         try {
-            if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
+            if (plaintext_email) { throw new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') }
             // Try to send HTML e-mail using sendmail
             def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
             sendmail_tf.withWriter { w -> w << sendmail_html }
@@ -364,13 +363,13 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     // Write summary e-mail HTML to a file
     def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
     output_hf.withWriter { w -> w << email_html }
-    FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
+    nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
     output_hf.delete()
 
     // Write summary e-mail TXT to a file
     def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt")
     output_tf.withWriter { w -> w << email_txt }
-    FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
+    nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
     output_tf.delete()
 }
 
@@ -378,7 +377,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
 // Print pipeline summary on completion
 //
 def completionSummary(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     if (workflow.success) {
         if (workflow.stats.ignoredCount == 0) {
             log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
@@ -395,7 +394,7 @@ def completionSummary(monochrome_logs=true) {
 //
 def imNotification(summary_params, hook_url) {
     def summary = [:]
-    for (group in summary_params.keySet()) {
+    summary_params.keySet().sort().each { group ->
         summary << summary_params[group]
     }
 
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
new file mode 100644
index 00000000..4994303e
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
@@ -0,0 +1,46 @@
+//
+// Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary
+//
+
+include { paramsSummaryLog   } from 'plugin/nf-schema'
+include { validateParameters } from 'plugin/nf-schema'
+
+workflow UTILS_NFSCHEMA_PLUGIN {
+
+    take:
+    input_workflow      // workflow: the workflow object used by nf-schema to get metadata from the workflow
+    validate_params     // boolean:  validate the parameters
+    parameters_schema   // string:   path to the parameters JSON schema.
+                        //           this has to be the same as the schema given to `validation.parametersSchema`
+                        //           when this input is empty it will automatically use the configured schema or
+                        //           "${projectDir}/nextflow_schema.json" as default. This input should not be empty
+                        //           for meta pipelines
+
+    main:
+
+    //
+    // Print parameter summary to stdout. This will display the parameters
+    // that differ from the default given in the JSON schema
+    //
+    if(parameters_schema) {
+        log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema)
+    } else {
+        log.info paramsSummaryLog(input_workflow)
+    }
+
+    //
+    // Validate the parameters using nextflow_schema.json or the schema
+    // given via the validation.parametersSchema configuration option
+    //
+    if(validate_params) {
+        if(parameters_schema) {
+            validateParameters(parameters_schema:parameters_schema)
+        } else {
+            validateParameters()
+        }
+    }
+
+    emit:
+    dummy_emit = true
+}
+
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
new file mode 100644
index 00000000..f7d9f028
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
@@ -0,0 +1,35 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "utils_nfschema_plugin"
+description: Run nf-schema to validate parameters and create a summary of changed parameters
+keywords:
+  - validation
+  - JSON schema
+  - plugin
+  - parameters
+  - summary
+components: []
+input:
+  - input_workflow:
+      type: object
+      description: |
+        The workflow object of the used pipeline.
+        This object contains meta data used to create the params summary log
+  - validate_params:
+      type: boolean
+      description: Validate the parameters and error if invalid.
+  - parameters_schema:
+      type: string
+      description: |
+        Path to the parameters JSON schema.
+        This has to be the same as the schema given to the `validation.parametersSchema` config
+        option. When this input is empty it will automatically use the configured schema or
+        "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way
+        for meta pipelines.
+output:
+  - dummy_emit:
+      type: boolean
+      description: Dummy emit to make nf-core subworkflows lint happy
+authors:
+  - "@nvnieuwk"
+maintainers:
+  - "@nvnieuwk"
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
new file mode 100644
index 00000000..842dc432
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
@@ -0,0 +1,117 @@
+nextflow_workflow {
+
+    name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN"
+    script "../main.nf"
+    workflow "UTILS_NFSCHEMA_PLUGIN"
+
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "subworkflows/utils_nfschema_plugin"
+    tag "plugin/nf-schema"
+
+    config "./nextflow.config"
+
+    test("Should run nothing") {
+
+        when {
+
+            params {
+                test_data   = ''
+            }
+
+            workflow {
+                """
+                validate_params = false
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = ""
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Should validate params") {
+
+        when {
+
+            params {
+                test_data   = ''
+                outdir      = 1
+            }
+
+            workflow {
+                """
+                validate_params = true
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = ""
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.failed },
+                { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } }
+            )
+        }
+    }
+
+    test("Should run nothing - custom schema") {
+
+        when {
+
+            params {
+                test_data   = ''
+            }
+
+            workflow {
+                """
+                validate_params = false
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Should validate params - custom schema") {
+
+        when {
+
+            params {
+                test_data   = ''
+                outdir      = 1
+            }
+
+            workflow {
+                """
+                validate_params = true
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.failed },
+                { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
new file mode 100644
index 00000000..0907ac58
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
@@ -0,0 +1,8 @@
+plugins {
+    id "nf-schema@2.1.0"
+}
+
+validation {
+    parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+    monochromeLogs = true
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
similarity index 95%
rename from subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
rename to subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
index 7626c1c9..331e0d2f 100644
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
@@ -1,10 +1,10 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
     "title": ". pipeline parameters",
     "description": "",
     "type": "object",
-    "definitions": {
+    "$defs": {
         "input_output_options": {
             "title": "Input/output options",
             "type": "object",
@@ -87,10 +87,10 @@
     },
     "allOf": [
         {
-            "$ref": "#/definitions/input_output_options"
+            "$ref": "#/$defs/input_output_options"
         },
         {
-            "$ref": "#/definitions/generic_options"
+            "$ref": "#/$defs/generic_options"
         }
     ]
 }
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
deleted file mode 100644
index 2585b65d..00000000
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
+++ /dev/null
@@ -1,62 +0,0 @@
-//
-// Subworkflow that uses the nf-validation plugin to render help text and parameter summary
-//
-
-/*
-========================================================================================
-    IMPORT NF-VALIDATION PLUGIN
-========================================================================================
-*/
-
-include { paramsHelp         } from 'plugin/nf-validation'
-include { paramsSummaryLog   } from 'plugin/nf-validation'
-include { validateParameters } from 'plugin/nf-validation'
-
-/*
-========================================================================================
-    SUBWORKFLOW DEFINITION
-========================================================================================
-*/
-
-workflow UTILS_NFVALIDATION_PLUGIN {
-
-    take:
-    print_help       // boolean: print help
-    workflow_command //  string: default commmand used to run pipeline
-    pre_help_text    //  string: string to be printed before help text and summary log
-    post_help_text   //  string: string to be printed after help text and summary log
-    validate_params  // boolean: validate parameters
-    schema_filename  //    path: JSON schema file, null to use default value
-
-    main:
-
-    log.debug "Using schema file: ${schema_filename}"
-
-    // Default values for strings
-    pre_help_text    = pre_help_text    ?: ''
-    post_help_text   = post_help_text   ?: ''
-    workflow_command = workflow_command ?: ''
-
-    //
-    // Print help message if needed
-    //
-    if (print_help) {
-        log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text
-        System.exit(0)
-    }
-
-    //
-    // Print parameter summary to stdout
-    //
-    log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text
-
-    //
-    // Validate parameters relative to the parameter JSON schema
-    //
-    if (validate_params){
-        validateParameters(parameters_schema: schema_filename)
-    }
-
-    emit:
-    dummy_emit = true
-}
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
deleted file mode 100644
index 3d4a6b04..00000000
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
+++ /dev/null
@@ -1,44 +0,0 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: "UTILS_NFVALIDATION_PLUGIN"
-description: Use nf-validation to initiate and validate a pipeline
-keywords:
-  - utility
-  - pipeline
-  - initialise
-  - validation
-components: []
-input:
-  - print_help:
-      type: boolean
-      description: |
-        Print help message and exit
-  - workflow_command:
-      type: string
-      description: |
-        The command to run the workflow e.g. "nextflow run main.nf"
-  - pre_help_text:
-      type: string
-      description: |
-        Text to print before the help message
-  - post_help_text:
-      type: string
-      description: |
-        Text to print after the help message
-  - validate_params:
-      type: boolean
-      description: |
-        Validate the parameters and error if invalid.
-  - schema_filename:
-      type: string
-      description: |
-        The filename of the schema to validate against.
-output:
-  - dummy_emit:
-      type: boolean
-      description: |
-        Dummy emit to make nf-core subworkflows lint happy
-authors:
-  - "@adamrtalbot"
-maintainers:
-  - "@adamrtalbot"
-  - "@maxulysse"
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
deleted file mode 100644
index 5784a33f..00000000
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
+++ /dev/null
@@ -1,200 +0,0 @@
-nextflow_workflow {
-
-    name "Test Workflow UTILS_NFVALIDATION_PLUGIN"
-    script "../main.nf"
-    workflow "UTILS_NFVALIDATION_PLUGIN"
-    tag "subworkflows"
-    tag "subworkflows_nfcore"
-    tag "plugin/nf-validation"
-    tag "'plugin/nf-validation'"
-    tag "utils_nfvalidation_plugin"
-    tag "subworkflows/utils_nfvalidation_plugin"
-
-    test("Should run nothing") {
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-
-            workflow {
-                """
-                help             = false
-                workflow_command = null
-                pre_help_text    = null
-                post_help_text   = null
-                validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success }
-            )
-        }
-    }
-
-    test("Should run help") {
-
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-            workflow {
-                """
-                help             = true
-                workflow_command = null
-                pre_help_text    = null
-                post_help_text   = null
-                validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert workflow.exitStatus == 0 },
-                { assert workflow.stdout.any { it.contains('Input/output options') } },
-                { assert workflow.stdout.any { it.contains('--outdir') } }
-            )
-        }
-    }
-
-    test("Should run help with command") {
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-            workflow {
-                """
-                help             = true
-                workflow_command = "nextflow run noorg/doesntexist"
-                pre_help_text    = null
-                post_help_text   = null
-                validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert workflow.exitStatus == 0 },
-                { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } },
-                { assert workflow.stdout.any { it.contains('Input/output options') } },
-                { assert workflow.stdout.any { it.contains('--outdir') } }
-            )
-        }
-    }
-
-    test("Should run help with extra text") {
-
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-            workflow {
-                """
-                help             = true
-                workflow_command = "nextflow run noorg/doesntexist"
-                pre_help_text    = "pre-help-text"
-                post_help_text   = "post-help-text"
-                validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert workflow.exitStatus == 0 },
-                { assert workflow.stdout.any { it.contains('pre-help-text') } },
-                { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } },
-                { assert workflow.stdout.any { it.contains('Input/output options') } },
-                { assert workflow.stdout.any { it.contains('--outdir') } },
-                { assert workflow.stdout.any { it.contains('post-help-text') } }
-            )
-        }
-    }
-
-    test("Should validate params") {
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-                outdir          = 1
-            }
-            workflow {
-                """
-                help             = false
-                workflow_command = null
-                pre_help_text    = null
-                post_help_text   = null
-                validate_params  = true
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.failed },
-                { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } }
-            )
-        }
-    }
-}
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
deleted file mode 100644
index 60b1cfff..00000000
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-subworkflows/utils_nfvalidation_plugin:
-  - subworkflows/nf-core/utils_nfvalidation_plugin/**
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index cf7a85c4..af3719c2 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -3,10 +3,9 @@
     IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
-
 include { FASTQC                 } from '../modules/nf-core/fastqc/main'
 include { MULTIQC                } from '../modules/nf-core/multiqc/main'
-include { paramsSummaryMap       } from 'plugin/nf-validation'
+include { paramsSummaryMap       } from 'plugin/nf-schema'
 include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline'
@@ -21,12 +20,10 @@ workflow SEQINSPECTOR {
 
     take:
     ch_samplesheet // channel: samplesheet read in from --input
-
     main:
 
     ch_versions = Channel.empty()
     ch_multiqc_files = Channel.empty()
-
     //
     // MODULE: Run FastQC
     //
@@ -42,11 +39,12 @@ workflow SEQINSPECTOR {
     softwareVersionsToYAML(ch_versions)
         .collectFile(
             storeDir: "${params.outdir}/pipeline_info",
-            name: 'nf_core_pipeline_software_mqc_versions.yml',
+            name: 'nf_core_'  + 'pipeline_software_' +  'mqc_'  + 'versions.yml',
             sort: true,
             newLine: true
         ).set { ch_collated_versions }
 
+
     //
     // MODULE: MultiQC
     //
@@ -59,18 +57,19 @@ workflow SEQINSPECTOR {
         Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
         Channel.empty()
 
+    
     summary_params      = paramsSummaryMap(
         workflow, parameters_schema: "nextflow_schema.json")
     ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
-
+    ch_multiqc_files = ch_multiqc_files.mix(
+        ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+    
     ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
         file(params.multiqc_methods_description, checkIfExists: true) :
         file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
     ch_methods_description                = Channel.value(
         methodsDescriptionText(ch_multiqc_custom_methods_description))
 
-    ch_multiqc_files = ch_multiqc_files.mix(
-        ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
     ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
     ch_multiqc_files = ch_multiqc_files.mix(
         ch_methods_description.collectFile(
@@ -83,12 +82,14 @@ workflow SEQINSPECTOR {
         ch_multiqc_files.collect(),
         ch_multiqc_config.toList(),
         ch_multiqc_custom_config.toList(),
-        ch_multiqc_logo.toList()
+        ch_multiqc_logo.toList(),
+        [],
+        []
     )
 
-    emit:
-    multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
+    emit:multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
     versions       = ch_versions                 // channel: [ path(versions.yml) ]
+
 }
 
 /*

From d5d1a04b0b48531e74fa8e63f7a994f05dcd7cc8 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Wed, 9 Oct 2024 11:07:36 +0000
Subject: [PATCH 052/530] Template update for nf-core/tools version 3.0.1

---
 .editorconfig                                 |   4 -
 .github/CONTRIBUTING.md                       |   2 +-
 .github/workflows/awsfulltest.yml             |   6 +-
 .github/workflows/linting.yml                 |   4 +-
 .nf-core.yml                                  |   2 +-
 .prettierignore                               |   1 -
 docs/output.md                                |   1 -
 modules.json                                  |   6 +-
 modules/nf-core/multiqc/environment.yml       |   2 +-
 modules/nf-core/multiqc/main.nf               |   4 +-
 .../nf-core/multiqc/tests/main.nf.test.snap   |  26 +-
 nextflow.config                               |   8 +-
 .../main.nf                                   |  12 +-
 .../nf-core/utils_nextflow_pipeline/main.nf   |  46 ++-
 .../nf-core/utils_nfcore_pipeline/main.nf     | 279 ++++++++++--------
 15 files changed, 209 insertions(+), 194 deletions(-)

diff --git a/.editorconfig b/.editorconfig
index e1058815..72dda289 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -11,7 +11,6 @@ indent_style = space
 [*.{md,yml,yaml,html,css,scss,js}]
 indent_size = 2
 
-
 # These files are edited and tested upstream in nf-core/modules
 [/modules/nf-core/**]
 charset = unset
@@ -26,12 +25,9 @@ insert_final_newline = unset
 trim_trailing_whitespace = unset
 indent_style = unset
 
-
-
 [/assets/email*]
 indent_size = unset
 
-
 # ignore python and markdown
 [*.{py,md}]
 indent_style = unset
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 78893ac8..4bcb559a 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -90,7 +90,7 @@ Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json
 
 ### Default processes resource requirements
 
-Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
+Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
 
 The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.
 
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index c9462a57..5fdd2769 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -14,16 +14,18 @@ on:
 jobs:
   run-platform:
     name: Run AWS full tests
-    if: github.repository == 'nf-core/seqinspector' && github.event.review.state == 'approved'
+    # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered
+    if: github.repository == 'nf-core/seqinspector' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
       - uses: octokit/request-action@v2.x
         id: check_approvals
         with:
-          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.review.number }}/reviews
+          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       - id: test_variables
+        if: github.event_name != 'workflow_dispatch'
         run: |
           JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
           CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index b882838a..a502573c 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -42,10 +42,10 @@ jobs:
           architecture: "x64"
 
       - name: read .nf-core.yml
-        uses: pietrobolcato/action-read-yaml@1.0.0
+        uses: pietrobolcato/action-read-yaml@1.1.0
         id: read_yml
         with:
-          config: ${{ github.workspace }}/.nf-core.yaml
+          config: ${{ github.workspace }}/.nf-core.yml
 
       - name: Install dependencies
         run: |
diff --git a/.nf-core.yml b/.nf-core.yml
index ca26523b..4e856727 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,6 +1,6 @@
 bump_version: null
 lint: null
-nf_core_version: 3.0.0
+nf_core_version: 3.0.1
 org_path: null
 repository_type: pipeline
 template:
diff --git a/.prettierignore b/.prettierignore
index 610e5069..437d763d 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -1,4 +1,3 @@
-
 email_template.html
 adaptivecard.json
 slackreport.json
diff --git a/docs/output.md b/docs/output.md
index 9184bd0a..e8665e59 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -14,7 +14,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 - [FastQC](#fastqc) - Raw read QC
 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
-
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
 ### FastQC
diff --git a/modules.json b/modules.json
index 0ab8a797..41789602 100644
--- a/modules.json
+++ b/modules.json
@@ -12,7 +12,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c",
                         "installed_by": ["modules"]
                     }
                 }
@@ -21,12 +21,12 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352",
+                        "git_sha": "9d05360da397692321d377b6102d2fb22507c6ef",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab",
+                        "git_sha": "772684d9d66f37b650c8ba5146ac1ee3ecba2acb",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index f1cd99b0..6f5b867b 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::multiqc=1.24.1
+  - bioconda::multiqc=1.25.1
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index b9ccebdb..9724d2f3 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,8 +3,8 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.25--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.25--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index b779e469..2fcbb5ff 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd"
+                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-10T12:41:34.562023"
+        "timestamp": "2024-10-02T17:51:46.317523"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd"
+                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-10T11:27:11.933869532"
+        "timestamp": "2024-10-02T17:52:20.680978"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd"
+                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-10T11:26:56.709849369"
+        "timestamp": "2024-10-02T17:52:09.185842"
     }
-}
+}
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index 90df1661..caea85ac 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -12,10 +12,12 @@ params {
     // TODO nf-core: Specify your pipeline's command line flags
     // Input options
     input                      = null
+
     // References
     genome                     = null
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
     igenomes_ignore            = false
+
     // MultiQC options
     multiqc_config             = null
     multiqc_title              = null
@@ -36,6 +38,7 @@ params {
     show_hidden                  = false
     version                      = false
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
+
     // Config options
     config_profile_name        = null
     config_profile_description = null
@@ -44,9 +47,9 @@ params {
     custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
     config_profile_contact     = null
     config_profile_url         = null
+
     // Schema validation default options
     validate_params            = true
-    
 }
 
 // Load base.config by default for all pipelines
@@ -161,6 +164,7 @@ includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${pa
 // Load nf-core/seqinspector custom profiles from different institutions.
 // TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
 // includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/seqinspector.config" : "/dev/null"
+
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
 // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
 // Set to your registry if you have a mirror of containers
@@ -172,6 +176,7 @@ charliecloud.registry = 'quay.io'
 
 // Load igenomes.config if required
 includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'
+
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container
 // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
 // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
@@ -263,4 +268,3 @@ validation {
 
 // Load modules.config for DSL2 module specific options
 includeConfig 'conf/modules.config'
-
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index 2571a5f5..b2558211 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -18,9 +18,9 @@ include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
 include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW TO INITIALISE PIPELINE
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow PIPELINE_INITIALISATION {
@@ -99,9 +99,9 @@ workflow PIPELINE_INITIALISATION {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW FOR PIPELINE COMPLETION
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow PIPELINE_COMPLETION {
@@ -147,9 +147,9 @@ workflow PIPELINE_COMPLETION {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 //
 // Check and validate pipeline parameters
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index 28e32b20..2b0dc67a 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -3,13 +3,12 @@
 //
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW DEFINITION
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow UTILS_NEXTFLOW_PIPELINE {
-
     take:
     print_version        // boolean: print version
     dump_parameters      // boolean: dump parameters
@@ -22,7 +21,7 @@ workflow UTILS_NEXTFLOW_PIPELINE {
     // Print workflow version and exit on --version
     //
     if (print_version) {
-        log.info "${workflow.manifest.name} ${getWorkflowVersion()}"
+        log.info("${workflow.manifest.name} ${getWorkflowVersion()}")
         System.exit(0)
     }
 
@@ -45,9 +44,9 @@ workflow UTILS_NEXTFLOW_PIPELINE {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 //
@@ -72,11 +71,11 @@ def getWorkflowVersion() {
 // Dump pipeline parameters to a JSON file
 //
 def dumpParametersToJSON(outdir) {
-    def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
-    def filename   = "params_${timestamp}.json"
-    def temp_pf    = new File(workflow.launchDir.toString(), ".${filename}")
-    def jsonStr    = groovy.json.JsonOutput.toJson(params)
-    temp_pf.text   = groovy.json.JsonOutput.prettyPrint(jsonStr)
+    def timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')
+    def filename  = "params_${timestamp}.json"
+    def temp_pf   = new File(workflow.launchDir.toString(), ".${filename}")
+    def jsonStr   = groovy.json.JsonOutput.toJson(params)
+    temp_pf.text  = groovy.json.JsonOutput.prettyPrint(jsonStr)
 
     nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
     temp_pf.delete()
@@ -91,9 +90,14 @@ def checkCondaChannels() {
     try {
         def config = parser.load("conda config --show channels".execute().text)
         channels = config.channels
-    } catch(NullPointerException | IOException e) {
-        log.warn "Could not verify conda channel configuration."
-        return
+    }
+    catch (NullPointerException e) {
+        log.warn("Could not verify conda channel configuration.")
+        return null
+    }
+    catch (IOException e) {
+        log.warn("Could not verify conda channel configuration.")
+        return null
     }
 
     // Check that all channels are present
@@ -106,19 +110,13 @@ def checkCondaChannels() {
 
     required_channels_in_order.eachWithIndex { channel, index ->
         if (index < required_channels_in_order.size() - 1) {
-            channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index+1]))
+            channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index + 1]))
         }
     }
 
     if (channels_missing | channel_priority_violation) {
-        log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-            "  There is a problem with your Conda configuration!\n\n" +
-            "  You will need to set-up the conda-forge and bioconda channels correctly.\n" +
-            "  Please refer to https://bioconda.github.io/\n" +
-            "  The observed channel order is \n" +
-            "  ${channels}\n" +
-            "  but the following channel order is required:\n" +
-            "  ${required_channels_in_order}\n" +
-            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+        log.warn(
+            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + "  There is a problem with your Conda configuration!\n\n" + "  You will need to set-up the conda-forge and bioconda channels correctly.\n" + "  Please refer to https://bioconda.github.io/\n" + "  The observed channel order is \n" + "  ${channels}\n" + "  but the following channel order is required:\n" + "  ${required_channels_in_order}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+        )
     }
 }
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index cbd8495b..b78273ca 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -3,13 +3,12 @@
 //
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW DEFINITION
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow UTILS_NFCORE_PIPELINE {
-
     take:
     nextflow_cli_args
 
@@ -22,9 +21,9 @@ workflow UTILS_NFCORE_PIPELINE {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 //
@@ -33,12 +32,9 @@ workflow UTILS_NFCORE_PIPELINE {
 def checkConfigProvided() {
     def valid_config = true as Boolean
     if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
-        log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
-            "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
-            "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" +
-            "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" +
-            "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" +
-            "Please refer to the quick start section and usage docs for the pipeline.\n "
+        log.warn(
+            "[${workflow.manifest.name}] You are attempting to run the pipeline without any custom configuration!\n\n" + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + "Please refer to the quick start section and usage docs for the pipeline.\n "
+        )
         valid_config = false
     }
     return valid_config
@@ -49,12 +45,14 @@ def checkConfigProvided() {
 //
 def checkProfileProvided(nextflow_cli_args) {
     if (workflow.profile.endsWith(',')) {
-        error "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" +
-            "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+        error(
+            "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+        )
     }
     if (nextflow_cli_args[0]) {
-        log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" +
-            "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+        log.warn(
+            "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+        )
     }
 }
 
@@ -70,13 +68,7 @@ def workflowCitation() {
     manifest_doi.each { doi_ref ->
         temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
     }
-    return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
-        "* The pipeline\n" +
-        temp_doi_ref + "\n" +
-        "* The nf-core framework\n" +
-        "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
-        "* Software dependencies\n" +
-        "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
+    return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + "* The nf-core framework\n" + "  https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
 }
 
 //
@@ -102,7 +94,7 @@ def getWorkflowVersion() {
 //
 def processVersionsFromYAML(yaml_file) {
     def yaml = new org.yaml.snakeyaml.Yaml()
-    def versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
+    def versions = yaml.load(yaml_file).collectEntries { k, v -> [k.tokenize(':')[-1], v] }
     return yaml.dumpAsMap(versions).trim()
 }
 
@@ -112,8 +104,8 @@ def processVersionsFromYAML(yaml_file) {
 def workflowVersionToYAML() {
     return """
     Workflow:
-        $workflow.manifest.name: ${getWorkflowVersion()}
-        Nextflow: $workflow.nextflow.version
+        ${workflow.manifest.name}: ${getWorkflowVersion()}
+        Nextflow: ${workflow.nextflow.version}
     """.stripIndent().trim()
 }
 
@@ -121,11 +113,7 @@ def workflowVersionToYAML() {
 // Get channel of software versions used in pipeline in YAML format
 //
 def softwareVersionsToYAML(ch_versions) {
-    return ch_versions
-                .unique()
-                .map { version -> processVersionsFromYAML(version) }
-                .unique()
-                .mix(Channel.of(workflowVersionToYAML()))
+    return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML()))
 }
 
 //
@@ -133,25 +121,31 @@ def softwareVersionsToYAML(ch_versions) {
 //
 def paramsSummaryMultiqc(summary_params) {
     def summary_section = ''
-    summary_params.keySet().each { group ->
-        def group_params = summary_params.get(group)  // This gets the parameters of that particular group
-        if (group_params) {
-            summary_section += "    <p style=\"font-size:110%\"><b>$group</b></p>\n"
-            summary_section += "    <dl class=\"dl-horizontal\">\n"
-            group_params.keySet().sort().each { param ->
-                summary_section += "        <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
+    summary_params
+        .keySet()
+        .each { group ->
+            def group_params = summary_params.get(group)
+            // This gets the parameters of that particular group
+            if (group_params) {
+                summary_section += "    <p style=\"font-size:110%\"><b>${group}</b></p>\n"
+                summary_section += "    <dl class=\"dl-horizontal\">\n"
+                group_params
+                    .keySet()
+                    .sort()
+                    .each { param ->
+                        summary_section += "        <dt>${param}</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
+                    }
+                summary_section += "    </dl>\n"
             }
-            summary_section += "    </dl>\n"
         }
-    }
 
-    def yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" as String
-    yaml_file_text        += "description: ' - this information is collected when the pipeline is started.'\n"
-    yaml_file_text        += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
-    yaml_file_text        += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
-    yaml_file_text        += "plot_type: 'html'\n"
-    yaml_file_text        += "data: |\n"
-    yaml_file_text        += "${summary_section}"
+    def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String
+    yaml_file_text     += "description: ' - this information is collected when the pipeline is started.'\n"
+    yaml_file_text     += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
+    yaml_file_text     += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
+    yaml_file_text     += "plot_type: 'html'\n"
+    yaml_file_text     += "data: |\n"
+    yaml_file_text     += "${summary_section}"
 
     return yaml_file_text
 }
@@ -199,54 +193,54 @@ def logColours(monochrome_logs=true) {
     colorcodes['hidden']     = monochrome_logs ? '' : "\033[8m"
 
     // Regular Colors
-    colorcodes['black']      = monochrome_logs ? '' : "\033[0;30m"
-    colorcodes['red']        = monochrome_logs ? '' : "\033[0;31m"
-    colorcodes['green']      = monochrome_logs ? '' : "\033[0;32m"
-    colorcodes['yellow']     = monochrome_logs ? '' : "\033[0;33m"
-    colorcodes['blue']       = monochrome_logs ? '' : "\033[0;34m"
-    colorcodes['purple']     = monochrome_logs ? '' : "\033[0;35m"
-    colorcodes['cyan']       = monochrome_logs ? '' : "\033[0;36m"
-    colorcodes['white']      = monochrome_logs ? '' : "\033[0;37m"
+    colorcodes['black']  = monochrome_logs ? '' : "\033[0;30m"
+    colorcodes['red']    = monochrome_logs ? '' : "\033[0;31m"
+    colorcodes['green']  = monochrome_logs ? '' : "\033[0;32m"
+    colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m"
+    colorcodes['blue']   = monochrome_logs ? '' : "\033[0;34m"
+    colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m"
+    colorcodes['cyan']   = monochrome_logs ? '' : "\033[0;36m"
+    colorcodes['white']  = monochrome_logs ? '' : "\033[0;37m"
 
     // Bold
-    colorcodes['bblack']     = monochrome_logs ? '' : "\033[1;30m"
-    colorcodes['bred']       = monochrome_logs ? '' : "\033[1;31m"
-    colorcodes['bgreen']     = monochrome_logs ? '' : "\033[1;32m"
-    colorcodes['byellow']    = monochrome_logs ? '' : "\033[1;33m"
-    colorcodes['bblue']      = monochrome_logs ? '' : "\033[1;34m"
-    colorcodes['bpurple']    = monochrome_logs ? '' : "\033[1;35m"
-    colorcodes['bcyan']      = monochrome_logs ? '' : "\033[1;36m"
-    colorcodes['bwhite']     = monochrome_logs ? '' : "\033[1;37m"
+    colorcodes['bblack']  = monochrome_logs ? '' : "\033[1;30m"
+    colorcodes['bred']    = monochrome_logs ? '' : "\033[1;31m"
+    colorcodes['bgreen']  = monochrome_logs ? '' : "\033[1;32m"
+    colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m"
+    colorcodes['bblue']   = monochrome_logs ? '' : "\033[1;34m"
+    colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m"
+    colorcodes['bcyan']   = monochrome_logs ? '' : "\033[1;36m"
+    colorcodes['bwhite']  = monochrome_logs ? '' : "\033[1;37m"
 
     // Underline
-    colorcodes['ublack']     = monochrome_logs ? '' : "\033[4;30m"
-    colorcodes['ured']       = monochrome_logs ? '' : "\033[4;31m"
-    colorcodes['ugreen']     = monochrome_logs ? '' : "\033[4;32m"
-    colorcodes['uyellow']    = monochrome_logs ? '' : "\033[4;33m"
-    colorcodes['ublue']      = monochrome_logs ? '' : "\033[4;34m"
-    colorcodes['upurple']    = monochrome_logs ? '' : "\033[4;35m"
-    colorcodes['ucyan']      = monochrome_logs ? '' : "\033[4;36m"
-    colorcodes['uwhite']     = monochrome_logs ? '' : "\033[4;37m"
+    colorcodes['ublack']  = monochrome_logs ? '' : "\033[4;30m"
+    colorcodes['ured']    = monochrome_logs ? '' : "\033[4;31m"
+    colorcodes['ugreen']  = monochrome_logs ? '' : "\033[4;32m"
+    colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m"
+    colorcodes['ublue']   = monochrome_logs ? '' : "\033[4;34m"
+    colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m"
+    colorcodes['ucyan']   = monochrome_logs ? '' : "\033[4;36m"
+    colorcodes['uwhite']  = monochrome_logs ? '' : "\033[4;37m"
 
     // High Intensity
-    colorcodes['iblack']     = monochrome_logs ? '' : "\033[0;90m"
-    colorcodes['ired']       = monochrome_logs ? '' : "\033[0;91m"
-    colorcodes['igreen']     = monochrome_logs ? '' : "\033[0;92m"
-    colorcodes['iyellow']    = monochrome_logs ? '' : "\033[0;93m"
-    colorcodes['iblue']      = monochrome_logs ? '' : "\033[0;94m"
-    colorcodes['ipurple']    = monochrome_logs ? '' : "\033[0;95m"
-    colorcodes['icyan']      = monochrome_logs ? '' : "\033[0;96m"
-    colorcodes['iwhite']     = monochrome_logs ? '' : "\033[0;97m"
+    colorcodes['iblack']  = monochrome_logs ? '' : "\033[0;90m"
+    colorcodes['ired']    = monochrome_logs ? '' : "\033[0;91m"
+    colorcodes['igreen']  = monochrome_logs ? '' : "\033[0;92m"
+    colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m"
+    colorcodes['iblue']   = monochrome_logs ? '' : "\033[0;94m"
+    colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m"
+    colorcodes['icyan']   = monochrome_logs ? '' : "\033[0;96m"
+    colorcodes['iwhite']  = monochrome_logs ? '' : "\033[0;97m"
 
     // Bold High Intensity
-    colorcodes['biblack']    = monochrome_logs ? '' : "\033[1;90m"
-    colorcodes['bired']      = monochrome_logs ? '' : "\033[1;91m"
-    colorcodes['bigreen']    = monochrome_logs ? '' : "\033[1;92m"
-    colorcodes['biyellow']   = monochrome_logs ? '' : "\033[1;93m"
-    colorcodes['biblue']     = monochrome_logs ? '' : "\033[1;94m"
-    colorcodes['bipurple']   = monochrome_logs ? '' : "\033[1;95m"
-    colorcodes['bicyan']     = monochrome_logs ? '' : "\033[1;96m"
-    colorcodes['biwhite']    = monochrome_logs ? '' : "\033[1;97m"
+    colorcodes['biblack']  = monochrome_logs ? '' : "\033[1;90m"
+    colorcodes['bired']    = monochrome_logs ? '' : "\033[1;91m"
+    colorcodes['bigreen']  = monochrome_logs ? '' : "\033[1;92m"
+    colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m"
+    colorcodes['biblue']   = monochrome_logs ? '' : "\033[1;94m"
+    colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m"
+    colorcodes['bicyan']   = monochrome_logs ? '' : "\033[1;96m"
+    colorcodes['biwhite']  = monochrome_logs ? '' : "\033[1;97m"
 
     return colorcodes
 }
@@ -261,14 +255,15 @@ def attachMultiqcReport(multiqc_report) {
             mqc_report = multiqc_report.getVal()
             if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
                 if (mqc_report.size() > 1) {
-                    log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one"
+                    log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one")
                 }
                 mqc_report = mqc_report[0]
             }
         }
-    } catch (all) {
+    }
+    catch (Exception all) {
         if (multiqc_report) {
-            log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email"
+            log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email")
         }
     }
     return mqc_report
@@ -280,26 +275,35 @@ def attachMultiqcReport(multiqc_report) {
 def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) {
 
     // Set up the e-mail variables
-    def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
+    def subject = "[${workflow.manifest.name}] Successful: ${workflow.runName}"
     if (!workflow.success) {
-        subject = "[$workflow.manifest.name] FAILED: $workflow.runName"
+        subject = "[${workflow.manifest.name}] FAILED: ${workflow.runName}"
     }
 
     def summary = [:]
-    summary_params.keySet().sort().each { group ->
-        summary << summary_params[group]
-    }
+    summary_params
+        .keySet()
+        .sort()
+        .each { group ->
+            summary << summary_params[group]
+        }
 
     def misc_fields = [:]
     misc_fields['Date Started']              = workflow.start
     misc_fields['Date Completed']            = workflow.complete
     misc_fields['Pipeline script file path'] = workflow.scriptFile
     misc_fields['Pipeline script hash ID']   = workflow.scriptId
-    if (workflow.repository) misc_fields['Pipeline repository Git URL']    = workflow.repository
-    if (workflow.commitId)   misc_fields['Pipeline repository Git Commit'] = workflow.commitId
-    if (workflow.revision)   misc_fields['Pipeline Git branch/tag']        = workflow.revision
-    misc_fields['Nextflow Version']           = workflow.nextflow.version
-    misc_fields['Nextflow Build']             = workflow.nextflow.build
+    if (workflow.repository) {
+        misc_fields['Pipeline repository Git URL']    = workflow.repository
+    }
+    if (workflow.commitId) {
+        misc_fields['Pipeline repository Git Commit'] = workflow.commitId
+    }
+    if (workflow.revision) {
+        misc_fields['Pipeline Git branch/tag']        = workflow.revision
+    }
+    misc_fields['Nextflow Version']          = workflow.nextflow.version
+    misc_fields['Nextflow Build']            = workflow.nextflow.build
     misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
 
     def email_fields = [:]
@@ -337,7 +341,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
 
     // Render the sendmail template
     def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit
-    def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ]
+    def smail_fields           = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()]
     def sf                     = new File("${workflow.projectDir}/assets/sendmail_template.txt")
     def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
     def sendmail_html          = sendmail_template.toString()
@@ -346,30 +350,32 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     def colors = logColours(monochrome_logs) as Map
     if (email_address) {
         try {
-            if (plaintext_email) { throw new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') }
+            if (plaintext_email) {
+new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML')            }
             // Try to send HTML e-mail using sendmail
             def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
             sendmail_tf.withWriter { w -> w << sendmail_html }
-            [ 'sendmail', '-t' ].execute() << sendmail_html
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
-        } catch (all) {
+            ['sendmail', '-t'].execute() << sendmail_html
+            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-")
+        }
+        catch (Exception all) {
             // Catch failures and try with plaintext
-            def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
+            def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address]
             mail_cmd.execute() << email_html
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-"
+            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (mail)-")
         }
     }
 
     // Write summary e-mail HTML to a file
     def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
     output_hf.withWriter { w -> w << email_html }
-    nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
+    nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html")
     output_hf.delete()
 
     // Write summary e-mail TXT to a file
     def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt")
     output_tf.withWriter { w -> w << email_txt }
-    nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
+    nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt")
     output_tf.delete()
 }
 
@@ -380,12 +386,14 @@ def completionSummary(monochrome_logs=true) {
     def colors = logColours(monochrome_logs) as Map
     if (workflow.success) {
         if (workflow.stats.ignoredCount == 0) {
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
-        } else {
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-"
+            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Pipeline completed successfully${colors.reset}-")
+        }
+        else {
+            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-")
         }
-    } else {
-        log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-"
+    }
+    else {
+        log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-")
     }
 }
 
@@ -394,21 +402,30 @@ def completionSummary(monochrome_logs=true) {
 //
 def imNotification(summary_params, hook_url) {
     def summary = [:]
-    summary_params.keySet().sort().each { group ->
-        summary << summary_params[group]
-    }
+    summary_params
+        .keySet()
+        .sort()
+        .each { group ->
+            summary << summary_params[group]
+        }
 
     def misc_fields = [:]
-    misc_fields['start']                                = workflow.start
-    misc_fields['complete']                             = workflow.complete
-    misc_fields['scriptfile']                           = workflow.scriptFile
-    misc_fields['scriptid']                             = workflow.scriptId
-    if (workflow.repository) misc_fields['repository']  = workflow.repository
-    if (workflow.commitId)   misc_fields['commitid']    = workflow.commitId
-    if (workflow.revision)   misc_fields['revision']    = workflow.revision
-    misc_fields['nxf_version']                          = workflow.nextflow.version
-    misc_fields['nxf_build']                            = workflow.nextflow.build
-    misc_fields['nxf_timestamp']                        = workflow.nextflow.timestamp
+    misc_fields['start']          = workflow.start
+    misc_fields['complete']       = workflow.complete
+    misc_fields['scriptfile']     = workflow.scriptFile
+    misc_fields['scriptid']       = workflow.scriptId
+    if (workflow.repository) {
+        misc_fields['repository'] = workflow.repository
+    }
+    if (workflow.commitId) {
+        misc_fields['commitid']   = workflow.commitId
+    }
+    if (workflow.revision) {
+        misc_fields['revision']   = workflow.revision
+    }
+    misc_fields['nxf_version']    = workflow.nextflow.version
+    misc_fields['nxf_build']      = workflow.nextflow.build
+    misc_fields['nxf_timestamp']  = workflow.nextflow.timestamp
 
     def msg_fields = [:]
     msg_fields['version']      = getWorkflowVersion()
@@ -433,13 +450,13 @@ def imNotification(summary_params, hook_url) {
     def json_message  = json_template.toString()
 
     // POST
-    def post = new URL(hook_url).openConnection();
+    def post = new URL(hook_url).openConnection()
     post.setRequestMethod("POST")
     post.setDoOutput(true)
     post.setRequestProperty("Content-Type", "application/json")
-    post.getOutputStream().write(json_message.getBytes("UTF-8"));
-    def postRC = post.getResponseCode();
-    if (! postRC.equals(200)) {
-        log.warn(post.getErrorStream().getText());
+    post.getOutputStream().write(json_message.getBytes("UTF-8"))
+    def postRC = post.getResponseCode()
+    if (!postRC.equals(200)) {
+        log.warn(post.getErrorStream().getText())
     }
 }

From 7566c9fb5396391f4a321806484ece1c1fd627f1 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Fri, 11 Oct 2024 12:35:06 +0000
Subject: [PATCH 053/530] Template update for nf-core/tools version 3.0.2

---
 .github/workflows/ci.yml                      | 60 +++++++++++++------
 .../workflows/template_version_comment.yml    | 21 ++++---
 .gitignore                                    |  1 +
 .nf-core.yml                                  |  2 +-
 main.nf                                       |  2 +-
 modules.json                                  |  6 +-
 modules/nf-core/multiqc/main.nf               |  2 +-
 nextflow.config                               |  4 +-
 .../main.nf                                   |  4 +-
 .../nf-core/utils_nextflow_pipeline/main.nf   | 30 +++++-----
 .../nf-core/utils_nfcore_pipeline/main.nf     | 10 ++--
 workflows/seqinspector.nf                     |  2 -
 12 files changed, 86 insertions(+), 58 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 5666673f..81d03080 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -11,6 +11,8 @@ on:
 
 env:
   NXF_ANSI_LOG: false
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
@@ -18,7 +20,7 @@ concurrency:
 
 jobs:
   test:
-    name: Run pipeline with test data
+    name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
     # Only run on push if this is the nf-core dev branch (merged PRs)
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/seqinspector') }}"
     runs-on: ubuntu-latest
@@ -27,33 +29,57 @@ jobs:
         NXF_VER:
           - "24.04.2"
           - "latest-everything"
+        profile:
+          - "conda"
+          - "docker"
+          - "singularity"
+        test_name:
+          - "test"
+        isMaster:
+          - ${{ github.base_ref == 'master' }}
+        # Exclude conda and singularity on dev
+        exclude:
+          - isMaster: false
+            profile: "conda"
+          - isMaster: false
+            profile: "singularity"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - name: Install Nextflow
+      - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Disk space cleanup
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+      - name: Set up Apptainer
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-apptainer@main
 
-      - name: Run pipeline with test data (docker)
-        # TODO nf-core: You can customise CI pipeline run tests as required
-        # For example: adding multiple test runs with different parameters
-        # Remember that you can parallelise this by using strategy.matrix
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          mkdir -p $NXF_SINGULARITY_CACHEDIR
+          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+
+      - name: Set up Miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
+        with:
+          miniconda-version: "latest"
+          auto-update-conda: true
+          conda-solver: libmamba
+          channels: conda-forge,bioconda
 
-      - name: Run pipeline with test data (singularity)
-        # TODO nf-core: You can customise CI pipeline run tests as required
+      - name: Set up Conda
+        if: matrix.profile == 'conda'
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,singularity --outdir ./results
-        if: "${{ github.base_ref == 'master' }}"
+          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
+          echo $(realpath python) >> $GITHUB_PATH
+
+      - name: Clean up Disk space
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - name: Run pipeline with test data (conda)
-        # TODO nf-core: You can customise CI pipeline run tests as required
+      - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,conda --outdir ./results
-        if: "${{ github.base_ref == 'master' }}"
+          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results
diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml
index 9dea41f0..e8aafe44 100644
--- a/.github/workflows/template_version_comment.yml
+++ b/.github/workflows/template_version_comment.yml
@@ -10,9 +10,11 @@ jobs:
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
 
       - name: Read template version from .nf-core.yml
-        uses: pietrobolcato/action-read-yaml@1.0.0
+        uses: nichmor/minimal-read-yaml@v0.0.2
         id: read_yml
         with:
           config: ${{ github.workspace }}/.nf-core.yml
@@ -24,20 +26,21 @@ jobs:
 
       - name: Check nf-core outdated
         id: nf_core_outdated
-        run: pip list --outdated | grep nf-core
+        run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV}
 
       - name: Post nf-core template version comment
         uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         if: |
-          ${{ steps.nf_core_outdated.outputs.stdout }} =~ 'nf-core'
+          contains(env.OUTPUT, 'nf-core')
         with:
           repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
           allow-repeats: false
           message: |
-            ## :warning: Newer version of the nf-core template is available.
-
-            Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}.
-            Please update your pipeline to the latest version.
-
-            For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).
+            > [!WARNING]
+            > Newer version of the nf-core template is available.
+            >
+            > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}.
+            > Please update your pipeline to the latest version.
+            >
+            > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).
           #
diff --git a/.gitignore b/.gitignore
index 5124c9ac..a42ce016 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,3 +6,4 @@ results/
 testing/
 testing*
 *.pyc
+null/
diff --git a/.nf-core.yml b/.nf-core.yml
index 4e856727..fb856008 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,6 +1,6 @@
 bump_version: null
 lint: null
-nf_core_version: 3.0.1
+nf_core_version: 3.0.2
 org_path: null
 repository_type: pipeline
 template:
diff --git a/main.nf b/main.nf
index df5d2162..58e593b1 100644
--- a/main.nf
+++ b/main.nf
@@ -76,7 +76,7 @@ workflow {
         params.outdir,
         params.input
     )
-    
+
     //
     // WORKFLOW: Run main workflow
     //
diff --git a/modules.json b/modules.json
index 41789602..8e632d50 100644
--- a/modules.json
+++ b/modules.json
@@ -12,7 +12,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c",
+                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                         "installed_by": ["modules"]
                     }
                 }
@@ -21,12 +21,12 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "9d05360da397692321d377b6102d2fb22507c6ef",
+                        "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "772684d9d66f37b650c8ba5146ac1ee3ecba2acb",
+                        "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 9724d2f3..cc0643e1 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -52,7 +52,7 @@ process MULTIQC {
     stub:
     """
     mkdir multiqc_data
-    touch multiqc_plots
+    mkdir multiqc_plots
     touch multiqc_report.html
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/nextflow.config b/nextflow.config
index caea85ac..1c1ca6b1 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -254,10 +254,10 @@ validation {
 """
         afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "  https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
 * The nf-core framework
-  https://doi.org/10.1038/s41587-020-0439-x
+    https://doi.org/10.1038/s41587-020-0439-x
 
 * Software dependencies
-  https://github.com/${manifest.name}/blob/master/CITATIONS.md
+    https://github.com/${manifest.name}/blob/master/CITATIONS.md
 """
     }
     summary {
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index b2558211..8384b833 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -47,7 +47,6 @@ workflow PIPELINE_INITIALISATION {
         workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1
     )
 
-    
     //
     // Validate parameters and generate parameter summary to stdout
     //
@@ -56,7 +55,6 @@ workflow PIPELINE_INITIALISATION {
         validate_params,
         null
     )
-    
 
     //
     // Check config provided to the pipeline
@@ -64,6 +62,7 @@ workflow PIPELINE_INITIALISATION {
     UTILS_NFCORE_PIPELINE (
         nextflow_cli_args
     )
+
     //
     // Custom validation for pipeline parameters
     //
@@ -110,7 +109,6 @@ workflow PIPELINE_COMPLETION {
     email           //  string: email address
     email_on_fail   //  string: email address sent on pipeline failure
     plaintext_email // boolean: Send plain-text email instead of HTML
-    
     outdir          //    path: Path to output directory where results will be published
     monochrome_logs // boolean: Disable ANSI colour codes in log output
     hook_url        //  string: hook URL for notifications
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index 2b0dc67a..0fcbf7b3 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -3,9 +3,9 @@
 //
 
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW DEFINITION
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow UTILS_NEXTFLOW_PIPELINE {
@@ -44,9 +44,9 @@ workflow UTILS_NEXTFLOW_PIPELINE {
 }
 
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 //
@@ -106,17 +106,19 @@ def checkCondaChannels() {
     def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
 
     // Check that they are in the right order
-    def channel_priority_violation = false
-
-    required_channels_in_order.eachWithIndex { channel, index ->
-        if (index < required_channels_in_order.size() - 1) {
-            channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index + 1]))
-        }
-    }
+    def channel_priority_violation = required_channels_in_order != channels.findAll { ch -> ch in required_channels_in_order }
 
     if (channels_missing | channel_priority_violation) {
-        log.warn(
-            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + "  There is a problem with your Conda configuration!\n\n" + "  You will need to set-up the conda-forge and bioconda channels correctly.\n" + "  Please refer to https://bioconda.github.io/\n" + "  The observed channel order is \n" + "  ${channels}\n" + "  but the following channel order is required:\n" + "  ${required_channels_in_order}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-        )
+        log.warn """\
+        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+            There is a problem with your Conda configuration!
+            You will need to set-up the conda-forge and bioconda channels correctly.
+            Please refer to https://bioconda.github.io/
+            The observed channel order is
+            ${channels}
+            but the following channel order is required:
+            ${required_channels_in_order}
+        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+        """.stripIndent(true)
     }
 }
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index b78273ca..5cb7bafe 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -3,9 +3,9 @@
 //
 
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW DEFINITION
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow UTILS_NFCORE_PIPELINE {
@@ -21,9 +21,9 @@ workflow UTILS_NFCORE_PIPELINE {
 }
 
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 //
@@ -62,7 +62,7 @@ def checkProfileProvided(nextflow_cli_args) {
 def workflowCitation() {
     def temp_doi_ref = ""
     def manifest_doi = workflow.manifest.doi.tokenize(",")
-    // Using a loop to handle multiple DOIs
+    // Handling multiple DOIs
     // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
     // Removing ` ` since the manifest.doi is a string and not a proper list
     manifest_doi.each { doi_ref ->
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index af3719c2..4a9df1ca 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -57,13 +57,11 @@ workflow SEQINSPECTOR {
         Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
         Channel.empty()
 
-    
     summary_params      = paramsSummaryMap(
         workflow, parameters_schema: "nextflow_schema.json")
     ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
     ch_multiqc_files = ch_multiqc_files.mix(
         ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
-    
     ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
         file(params.multiqc_methods_description, checkIfExists: true) :
         file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)

From 1faa8db5858b1c780e1f42b1b2da1cda462ffe51 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Mon, 28 Oct 2024 11:12:03 +0000
Subject: [PATCH 054/530] nf-core tools 3.0.2 modules update

---
 modules.json                                  |   4 +-
 modules/nf-core/fastqc/environment.yml        |   2 -
 modules/nf-core/fastqc/main.nf                |   5 +-
 modules/nf-core/fastqc/meta.yml               |  57 +--
 modules/nf-core/fastqc/tests/main.nf.test     | 225 ++++++++---
 .../nf-core/fastqc/tests/main.nf.test.snap    | 370 ++++++++++++++++--
 modules/nf-core/multiqc/environment.yml       |   4 +-
 modules/nf-core/multiqc/main.nf               |   6 +-
 modules/nf-core/multiqc/meta.yml              |  91 +++--
 .../nf-core/multiqc/tests/main.nf.test.snap   |  26 +-
 10 files changed, 603 insertions(+), 187 deletions(-)

diff --git a/modules.json b/modules.json
index 70f3486c..a84d111b 100644
--- a/modules.json
+++ b/modules.json
@@ -7,12 +7,12 @@
                 "nf-core": {
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "19ca321db5d8bd48923262c2eca6422359633491",
+                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                         "installed_by": ["modules"]
                     }
                 }
diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml
index 1787b38a..691d4c76 100644
--- a/modules/nf-core/fastqc/environment.yml
+++ b/modules/nf-core/fastqc/environment.yml
@@ -1,7 +1,5 @@
-name: fastqc
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::fastqc=0.12.1
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index d79f1c86..d8989f48 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -26,7 +26,10 @@ process FASTQC {
     def rename_to = old_new_pairs*.join(' ').join(' ')
     def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
 
-    def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB')
+    // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory)
+    // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222
+    // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label
+    def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus
     // FastQC memory value allowed range (100 - 10000)
     def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
 
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
index ee5507e0..4827da7a 100644
--- a/modules/nf-core/fastqc/meta.yml
+++ b/modules/nf-core/fastqc/meta.yml
@@ -16,35 +16,44 @@ tools:
       homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
       documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
       licence: ["GPL-2.0-only"]
+      identifier: biotools:fastqc
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: |
-        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-        respectively.
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: file
+        description: |
+          List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+          respectively.
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - html:
-      type: file
-      description: FastQC report
-      pattern: "*_{fastqc.html}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.html":
+          type: file
+          description: FastQC report
+          pattern: "*_{fastqc.html}"
   - zip:
-      type: file
-      description: FastQC report archive
-      pattern: "*_{fastqc.zip}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.zip":
+          type: file
+          description: FastQC report archive
+          pattern: "*_{fastqc.zip}"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@drpatelh"
   - "@grst"
diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test
index 70edae4d..e9d79a07 100644
--- a/modules/nf-core/fastqc/tests/main.nf.test
+++ b/modules/nf-core/fastqc/tests/main.nf.test
@@ -23,17 +23,14 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it.
-            // looks like this: <div id="header_filename">Mon 2 Oct 2023<br/>test.gz</div>
-            // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039
-
-            { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
-            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
-            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_single") }
+                { assert process.success },
+                // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it.
+                // looks like this: <div id="header_filename">Mon 2 Oct 2023<br/>test.gz</div>
+                // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039
+                { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+                { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -54,16 +51,14 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
-            { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
-            { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
-            { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
-            { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-            { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_paired") }
+                { assert process.success },
+                { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
+                { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
+                { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
+                { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
+                { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -83,13 +78,11 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
-            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
-            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") }
+                { assert process.success },
+                { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+                { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -109,13 +102,11 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
-            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
-            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_bam") }
+                { assert process.success },
+                { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+                { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -138,22 +129,20 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
-            { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
-            { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" },
-            { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" },
-            { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
-            { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
-            { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" },
-            { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" },
-            { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-            { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-            { assert path(process.out.html[0][1][2]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-            { assert path(process.out.html[0][1][3]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_multiple") }
+                { assert process.success },
+                { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
+                { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
+                { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" },
+                { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" },
+                { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
+                { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
+                { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" },
+                { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" },
+                { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert path(process.out.html[0][1][2]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert path(process.out.html[0][1][3]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -173,21 +162,18 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" },
-            { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" },
-            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") }
+                { assert process.success },
+                { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" },
+                { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" },
+                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
 
     test("sarscov2 single-end [fastq] - stub") {
 
-        options "-stub"
-
+    options "-stub"
         when {
             process {
                 """
@@ -201,12 +187,123 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-            { assert snapshot(process.out.html.collect { file(it[1]).getName() } +
-                                process.out.zip.collect { file(it[1]).getName() } +
-                                process.out.versions ).match("fastqc_stub") }
+                { assert process.success },
+                { assert snapshot(process.out).match() }
             )
         }
     }
 
+    test("sarscov2 paired-end [fastq] - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 interleaved [fastq] - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true)
+                ])
+            """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 paired-end [bam] - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 multiple [fastq] - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 custom_prefix - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'mysample', single_end:true ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
 }
diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap
index 86f7c311..d5db3092 100644
--- a/modules/nf-core/fastqc/tests/main.nf.test.snap
+++ b/modules/nf-core/fastqc/tests/main.nf.test.snap
@@ -1,88 +1,392 @@
 {
-    "fastqc_versions_interleaved": {
+    "sarscov2 custom_prefix": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:40:07.293713"
+        "timestamp": "2024-07-22T11:02:16.374038"
     },
-    "fastqc_stub": {
+    "sarscov2 single-end [fastq] - stub": {
         "content": [
-            [
-                "test.html",
-                "test.zip",
-                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-            ]
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:24.993809"
+    },
+    "sarscov2 custom_prefix - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:31:01.425198"
+        "timestamp": "2024-07-22T11:03:10.93942"
     },
-    "fastqc_versions_multiple": {
+    "sarscov2 interleaved [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:40:55.797907"
+        "timestamp": "2024-07-22T11:01:42.355718"
     },
-    "fastqc_versions_bam": {
+    "sarscov2 paired-end [bam]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:40:26.795862"
+        "timestamp": "2024-07-22T11:01:53.276274"
     },
-    "fastqc_versions_single": {
+    "sarscov2 multiple [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:39:27.043675"
+        "timestamp": "2024-07-22T11:02:05.527626"
     },
-    "fastqc_versions_paired": {
+    "sarscov2 paired-end [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:01:31.188871"
+    },
+    "sarscov2 paired-end [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:34.273566"
+    },
+    "sarscov2 multiple [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:39:47.584191"
+        "timestamp": "2024-07-22T11:03:02.304411"
     },
-    "fastqc_versions_custom_prefix": {
+    "sarscov2 single-end [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:01:19.095607"
+    },
+    "sarscov2 interleaved [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:44.640184"
+    },
+    "sarscov2 paired-end [bam] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:41:14.576531"
+        "timestamp": "2024-07-22T11:02:53.550742"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index a31464c9..6f5b867b 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -1,7 +1,5 @@
-name: multiqc
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::multiqc=1.24.1
+  - bioconda::multiqc=1.25.1
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index ceaec139..cc0643e1 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,8 +3,8 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.24.1--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.24.1--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
@@ -52,7 +52,7 @@ process MULTIQC {
     stub:
     """
     mkdir multiqc_data
-    touch multiqc_plots
+    mkdir multiqc_plots
     touch multiqc_report.html
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index 382c08cb..b16c1879 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -1,5 +1,6 @@
 name: multiqc
-description: Aggregate results from bioinformatics analyses across many samples into a single report
+description: Aggregate results from bioinformatics analyses across many samples into
+  a single report
 keywords:
   - QC
   - bioinformatics tools
@@ -12,53 +13,59 @@ tools:
       homepage: https://multiqc.info/
       documentation: https://multiqc.info/docs/
       licence: ["GPL-3.0-or-later"]
+      identifier: biotools:multiqc
 input:
-  - multiqc_files:
-      type: file
-      description: |
-        List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
-  - multiqc_config:
-      type: file
-      description: Optional config yml for MultiQC
-      pattern: "*.{yml,yaml}"
-  - extra_multiqc_config:
-      type: file
-      description: Second optional config yml for MultiQC. Will override common sections in multiqc_config.
-      pattern: "*.{yml,yaml}"
-  - multiqc_logo:
-      type: file
-      description: Optional logo file for MultiQC
-      pattern: "*.{png}"
-  - replace_names:
-      type: file
-      description: |
-        Optional two-column sample renaming file. First column a set of
-        patterns, second column a set of corresponding replacements. Passed via
-        MultiQC's `--replace-names` option.
-      pattern: "*.{tsv}"
-  - sample_names:
-      type: file
-      description: |
-        Optional TSV file with headers, passed to the MultiQC --sample_names
-        argument.
-      pattern: "*.{tsv}"
+  - - multiqc_files:
+        type: file
+        description: |
+          List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
+  - - multiqc_config:
+        type: file
+        description: Optional config yml for MultiQC
+        pattern: "*.{yml,yaml}"
+  - - extra_multiqc_config:
+        type: file
+        description: Second optional config yml for MultiQC. Will override common sections
+          in multiqc_config.
+        pattern: "*.{yml,yaml}"
+  - - multiqc_logo:
+        type: file
+        description: Optional logo file for MultiQC
+        pattern: "*.{png}"
+  - - replace_names:
+        type: file
+        description: |
+          Optional two-column sample renaming file. First column a set of
+          patterns, second column a set of corresponding replacements. Passed via
+          MultiQC's `--replace-names` option.
+        pattern: "*.{tsv}"
+  - - sample_names:
+        type: file
+        description: |
+          Optional TSV file with headers, passed to the MultiQC --sample_names
+          argument.
+        pattern: "*.{tsv}"
 output:
   - report:
-      type: file
-      description: MultiQC report file
-      pattern: "multiqc_report.html"
+      - "*multiqc_report.html":
+          type: file
+          description: MultiQC report file
+          pattern: "multiqc_report.html"
   - data:
-      type: directory
-      description: MultiQC data dir
-      pattern: "multiqc_data"
+      - "*_data":
+          type: directory
+          description: MultiQC data dir
+          pattern: "multiqc_data"
   - plots:
-      type: file
-      description: Plots created by MultiQC
-      pattern: "*_data"
+      - "*_plots":
+          type: file
+          description: Plots created by MultiQC
+          pattern: "*_data"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@abhi18av"
   - "@bunop"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index 83fa080c..2fcbb5ff 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760"
+                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-10T12:41:34.562023"
+        "timestamp": "2024-10-02T17:51:46.317523"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760"
+                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-10T11:27:11.933869532"
+        "timestamp": "2024-10-02T17:52:20.680978"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760"
+                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-10T11:26:56.709849369"
+        "timestamp": "2024-10-02T17:52:09.185842"
     }
-}
+}
\ No newline at end of file

From 6caa3f2d4d39364c8b5283f09be9fda8052bf7d3 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Mon, 28 Oct 2024 13:30:37 +0000
Subject: [PATCH 055/530] merge fix

---
 .../local/utils_nfcore_seqinspector_pipeline/main.nf         | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index c2270583..a84e064f 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -74,6 +74,7 @@ workflow PIPELINE_INITIALISATION {
 
     Channel
         .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
+        .toList()
         .flatMap { it.withIndex().collect {  entry, idx -> entry + "${idx+1}" } }
         .map {
             meta, fastq_1, fastq_2, idx ->
@@ -94,8 +95,8 @@ workflow PIPELINE_INITIALISATION {
                 }
         }
         .groupTuple()
-        .map { samplesheet ->
-            validateInputSamplesheet(samplesheet)
+        .map {
+            validateInputSamplesheet(it) // Applies additional group validation checks that schema_input.json cannot do.
         }
         .transpose() // Replace the map below
         // .map {

From da6f21e20cf0135fc9efe42b1921c35a4a1636fe Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Mon, 28 Oct 2024 13:30:48 +0000
Subject: [PATCH 056/530] update snapshots

---
 tests/MiSeq.main.nf.test.snap       |  8 ++++----
 tests/NovaSeq6000.main.nf.test.snap | 24 ++++++++++++------------
 tests/PromethION.main.nf.test.snap  | 10 +++++-----
 3 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 9dacaf8a..4613d525 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -3,13 +3,13 @@
         "content": [
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
-            "multiqc_general_stats.txt:md5,962713a1473a318f2cb29bb5290c4c8e",
-            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5"
+            "multiqc_general_stats.txt:md5,5b28a83b14cb2fe88d084d08900ebdbf",
+            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3"
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-09-10T08:57:05.870194"
+        "timestamp": "2024-10-28T13:18:10.3675973"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index 3f27e5a2..ee3c22b7 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -3,29 +3,29 @@
         "content": [
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d",
-            "multiqc_general_stats.txt:md5,d521de54d1e659bf7892105f7d23d4db",
-            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5",
+            "multiqc_general_stats.txt:md5,25abe0f6a35eb4a3b056fc3cf5c13732",
+            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
-            "multiqc_general_stats.txt:md5,d52544eb1a505c889a2f9117cf94a5fa",
-            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5",
+            "multiqc_general_stats.txt:md5,90ee35137492b80aab36ef67f72d8921",
+            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
-            "multiqc_general_stats.txt:md5,5b1190093085ef073d4bd5818c9cde79",
-            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5",
+            "multiqc_general_stats.txt:md5,d62a2fc39e674d98783d408791803148",
+            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
-            "multiqc_general_stats.txt:md5,79c1090dd8a97912893f8491641b9dc9",
-            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5",
+            "multiqc_general_stats.txt:md5,2f09b8f199ac40cf67ba50843cebd29c",
+            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
-            "multiqc_general_stats.txt:md5,41611bd5ab9e79425c466bf976b03bdc",
-            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5"
+            "multiqc_general_stats.txt:md5,6a1c16f068d7ba3a9225a17eb570ed9a",
+            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3"
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-09-10T08:58:26.732622"
+        "timestamp": "2024-10-28T13:19:13.226135825"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index fb8cda25..026a8cd2 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -2,14 +2,14 @@
     "PromethION data test": {
         "content": [
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,35984961f25a0d4e7352cab4d5650178",
-            "multiqc_general_stats.txt:md5,1465b0b1959e3864b28ecc2340df351b",
-            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5"
+            "multiqc_fastqc.txt:md5,1a4b472e13cadc770832b0e20d1de7b0",
+            "multiqc_general_stats.txt:md5,409cefc7f17f95d176ced6032bf8fb32",
+            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3"
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-09-10T08:58:57.180636"
+        "timestamp": "2024-10-28T13:19:57.261730412"
     }
 }
\ No newline at end of file

From dde2a8d93a6ec79b132b3d3123547fa81b6286bc Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Mon, 28 Oct 2024 13:38:38 +0000
Subject: [PATCH 057/530] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3aa5bacc..b0b12de1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 
 - [#20](https://github.com/nf-core/seqinspector/pull/20) Use tags to generate group reports
 - [#13](https://github.com/nf-core/seqinspector/pull/13) Generate reports per run, per project and per lane.
+- [#49](https://github.com/nf-core/seqinspector/pull/49) Merge with template 3.0.2.
 
 ### `Fixed`
 

From ea5fc892deff6bfbf8d23bba48cfe2a6e57d1b02 Mon Sep 17 00:00:00 2001
From: ngarcia <natalia.garcia@nanoporetech.com>
Date: Mon, 28 Oct 2024 13:16:54 +0000
Subject: [PATCH 058/530] add subsampling

---
 modules.json                                  |  5 +
 modules/nf-core/seqtk/sample/environment.yml  |  5 +
 modules/nf-core/seqtk/sample/main.nf          | 58 +++++++++++
 modules/nf-core/seqtk/sample/meta.yml         | 52 ++++++++++
 .../nf-core/seqtk/sample/tests/main.nf.test   | 80 ++++++++++++++++
 .../seqtk/sample/tests/main.nf.test.snap      | 95 +++++++++++++++++++
 .../seqtk/sample/tests/standard.config        |  6 ++
 modules/nf-core/seqtk/sample/tests/tags.yml   |  2 +
 nextflow.config                               |  2 +-
 nextflow_schema.json                          |  7 ++
 workflows/seqinspector.nf                     | 17 +++-
 11 files changed, 327 insertions(+), 2 deletions(-)
 create mode 100644 modules/nf-core/seqtk/sample/environment.yml
 create mode 100644 modules/nf-core/seqtk/sample/main.nf
 create mode 100644 modules/nf-core/seqtk/sample/meta.yml
 create mode 100644 modules/nf-core/seqtk/sample/tests/main.nf.test
 create mode 100644 modules/nf-core/seqtk/sample/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/seqtk/sample/tests/standard.config
 create mode 100644 modules/nf-core/seqtk/sample/tests/tags.yml

diff --git a/modules.json b/modules.json
index 8e632d50..f01f2a64 100644
--- a/modules.json
+++ b/modules.json
@@ -14,6 +14,11 @@
                         "branch": "master",
                         "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                         "installed_by": ["modules"]
+                    },
+                    "seqtk/sample": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
                     }
                 }
             },
diff --git a/modules/nf-core/seqtk/sample/environment.yml b/modules/nf-core/seqtk/sample/environment.yml
new file mode 100644
index 00000000..693aa5c1
--- /dev/null
+++ b/modules/nf-core/seqtk/sample/environment.yml
@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::seqtk=1.4
diff --git a/modules/nf-core/seqtk/sample/main.nf b/modules/nf-core/seqtk/sample/main.nf
new file mode 100644
index 00000000..ea9b839e
--- /dev/null
+++ b/modules/nf-core/seqtk/sample/main.nf
@@ -0,0 +1,58 @@
+process SEQTK_SAMPLE {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/seqtk:1.4--he4a0461_1' :
+        'biocontainers/seqtk:1.4--he4a0461_1' }"
+
+    input:
+    tuple val(meta), path(reads), val(sample_size)
+
+    output:
+    tuple val(meta), path("*.fastq.gz"), emit: reads
+    path "versions.yml"                , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args   = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    if (!(args ==~ /.*-s[0-9]+.*/)) {
+        args += " -s100"
+    }
+    if ( !sample_size ) {
+        error "SEQTK/SAMPLE must have a sample_size value included"
+    }
+    """
+    printf "%s\\n" $reads | while read f;
+    do
+        seqtk \\
+            sample \\
+            $args \\
+            \$f \\
+            $sample_size \\
+            | gzip --no-name > ${prefix}_\$(basename \$f)
+    done
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    echo "" | gzip > ${prefix}.fastq.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+}
diff --git a/modules/nf-core/seqtk/sample/meta.yml b/modules/nf-core/seqtk/sample/meta.yml
new file mode 100644
index 00000000..42f67d8f
--- /dev/null
+++ b/modules/nf-core/seqtk/sample/meta.yml
@@ -0,0 +1,52 @@
+name: seqtk_sample
+description: Subsample reads from FASTQ files
+keywords:
+  - sample
+  - fastx
+  - reads
+tools:
+  - seqtk:
+      description: Seqtk is a fast and lightweight tool for processing sequences in
+        the FASTA or FASTQ format. Seqtk sample command subsamples sequences.
+      homepage: https://github.com/lh3/seqtk
+      documentation: https://docs.csc.fi/apps/seqtk/
+      tool_dev_url: https://github.com/lh3/seqtk
+      licence: ["MIT"]
+      identifier: biotools:seqtk
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: file
+        description: List of input FastQ files
+        pattern: "*.{fastq.gz}"
+    - sample_size:
+        type: integer
+        description: Number of reads to sample.
+output:
+  - reads:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.fastq.gz":
+          type: file
+          description: Subsampled FastQ files
+          pattern: "*.{fastq.gz}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@kaurravneet4123"
+  - "@sidorov-si"
+  - "@adamrtalbot"
+maintainers:
+  - "@kaurravneet4123"
+  - "@sidorov-si"
+  - "@adamrtalbot"
diff --git a/modules/nf-core/seqtk/sample/tests/main.nf.test b/modules/nf-core/seqtk/sample/tests/main.nf.test
new file mode 100644
index 00000000..c121c9d9
--- /dev/null
+++ b/modules/nf-core/seqtk/sample/tests/main.nf.test
@@ -0,0 +1,80 @@
+nextflow_process {
+
+    name "Test Process SEQTK_SAMPLE"
+    script "modules/nf-core/seqtk/sample/main.nf"
+    process "SEQTK_SAMPLE"
+    config "./standard.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "seqtk"
+    tag "seqtk/sample"
+
+    test("sarscov2_sample_singleend_fqgz") {
+
+        when {
+            process {
+                """
+                input[0] =  [
+                                [ id:'test', single_end:true ],
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                                50
+                            ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2_sample_pairedend_fqgz") {
+
+        when {
+            process {
+                """
+                input[0] =  [
+                                [ id:'test', single_end:true ],
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                                50
+                            ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2_sample_singlend_fqgz_stub") {
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] =  [
+                                [ id:'test', single_end:true ],
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                                50
+                            ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/seqtk/sample/tests/main.nf.test.snap b/modules/nf-core/seqtk/sample/tests/main.nf.test.snap
new file mode 100644
index 00000000..a9fec3c4
--- /dev/null
+++ b/modules/nf-core/seqtk/sample/tests/main.nf.test.snap
@@ -0,0 +1,95 @@
+{
+    "sarscov2_sample_singlend_fqgz_stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.sampled.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.sampled.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806"
+                ]
+            }
+        ],
+        "timestamp": "2024-02-22T15:58:45.902956"
+    },
+    "sarscov2_sample_pairedend_fqgz": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.sampled_test_1.fastq.gz:md5,e5f44fafd7351c5abb9925a075132941"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.sampled_test_1.fastq.gz:md5,e5f44fafd7351c5abb9925a075132941"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806"
+                ]
+            }
+        ],
+        "timestamp": "2024-02-22T15:58:37.679954"
+    },
+    "sarscov2_sample_singleend_fqgz": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.sampled_test_1.fastq.gz:md5,e5f44fafd7351c5abb9925a075132941"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.sampled_test_1.fastq.gz:md5,e5f44fafd7351c5abb9925a075132941"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806"
+                ]
+            }
+        ],
+        "timestamp": "2024-02-22T15:58:29.474491"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/seqtk/sample/tests/standard.config b/modules/nf-core/seqtk/sample/tests/standard.config
new file mode 100644
index 00000000..b2dd4b9f
--- /dev/null
+++ b/modules/nf-core/seqtk/sample/tests/standard.config
@@ -0,0 +1,6 @@
+process {
+    withName: SEQTK_SAMPLE {
+        ext.args = '-s100'
+        ext.prefix = { "${meta.id}.sampled" }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/seqtk/sample/tests/tags.yml b/modules/nf-core/seqtk/sample/tests/tags.yml
new file mode 100644
index 00000000..e5d113b8
--- /dev/null
+++ b/modules/nf-core/seqtk/sample/tests/tags.yml
@@ -0,0 +1,2 @@
+seqtk/sample:
+  - "modules/nf-core/seqtk/sample/**"
diff --git a/nextflow.config b/nextflow.config
index 50c1ecbb..10bcb897 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -12,7 +12,7 @@ params {
     // TODO nf-core: Specify your pipeline's command line flags
     // Input options
     input                      = null
-
+    sample_size                = null
     // References
     genome                     = null
     fasta                      = null
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 88fd607b..f87e525f 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -23,8 +23,15 @@
                     "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/seqinspector/usage#samplesheet-input).",
                     "fa_icon": "fas fa-file-csv"
                 },
+                "sample_size": {
+                    "type": "integer",
+                    "default": null,
+                    "description": "Subset this number of reads.",
+                    "help_text": "Samples will be subsetted to this number of reads. If null, no subsampling will be performed."
+                },
                 "outdir": {
                     "type": "string",
+                    "default": null,
                     "format": "directory-path",
                     "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
                     "fa_icon": "fas fa-folder-open"
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index ea628117..70b89679 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -3,6 +3,8 @@
     IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
+
+include { SEQTK_SAMPLE                  } from '../modules/nf-core/seqtk/sample/main'
 include { FASTQC                        } from '../modules/nf-core/fastqc/main'
 
 include { MULTIQC as MULTIQC_GLOBAL     } from '../modules/nf-core/multiqc/main'
@@ -30,11 +32,24 @@ workflow SEQINSPECTOR {
     ch_multiqc_extra_files = Channel.empty()
     ch_multiqc_reports     = Channel.empty()
 
+    //
+    // MODULE: Run Seqkit sample to perform subsampling
+    //
+    if (params.sample_size) {
+        ch_sample_sized = SEQTK_SAMPLE(ch_samplesheet.map {
+            meta, reads -> [meta, reads, params.sample_size]
+        }).reads
+        ch_versions = ch_versions.mix(SEQTK_SAMPLE.out.versions.first())
+    } else {
+        // No do subsample
+        ch_sample_sized = ch_samplesheet
+    }
+
     //
     // MODULE: Run FastQC
     //
     FASTQC (
-        ch_samplesheet
+        ch_sample_sized
     )
     ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip)
     ch_versions = ch_versions.mix(FASTQC.out.versions.first())

From 9b2808c62e95099d20615ef0746e209adab33b5a Mon Sep 17 00:00:00 2001
From: ngarcia <natalia.garcia@nanoporetech.com>
Date: Mon, 28 Oct 2024 14:03:06 +0000
Subject: [PATCH 059/530] add subsampling nf-test

---
 tests/NovaSeq6000.main_subsample.nf.test      | 50 +++++++++++++++++++
 .../NovaSeq6000.main_subsample.nf.test.config |  8 +++
 2 files changed, 58 insertions(+)
 create mode 100644 tests/NovaSeq6000.main_subsample.nf.test
 create mode 100644 tests/NovaSeq6000.main_subsample.nf.test.config

diff --git a/tests/NovaSeq6000.main_subsample.nf.test b/tests/NovaSeq6000.main_subsample.nf.test
new file mode 100644
index 00000000..0919bc23
--- /dev/null
+++ b/tests/NovaSeq6000.main_subsample.nf.test
@@ -0,0 +1,50 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf on NovaSeq6000 data"
+    script "../main.nf"
+    tag "seqinspector"
+    tag "PIPELINE"
+
+    test("NovaSeq6000 data test") {
+
+        when {
+            config "./NovaSeq6000.main_subsample.nf.test.config"
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_software_versions.txt"),
+
+                    path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_software_versions.txt"),
+
+                    path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt"),
+
+                    path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_software_versions.txt"),
+
+                    path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_software_versions.txt"),
+                    ).match()
+                },
+            )
+        }
+    }
+}
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.config b/tests/NovaSeq6000.main_subsample.nf.test.config
new file mode 100644
index 00000000..acda74dd
--- /dev/null
+++ b/tests/NovaSeq6000.main_subsample.nf.test.config
@@ -0,0 +1,8 @@
+// Load the basic test config
+includeConfig 'nextflow.config'
+
+// Load the correct samplesheet for that test
+params {
+    input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
+    sample_size = 90
+}

From a39925c8deed21a2fca735d91a6df9bca034ad6e Mon Sep 17 00:00:00 2001
From: ngarcia <natalia.garcia@nanoporetech.com>
Date: Mon, 28 Oct 2024 14:09:57 +0000
Subject: [PATCH 060/530] add snapshots

---
 tests/NovaSeq6000.main_subsample.nf.test.snap | 31 +++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 tests/NovaSeq6000.main_subsample.nf.test.snap

diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
new file mode 100644
index 00000000..d1dbe4a7
--- /dev/null
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -0,0 +1,31 @@
+{
+    "NovaSeq6000 data test": {
+        "content": [
+            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_fastqc.txt:md5,aba942d1e6996b579f19798e5673f514",
+            "multiqc_general_stats.txt:md5,c4f40f2313aadc38619e7487226e8d93",
+            "multiqc_software_versions.txt:md5,b7d1ca14785a9361f0a39ce1b6a02686",
+            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8",
+            "multiqc_general_stats.txt:md5,d5d73d2888cd9895e5f116e5b869e73c",
+            "multiqc_software_versions.txt:md5,b7d1ca14785a9361f0a39ce1b6a02686",
+            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_fastqc.txt:md5,ff996e1d3dc4a46e0c9535e54d51ccab",
+            "multiqc_general_stats.txt:md5,d01ec30a262b69bc5749b0ed108a950a",
+            "multiqc_software_versions.txt:md5,b7d1ca14785a9361f0a39ce1b6a02686",
+            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_fastqc.txt:md5,3df36ecfe76b25b0c22dcda84bce2b3b",
+            "multiqc_general_stats.txt:md5,4dffc0d1169c49adde819d4467ffb775",
+            "multiqc_software_versions.txt:md5,b7d1ca14785a9361f0a39ce1b6a02686",
+            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_fastqc.txt:md5,ce61b4ce4b1d76ec3f20de3bf0c9ec7f",
+            "multiqc_general_stats.txt:md5,05f8dfeea9fca7f4c16ba9d553af4c69",
+            "multiqc_software_versions.txt:md5,b7d1ca14785a9361f0a39ce1b6a02686"
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-28T14:05:44.868455454"
+    }
+}
\ No newline at end of file

From 23f52fb325ae74256cb00a9721ec765d86799009 Mon Sep 17 00:00:00 2001
From: ngarcia <natalia.garcia@nanoporetech.com>
Date: Mon, 28 Oct 2024 14:20:03 +0000
Subject: [PATCH 061/530] better name

---
 tests/NovaSeq6000.main_subsample.nf.test | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/NovaSeq6000.main_subsample.nf.test b/tests/NovaSeq6000.main_subsample.nf.test
index 0919bc23..72851f91 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test
+++ b/tests/NovaSeq6000.main_subsample.nf.test
@@ -1,11 +1,11 @@
 nextflow_pipeline {
 
-    name "Test Workflow main.nf on NovaSeq6000 data"
+    name "Test Workflow main.nf on NovaSeq6000 data sample size 90"
     script "../main.nf"
     tag "seqinspector"
     tag "PIPELINE"
 
-    test("NovaSeq6000 data test") {
+    test("NovaSeq6000 data test sample size") {
 
         when {
             config "./NovaSeq6000.main_subsample.nf.test.config"

From ef66577d5e1e3f6a338e66104267bc28888e1319 Mon Sep 17 00:00:00 2001
From: ngarcia <natalia.garcia@nanoporetech.com>
Date: Mon, 28 Oct 2024 14:52:09 +0000
Subject: [PATCH 062/530] update docs

---
 docs/output.md  | 13 +++++++++++++
 docs/usage.md   |  5 +++++
 nextflow.config |  2 +-
 3 files changed, 19 insertions(+), 1 deletion(-)

diff --git a/docs/output.md b/docs/output.md
index e14c3ad6..a8257513 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -10,10 +10,23 @@ The directories listed below will be created in the results directory after the
 
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
+- [seqkit](#seqkit) - Subsample a specific number of reads per sample
 - [FastQC](#fastqc) - Raw read QC
 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
+### Seqkit
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `seqtk/`
+  - `*_fastq`: FastQ file after being subsampled to the sample_size value.
+
+</details>
+
+[SeqKit](https://bioinf.shenwei.me/seqkit/) samples sequences by number. For further reading and documentation see the [FastQC help pages](https://bioinf.shenwei.me/seqkit/usage/#sample).
+
 ### FastQC
 
 <details markdown="1">
diff --git a/docs/usage.md b/docs/usage.md
index d75e0fbd..c11b270f 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -93,6 +93,11 @@ genome: 'GRCh37'
 
 You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch).
 
+Optionally, the `sample_size` parameter allows you to subset a random number of reads to be analysed.
+```bash
+nextflow run nf-core/seqinspector --input ./samplesheet.csv --outdir ./results --sample_size 90 -profile docker
+```
+
 ### Updating the pipeline
 
 When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline:
diff --git a/nextflow.config b/nextflow.config
index 10bcb897..38eb3127 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -12,7 +12,7 @@ params {
     // TODO nf-core: Specify your pipeline's command line flags
     // Input options
     input                      = null
-    sample_size                = null
+    sample_size                = 0
     // References
     genome                     = null
     fasta                      = null

From 5ce6a098c5bd5fb856d0747b90c7de0f49c14a1c Mon Sep 17 00:00:00 2001
From: ngarcia <natalia.garcia@nanoporetech.com>
Date: Mon, 28 Oct 2024 14:52:21 +0000
Subject: [PATCH 063/530] change default to 0

---
 nextflow_schema.json      | 4 ++--
 workflows/seqinspector.nf | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index f87e525f..edb18ea0 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -25,9 +25,9 @@
                 },
                 "sample_size": {
                     "type": "integer",
-                    "default": null,
+                    "default": 0,
                     "description": "Subset this number of reads.",
-                    "help_text": "Samples will be subsetted to this number of reads. If null, no subsampling will be performed."
+                    "help_text": "Samples will be subsetted to this number of reads. If 0 (default), no subsampling will be performed."
                 },
                 "outdir": {
                     "type": "string",
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 70b89679..91a699da 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -35,7 +35,7 @@ workflow SEQINSPECTOR {
     //
     // MODULE: Run Seqkit sample to perform subsampling
     //
-    if (params.sample_size) {
+    if (params.sample_size > 0 ) {
         ch_sample_sized = SEQTK_SAMPLE(ch_samplesheet.map {
             meta, reads -> [meta, reads, params.sample_size]
         }).reads

From 9c449ca83b4e4a0be74e2ddbeb07336147e8f540 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Mon, 28 Oct 2024 14:56:37 +0000
Subject: [PATCH 064/530] Fran's draft

---
 modules.json                                  |  5 ++
 .../fastqscreen/fastqscreen/environment.yml   |  9 ++
 .../nf-core/fastqscreen/fastqscreen/main.nf   | 54 ++++++++++++
 .../nf-core/fastqscreen/fastqscreen/meta.yml  | 44 ++++++++++
 .../fastqscreen/tests/main.nf.test            | 87 +++++++++++++++++++
 .../fastqscreen/tests/main.nf.test.snap       | 81 +++++++++++++++++
 .../fastqscreen/fastqscreen/tests/tags.yml    |  2 +
 nextflow.config                               |  1 +
 nextflow_schema.json                          |  5 ++
 workflows/seqinspector.nf                     | 12 +++
 10 files changed, 300 insertions(+)
 create mode 100644 modules/nf-core/fastqscreen/fastqscreen/environment.yml
 create mode 100644 modules/nf-core/fastqscreen/fastqscreen/main.nf
 create mode 100644 modules/nf-core/fastqscreen/fastqscreen/meta.yml
 create mode 100644 modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test
 create mode 100644 modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml

diff --git a/modules.json b/modules.json
index 8e632d50..cb726e0d 100644
--- a/modules.json
+++ b/modules.json
@@ -10,6 +10,11 @@
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
+                    "fastqscreen/fastqscreen": {
+                        "branch": "master",
+                        "git_sha": "e1316cdcbef318b9cdfd35586423f8337c3d45f0",
+                        "installed_by": ["modules"]
+                    },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
diff --git a/modules/nf-core/fastqscreen/fastqscreen/environment.yml b/modules/nf-core/fastqscreen/fastqscreen/environment.yml
new file mode 100644
index 00000000..5097f091
--- /dev/null
+++ b/modules/nf-core/fastqscreen/fastqscreen/environment.yml
@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "fastqscreen_fastqscreen"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::fastq-screen=0.15.3"
diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
new file mode 100644
index 00000000..8686f200
--- /dev/null
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -0,0 +1,54 @@
+process FASTQSCREEN_FASTQSCREEN {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/fastq-screen:0.15.3--pl5321hdfd78af_0':
+        'biocontainers/fastq-screen:0.15.3--pl5321hdfd78af_0'}"
+
+    input:
+    tuple val(meta), path(reads)  // .fastq files
+    path database
+
+    output:
+    tuple val(meta), path("*.txt") , emit: txt
+    tuple val(meta), path("*.png") , emit: png
+    tuple val(meta), path("*.html"), emit: html
+    path "versions.yml"            , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args ?: ""
+
+    """
+    fastq_screen --threads ${task.cpus} \\
+        --aligner bowtie2 \\
+        --conf ${database}/fastq_screen.conf \\
+        $reads \\
+        $args \\
+        --outdir .
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch test_1_screen.html
+    touch test_1_screen.png
+    touch test_1_screen.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//')
+    END_VERSIONS
+    """
+
+}
diff --git a/modules/nf-core/fastqscreen/fastqscreen/meta.yml b/modules/nf-core/fastqscreen/fastqscreen/meta.yml
new file mode 100644
index 00000000..623dacf7
--- /dev/null
+++ b/modules/nf-core/fastqscreen/fastqscreen/meta.yml
@@ -0,0 +1,44 @@
+name: fastqscreen_fastqscreen
+description: Align reads to multiple reference genomes using fastq-screen
+keywords:
+  - align
+  - map
+  - fasta
+  - fastq
+  - genome
+  - reference
+tools:
+  - "fastqscreen":
+      description: "FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect."
+      homepage: "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/"
+      documentation: "https://stevenwingett.github.io/FastQ-Screen/"
+      tool_dev_url: "https://github.com/StevenWingett/FastQ-Screen/archive/refs/tags/v0.15.3.zip"
+      doi: "10.5281/zenodo.5838377"
+      licence: ["GPL-3.0-or-later"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: |
+        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+        respectively.
+  - database:
+      type: directory
+      description: fastq screen database folder containing config file and index folders
+      pattern: "FastQ_Screen_Genomes"
+output:
+  - fastq_screen:
+      type: directory
+      description: Output fastq_screen file containing alignment statistics
+      pattern: "*.{_fq_screen}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@snesic"
+  - "@JPejovicApis"
diff --git a/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test b/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test
new file mode 100644
index 00000000..6d858a4d
--- /dev/null
+++ b/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test
@@ -0,0 +1,87 @@
+nextflow_process {
+
+    name "Test Process FASTQSCREEN_FASTQSCREEN"
+    script "../main.nf"
+    process "FASTQSCREEN_FASTQSCREEN"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bowtie2/build"
+    tag "fastqscreen"
+    tag "fastqscreen/buildfromindex"
+    tag "fastqscreen/fastqscreen"
+
+    setup {
+
+        run("BOWTIE2_BUILD") {
+            script "../../../bowtie2/build/main.nf"
+            process {
+                """
+                input[0] =  Channel.from([
+                                    [[id: "sarscov2"], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)],
+                                    [[id: "human"]   , file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)]
+                            ])
+                """
+            }
+        }
+
+        run("FASTQSCREEN_BUILDFROMINDEX") {
+            script "../../../fastqscreen/buildfromindex/main.nf"
+            process {
+                """
+                input[0] = BOWTIE2_BUILD.out.index.map{meta, index -> meta.id}.collect()
+                input[1] = BOWTIE2_BUILD.out.index.map{meta, index -> index}.collect()
+                """
+            }
+        }
+    }
+
+    test("sarscov2 - human") {
+
+        when {
+            process {
+                """
+                input[0] =  [[ id:'test', single_end:true ],
+                             [file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+                            ]
+                input[1] = FASTQSCREEN_BUILDFROMINDEX.out.database
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.version).match("version") },
+                { assert file(process.out.txt.get(0).get(1)).exists() },
+                { assert file(process.out.png.get(0).get(1)).exists() },
+                { assert file(process.out.html.get(0).get(1)).exists() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - human - stub") {
+
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] =  [[ id:'test', single_end:true ],
+                             [file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+                            ]
+                input[1] = FASTQSCREEN_BUILDFROMINDEX.out.database
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap b/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap
new file mode 100644
index 00000000..b2450191
--- /dev/null
+++ b/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap
@@ -0,0 +1,81 @@
+{
+    "version": {
+        "content": null,
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-30T14:22:56.541922683"
+    },
+    "sarscov2 - human - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_1_screen.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_1_screen.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_1_screen.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,8ac0239b5103352958d9a9e562b23103"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_1_screen.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "png": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_1_screen.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test_1_screen.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8ac0239b5103352958d9a9e562b23103"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-30T14:23:12.70922619"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml b/modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml
new file mode 100644
index 00000000..b03bfb45
--- /dev/null
+++ b/modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml
@@ -0,0 +1,2 @@
+fastqscreen/fastqscreen:
+  - "modules/nf-core/fastqscreen/fastqscreen/**"
diff --git a/nextflow.config b/nextflow.config
index 50c1ecbb..210f03ef 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -17,6 +17,7 @@ params {
     genome                     = null
     fasta                      = null
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
+    config_fastq_screen        = "${projectDir}/modules/nf-core/fastqscreen/references"
     igenomes_ignore            = false
 
     // MultiQC options
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 88fd607b..f18a5f19 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -65,6 +65,11 @@
                     "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
                     "fa_icon": "far fa-file-code"
                 },
+                "config_fastq_screen": {
+                    "type": "string",
+                    "description": "path to directory with fastq_screen config (fastq_screen.conf)",
+                    "fa_icon": "fas fa-braille"
+                },
                 "igenomes_ignore": {
                     "type": "boolean",
                     "description": "Do not load the iGenomes reference config.",
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index ea628117..6ec9ca9f 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -4,6 +4,7 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 include { FASTQC                        } from '../modules/nf-core/fastqc/main'
+include { FASTQSCREEN_FASTQSCREEN       } from '../modules/nf-core/fastqscreen/fastqscreen/main'
 
 include { MULTIQC as MULTIQC_GLOBAL     } from '../modules/nf-core/multiqc/main'
 include { MULTIQC as MULTIQC_PER_TAG    } from '../modules/nf-core/multiqc/main'
@@ -39,6 +40,17 @@ workflow SEQINSPECTOR {
     ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip)
     ch_versions = ch_versions.mix(FASTQC.out.versions.first())
 
+    //
+    // MODULE: Run FastQ Screen
+    //
+
+    FASTQSCREEN_FASTQSCREEN (
+        ch_samplesheet,
+        Channel.fromPath(params.config_fastq_screen)
+    )
+    ch_multiqc_files = ch_multiqc_files.mix(FASTQSCREEN_FASTQSCREEN.out.txt)
+    ch_versions = ch_versions.mix(FASTQSCREEN_FASTQSCREEN.out.versions.first())
+
     //
     // Collate and save software versions
     //

From 47c59f3caea301e1af31c0dd3db64ae439a673d9 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Mon, 28 Oct 2024 15:02:08 +0000
Subject: [PATCH 065/530] nf-core modules update --> fastqscreen

---
 modules.json                                  |  2 +-
 .../fastqscreen/fastqscreen/environment.yml   |  3 +-
 .../nf-core/fastqscreen/fastqscreen/main.nf   | 10 +--
 .../nf-core/fastqscreen/fastqscreen/meta.yml  | 78 +++++++++++++------
 .../fastqscreen/tests/main.nf.test            | 32 +++++++-
 .../fastqscreen/tests/main.nf.test.snap       | 65 ++++++++++++++--
 .../fastqscreen/tests/nextflow.config         |  5 ++
 7 files changed, 157 insertions(+), 38 deletions(-)
 create mode 100644 modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config

diff --git a/modules.json b/modules.json
index cb726e0d..f8b48550 100644
--- a/modules.json
+++ b/modules.json
@@ -12,7 +12,7 @@
                     },
                     "fastqscreen/fastqscreen": {
                         "branch": "master",
-                        "git_sha": "e1316cdcbef318b9cdfd35586423f8337c3d45f0",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
diff --git a/modules/nf-core/fastqscreen/fastqscreen/environment.yml b/modules/nf-core/fastqscreen/fastqscreen/environment.yml
index 5097f091..c63c61e2 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/environment.yml
+++ b/modules/nf-core/fastqscreen/fastqscreen/environment.yml
@@ -1,9 +1,8 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-name: "fastqscreen_fastqscreen"
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - "bioconda::fastq-screen=0.15.3"
+  - bioconda::perl-gdgraph=1.54
diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index 8686f200..88c4e5c5 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -12,10 +12,11 @@ process FASTQSCREEN_FASTQSCREEN {
     path database
 
     output:
-    tuple val(meta), path("*.txt") , emit: txt
-    tuple val(meta), path("*.png") , emit: png
-    tuple val(meta), path("*.html"), emit: html
-    path "versions.yml"            , emit: versions
+    tuple val(meta), path("*.txt")     , emit: txt
+    tuple val(meta), path("*.png")     , emit: png  , optional: true
+    tuple val(meta), path("*.html")    , emit: html
+    tuple val(meta), path("*.fastq.gz"), emit: fastq, optional: true
+    path "versions.yml"                , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -30,7 +31,6 @@ process FASTQSCREEN_FASTQSCREEN {
         --conf ${database}/fastq_screen.conf \\
         $reads \\
         $args \\
-        --outdir .
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/fastqscreen/fastqscreen/meta.yml b/modules/nf-core/fastqscreen/fastqscreen/meta.yml
index 623dacf7..39c86b4f 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/meta.yml
+++ b/modules/nf-core/fastqscreen/fastqscreen/meta.yml
@@ -9,36 +9,70 @@ keywords:
   - reference
 tools:
   - "fastqscreen":
-      description: "FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect."
+      description: "FastQ Screen allows you to screen a library of sequences in FastQ
+        format against a set of sequence databases so you can see if the composition
+        of the library matches with what you expect."
       homepage: "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/"
       documentation: "https://stevenwingett.github.io/FastQ-Screen/"
       tool_dev_url: "https://github.com/StevenWingett/FastQ-Screen/archive/refs/tags/v0.15.3.zip"
       doi: "10.5281/zenodo.5838377"
       licence: ["GPL-3.0-or-later"]
+      identifier: ""
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: |
-        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-        respectively.
-  - database:
-      type: directory
-      description: fastq screen database folder containing config file and index folders
-      pattern: "FastQ_Screen_Genomes"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: file
+        description: |
+          List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+          respectively.
+  - - database:
+        type: directory
+        description: fastq screen database folder containing config file and index folders
+        pattern: "FastQ_Screen_Genomes"
 output:
-  - fastq_screen:
-      type: directory
-      description: Output fastq_screen file containing alignment statistics
-      pattern: "*.{_fq_screen}"
+  - txt:
+      - meta:
+          type: map
+          description: Groovy Map containing sample information
+      - "*.txt":
+          type: file
+          description: TXT file containing alignment statistics
+          pattern: "*.txt"
+  - png:
+      - meta:
+          type: map
+          description: Groovy Map containing sample information
+      - "*.png":
+          type: file
+          description: PNG file with graphical representation of alignments
+          pattern: "*.png"
+  - html:
+      - meta:
+          type: map
+          description: Groovy Map containing sample information
+      - "*.html":
+          type: file
+          description: HTML file containing mapping results as a table and graphical representation
+          pattern: "*.html"
+  - fastq:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.fastq.gz":
+          type: file
+          description: FastQ file containing reads that did not align to any database (optional)
+          pattern: "*.fastq.gz"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@snesic"
   - "@JPejovicApis"
diff --git a/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test b/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test
index 6d858a4d..71230a22 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test
+++ b/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test
@@ -10,6 +10,8 @@ nextflow_process {
     tag "fastqscreen"
     tag "fastqscreen/buildfromindex"
     tag "fastqscreen/fastqscreen"
+    tag "buildfromindex"
+    tag "modules_fastqscreen"
 
     setup {
 
@@ -52,7 +54,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.version).match("version") },
+                { assert snapshot(process.out.version).match() },
                 { assert file(process.out.txt.get(0).get(1)).exists() },
                 { assert file(process.out.png.get(0).get(1)).exists() },
                 { assert file(process.out.html.get(0).get(1)).exists() }
@@ -61,6 +63,34 @@ nextflow_process {
 
     }
 
+    test("sarscov2 - human - tags") {
+        config './nextflow.config'
+        when {
+            process {
+                """
+                input[0] =  [[ id:'test', single_end:false ],
+                             [file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
+                            ]
+                input[1] = FASTQSCREEN_BUILDFROMINDEX.out.database
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.version,
+                    process.out.txt,
+                    process.out.fastq,
+                    path(process.out.html.get(0).get(1)).readLines()[0..10],
+                    path(process.out.png.get(0).get(1)).exists()
+                    ).match() }
+            )
+        }
+
+    }
+
     test("sarscov2 - human - stub") {
 
         options "-stub"
diff --git a/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap b/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap
index b2450191..2afffdea 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap
+++ b/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap
@@ -1,11 +1,56 @@
 {
-    "version": {
+    "sarscov2 - human": {
         "content": null,
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-04-30T14:22:56.541922683"
+        "timestamp": "2024-08-31T05:42:29.972454812"
+    },
+    "sarscov2 - human - tags": {
+        "content": [
+            null,
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_1_screen.txt:md5,b0b0ea58bc26ebaa4d573a85e7898f25"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "test_1.tagged.fastq.gz:md5,f742b162c43ce28f80b89608d5c47f3d",
+                        "test_1.tagged_filter.fastq.gz:md5,28527a76bb0bb3fce0ee76afe01e90aa"
+                    ]
+                ]
+            ],
+            [
+                "<!DOCTYPE html>",
+                "<html>",
+                "",
+                "",
+                "<!-- Style, and Plotly code -->",
+                "<head>",
+                "\t<meta http-equiv=\"content-type\" content=\"text/html; charset=UTF-8\">",
+                "\t<title>FastQ Screen Processing Report - test_1.fastq.gz</title>",
+                "\t<style type=\"text/css\">",
+                "\t\tbody {",
+                "\t\t\tfont-family: Arial, sans-serif;"
+            ],
+            true
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-31T06:23:02.73675229"
     },
     "sarscov2 - human - stub": {
         "content": [
@@ -38,7 +83,13 @@
                     ]
                 ],
                 "3": [
+                    
+                ],
+                "4": [
                     "versions.yml:md5,8ac0239b5103352958d9a9e562b23103"
+                ],
+                "fastq": [
+                    
                 ],
                 "html": [
                     [
@@ -73,9 +124,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-04-30T14:23:12.70922619"
+        "timestamp": "2024-08-31T05:45:54.845041829"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config b/modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config
new file mode 100644
index 00000000..ccf580b7
--- /dev/null
+++ b/modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: FASTQSCREEN_FASTQSCREEN {
+        ext.args = "--tag --filter 10"
+    }
+}

From 1f17971e5b2a14ce3f4f9438c7cf2d043813ee12 Mon Sep 17 00:00:00 2001
From: ngarcia <natalia.garcia@nanoporetech.com>
Date: Mon, 28 Oct 2024 15:15:17 +0000
Subject: [PATCH 066/530] update snapshot

---
 tests/MiSeq.main.nf.test.snap                 |  8 ++++----
 tests/NovaSeq6000.main.nf.test.snap           | 16 ++++++++--------
 tests/NovaSeq6000.main_subsample.nf.test.snap | 14 +++++++-------
 tests/PromethION.main.nf.test.snap            |  8 ++++----
 4 files changed, 23 insertions(+), 23 deletions(-)

diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 4613d525..d60f627d 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -4,12 +4,12 @@
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
             "multiqc_general_stats.txt:md5,5b28a83b14cb2fe88d084d08900ebdbf",
-            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3"
+            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5"
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.1",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-28T13:18:10.3675973"
+        "timestamp": "2024-10-28T15:06:30.86052858"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index ee3c22b7..5ac1e09d 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -4,28 +4,28 @@
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d",
             "multiqc_general_stats.txt:md5,25abe0f6a35eb4a3b056fc3cf5c13732",
-            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3",
+            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
             "multiqc_general_stats.txt:md5,90ee35137492b80aab36ef67f72d8921",
-            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3",
+            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
             "multiqc_general_stats.txt:md5,d62a2fc39e674d98783d408791803148",
-            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3",
+            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
             "multiqc_general_stats.txt:md5,2f09b8f199ac40cf67ba50843cebd29c",
-            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3",
+            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
             "multiqc_general_stats.txt:md5,6a1c16f068d7ba3a9225a17eb570ed9a",
-            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3"
+            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5"
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.1",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-28T13:19:13.226135825"
+        "timestamp": "2024-10-28T15:07:59.897711748"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index d1dbe4a7..c37e51cc 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -1,31 +1,31 @@
 {
-    "NovaSeq6000 data test": {
+    "NovaSeq6000 data test sample size": {
         "content": [
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,aba942d1e6996b579f19798e5673f514",
-            "multiqc_general_stats.txt:md5,c4f40f2313aadc38619e7487226e8d93",
+            "multiqc_general_stats.txt:md5,ad1ec9c64cbdb1131a26aeb6de51e31c",
             "multiqc_software_versions.txt:md5,b7d1ca14785a9361f0a39ce1b6a02686",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8",
-            "multiqc_general_stats.txt:md5,d5d73d2888cd9895e5f116e5b869e73c",
+            "multiqc_general_stats.txt:md5,c73c8d10568a56f6534d280fff701e60",
             "multiqc_software_versions.txt:md5,b7d1ca14785a9361f0a39ce1b6a02686",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,ff996e1d3dc4a46e0c9535e54d51ccab",
-            "multiqc_general_stats.txt:md5,d01ec30a262b69bc5749b0ed108a950a",
+            "multiqc_general_stats.txt:md5,834e1868b887171cfda72029bbbe2d3f",
             "multiqc_software_versions.txt:md5,b7d1ca14785a9361f0a39ce1b6a02686",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,3df36ecfe76b25b0c22dcda84bce2b3b",
-            "multiqc_general_stats.txt:md5,4dffc0d1169c49adde819d4467ffb775",
+            "multiqc_general_stats.txt:md5,274a001b007521970f14d68bd176e5be",
             "multiqc_software_versions.txt:md5,b7d1ca14785a9361f0a39ce1b6a02686",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,ce61b4ce4b1d76ec3f20de3bf0c9ec7f",
-            "multiqc_general_stats.txt:md5,05f8dfeea9fca7f4c16ba9d553af4c69",
+            "multiqc_general_stats.txt:md5,d476ad59458a035a329605d5284b6012",
             "multiqc_software_versions.txt:md5,b7d1ca14785a9361f0a39ce1b6a02686"
         ],
         "meta": {
             "nf-test": "0.9.1",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-28T14:05:44.868455454"
+        "timestamp": "2024-10-28T15:09:41.503580136"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index 026a8cd2..1232678d 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -4,12 +4,12 @@
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,1a4b472e13cadc770832b0e20d1de7b0",
             "multiqc_general_stats.txt:md5,409cefc7f17f95d176ced6032bf8fb32",
-            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3"
+            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5"
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.1",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-28T13:19:57.261730412"
+        "timestamp": "2024-10-28T15:10:20.186073387"
     }
 }
\ No newline at end of file

From 09cd0da35368e2a185bdda327074303653d4fbca Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Mon, 28 Oct 2024 15:15:37 +0000
Subject: [PATCH 067/530] add fastq_screen.conf

---
 conf/fastq_screen.conf | 64 ++++++++++++++++++++++++++++++++++++++++++
 nextflow.config        |  2 +-
 2 files changed, 65 insertions(+), 1 deletion(-)
 create mode 100644 conf/fastq_screen.conf

diff --git a/conf/fastq_screen.conf b/conf/fastq_screen.conf
new file mode 100644
index 00000000..aaa19641
--- /dev/null
+++ b/conf/fastq_screen.conf
@@ -0,0 +1,64 @@
+# This is a configuration file for fastq_screen
+
+###########
+## Bowtie #
+###########
+## If the bowtie binary is not in your PATH then you can
+## set this value to tell the program where to find it.
+## Uncomment the line below and set the appropriate location
+##
+
+#BOWTIE2 /sw/data/uppnex/reference/sw/mf/bioinfo-tools/pipelines/bowtie2/2.1.0/bowtie2
+
+############
+## Threads #
+############
+## Bowtie can be made to run across multiple CPU cores to
+## speed up your searches. Set this value to the number
+## of cores you want to use for your searches.
+
+#THREADS                16
+
+##############
+## Databases #
+##############
+## This section allows you to configure multiple databases
+## to search against in your screen.  For each database
+## you need to provide a database name (which can't contain
+## spaces) and the location of the bowtie indices which
+## you created for that database.
+##
+## The default entries shown below are only suggested examples
+## you can add as many DATABASE sections as you like, and you
+## can comment out or remove as many of the existing entries
+## as you like.
+##
+## Either the original bowtie or bowtie 2 may be used for the
+## mapping. Specify the aligner to use with the command line
+## flag --aligner with arguments 'bowtie' (default) or
+## 'bowtie2'.
+##
+## The configuration file may list paths to both bowtie and
+## bowtie2 indices, which are specified with either 'BOWTIE'
+## or 'BOWTIE2' after the path (leaving unspecified will
+## default to bowtie). While the configuration file may list
+## paths to both bowtie and bowtie2 indices, only one aligner
+## will be used for the mapping, as specified by the --aligner
+## flag.
+##
+## For example:
+## DATABASE     Human_Bowtie    /data/public/Genomes/Human_Bowtie/GRCh37/Homo_sapiens.GRCh37 BOWTIE
+## DATABASE     Human_Bowtie    /data/public/Genomes/Human_Bowtie/GRCh37/Homo_sapiens.GRCh37
+## DATABASE     Human_Bowtie2   /data/public/Genomes/Human_Bowtie2/GRCh37/Homo_sapiens.GRCh37 BOWTIE2
+
+## E. coli (igenomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1)
+DATABASE    Ecoli   ../../../modules/nf-core/fastqscreen/references/genome_ecoli/genome BOWTIE2
+
+## M. tuberculosis (igenomes/Mycobacterium_tuberculosis_H37RV/Ensembl/H37Rv.EB1)
+DATABASE    Tuberculosis   ../../../modules/nf-core/fastqscreen/references/genome_tuberculosis/genome BOWTIE2
+
+## PhiX (/igenomes/PhiX/Illumina/RTA)
+DATABASE    PhiX   ../../../modules/nf-core/fastqscreen/references/genome_phix/genome BOWTIE2
+
+##S. cerevisiae (igenomes/Saccharomyces_cerevisiae/Ensembl/EF4)
+DATABASE    Scerevisiae   ../../../modules/nf-core/fastqscreen/references/genome_cerevisiae/genome BOWTIE2
diff --git a/nextflow.config b/nextflow.config
index 210f03ef..1600a70b 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -17,7 +17,7 @@ params {
     genome                     = null
     fasta                      = null
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
-    config_fastq_screen        = "${projectDir}/modules/nf-core/fastqscreen/references"
+    config_fastq_screen        = "${projectDir}/conf"
     igenomes_ignore            = false
 
     // MultiQC options

From 73a2aef575ef96e2f453e65aad2c5a0161705a00 Mon Sep 17 00:00:00 2001
From: ngarcia <natalia.garcia@nanoporetech.com>
Date: Mon, 28 Oct 2024 15:43:30 +0000
Subject: [PATCH 068/530] prettify docs

---
 docs/usage.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/usage.md b/docs/usage.md
index c11b270f..0cbd8f5d 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -94,6 +94,7 @@ genome: 'GRCh37'
 You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch).
 
 Optionally, the `sample_size` parameter allows you to subset a random number of reads to be analysed.
+
 ```bash
 nextflow run nf-core/seqinspector --input ./samplesheet.csv --outdir ./results --sample_size 90 -profile docker
 ```

From 5a69f5ea2844641ceab090dbc3bdca9249b52e3a Mon Sep 17 00:00:00 2001
From: ngarcia <natalia.garcia@nanoporetech.com>
Date: Mon, 28 Oct 2024 15:53:19 +0000
Subject: [PATCH 069/530] update changelog

---
 CHANGELOG.md   | 1 +
 docs/output.md | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b0b12de1..bad5a09b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,6 +12,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#20](https://github.com/nf-core/seqinspector/pull/20) Use tags to generate group reports
 - [#13](https://github.com/nf-core/seqinspector/pull/13) Generate reports per run, per project and per lane.
 - [#49](https://github.com/nf-core/seqinspector/pull/49) Merge with template 3.0.2.
+- [#50](https://github.com/nf-core/seqinspector/pull/50) Add an optional subsampling step.
 
 ### `Fixed`
 
diff --git a/docs/output.md b/docs/output.md
index a8257513..aef433b2 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -25,7 +25,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 </details>
 
-[SeqKit](https://bioinf.shenwei.me/seqkit/) samples sequences by number. For further reading and documentation see the [FastQC help pages](https://bioinf.shenwei.me/seqkit/usage/#sample).
+[SeqKit](https://bioinf.shenwei.me/seqkit/) samples sequences by number. For further reading and documentation see the [Sekit sample](https://bioinf.shenwei.me/seqkit/usage/#sample).
 
 ### FastQC
 

From e9fdeab5b6b24cb9017ce7491243b325c58e106e Mon Sep 17 00:00:00 2001
From: ngarcia <natalia.garcia@nanoporetech.com>
Date: Mon, 28 Oct 2024 15:54:54 +0000
Subject: [PATCH 070/530] typo

---
 docs/output.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/output.md b/docs/output.md
index aef433b2..f2048f07 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -25,7 +25,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 </details>
 
-[SeqKit](https://bioinf.shenwei.me/seqkit/) samples sequences by number. For further reading and documentation see the [Sekit sample](https://bioinf.shenwei.me/seqkit/usage/#sample).
+[SeqKit](https://bioinf.shenwei.me/seqkit/) samples sequences by number. For further reading and documentation see the [Seqkit sample](https://bioinf.shenwei.me/seqkit/usage/#sample).
 
 ### FastQC
 

From 9f5cd983c80c489dba0bb07958f0649e6c2f3065 Mon Sep 17 00:00:00 2001
From: ngarcia <natalia.garcia@nanoporetech.com>
Date: Tue, 29 Oct 2024 08:47:48 +0000
Subject: [PATCH 071/530] suggestions

---
 docs/output.md       | 6 +++---
 docs/usage.md        | 4 ++--
 nextflow_schema.json | 4 ++--
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/docs/output.md b/docs/output.md
index f2048f07..2d4efb02 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -10,12 +10,12 @@ The directories listed below will be created in the results directory after the
 
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
-- [seqkit](#seqkit) - Subsample a specific number of reads per sample
+- [Seqtk](#seqtk) - Subsample a specific number of reads per sample
 - [FastQC](#fastqc) - Raw read QC
 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
-### Seqkit
+### Seqtk
 
 <details markdown="1">
 <summary>Output files</summary>
@@ -25,7 +25,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 </details>
 
-[SeqKit](https://bioinf.shenwei.me/seqkit/) samples sequences by number. For further reading and documentation see the [Seqkit sample](https://bioinf.shenwei.me/seqkit/usage/#sample).
+[Seqtk](https://github.com/lh3/seqtk) samples sequences by number.
 
 ### FastQC
 
diff --git a/docs/usage.md b/docs/usage.md
index 0cbd8f5d..31ab91ef 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -93,10 +93,10 @@ genome: 'GRCh37'
 
 You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch).
 
-Optionally, the `sample_size` parameter allows you to subset a random number of reads to be analysed.
+Optionally, the `sample_size` parameter allows you to subset a random number of reads to be analysed. Note that it refers to an absolute number.
 
 ```bash
-nextflow run nf-core/seqinspector --input ./samplesheet.csv --outdir ./results --sample_size 90 -profile docker
+nextflow run nf-core/seqinspector --input ./samplesheet.csv --outdir ./results --sample_size 1000000 -profile docker
 ```
 
 ### Updating the pipeline
diff --git a/nextflow_schema.json b/nextflow_schema.json
index edb18ea0..49742b28 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -26,8 +26,8 @@
                 "sample_size": {
                     "type": "integer",
                     "default": 0,
-                    "description": "Subset this number of reads.",
-                    "help_text": "Samples will be subsetted to this number of reads. If 0 (default), no subsampling will be performed."
+                    "description": "Take this number of reads as a subset.",
+                    "help_text": "Choose the size of the subset or 0, if no subsampling shall be performed. Note that it refers to an absolute number."
                 },
                 "outdir": {
                     "type": "string",

From 2533e58425cc2efc5428b70591a128568091ad05 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 29 Oct 2024 09:57:43 +0100
Subject: [PATCH 072/530] hack out some ideas

---
 workflows/seqinspector.nf | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 6ec9ca9f..a0e9d900 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -44,6 +44,14 @@ workflow SEQINSPECTOR {
     // MODULE: Run FastQ Screen
     //
 
+    Channel.fromPath(params.config_fastq_screen)
+        .splitText()
+    .filter // TODO anything that doesn't have "database"
+        .collect()
+
+    file(list_of_configs)
+    // TODO write configs to text file?
+
     FASTQSCREEN_FASTQSCREEN (
         ch_samplesheet,
         Channel.fromPath(params.config_fastq_screen)

From 17cd0732e42dea169eac519c8730a36149f6b188 Mon Sep 17 00:00:00 2001
From: ngarcia <natalia.garcia@nanoporetech.com>
Date: Tue, 29 Oct 2024 09:14:24 +0000
Subject: [PATCH 073/530] switch to original reads for fastqc

---
 workflows/seqinspector.nf | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 91a699da..a89bd5c5 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -36,20 +36,28 @@ workflow SEQINSPECTOR {
     // MODULE: Run Seqkit sample to perform subsampling
     //
     if (params.sample_size > 0 ) {
-        ch_sample_sized = SEQTK_SAMPLE(ch_samplesheet.map {
-            meta, reads -> [meta, reads, params.sample_size]
-        }).reads
+        ch_sample_sized = ch_samplesheet.join(
+            SEQTK_SAMPLE(
+                ch_samplesheet.map {
+                    meta, reads -> [meta, reads, params.sample_size]
+                }
+            ).reads, by: [0]
+        )
         ch_versions = ch_versions.mix(SEQTK_SAMPLE.out.versions.first())
     } else {
         // No do subsample
-        ch_sample_sized = ch_samplesheet
+        ch_sample_sized = ch_samplesheet.map {
+            meta, reads -> [meta, reads, []]
+        }
     }
 
     //
     // MODULE: Run FastQC
     //
     FASTQC (
-        ch_sample_sized
+        ch_sample_sized.map {
+            meta, reads, subsampled -> [meta, reads]
+        }
     )
     ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip)
     ch_versions = ch_versions.mix(FASTQC.out.versions.first())

From a06126db89cfc4868d635a09ad455fd7696757be Mon Sep 17 00:00:00 2001
From: ngarcia <natalia.garcia@nanoporetech.com>
Date: Tue, 29 Oct 2024 09:15:38 +0000
Subject: [PATCH 074/530] update snapshot

---
 tests/NovaSeq6000.main_subsample.nf.test.snap | 22 +++++++++----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index c37e51cc..ee118c94 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -2,30 +2,30 @@
     "NovaSeq6000 data test sample size": {
         "content": [
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,aba942d1e6996b579f19798e5673f514",
-            "multiqc_general_stats.txt:md5,ad1ec9c64cbdb1131a26aeb6de51e31c",
+            "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d",
+            "multiqc_general_stats.txt:md5,25abe0f6a35eb4a3b056fc3cf5c13732",
             "multiqc_software_versions.txt:md5,b7d1ca14785a9361f0a39ce1b6a02686",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8",
-            "multiqc_general_stats.txt:md5,c73c8d10568a56f6534d280fff701e60",
+            "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
+            "multiqc_general_stats.txt:md5,90ee35137492b80aab36ef67f72d8921",
             "multiqc_software_versions.txt:md5,b7d1ca14785a9361f0a39ce1b6a02686",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,ff996e1d3dc4a46e0c9535e54d51ccab",
-            "multiqc_general_stats.txt:md5,834e1868b887171cfda72029bbbe2d3f",
+            "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
+            "multiqc_general_stats.txt:md5,d62a2fc39e674d98783d408791803148",
             "multiqc_software_versions.txt:md5,b7d1ca14785a9361f0a39ce1b6a02686",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,3df36ecfe76b25b0c22dcda84bce2b3b",
-            "multiqc_general_stats.txt:md5,274a001b007521970f14d68bd176e5be",
+            "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
+            "multiqc_general_stats.txt:md5,2f09b8f199ac40cf67ba50843cebd29c",
             "multiqc_software_versions.txt:md5,b7d1ca14785a9361f0a39ce1b6a02686",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,ce61b4ce4b1d76ec3f20de3bf0c9ec7f",
-            "multiqc_general_stats.txt:md5,d476ad59458a035a329605d5284b6012",
+            "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
+            "multiqc_general_stats.txt:md5,6a1c16f068d7ba3a9225a17eb570ed9a",
             "multiqc_software_versions.txt:md5,b7d1ca14785a9361f0a39ce1b6a02686"
         ],
         "meta": {
             "nf-test": "0.9.1",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-28T15:09:41.503580136"
+        "timestamp": "2024-10-29T09:15:03.224117679"
     }
 }
\ No newline at end of file

From 938a6092e9f67035dd2fdb0ff83772e5334147e2 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 29 Oct 2024 10:33:48 +0100
Subject: [PATCH 075/530] test: Update path for database

---
 conf/fastq_screen.conf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/conf/fastq_screen.conf b/conf/fastq_screen.conf
index aaa19641..f170f285 100644
--- a/conf/fastq_screen.conf
+++ b/conf/fastq_screen.conf
@@ -52,10 +52,10 @@
 ## DATABASE     Human_Bowtie2   /data/public/Genomes/Human_Bowtie2/GRCh37/Homo_sapiens.GRCh37 BOWTIE2
 
 ## E. coli (igenomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1)
-DATABASE    Ecoli   ../../../modules/nf-core/fastqscreen/references/genome_ecoli/genome BOWTIE2
+DATABASE    Ecoli   ./database/EB1 BOWTIE2
 
 ## M. tuberculosis (igenomes/Mycobacterium_tuberculosis_H37RV/Ensembl/H37Rv.EB1)
-DATABASE    Tuberculosis   ../../../modules/nf-core/fastqscreen/references/genome_tuberculosis/genome BOWTIE2
+DATABASE    Tuberculosis   ./references/genome_tuberculosis/genome BOWTIE2
 
 ## PhiX (/igenomes/PhiX/Illumina/RTA)
 DATABASE    PhiX   ../../../modules/nf-core/fastqscreen/references/genome_phix/genome BOWTIE2

From 2918075bc7f0d54b142528bdd6e4b64cee336488 Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Tue, 29 Oct 2024 10:51:33 +0100
Subject: [PATCH 076/530] Add CI config for parallellized and economical
 nf-test runs, ripped from nf-test docs

---
 .github/workflows/nf-test.yml | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 .github/workflows/nf-test.yml

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
new file mode 100644
index 00000000..cf8def06
--- /dev/null
+++ b/.github/workflows/nf-test.yml
@@ -0,0 +1,34 @@
+name: nf-test
+
+on: [push, pull_request]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        shard: [1, 2, 3, 4]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up JDK 11
+        uses: actions/setup-java@v2
+        with:
+          java-version: '11'
+          distribution: 'adopt'
+
+      - name: Setup Nextflow latest-edge
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "latest-edge"
+
+      - name: Install nf-test
+        run: |
+          wget -qO- https://get.nf-test.com | bash
+          sudo mv nf-test /usr/local/bin/
+
+      - name: Run Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }})
+        run: nf-test test --ci --shard ${{ matrix.shard }}/${{ strategy.job-total }} --changed-since HEAD^

From 59bcca68375138fda836c3f92dcdd0d26214e350 Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Tue, 29 Oct 2024 10:53:07 +0100
Subject: [PATCH 077/530] Add nf-test config to trigger full test on changes to
 critical files

---
 .nf-test.config | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 .nf-test.config

diff --git a/.nf-test.config b/.nf-test.config
new file mode 100644
index 00000000..359a8b5f
--- /dev/null
+++ b/.nf-test.config
@@ -0,0 +1,5 @@
+config {
+    ...
+    triggers 'nextflow.config', 'nf-test.config', 'test-data/**/*'
+    ...
+}

From 00081e31941aaa5887e5ddc28e5c492027ccf732 Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Tue, 29 Oct 2024 10:57:02 +0100
Subject: [PATCH 078/530] prettier lint

---
 .github/workflows/nf-test.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index cf8def06..d7e81844 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -17,8 +17,8 @@ jobs:
       - name: Set up JDK 11
         uses: actions/setup-java@v2
         with:
-          java-version: '11'
-          distribution: 'adopt'
+          java-version: "11"
+          distribution: "adopt"
 
       - name: Setup Nextflow latest-edge
         uses: nf-core/setup-nextflow@v1

From 4a33c3b4ebd24513323e4751d304cc41d3f54a09 Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Tue, 29 Oct 2024 11:00:58 +0100
Subject: [PATCH 079/530] Bump changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b0b12de1..c682d313 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,6 +12,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#20](https://github.com/nf-core/seqinspector/pull/20) Use tags to generate group reports
 - [#13](https://github.com/nf-core/seqinspector/pull/13) Generate reports per run, per project and per lane.
 - [#49](https://github.com/nf-core/seqinspector/pull/49) Merge with template 3.0.2.
+- [#51](https://github.com/nf-core/seqinspector/pull/51) Add nf-test to CI.
 
 ### `Fixed`
 

From 5e3602db2b4f97a787fd390e02dbec2da1689e77 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 29 Oct 2024 11:14:00 +0100
Subject: [PATCH 080/530] Hack ideas

---
 workflows/seqinspector.nf | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index a0e9d900..20bec7a8 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -46,15 +46,23 @@ workflow SEQINSPECTOR {
 
     Channel.fromPath(params.config_fastq_screen)
         .splitText()
-    .filter // TODO anything that doesn't have "database"
+        .filter(!it.contains('database')) // TODO anything that doesn't have "database"
         .collect()
+        .view()
 
-    file(list_of_configs)
-    // TODO write configs to text file?
+    if(params.database_tar.endsWith('.tar.gz')) {
+        UNTAR (
+            params.database_tar,
+        )
+        ch_database = UNTAR.out.untar
+    } else {
+        ch_database = params.database_tar
+    }
 
     FASTQSCREEN_FASTQSCREEN (
         ch_samplesheet,
-        Channel.fromPath(params.config_fastq_screen)
+        Channel.fromPath(params.config_fastq_screen),
+        ch_database,
     )
     ch_multiqc_files = ch_multiqc_files.mix(FASTQSCREEN_FASTQSCREEN.out.txt)
     ch_versions = ch_versions.mix(FASTQSCREEN_FASTQSCREEN.out.versions.first())

From f1b954962cea9b725192c18eed4f10e77d88c9d0 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Tue, 29 Oct 2024 10:34:45 +0000
Subject: [PATCH 081/530] Add modules testdata base path to test config and
 trim out resource limits

---
 tests/nextflow.config | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/tests/nextflow.config b/tests/nextflow.config
index 8d9ef461..1e56f44d 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -8,14 +8,8 @@ params {
     config_profile_name        = 'nf-test profile'
     config_profile_description = 'Configuration profile to use for nf-test.'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '3.GB'
-    max_time   = '2.h'
-
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
+    modules_testdata_base_path   = 's3://ngi-igenomes/testdata/nf-core/modules/'
 
     validationSchemaIgnoreParams = 'genomes,igenomes_base,pipelines_testdata_base_path'
-
-
 }

From 78edf3af35e8a05807c2dec2e254a169ef2b9553 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 29 Oct 2024 11:36:11 +0100
Subject: [PATCH 082/530] Initial datasheet example

---
 assets/databasesheet.csv | 9 +++++++++
 1 file changed, 9 insertions(+)
 create mode 100644 assets/databasesheet.csv

diff --git a/assets/databasesheet.csv b/assets/databasesheet.csv
new file mode 100644
index 00000000..9923e8d8
--- /dev/null
+++ b/assets/databasesheet.csv
@@ -0,0 +1,9 @@
+name,index,aligner
+Ecoli,./database/EB1,BOWTIE2
+Ecoli,s3://ngi-igenomes/database/EB1,BOWTIE2
+## M. tuberculosis (igenomes/Mycobacterium_tuberculosis_H37RV/Ensembl/H37Rv.EB1)
+Tuberculosis,./references/genome_tuberculosis/genome,BOWTIE2
+## PhiX (/igenomes/PhiX/Illumina/RTA)
+PhiX,../../../modules/nf-core/fastqscreen/references/genome_phix/genome,BOWTIE2
+##S. cerevisiae (igenomes/Saccharomyces_cerevisiae/Ensembl/EF4)
+Scerevisiae,../../../modules/nf-core/fastqscreen/references/genome_cerevisiae/genome,BOWTIE2

From 7ae5cd6e6dccf1c0edd6ed3950bce515457bc8ea Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 29 Oct 2024 11:44:19 +0100
Subject: [PATCH 083/530] refactor: Rework fastqscreen with new ideas

---
 assets/databasesheet.csv                      |  9 +----
 assets/schema_database.json                   | 32 +++++++++++++++
 conf/test.config                              |  1 +
 main.nf                                       |  7 +++-
 modules.json                                  |  3 +-
 .../fastqscreen/fastqscreen-fastqscreen.diff  | 40 +++++++++++++++++++
 .../nf-core/fastqscreen/fastqscreen/main.nf   | 13 +++---
 workflows/seqinspector.nf                     | 23 ++++-------
 8 files changed, 96 insertions(+), 32 deletions(-)
 create mode 100644 assets/schema_database.json
 create mode 100644 modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff

diff --git a/assets/databasesheet.csv b/assets/databasesheet.csv
index 9923e8d8..f300a046 100644
--- a/assets/databasesheet.csv
+++ b/assets/databasesheet.csv
@@ -1,9 +1,2 @@
 name,index,aligner
-Ecoli,./database/EB1,BOWTIE2
-Ecoli,s3://ngi-igenomes/database/EB1,BOWTIE2
-## M. tuberculosis (igenomes/Mycobacterium_tuberculosis_H37RV/Ensembl/H37Rv.EB1)
-Tuberculosis,./references/genome_tuberculosis/genome,BOWTIE2
-## PhiX (/igenomes/PhiX/Illumina/RTA)
-PhiX,../../../modules/nf-core/fastqscreen/references/genome_phix/genome,BOWTIE2
-##S. cerevisiae (igenomes/Saccharomyces_cerevisiae/Ensembl/EF4)
-Scerevisiae,../../../modules/nf-core/fastqscreen/references/genome_cerevisiae/genome,BOWTIE2
+PhiX,s3://ngi-igenomes/igenomes/PhiX/Illumina/RTA/Sequence/Bowtie2Index/,BOWTIE2
diff --git a/assets/schema_database.json b/assets/schema_database.json
new file mode 100644
index 00000000..df54284e
--- /dev/null
+++ b/assets/schema_database.json
@@ -0,0 +1,32 @@
+{
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "$id": "https://raw.githubusercontent.com/nf-core/seqinspector/master/assets/schema_database.json",
+    "title": "nf-core/seqinspector pipeline - params.databasesheet schema",
+    "description": "Schema for the file provided with params.databasesheet",
+    "type": "array",
+    "items": {
+        "type": "object",
+        "properties": {
+            "name": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "The database name for fastq screen",
+                "meta": ["database_name"]
+            },
+            "index": {
+                "type": "string",
+                "format": "file-path",
+                "exists": true,
+                "pattern": "^\\S+$",
+                "errorMessage": "Path to the aligner index"
+            },
+            "aligner": {
+                "type": "string",
+                "enum": ["BOWTIE", "BOWTIE2", "BWA", "MINIMAP2"],
+                "errorMessage": "Specify the aligner to use for the mapping. Valid arguments are 'bowtie', bowtie2' (default), 'bwa' or 'minimap2'.",
+                "meta": ["database_notes"]
+            }
+        },
+        "required": ["name", "index", "aligner"]
+    }
+}
diff --git a/conf/test.config b/conf/test.config
index 76a7ad03..c0324318 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -26,6 +26,7 @@ params {
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
     input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
+    database_sheet = "${projectDir}/assets/databasesheet.csv"
 
     // Genome references
     genome = 'R64-1-1'
diff --git a/main.nf b/main.nf
index 85027a4b..79e8a33d 100644
--- a/main.nf
+++ b/main.nf
@@ -44,6 +44,7 @@ workflow NFCORE_SEQINSPECTOR {
 
     take:
     samplesheet // channel: samplesheet read in from --input
+    database_sheet
 
     main:
 
@@ -51,7 +52,8 @@ workflow NFCORE_SEQINSPECTOR {
     // WORKFLOW: Run pipeline
     //
     SEQINSPECTOR (
-        samplesheet
+        samplesheet,
+        database_sheet,
     )
     emit:
     global_report   = SEQINSPECTOR.out.global_report    // channel: /path/to/multiqc_report.html
@@ -83,7 +85,8 @@ workflow {
     // WORKFLOW: Run main workflow
     //
     NFCORE_SEQINSPECTOR (
-        PIPELINE_INITIALISATION.out.samplesheet
+        PIPELINE_INITIALISATION.out.samplesheet,
+        params.database_sheet,
     )
     //
     // SUBWORKFLOW: Run completion tasks
diff --git a/modules.json b/modules.json
index f8b48550..cb48bc3d 100644
--- a/modules.json
+++ b/modules.json
@@ -13,7 +13,8 @@
                     "fastqscreen/fastqscreen": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff"
                     },
                     "multiqc": {
                         "branch": "master",
diff --git a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
new file mode 100644
index 00000000..e8ff52e0
--- /dev/null
+++ b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
@@ -0,0 +1,40 @@
+Changes in module 'nf-core/fastqscreen/fastqscreen'
+'modules/nf-core/fastqscreen/fastqscreen/environment.yml' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/meta.yml' is unchanged
+Changes in 'fastqscreen/fastqscreen/main.nf':
+--- modules/nf-core/fastqscreen/fastqscreen/main.nf
++++ modules/nf-core/fastqscreen/fastqscreen/main.nf
+@@ -9,7 +9,7 @@
+ 
+     input:
+     tuple val(meta), path(reads)  // .fastq files
+-    path database
++    tuple val(meta), path(database) // [[database_name,  database_notes], database_path]
+ 
+     output:
+     tuple val(meta), path("*.txt")     , emit: txt
+@@ -24,11 +24,14 @@
+     script:
+     def prefix = task.ext.prefix ?: "${meta.id}"
+     def args = task.ext.args ?: ""
++    // 'Database name','Genome path and basename','Notes'
++    """
++    fastq_screen --add_genome \\
++        '$meta.database_name','$database_path','$meta.database_notes'
+ 
+-    """
+-    fastq_screen --threads ${task.cpus} \\
+-        --aligner bowtie2 \\
+-        --conf ${database}/fastq_screen.conf \\
++    fastq_screen
++        --conf fastq_screen.conf \\
++        --threads ${task.cpus} \\
+         $reads \\
+         $args \\
+ 
+
+'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test' is unchanged
+************************************************************
diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index 88c4e5c5..0106e6e8 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -9,7 +9,7 @@ process FASTQSCREEN_FASTQSCREEN {
 
     input:
     tuple val(meta), path(reads)  // .fastq files
-    path database
+    tuple val(meta), path(database) // [[database_name,  database_notes], database_path]
 
     output:
     tuple val(meta), path("*.txt")     , emit: txt
@@ -24,11 +24,14 @@ process FASTQSCREEN_FASTQSCREEN {
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
     def args = task.ext.args ?: ""
-
+    // 'Database name','Genome path and basename','Notes'
     """
-    fastq_screen --threads ${task.cpus} \\
-        --aligner bowtie2 \\
-        --conf ${database}/fastq_screen.conf \\
+    fastq_screen --add_genome \\
+        '$meta.database_name','$database_path','$meta.database_notes'
+
+    fastq_screen
+        --conf fastq_screen.conf \\
+        --threads ${task.cpus} \\
         $reads \\
         $args \\
 
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 20bec7a8..d283c2ac 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -1,3 +1,5 @@
+include { samplesheetToList } from 'plugin/nf-schema'
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS
@@ -24,6 +26,8 @@ workflow SEQINSPECTOR {
 
     take:
     ch_samplesheet // channel: samplesheet read in from --input
+    ch_databasesheet // channel: database sheet read in from --database_sheet
+
     main:
 
     ch_versions            = Channel.empty()
@@ -43,26 +47,13 @@ workflow SEQINSPECTOR {
     //
     // MODULE: Run FastQ Screen
     //
-
-    Channel.fromPath(params.config_fastq_screen)
-        .splitText()
-        .filter(!it.contains('database')) // TODO anything that doesn't have "database"
-        .collect()
+    ch_databases = Channel
+        .fromList(samplesheetToList(ch_databasesheet, "${projectDir}/assets/schema_database.json"))
         .view()
 
-    if(params.database_tar.endsWith('.tar.gz')) {
-        UNTAR (
-            params.database_tar,
-        )
-        ch_database = UNTAR.out.untar
-    } else {
-        ch_database = params.database_tar
-    }
-
     FASTQSCREEN_FASTQSCREEN (
         ch_samplesheet,
-        Channel.fromPath(params.config_fastq_screen),
-        ch_database,
+        ch_databases,
     )
     ch_multiqc_files = ch_multiqc_files.mix(FASTQSCREEN_FASTQSCREEN.out.txt)
     ch_versions = ch_versions.mix(FASTQSCREEN_FASTQSCREEN.out.versions.first())

From eb92baab3c17da74a6902477fd179d40e2e836e0 Mon Sep 17 00:00:00 2001
From: ngarcia <natalia.garcia@nanoporetech.com>
Date: Tue, 29 Oct 2024 11:14:12 +0000
Subject: [PATCH 084/530] back to the past

---
 workflows/seqinspector.nf | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index a89bd5c5..972b2f31 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -36,18 +36,16 @@ workflow SEQINSPECTOR {
     // MODULE: Run Seqkit sample to perform subsampling
     //
     if (params.sample_size > 0 ) {
-        ch_sample_sized = ch_samplesheet.join(
-            SEQTK_SAMPLE(
-                ch_samplesheet.map {
-                    meta, reads -> [meta, reads, params.sample_size]
-                }
-            ).reads, by: [0]
-        )
+        ch_sample_sized = SEQTK_SAMPLE(
+            ch_samplesheet.map {
+                meta, reads -> [meta, reads, params.sample_size]
+            }
+        ).reads
         ch_versions = ch_versions.mix(SEQTK_SAMPLE.out.versions.first())
     } else {
         // No do subsample
         ch_sample_sized = ch_samplesheet.map {
-            meta, reads -> [meta, reads, []]
+            meta, reads -> [meta, reads]
         }
     }
 
@@ -56,7 +54,7 @@ workflow SEQINSPECTOR {
     //
     FASTQC (
         ch_sample_sized.map {
-            meta, reads, subsampled -> [meta, reads]
+            meta, subsampled -> [meta, subsampled]
         }
     )
     ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip)

From 22aaafb1fa22acc353a0655bec43b348e40366dd Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 29 Oct 2024 12:20:59 +0100
Subject: [PATCH 085/530] chore: Bump fastq-screen

---
 modules/nf-core/fastqscreen/fastqscreen/environment.yml | 8 +++++++-
 modules/nf-core/fastqscreen/fastqscreen/main.nf         | 4 ++--
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/modules/nf-core/fastqscreen/fastqscreen/environment.yml b/modules/nf-core/fastqscreen/fastqscreen/environment.yml
index c63c61e2..7d4c8922 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/environment.yml
+++ b/modules/nf-core/fastqscreen/fastqscreen/environment.yml
@@ -4,5 +4,11 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::fastq-screen=0.15.3"
+  - bioconda::fastq-screen=0.16.0
   - bioconda::perl-gdgraph=1.54
+  # - gzip
+  # - SAMtools
+  # - bowtie
+  # - bowtie2
+  # - bwa
+  # - bismark
diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index 0106e6e8..c792707e 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -4,8 +4,8 @@ process FASTQSCREEN_FASTQSCREEN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/fastq-screen:0.15.3--pl5321hdfd78af_0':
-        'biocontainers/fastq-screen:0.15.3--pl5321hdfd78af_0'}"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fc/fc53eee7ca23c32220a9662fbb63c67769756544b6d74a1ee85cf439ea79a7ee/data' :
+        'community.wave.seqera.io/library/fastq-screen_perl-gdgraph:5c1786a5d5bc1309'}"
 
     input:
     tuple val(meta), path(reads)  // .fastq files

From c2026e660fed98988f1e8c8c2ee9e8ca164d9136 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 29 Oct 2024 13:00:00 +0100
Subject: [PATCH 086/530] fix: Give up on fastq_screen writing it's own config

---
 modules/nf-core/fastqscreen/fastqscreen/main.nf | 12 +++++++-----
 workflows/seqinspector.nf                       |  1 -
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index c792707e..771c6acf 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -1,5 +1,5 @@
 process FASTQSCREEN_FASTQSCREEN {
-    tag "$meta.id"
+    tag "$meta.id | $meta2.database_name"
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
@@ -9,7 +9,7 @@ process FASTQSCREEN_FASTQSCREEN {
 
     input:
     tuple val(meta), path(reads)  // .fastq files
-    tuple val(meta), path(database) // [[database_name,  database_notes], database_path]
+    tuple val(meta2), path(database) // [[database_name,  database_notes], database_path]
 
     output:
     tuple val(meta), path("*.txt")     , emit: txt
@@ -26,12 +26,14 @@ process FASTQSCREEN_FASTQSCREEN {
     def args = task.ext.args ?: ""
     // 'Database name','Genome path and basename','Notes'
     """
-    fastq_screen --add_genome \\
-        '$meta.database_name','$database_path','$meta.database_notes'
+    echo "Writing config"
+    echo "DATABASE    ${meta2.database_name}    ./${database}/genome    ${meta2.database_notes}" > fastq_screen.conf
+    echo "Wrote config"
 
-    fastq_screen
+    fastq_screen \\
         --conf fastq_screen.conf \\
         --threads ${task.cpus} \\
+        --aligner ${meta2.database_notes.toLowerCase()} \\
         $reads \\
         $args \\
 
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index d283c2ac..ad6dc2cb 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -49,7 +49,6 @@ workflow SEQINSPECTOR {
     //
     ch_databases = Channel
         .fromList(samplesheetToList(ch_databasesheet, "${projectDir}/assets/schema_database.json"))
-        .view()
 
     FASTQSCREEN_FASTQSCREEN (
         ch_samplesheet,

From 53f10c309ba2ef850d2bb867ffaebc4148e941ec Mon Sep 17 00:00:00 2001
From: ngarcia <natalia.garcia@nanoporetech.com>
Date: Tue, 29 Oct 2024 13:35:36 +0000
Subject: [PATCH 087/530] update README

---
 README.md                 | 5 +++--
 workflows/seqinspector.nf | 6 ++----
 2 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index f647af08..6cf36dcc 100644
--- a/README.md
+++ b/README.md
@@ -31,8 +31,9 @@
      workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->
 <!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
 
-1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))
+2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
+3. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
 
 ## Usage
 
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 972b2f31..2fbb2348 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -33,7 +33,7 @@ workflow SEQINSPECTOR {
     ch_multiqc_reports     = Channel.empty()
 
     //
-    // MODULE: Run Seqkit sample to perform subsampling
+    // MODULE: Run Seqtk sample to perform subsampling
     //
     if (params.sample_size > 0 ) {
         ch_sample_sized = SEQTK_SAMPLE(
@@ -44,9 +44,7 @@ workflow SEQINSPECTOR {
         ch_versions = ch_versions.mix(SEQTK_SAMPLE.out.versions.first())
     } else {
         // No do subsample
-        ch_sample_sized = ch_samplesheet.map {
-            meta, reads -> [meta, reads]
-        }
+        ch_sample_sized = ch_samplesheet
     }
 
     //

From 87693061a4f1d7e6e084eca26bac0a4a88720a6a Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 29 Oct 2024 13:05:42 +0100
Subject: [PATCH 088/530] test: Update databases

---
 assets/databasesheet.csv                        | 2 ++
 modules/nf-core/fastqscreen/fastqscreen/main.nf | 2 +-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/assets/databasesheet.csv b/assets/databasesheet.csv
index f300a046..150f8318 100644
--- a/assets/databasesheet.csv
+++ b/assets/databasesheet.csv
@@ -1,2 +1,4 @@
 name,index,aligner
+Ecoli,s3://ngi-igenomes/igenomes/Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/Bowtie2Index/,BOWTIE2
 PhiX,s3://ngi-igenomes/igenomes/PhiX/Illumina/RTA/Sequence/Bowtie2Index/,BOWTIE2
+Scerevisiae,s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/NCBI/build3.1/Sequence/Bowtie2Index/,BOWTIE2
diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index 771c6acf..eab5afb1 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -35,7 +35,7 @@ process FASTQSCREEN_FASTQSCREEN {
         --threads ${task.cpus} \\
         --aligner ${meta2.database_notes.toLowerCase()} \\
         $reads \\
-        $args \\
+        $args
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From b79c1e6745617ee0624f2e1013afabddd3eabbab Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 29 Oct 2024 14:32:09 +0100
Subject: [PATCH 089/530] fix: Run every sample and every DB

---
 modules/nf-core/fastqscreen/fastqscreen/main.nf | 4 ++--
 workflows/seqinspector.nf                       | 3 +--
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index eab5afb1..5037db6a 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -8,8 +8,8 @@ process FASTQSCREEN_FASTQSCREEN {
         'community.wave.seqera.io/library/fastq-screen_perl-gdgraph:5c1786a5d5bc1309'}"
 
     input:
-    tuple val(meta), path(reads)  // .fastq files
-    tuple val(meta2), path(database) // [[database_name,  database_notes], database_path]
+    // NOTE for meta 2 and database [[database_name,  database_notes], database_path]
+    tuple val(meta), path(reads), val(meta2), path(database)
 
     output:
     tuple val(meta), path("*.txt")     , emit: txt
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index ad6dc2cb..75ea2d6c 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -51,8 +51,7 @@ workflow SEQINSPECTOR {
         .fromList(samplesheetToList(ch_databasesheet, "${projectDir}/assets/schema_database.json"))
 
     FASTQSCREEN_FASTQSCREEN (
-        ch_samplesheet,
-        ch_databases,
+        ch_samplesheet.combine(ch_databases)
     )
     ch_multiqc_files = ch_multiqc_files.mix(FASTQSCREEN_FASTQSCREEN.out.txt)
     ch_versions = ch_versions.mix(FASTQSCREEN_FASTQSCREEN.out.versions.first())

From c54681eeafa1942da306748129a1a61cb285612a Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Tue, 29 Oct 2024 13:39:41 +0000
Subject: [PATCH 090/530] nf-core subworkflows update to apply fix

---
 modules.json                                           |  4 ++--
 .../tests/main.workflow.nf.test                        | 10 ++++++----
 .../nf-core/utils_nfschema_plugin/tests/main.nf.test   |  4 ++--
 workflows/seqinspector.nf                              |  4 ++--
 4 files changed, 12 insertions(+), 10 deletions(-)

diff --git a/modules.json b/modules.json
index 8e632d50..a27c7506 100644
--- a/modules.json
+++ b/modules.json
@@ -21,7 +21,7 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",
+                        "git_sha": "56372688d8979092cafbe0c5c3895b491166ca1c",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
@@ -31,7 +31,7 @@
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c",
+                        "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
index ca964ce8..02dbf094 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
@@ -52,10 +52,12 @@ nextflow_workflow {
         }
 
         then {
-            assertAll(
-                { assert workflow.success },
-                { assert workflow.stdout.contains("nextflow_workflow v9.9.9") }
-            )
+            expect {
+                with(workflow) {
+                    assert success
+                    assert "nextflow_workflow v9.9.9" in stdout
+                }
+            }
         }
     }
 
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
index 842dc432..8fb30164 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
@@ -42,7 +42,7 @@ nextflow_workflow {
 
             params {
                 test_data   = ''
-                outdir      = 1
+                outdir      = null
             }
 
             workflow {
@@ -94,7 +94,7 @@ nextflow_workflow {
 
             params {
                 test_data   = ''
-                outdir      = 1
+                outdir      = null
             }
 
             workflow {
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index ea628117..d1fb2891 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -138,9 +138,9 @@ workflow SEQINSPECTOR {
     )
 
     emit:
-    global_report = MULTIQC_GLOBAL.out.report.toList()      // channel: /path/to/multiqc_report.html
+    global_report   = MULTIQC_GLOBAL.out.report.toList()    // channel: /path/to/multiqc_report.html
     grouped_reports = MULTIQC_PER_TAG.out.report.toList()   // channel: [ /path/to/multiqc_report.html ]
-    versions       = ch_versions                            // channel: [ path(versions.yml) ]
+    versions        = ch_versions                           // channel: [ path(versions.yml) ]
 }
 
 /*

From 8a7c6d6139738be06d6c6f510a04af05f033b260 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Tue, 29 Oct 2024 13:43:56 +0000
Subject: [PATCH 091/530] simplify CI, always run

---
 .github/workflows/nf-test.yml | 4 +---
 .nf-test.config               | 5 -----
 2 files changed, 1 insertion(+), 8 deletions(-)
 delete mode 100644 .nf-test.config

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index d7e81844..b6276bfd 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -11,8 +11,6 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
 
       - name: Set up JDK 11
         uses: actions/setup-java@v2
@@ -31,4 +29,4 @@ jobs:
           sudo mv nf-test /usr/local/bin/
 
       - name: Run Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }})
-        run: nf-test test --ci --shard ${{ matrix.shard }}/${{ strategy.job-total }} --changed-since HEAD^
+        run: nf-test test --ci --shard ${{ matrix.shard }}/${{ strategy.job-total }}
diff --git a/.nf-test.config b/.nf-test.config
deleted file mode 100644
index 359a8b5f..00000000
--- a/.nf-test.config
+++ /dev/null
@@ -1,5 +0,0 @@
-config {
-    ...
-    triggers 'nextflow.config', 'nf-test.config', 'test-data/**/*'
-    ...
-}

From 700c6c4970748466cdcb343133dc0787a1fbf89d Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Tue, 29 Oct 2024 13:48:10 +0000
Subject: [PATCH 092/530] try specifying cwd as arg in nf-test command

---
 .github/workflows/nf-test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index b6276bfd..b0d7b8e8 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -29,4 +29,4 @@ jobs:
           sudo mv nf-test /usr/local/bin/
 
       - name: Run Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }})
-        run: nf-test test --ci --shard ${{ matrix.shard }}/${{ strategy.job-total }}
+        run: nf-test test --ci --shard ${{ matrix.shard }}/${{ strategy.job-total }} .

From fc0df3d4fbe97c12e747d7a6061e7d21bee28a22 Mon Sep 17 00:00:00 2001
From: ngarcia <natalia.garcia@nanoporetech.com>
Date: Tue, 29 Oct 2024 14:09:35 +0000
Subject: [PATCH 093/530] add module config

---
 conf/modules.config                           |  4 ++++
 tests/NovaSeq6000.main_subsample.nf.test.snap | 22 +++++++++----------
 2 files changed, 15 insertions(+), 11 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index c8838224..d3c597b3 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -18,6 +18,10 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
+    withName: SEQTK_SAMPLE {
+        ext.args = '-s100'
+    }
+
     withName: FASTQC {
         ext.args = '--quiet'
     }
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index ee118c94..27277ff0 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -2,30 +2,30 @@
     "NovaSeq6000 data test sample size": {
         "content": [
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d",
-            "multiqc_general_stats.txt:md5,25abe0f6a35eb4a3b056fc3cf5c13732",
+            "multiqc_fastqc.txt:md5,aba942d1e6996b579f19798e5673f514",
+            "multiqc_general_stats.txt:md5,ad1ec9c64cbdb1131a26aeb6de51e31c",
             "multiqc_software_versions.txt:md5,b7d1ca14785a9361f0a39ce1b6a02686",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
-            "multiqc_general_stats.txt:md5,90ee35137492b80aab36ef67f72d8921",
+            "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8",
+            "multiqc_general_stats.txt:md5,c73c8d10568a56f6534d280fff701e60",
             "multiqc_software_versions.txt:md5,b7d1ca14785a9361f0a39ce1b6a02686",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
-            "multiqc_general_stats.txt:md5,d62a2fc39e674d98783d408791803148",
+            "multiqc_fastqc.txt:md5,ff996e1d3dc4a46e0c9535e54d51ccab",
+            "multiqc_general_stats.txt:md5,834e1868b887171cfda72029bbbe2d3f",
             "multiqc_software_versions.txt:md5,b7d1ca14785a9361f0a39ce1b6a02686",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
-            "multiqc_general_stats.txt:md5,2f09b8f199ac40cf67ba50843cebd29c",
+            "multiqc_fastqc.txt:md5,3df36ecfe76b25b0c22dcda84bce2b3b",
+            "multiqc_general_stats.txt:md5,274a001b007521970f14d68bd176e5be",
             "multiqc_software_versions.txt:md5,b7d1ca14785a9361f0a39ce1b6a02686",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
-            "multiqc_general_stats.txt:md5,6a1c16f068d7ba3a9225a17eb570ed9a",
+            "multiqc_fastqc.txt:md5,ce61b4ce4b1d76ec3f20de3bf0c9ec7f",
+            "multiqc_general_stats.txt:md5,d476ad59458a035a329605d5284b6012",
             "multiqc_software_versions.txt:md5,b7d1ca14785a9361f0a39ce1b6a02686"
         ],
         "meta": {
             "nf-test": "0.9.1",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-29T09:15:03.224117679"
+        "timestamp": "2024-10-29T13:44:43.105472321"
     }
 }
\ No newline at end of file

From 7d46b1528a1f8bebd914c1184343d68595bdc549 Mon Sep 17 00:00:00 2001
From: ctuni <c.tuni.dominguez@gmail.com>
Date: Tue, 29 Oct 2024 15:23:39 +0100
Subject: [PATCH 094/530] added seqfu stats

---
 modules.json                                  |  5 ++
 modules/nf-core/seqfu/stats/environment.yml   |  7 ++
 modules/nf-core/seqfu/stats/main.nf           | 51 +++++++++++++
 modules/nf-core/seqfu/stats/meta.yml          | 60 +++++++++++++++
 .../nf-core/seqfu/stats/tests/main.nf.test    | 75 +++++++++++++++++++
 .../seqfu/stats/tests/main.nf.test.snap       | 56 ++++++++++++++
 modules/nf-core/seqfu/stats/tests/tags.yml    |  2 +
 workflows/seqinspector.nf                     | 11 +++
 8 files changed, 267 insertions(+)
 create mode 100644 modules/nf-core/seqfu/stats/environment.yml
 create mode 100644 modules/nf-core/seqfu/stats/main.nf
 create mode 100644 modules/nf-core/seqfu/stats/meta.yml
 create mode 100644 modules/nf-core/seqfu/stats/tests/main.nf.test
 create mode 100644 modules/nf-core/seqfu/stats/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/seqfu/stats/tests/tags.yml

diff --git a/modules.json b/modules.json
index 8e632d50..ae745d1d 100644
--- a/modules.json
+++ b/modules.json
@@ -14,6 +14,11 @@
                         "branch": "master",
                         "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                         "installed_by": ["modules"]
+                    },
+                    "seqfu/stats": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
                     }
                 }
             },
diff --git a/modules/nf-core/seqfu/stats/environment.yml b/modules/nf-core/seqfu/stats/environment.yml
new file mode 100644
index 00000000..8fa07dfc
--- /dev/null
+++ b/modules/nf-core/seqfu/stats/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::seqfu=1.20.3"
diff --git a/modules/nf-core/seqfu/stats/main.nf b/modules/nf-core/seqfu/stats/main.nf
new file mode 100644
index 00000000..0f8bb3e2
--- /dev/null
+++ b/modules/nf-core/seqfu/stats/main.nf
@@ -0,0 +1,51 @@
+process SEQFU_STATS {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/seqfu:1.20.3--h1eb128b_0':
+        'biocontainers/seqfu:1.20.3--h1eb128b_0' }"
+
+
+    input:
+    // stats can get one or more fasta or fastq files
+    tuple val(meta), path(files)
+
+    output:
+    tuple val(meta), path("*.tsv")    ,  emit: stats
+    tuple val(meta), path("*_mqc.txt"), emit: multiqc
+    path "versions.yml"               ,  emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    seqfu \\
+        stats \\
+        $args \\
+        --multiqc ${prefix}_mqc.txt \\
+        $files > ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seqfu: \$(seqfu version)
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_mqc.txt
+    seqfu stats ${prefix}_mqc.txt > ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seqfu: \$(samtools --version |& sed '1!d ; s/samtools //')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/seqfu/stats/meta.yml b/modules/nf-core/seqfu/stats/meta.yml
new file mode 100644
index 00000000..f534a3f5
--- /dev/null
+++ b/modules/nf-core/seqfu/stats/meta.yml
@@ -0,0 +1,60 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "seqfu_stats"
+description: Statistics for FASTA or FASTQ files
+keywords:
+  - seqfu
+  - stats
+  - n50
+tools:
+  - "seqfu":
+      description: "Cross-platform compiled suite of tools to manipulate and inspect
+        FASTA and FASTQ files"
+      homepage: "https://telatin.github.io/seqfu2/"
+      documentation: "https://telatin.github.io/seqfu2/"
+      tool_dev_url: "https://github.com/telatin/seqfu2"
+      doi: "10.3390/bioengineering8050059"
+      licence: ["GPL v3"]
+      identifier: biotools:seqfu
+
+input:
+  # Only when we have meta
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - files:
+        type: file
+        description: One or more FASTA or FASTQ files
+        pattern: "*.{fasta,fastq,fasta.gz,fastq.gz,fq,fq.gz}"
+output:
+  #Only when we have meta
+  - stats:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.tsv":
+          type: file
+          description: Tab-separated output file with basic sequence statistics.
+          pattern: "*.{tsv}"
+  - multiqc:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*_mqc.txt":
+          type: file
+          description: MultiQC ready table
+          pattern: "*.{_mqc.txt}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@telatin"
+maintainers:
+  - "@telatin"
diff --git a/modules/nf-core/seqfu/stats/tests/main.nf.test b/modules/nf-core/seqfu/stats/tests/main.nf.test
new file mode 100644
index 00000000..b889b2bb
--- /dev/null
+++ b/modules/nf-core/seqfu/stats/tests/main.nf.test
@@ -0,0 +1,75 @@
+nextflow_process {
+
+    name "Test Process SEQFU_STATS"
+    script "../main.nf"
+    process "SEQFU_STATS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "seqfu"
+    tag "seqfu/stats"
+
+    
+    test("seqfu stats - faa") {
+        // test with 1 FAA file (with  multiple sequences of different length)
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], 
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.stats },
+                { assert process.out.multiqc },
+                { assert process.out.stats.size() == 1 },
+                { assert snapshot(process.out.versions).match("versions-single") },
+                { assert snapshot(process.out.stats).match("stats-single") },
+                { assert path(process.out.stats.get(0).get(1)).md5 == "26141ef87ad8a6f59a6f283cc0a06fda" }
+            )
+        }
+
+    }
+
+    test("seqfu stats - multiple files") {
+        // test feeding a mix of files including compressed
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id:'test' ],
+                            [
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true),
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true),
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                            ]
+                        ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.stats },
+                { assert process.out.multiqc },
+                { assert process.out.stats.size() == 1 },
+                { assert path(process.out.versions[0]).readLines()[1].contains('.') },
+                { assert snapshot(process.out.stats).match("stats-multi") },
+                { assert snapshot(process.out.stats).md5().match("multi-lines") },
+                { assert path(process.out.stats[0][1]).readLines()[0] ==  'File\t#Seq\tTotal bp\tAvg\tN50\tN75\tN90\tauN\tMin\tMax' },
+                { assert path(process.out.multiqc[0][1]).readLines().join('\n').contains('genome.fasta') },
+                { assert path(process.out.multiqc[0][1]).readLines().join('\n').contains('proteome.fasta') }              
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/seqfu/stats/tests/main.nf.test.snap b/modules/nf-core/seqfu/stats/tests/main.nf.test.snap
new file mode 100644
index 00000000..8049c827
--- /dev/null
+++ b/modules/nf-core/seqfu/stats/tests/main.nf.test.snap
@@ -0,0 +1,56 @@
+{
+    "versions-single": {
+        "content": [
+            [
+                "versions.yml:md5,fd11b4665f68f22e7ad4c646ad3c56cd"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-19T20:21:50.896221522"
+    },
+    "multi-lines": {
+        "content": "d5ab14ce74939f856edc64c6a8d250d3",
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-19T20:22:03.775940585"
+    },
+    "stats-single": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.tsv:md5,26141ef87ad8a6f59a6f283cc0a06fda"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-19T20:21:50.937732021"
+    },
+    "stats-multi": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.tsv:md5,98102573ecf7e3b9e53db1c6e0f02b06"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-19T20:22:03.681146614"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/seqfu/stats/tests/tags.yml b/modules/nf-core/seqfu/stats/tests/tags.yml
new file mode 100644
index 00000000..2685ed43
--- /dev/null
+++ b/modules/nf-core/seqfu/stats/tests/tags.yml
@@ -0,0 +1,2 @@
+seqfu/stats:
+  - "modules/nf-core/seqfu/stats/**"
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index ea628117..53ceb0d0 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -4,6 +4,7 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 include { FASTQC                        } from '../modules/nf-core/fastqc/main'
+include { SEQFU_STATS                   } from '../modules/nf-core/seqfu/stats'
 
 include { MULTIQC as MULTIQC_GLOBAL     } from '../modules/nf-core/multiqc/main'
 include { MULTIQC as MULTIQC_PER_TAG    } from '../modules/nf-core/multiqc/main'
@@ -39,6 +40,16 @@ workflow SEQINSPECTOR {
     ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip)
     ch_versions = ch_versions.mix(FASTQC.out.versions.first())
 
+
+    //
+    // Module: Run SeqFu stats
+    //
+    SEQFU_STATS (
+        ch_samplesheet
+    )
+    ch_multiqc_files = ch_multiqc_files.mix(SEQFU_STATS.out.multiqc)
+    ch_versions = ch_versions.mix(SEQFU_STATS.out.versions.first())
+
     //
     // Collate and save software versions
     //

From 32e562210b5dc9f2dc3b0e15beed56a2677adcdd Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Tue, 29 Oct 2024 14:34:32 +0000
Subject: [PATCH 095/530] harmonize syntax and correct comment

---
 workflows/seqinspector.nf | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index d1fb2891..ab6cda41 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -87,10 +87,10 @@ workflow SEQINSPECTOR {
             .mix(ch_multiqc_extra_files)
             .collect(),
         ch_multiqc_config.toList(),
-        Channel.empty().toList(),
+        [],
         ch_multiqc_logo.toList(),
-        Channel.empty().toList(),
-        Channel.empty().toList()
+        [],
+        []
     )
 
     ch_tags = ch_multiqc_files
@@ -138,7 +138,7 @@ workflow SEQINSPECTOR {
     )
 
     emit:
-    global_report   = MULTIQC_GLOBAL.out.report.toList()    // channel: /path/to/multiqc_report.html
+    global_report   = MULTIQC_GLOBAL.out.report.toList()    // channel: [ /path/to/multiqc_report.html ]
     grouped_reports = MULTIQC_PER_TAG.out.report.toList()   // channel: [ /path/to/multiqc_report.html ]
     versions        = ch_versions                           // channel: [ path(versions.yml) ]
 }

From 2a27be79e92d28d8ded88f719c2706fc29a35410 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Tue, 29 Oct 2024 14:42:03 +0000
Subject: [PATCH 096/530] remove multiqc versions file from snapshot assertion,
 will fail if tests run on different nextflow versions

---
 tests/MiSeq.main.nf.test            | 1 -
 tests/MiSeq.main.nf.test.snap       | 5 ++---
 tests/NovaSeq6000.main.nf.test      | 5 -----
 tests/NovaSeq6000.main.nf.test.snap | 9 ++-------
 tests/PromethION.main.nf.test       | 1 -
 tests/PromethION.main.nf.test.snap  | 5 ++---
 6 files changed, 6 insertions(+), 20 deletions(-)

diff --git a/tests/MiSeq.main.nf.test b/tests/MiSeq.main.nf.test
index 8fbff4a3..246a05a5 100644
--- a/tests/MiSeq.main.nf.test
+++ b/tests/MiSeq.main.nf.test
@@ -21,7 +21,6 @@ nextflow_pipeline {
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_software_versions.txt"),
                     ).match()
                 }
             )
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 4613d525..0742b5a8 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -3,8 +3,7 @@
         "content": [
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
-            "multiqc_general_stats.txt:md5,5b28a83b14cb2fe88d084d08900ebdbf",
-            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3"
+            "multiqc_general_stats.txt:md5,5b28a83b14cb2fe88d084d08900ebdbf"
         ],
         "meta": {
             "nf-test": "0.9.0",
@@ -12,4 +11,4 @@
         },
         "timestamp": "2024-10-28T13:18:10.3675973"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/NovaSeq6000.main.nf.test b/tests/NovaSeq6000.main.nf.test
index d050399e..e24637cd 100644
--- a/tests/NovaSeq6000.main.nf.test
+++ b/tests/NovaSeq6000.main.nf.test
@@ -21,27 +21,22 @@ nextflow_pipeline {
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_software_versions.txt"),
 
                     path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_software_versions.txt"),
 
                     path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt"),
 
                     path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_software_versions.txt"),
 
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_software_versions.txt"),
                     ).match()
                 },
             )
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index ee3c22b7..fc38ac52 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -4,23 +4,18 @@
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d",
             "multiqc_general_stats.txt:md5,25abe0f6a35eb4a3b056fc3cf5c13732",
-            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
             "multiqc_general_stats.txt:md5,90ee35137492b80aab36ef67f72d8921",
-            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
             "multiqc_general_stats.txt:md5,d62a2fc39e674d98783d408791803148",
-            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
             "multiqc_general_stats.txt:md5,2f09b8f199ac40cf67ba50843cebd29c",
-            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
-            "multiqc_general_stats.txt:md5,6a1c16f068d7ba3a9225a17eb570ed9a",
-            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3"
+            "multiqc_general_stats.txt:md5,6a1c16f068d7ba3a9225a17eb570ed9a"
         ],
         "meta": {
             "nf-test": "0.9.0",
@@ -28,4 +23,4 @@
         },
         "timestamp": "2024-10-28T13:19:13.226135825"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/PromethION.main.nf.test b/tests/PromethION.main.nf.test
index 8fec8b33..ad6fe6d0 100644
--- a/tests/PromethION.main.nf.test
+++ b/tests/PromethION.main.nf.test
@@ -21,7 +21,6 @@ nextflow_pipeline {
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_software_versions.txt"),
                     ).match()
                 },
             )
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index 026a8cd2..875673c0 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -3,8 +3,7 @@
         "content": [
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,1a4b472e13cadc770832b0e20d1de7b0",
-            "multiqc_general_stats.txt:md5,409cefc7f17f95d176ced6032bf8fb32",
-            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3"
+            "multiqc_general_stats.txt:md5,409cefc7f17f95d176ced6032bf8fb32"
         ],
         "meta": {
             "nf-test": "0.9.0",
@@ -12,4 +11,4 @@
         },
         "timestamp": "2024-10-28T13:19:57.261730412"
     }
-}
\ No newline at end of file
+}

From 1560bd0ce6edee4c86e54dfc6472abc81bb57560 Mon Sep 17 00:00:00 2001
From: ctuni <c.tuni.dominguez@gmail.com>
Date: Tue, 29 Oct 2024 15:43:59 +0100
Subject: [PATCH 097/530] citations, usage, output, etc

---
 CHANGELOG.md   |  1 +
 CITATIONS.md   |  4 ++++
 docs/output.md | 14 ++++++++++++++
 3 files changed, 19 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b0b12de1..fb229c2b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,6 +12,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#20](https://github.com/nf-core/seqinspector/pull/20) Use tags to generate group reports
 - [#13](https://github.com/nf-core/seqinspector/pull/13) Generate reports per run, per project and per lane.
 - [#49](https://github.com/nf-core/seqinspector/pull/49) Merge with template 3.0.2.
+- [#56](https://github.com/nf-core/seqinspector/pull/56) Added SeqFu stats module.
 
 ### `Fixed`
 
diff --git a/CITATIONS.md b/CITATIONS.md
index ecbfb16e..b5b796eb 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -14,6 +14,10 @@
 
 > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
 
+- [SeqFu](https://telatin.github.io/seqfu2/)
+
+> Telatin A, Fariselli P, Birolo G. SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files. Bioengineering 2021, 8, 59. doi.org/10.3390/bioengineering8050059
+
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
 > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
diff --git a/docs/output.md b/docs/output.md
index e14c3ad6..1937c179 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -11,6 +11,7 @@ The directories listed below will be created in the results directory after the
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
 - [FastQC](#fastqc) - Raw read QC
+- [SeqFu Stats](#seqfu_stats) - Statistics for FASTA or FASTQ files
 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
@@ -27,6 +28,19 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
 
+#### SeqFu Stats
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `seqfu/`
+  - `*.tsv`: Tab-separated file containing quality metrics.
+  - `*_mqc.txt`: File containing the same quality metrics as the TSV file, ready to be read by MultiQC.
+
+</details>
+
+[SeqFu](https://telatin.github.io/seqfu2/) is general-purpose program to manipulate and parse information from FASTA/FASTQ files, supporting gzipped input files. Includes functions to interleave and de-interleave FASTQ files, to rename sequences and to count and print statistics on sequence lengths. In this pipeline, the `seqfu stats` module is used to produce general quality metrics statistics.
+
 ### MultiQC
 
 nf-core/seqinspector will generate the following MultiQC reports:

From 73381fbdfa9048aff3282483c1a26cd1e5aabd7c Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 29 Oct 2024 13:00:00 +0100
Subject: [PATCH 098/530] fix: Give up on fastq_screen writing it's own config

---
 .../fastqscreen/fastqscreen-fastqscreen.diff  | 51 +++++++++++++++----
 .../nf-core/fastqscreen/fastqscreen/main.nf   | 14 ++---
 workflows/seqinspector.nf                     |  1 -
 3 files changed, 50 insertions(+), 16 deletions(-)

diff --git a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
index e8ff52e0..e2f8a54d 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
+++ b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
@@ -1,37 +1,70 @@
 Changes in module 'nf-core/fastqscreen/fastqscreen'
-'modules/nf-core/fastqscreen/fastqscreen/environment.yml' is unchanged
+Changes in 'fastqscreen/fastqscreen/environment.yml':
+--- modules/nf-core/fastqscreen/fastqscreen/environment.yml
++++ modules/nf-core/fastqscreen/fastqscreen/environment.yml
+@@ -4,5 +4,11 @@
+   - conda-forge
+   - bioconda
+ dependencies:
+-  - "bioconda::fastq-screen=0.15.3"
++  - bioconda::fastq-screen=0.16.0
+   - bioconda::perl-gdgraph=1.54
++  # - gzip
++  # - SAMtools
++  # - bowtie
++  # - bowtie2
++  # - bwa
++  # - bismark
+
 'modules/nf-core/fastqscreen/fastqscreen/meta.yml' is unchanged
 Changes in 'fastqscreen/fastqscreen/main.nf':
 --- modules/nf-core/fastqscreen/fastqscreen/main.nf
 +++ modules/nf-core/fastqscreen/fastqscreen/main.nf
-@@ -9,7 +9,7 @@
+@@ -1,15 +1,15 @@
+ process FASTQSCREEN_FASTQSCREEN {
+-    tag "$meta.id"
++    tag "$meta.id | $meta2.database_name"
+     label 'process_medium'
+ 
+     conda "${moduleDir}/environment.yml"
+     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+-        'https://depot.galaxyproject.org/singularity/fastq-screen:0.15.3--pl5321hdfd78af_0':
+-        'biocontainers/fastq-screen:0.15.3--pl5321hdfd78af_0'}"
++        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fc/fc53eee7ca23c32220a9662fbb63c67769756544b6d74a1ee85cf439ea79a7ee/data' :
++        'community.wave.seqera.io/library/fastq-screen_perl-gdgraph:5c1786a5d5bc1309'}"
  
      input:
-     tuple val(meta), path(reads)  // .fastq files
+-    tuple val(meta), path(reads)  // .fastq files
 -    path database
-+    tuple val(meta), path(database) // [[database_name,  database_notes], database_path]
++    // NOTE for meta 2 and database [[database_name,  database_notes], database_path]
++    tuple val(meta), path(reads), val(meta2), path(database)
  
      output:
      tuple val(meta), path("*.txt")     , emit: txt
-@@ -24,11 +24,14 @@
+@@ -24,13 +24,18 @@
      script:
      def prefix = task.ext.prefix ?: "${meta.id}"
      def args = task.ext.args ?: ""
 +    // 'Database name','Genome path and basename','Notes'
 +    """
-+    fastq_screen --add_genome \\
-+        '$meta.database_name','$database_path','$meta.database_notes'
++    echo "Writing config"
++    echo "DATABASE    ${meta2.database_name}    ./${database}/genome    ${meta2.database_notes}" > fastq_screen.conf
++    echo "Wrote config"
  
 -    """
 -    fastq_screen --threads ${task.cpus} \\
 -        --aligner bowtie2 \\
 -        --conf ${database}/fastq_screen.conf \\
-+    fastq_screen
++    fastq_screen \\
 +        --conf fastq_screen.conf \\
 +        --threads ${task.cpus} \\
++        --aligner ${meta2.database_notes.toLowerCase()} \\
          $reads \\
-         $args \\
+-        $args \\
++        $args
  
+     cat <<-END_VERSIONS > versions.yml
+     "${task.process}":
 
 'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap' is unchanged
 'modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml' is unchanged
diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index c792707e..eab5afb1 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -1,5 +1,5 @@
 process FASTQSCREEN_FASTQSCREEN {
-    tag "$meta.id"
+    tag "$meta.id | $meta2.database_name"
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
@@ -9,7 +9,7 @@ process FASTQSCREEN_FASTQSCREEN {
 
     input:
     tuple val(meta), path(reads)  // .fastq files
-    tuple val(meta), path(database) // [[database_name,  database_notes], database_path]
+    tuple val(meta2), path(database) // [[database_name,  database_notes], database_path]
 
     output:
     tuple val(meta), path("*.txt")     , emit: txt
@@ -26,14 +26,16 @@ process FASTQSCREEN_FASTQSCREEN {
     def args = task.ext.args ?: ""
     // 'Database name','Genome path and basename','Notes'
     """
-    fastq_screen --add_genome \\
-        '$meta.database_name','$database_path','$meta.database_notes'
+    echo "Writing config"
+    echo "DATABASE    ${meta2.database_name}    ./${database}/genome    ${meta2.database_notes}" > fastq_screen.conf
+    echo "Wrote config"
 
-    fastq_screen
+    fastq_screen \\
         --conf fastq_screen.conf \\
         --threads ${task.cpus} \\
+        --aligner ${meta2.database_notes.toLowerCase()} \\
         $reads \\
-        $args \\
+        $args
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index d283c2ac..ad6dc2cb 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -49,7 +49,6 @@ workflow SEQINSPECTOR {
     //
     ch_databases = Channel
         .fromList(samplesheetToList(ch_databasesheet, "${projectDir}/assets/schema_database.json"))
-        .view()
 
     FASTQSCREEN_FASTQSCREEN (
         ch_samplesheet,

From 5d5c65017b9afdbdd584ed857e719e2aae931a48 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 29 Oct 2024 13:05:42 +0100
Subject: [PATCH 099/530] test: Update databases

---
 assets/databasesheet.csv | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/assets/databasesheet.csv b/assets/databasesheet.csv
index f300a046..150f8318 100644
--- a/assets/databasesheet.csv
+++ b/assets/databasesheet.csv
@@ -1,2 +1,4 @@
 name,index,aligner
+Ecoli,s3://ngi-igenomes/igenomes/Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/Bowtie2Index/,BOWTIE2
 PhiX,s3://ngi-igenomes/igenomes/PhiX/Illumina/RTA/Sequence/Bowtie2Index/,BOWTIE2
+Scerevisiae,s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/NCBI/build3.1/Sequence/Bowtie2Index/,BOWTIE2

From 7780d30ce900897118dd54b750ee3a60fd2bd124 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 29 Oct 2024 14:32:09 +0100
Subject: [PATCH 100/530] fix: Run every sample and every DB

---
 modules/nf-core/fastqscreen/fastqscreen/main.nf | 4 ++--
 workflows/seqinspector.nf                       | 3 +--
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index eab5afb1..5037db6a 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -8,8 +8,8 @@ process FASTQSCREEN_FASTQSCREEN {
         'community.wave.seqera.io/library/fastq-screen_perl-gdgraph:5c1786a5d5bc1309'}"
 
     input:
-    tuple val(meta), path(reads)  // .fastq files
-    tuple val(meta2), path(database) // [[database_name,  database_notes], database_path]
+    // NOTE for meta 2 and database [[database_name,  database_notes], database_path]
+    tuple val(meta), path(reads), val(meta2), path(database)
 
     output:
     tuple val(meta), path("*.txt")     , emit: txt
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index ad6dc2cb..75ea2d6c 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -51,8 +51,7 @@ workflow SEQINSPECTOR {
         .fromList(samplesheetToList(ch_databasesheet, "${projectDir}/assets/schema_database.json"))
 
     FASTQSCREEN_FASTQSCREEN (
-        ch_samplesheet,
-        ch_databases,
+        ch_samplesheet.combine(ch_databases)
     )
     ch_multiqc_files = ch_multiqc_files.mix(FASTQSCREEN_FASTQSCREEN.out.txt)
     ch_versions = ch_versions.mix(FASTQSCREEN_FASTQSCREEN.out.versions.first())

From 01aa53f5f5142be3c927e76fa0c06e9eec554d55 Mon Sep 17 00:00:00 2001
From: matrulda <matilda.aslin@medsci.uu.se>
Date: Wed, 30 Oct 2024 08:15:54 +0100
Subject: [PATCH 101/530] Update CONTRIBUTION regarding displaying tool results

---
 .github/CONTRIBUTING.md | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 4bcb559a..ed49905d 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -82,6 +82,12 @@ If you wish to contribute a new step, please use the following coding standards:
 9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
 10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
 
+### Things to consider regarding displaying results for a new tool
+
+- If a MultiQC module exist for the tool, use the standard settings for it to start with.
+- If no Multiqc module exists, the results of the tool should be made available in the results directory.
+- If a tool doesn’t produce output files, the stdout should be channeled into a output file that can be accessible from the outdir of the pipeline.
+
 ### Default values
 
 Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.

From 70efcfa67525b1f2d1e33209f0d77cb4e785861b Mon Sep 17 00:00:00 2001
From: matrulda <matilda.aslin@medsci.uu.se>
Date: Wed, 30 Oct 2024 08:25:32 +0100
Subject: [PATCH 102/530] Updated Changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c682d313..73a4af01 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#13](https://github.com/nf-core/seqinspector/pull/13) Generate reports per run, per project and per lane.
 - [#49](https://github.com/nf-core/seqinspector/pull/49) Merge with template 3.0.2.
 - [#51](https://github.com/nf-core/seqinspector/pull/51) Add nf-test to CI.
+- [#63](https://github.com/nf-core/seqinspector/pull/63) Contribution guidelines added about displaying results for new tools
 
 ### `Fixed`
 

From 14a27f071591eedb2d57e51b1710d6c31b8d184a Mon Sep 17 00:00:00 2001
From: matrulda <matilda.aslin@medsci.uu.se>
Date: Wed, 30 Oct 2024 09:59:43 +0100
Subject: [PATCH 103/530] Ignore files_unchanged for CONTRIBUTION.md

---
 .nf-core.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index fb856008..3765b89d 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,5 +1,7 @@
 bump_version: null
-lint: null
+lint:
+  files_unchanged:
+    - .github/CONTRIBUTING.md
 nf_core_version: 3.0.2
 org_path: null
 repository_type: pipeline

From 131b718c376f9978c6db2624534ba6b1ddee7259 Mon Sep 17 00:00:00 2001
From: ngarcia <natalia.garcia@nanoporetech.com>
Date: Wed, 30 Oct 2024 09:26:52 +0000
Subject: [PATCH 104/530] fix test

---
 tests/NovaSeq6000.main_subsample.nf.test      | 1 -
 tests/NovaSeq6000.main_subsample.nf.test.snap | 3 +--
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/tests/NovaSeq6000.main_subsample.nf.test b/tests/NovaSeq6000.main_subsample.nf.test
index 72851f91..efdc574f 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test
+++ b/tests/NovaSeq6000.main_subsample.nf.test
@@ -21,7 +21,6 @@ nextflow_pipeline {
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_software_versions.txt"),
 
                     path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt"),
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index fdb7c8c4..8e9ada04 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -4,7 +4,6 @@
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,aba942d1e6996b579f19798e5673f514",
             "multiqc_general_stats.txt:md5,ad1ec9c64cbdb1131a26aeb6de51e31c",
-            "multiqc_software_versions.txt:md5,b7d1ca14785a9361f0a39ce1b6a02686",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8",
             "multiqc_general_stats.txt:md5,c73c8d10568a56f6534d280fff701e60",
@@ -26,6 +25,6 @@
             "nf-test": "0.9.1",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-30T09:11:23.734754433"
+        "timestamp": "2024-10-30T09:25:16.689719475"
     }
 }
\ No newline at end of file

From 3ac419f0d25a8b1893364a3432a8c18dad6f8551 Mon Sep 17 00:00:00 2001
From: ngarcia <natalia.garcia@nanoporetech.com>
Date: Wed, 30 Oct 2024 09:38:34 +0000
Subject: [PATCH 105/530] add citation

---
 CITATIONS.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CITATIONS.md b/CITATIONS.md
index ecbfb16e..8a4e350b 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -18,6 +18,8 @@
 
 > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
+- [Seqtk](https://github.com/lh3/seqtk)
+
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)

From 227619bfc9d8f0d816e8070643935527ea0a9a72 Mon Sep 17 00:00:00 2001
From: ngarcia <natalia.garcia@nanoporetech.com>
Date: Wed, 30 Oct 2024 09:38:51 +0000
Subject: [PATCH 106/530] fix test

---
 tests/NovaSeq6000.main_subsample.nf.test      | 4 ----
 tests/NovaSeq6000.main_subsample.nf.test.snap | 8 ++------
 2 files changed, 2 insertions(+), 10 deletions(-)

diff --git a/tests/NovaSeq6000.main_subsample.nf.test b/tests/NovaSeq6000.main_subsample.nf.test
index efdc574f..fe2b0685 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test
+++ b/tests/NovaSeq6000.main_subsample.nf.test
@@ -25,22 +25,18 @@ nextflow_pipeline {
                     path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_software_versions.txt"),
 
                     path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt"),
 
                     path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_software_versions.txt"),
 
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_software_versions.txt"),
                     ).match()
                 },
             )
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index 8e9ada04..651973b1 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -7,24 +7,20 @@
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8",
             "multiqc_general_stats.txt:md5,c73c8d10568a56f6534d280fff701e60",
-            "multiqc_software_versions.txt:md5,b7d1ca14785a9361f0a39ce1b6a02686",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,ff996e1d3dc4a46e0c9535e54d51ccab",
             "multiqc_general_stats.txt:md5,834e1868b887171cfda72029bbbe2d3f",
-            "multiqc_software_versions.txt:md5,b7d1ca14785a9361f0a39ce1b6a02686",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,3df36ecfe76b25b0c22dcda84bce2b3b",
             "multiqc_general_stats.txt:md5,274a001b007521970f14d68bd176e5be",
-            "multiqc_software_versions.txt:md5,b7d1ca14785a9361f0a39ce1b6a02686",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,ce61b4ce4b1d76ec3f20de3bf0c9ec7f",
-            "multiqc_general_stats.txt:md5,d476ad59458a035a329605d5284b6012",
-            "multiqc_software_versions.txt:md5,b7d1ca14785a9361f0a39ce1b6a02686"
+            "multiqc_general_stats.txt:md5,d476ad59458a035a329605d5284b6012"
         ],
         "meta": {
             "nf-test": "0.9.1",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-30T09:25:16.689719475"
+        "timestamp": "2024-10-30T09:37:46.182191597"
     }
 }
\ No newline at end of file

From 9211091e48c820e6926cbde242130d0c1ec0da69 Mon Sep 17 00:00:00 2001
From: ctuni <c.tuni.dominguez@gmail.com>
Date: Wed, 30 Oct 2024 11:20:57 +0100
Subject: [PATCH 107/530] added seqfu config

---
 conf/modules.config | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/conf/modules.config b/conf/modules.config
index c8838224..e1f0350b 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -22,6 +22,15 @@ process {
         ext.args = '--quiet'
     }
 
+    withName: 'SEQFU_STATS' {
+        ext.args   = ''
+        publishDir = [
+            path: { "${params.outdir}/seqfu_stats" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: 'MULTIQC_GLOBAL' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [

From 166f1812d170a3aa4c435f537eb46a0fe8e48735 Mon Sep 17 00:00:00 2001
From: FranBonath <franziska.bonath@scilifelab.se>
Date: Wed, 30 Oct 2024 12:02:01 +0100
Subject: [PATCH 108/530] adding fastqscreen database parameter, updating docs

---
 CHANGELOG.md                |  1 +
 CITATIONS.md                |  4 ++++
 assets/schema_database.json |  4 ++--
 docs/output.md              | 17 +++++++++++++++++
 main.nf                     |  2 +-
 nextflow.config             |  3 +++
 nextflow_schema.json        |  9 ++++++++-
 workflows/seqinspector.nf   |  4 ++--
 8 files changed, 38 insertions(+), 6 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b0b12de1..e396512f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,6 +12,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#20](https://github.com/nf-core/seqinspector/pull/20) Use tags to generate group reports
 - [#13](https://github.com/nf-core/seqinspector/pull/13) Generate reports per run, per project and per lane.
 - [#49](https://github.com/nf-core/seqinspector/pull/49) Merge with template 3.0.2.
+- [#53](https://github.com/nf-core/seqinspector/pull/53) Add FastQ-Screen database multiplexing
 
 ### `Fixed`
 
diff --git a/CITATIONS.md b/CITATIONS.md
index ecbfb16e..9cbd9f80 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -14,6 +14,10 @@
 
 > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
 
+- [Fastqscreen](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)
+
+> Wingett SW and Andrews S. FastQ Screen: A tool for multi-genome mapping and quality control [version 2; referees: 4 approved]. F1000Research 2018, 7:1338 (https://doi.org/10.12688/f1000research.15931.2)
+
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
 > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
diff --git a/assets/schema_database.json b/assets/schema_database.json
index df54284e..e735ea42 100644
--- a/assets/schema_database.json
+++ b/assets/schema_database.json
@@ -1,8 +1,8 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/seqinspector/master/assets/schema_database.json",
-    "title": "nf-core/seqinspector pipeline - params.databasesheet schema",
-    "description": "Schema for the file provided with params.databasesheet",
+    "title": "nf-core/seqinspector pipeline - params.fastqscreen_databasesheet schema",
+    "description": "Schema for the file provided with params.fastq_screen_databasesheet",
     "type": "array",
     "items": {
         "type": "object",
diff --git a/docs/output.md b/docs/output.md
index e14c3ad6..337037d2 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -11,6 +11,7 @@ The directories listed below will be created in the results directory after the
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
 - [FastQC](#fastqc) - Raw read QC
+- [Fastqscreen](#fastqscreen) - mapping against a set of references for basic contamination QC
 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
@@ -27,6 +28,22 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
 
+### FASTQSCREEN
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `fastqc/`
+  - `*_screen.html`: Interactive graphical fastqscreen report which summaries the mapping of your sequences against each of your libraries.
+  - `*_screen.pdf`: Static graphical fastqscreen report which summaries the mapping of your sequences against each of your libraries.
+  - `*_screen.txt` : text based fastqscreen report which summaries the mapping of your sequences against each of your libraries.
+
+</details>
+
+[Fastqscreen](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/) allows you to set up a standard set of libraries against which all of your sequences can be searched. Your search libraries might contain the genomes of all of the organisms you work on, along with PhiX, Vectors or other contaminants commonly seen in sequencing experiments.
+
+It requires the supply of referenced (databases) in a config file. In order to parallelize the mapping of the different samples, in seqinspector, this a fastqscreen config file is generated for every sample/reference combination.
+
 ### MultiQC
 
 nf-core/seqinspector will generate the following MultiQC reports:
diff --git a/main.nf b/main.nf
index 79e8a33d..cd4af962 100644
--- a/main.nf
+++ b/main.nf
@@ -86,7 +86,7 @@ workflow {
     //
     NFCORE_SEQINSPECTOR (
         PIPELINE_INITIALISATION.out.samplesheet,
-        params.database_sheet,
+        params.fastqscreen_database_sheet,
     )
     //
     // SUBWORKFLOW: Run completion tasks
diff --git a/nextflow.config b/nextflow.config
index 1600a70b..42372b9e 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -20,6 +20,9 @@ params {
     config_fastq_screen        = "${projectDir}/conf"
     igenomes_ignore            = false
 
+    // Fastqscreen options
+    fastqscreen_database_sheet = './assets/databasesheet.csv'
+
     // MultiQC options
     multiqc_config             = null
     multiqc_title              = null
diff --git a/nextflow_schema.json b/nextflow_schema.json
index f18a5f19..8331a2e4 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -68,7 +68,8 @@
                 "config_fastq_screen": {
                     "type": "string",
                     "description": "path to directory with fastq_screen config (fastq_screen.conf)",
-                    "fa_icon": "fas fa-braille"
+                    "fa_icon": "fas fa-braille",
+                    "default": "/Users/franziska.franziska/workspace/seqinspector/conf"
                 },
                 "igenomes_ignore": {
                     "type": "boolean",
@@ -84,6 +85,12 @@
                     "fa_icon": "fas fa-ban",
                     "hidden": true,
                     "default": "s3://ngi-igenomes/igenomes/"
+                },
+                "fastqscreen_database_sheet": {
+                    "type": "string",
+                    "default": "./assets/databasesheet.csv",
+                    "fa_icon": "fas fa-search",
+                    "description": "list of reference genomes (databases) to be mapped against in fastqscreen"
                 }
             }
         },
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 75ea2d6c..535448dd 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -26,7 +26,7 @@ workflow SEQINSPECTOR {
 
     take:
     ch_samplesheet // channel: samplesheet read in from --input
-    ch_databasesheet // channel: database sheet read in from --database_sheet
+    ch_fastqscreen_databasesheet // channel: database sheet read in from --fastqscreen_database_sheet
 
     main:
 
@@ -48,7 +48,7 @@ workflow SEQINSPECTOR {
     // MODULE: Run FastQ Screen
     //
     ch_databases = Channel
-        .fromList(samplesheetToList(ch_databasesheet, "${projectDir}/assets/schema_database.json"))
+        .fromList(samplesheetToList(ch_fastqscreen_databasesheet, "${projectDir}/assets/schema_database.json"))
 
     FASTQSCREEN_FASTQSCREEN (
         ch_samplesheet.combine(ch_databases)

From 478e2cc0dddc0d61e9c7c4ee858f9763410e9941 Mon Sep 17 00:00:00 2001
From: Franziska Bonath <41994400+FranBonath@users.noreply.github.com>
Date: Thu, 7 Nov 2024 10:43:32 +0100
Subject: [PATCH 109/530] remove absolute path of fastqscreen config

---
 nextflow_schema.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 8331a2e4..ba1304e5 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -69,7 +69,7 @@
                     "type": "string",
                     "description": "path to directory with fastq_screen config (fastq_screen.conf)",
                     "fa_icon": "fas fa-braille",
-                    "default": "/Users/franziska.franziska/workspace/seqinspector/conf"
+                    "default": "./conf"
                 },
                 "igenomes_ignore": {
                     "type": "boolean",

From dc8f72991c3f7c1f24c8c2b0b6850dc39bb3676b Mon Sep 17 00:00:00 2001
From: Franziska Bonath <41994400+FranBonath@users.noreply.github.com>
Date: Thu, 7 Nov 2024 10:47:53 +0100
Subject: [PATCH 110/530] remove "projectDir" from path for fastqscreen config
 in nextflow.config

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 42372b9e..791764c5 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -17,7 +17,7 @@ params {
     genome                     = null
     fasta                      = null
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
-    config_fastq_screen        = "${projectDir}/conf"
+    config_fastq_screen        = "./conf"
     igenomes_ignore            = false
 
     // Fastqscreen options

From dd567b5695ff6a3fe9c03a380535558e3ce2eee3 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 7 Nov 2024 12:03:05 +0000
Subject: [PATCH 111/530] remove conf/fastq_screen.conf and it's references, as
 the file is built by the process on the fly

---
 conf/fastq_screen.conf | 64 ------------------------------------------
 nextflow.config        |  1 -
 nextflow_schema.json   |  6 ----
 3 files changed, 71 deletions(-)
 delete mode 100644 conf/fastq_screen.conf

diff --git a/conf/fastq_screen.conf b/conf/fastq_screen.conf
deleted file mode 100644
index f170f285..00000000
--- a/conf/fastq_screen.conf
+++ /dev/null
@@ -1,64 +0,0 @@
-# This is a configuration file for fastq_screen
-
-###########
-## Bowtie #
-###########
-## If the bowtie binary is not in your PATH then you can
-## set this value to tell the program where to find it.
-## Uncomment the line below and set the appropriate location
-##
-
-#BOWTIE2 /sw/data/uppnex/reference/sw/mf/bioinfo-tools/pipelines/bowtie2/2.1.0/bowtie2
-
-############
-## Threads #
-############
-## Bowtie can be made to run across multiple CPU cores to
-## speed up your searches. Set this value to the number
-## of cores you want to use for your searches.
-
-#THREADS                16
-
-##############
-## Databases #
-##############
-## This section allows you to configure multiple databases
-## to search against in your screen.  For each database
-## you need to provide a database name (which can't contain
-## spaces) and the location of the bowtie indices which
-## you created for that database.
-##
-## The default entries shown below are only suggested examples
-## you can add as many DATABASE sections as you like, and you
-## can comment out or remove as many of the existing entries
-## as you like.
-##
-## Either the original bowtie or bowtie 2 may be used for the
-## mapping. Specify the aligner to use with the command line
-## flag --aligner with arguments 'bowtie' (default) or
-## 'bowtie2'.
-##
-## The configuration file may list paths to both bowtie and
-## bowtie2 indices, which are specified with either 'BOWTIE'
-## or 'BOWTIE2' after the path (leaving unspecified will
-## default to bowtie). While the configuration file may list
-## paths to both bowtie and bowtie2 indices, only one aligner
-## will be used for the mapping, as specified by the --aligner
-## flag.
-##
-## For example:
-## DATABASE     Human_Bowtie    /data/public/Genomes/Human_Bowtie/GRCh37/Homo_sapiens.GRCh37 BOWTIE
-## DATABASE     Human_Bowtie    /data/public/Genomes/Human_Bowtie/GRCh37/Homo_sapiens.GRCh37
-## DATABASE     Human_Bowtie2   /data/public/Genomes/Human_Bowtie2/GRCh37/Homo_sapiens.GRCh37 BOWTIE2
-
-## E. coli (igenomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1)
-DATABASE    Ecoli   ./database/EB1 BOWTIE2
-
-## M. tuberculosis (igenomes/Mycobacterium_tuberculosis_H37RV/Ensembl/H37Rv.EB1)
-DATABASE    Tuberculosis   ./references/genome_tuberculosis/genome BOWTIE2
-
-## PhiX (/igenomes/PhiX/Illumina/RTA)
-DATABASE    PhiX   ../../../modules/nf-core/fastqscreen/references/genome_phix/genome BOWTIE2
-
-##S. cerevisiae (igenomes/Saccharomyces_cerevisiae/Ensembl/EF4)
-DATABASE    Scerevisiae   ../../../modules/nf-core/fastqscreen/references/genome_cerevisiae/genome BOWTIE2
diff --git a/nextflow.config b/nextflow.config
index 0c7668c9..9b9a8bd4 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -17,7 +17,6 @@ params {
     genome                     = null
     fasta                      = null
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
-    config_fastq_screen        = "./conf"
     igenomes_ignore            = false
 
     // Fastqscreen options
diff --git a/nextflow_schema.json b/nextflow_schema.json
index b464e2a6..b320d2be 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -72,12 +72,6 @@
                     "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
                     "fa_icon": "far fa-file-code"
                 },
-                "config_fastq_screen": {
-                    "type": "string",
-                    "description": "path to directory with fastq_screen config (fastq_screen.conf)",
-                    "fa_icon": "fas fa-braille",
-                    "default": "./conf"
-                },
                 "igenomes_ignore": {
                     "type": "boolean",
                     "description": "Do not load the iGenomes reference config.",

From 5750d622d1cf0a904ea2d2b4a5f97e2ff2cbb386 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 7 Nov 2024 12:03:40 +0000
Subject: [PATCH 112/530] remove diff dump, I don't see why it should be here

---
 .../fastqscreen/fastqscreen-fastqscreen.diff  | 73 -------------------
 1 file changed, 73 deletions(-)
 delete mode 100644 modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff

diff --git a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
deleted file mode 100644
index e2f8a54d..00000000
--- a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
+++ /dev/null
@@ -1,73 +0,0 @@
-Changes in module 'nf-core/fastqscreen/fastqscreen'
-Changes in 'fastqscreen/fastqscreen/environment.yml':
---- modules/nf-core/fastqscreen/fastqscreen/environment.yml
-+++ modules/nf-core/fastqscreen/fastqscreen/environment.yml
-@@ -4,5 +4,11 @@
-   - conda-forge
-   - bioconda
- dependencies:
--  - "bioconda::fastq-screen=0.15.3"
-+  - bioconda::fastq-screen=0.16.0
-   - bioconda::perl-gdgraph=1.54
-+  # - gzip
-+  # - SAMtools
-+  # - bowtie
-+  # - bowtie2
-+  # - bwa
-+  # - bismark
-
-'modules/nf-core/fastqscreen/fastqscreen/meta.yml' is unchanged
-Changes in 'fastqscreen/fastqscreen/main.nf':
---- modules/nf-core/fastqscreen/fastqscreen/main.nf
-+++ modules/nf-core/fastqscreen/fastqscreen/main.nf
-@@ -1,15 +1,15 @@
- process FASTQSCREEN_FASTQSCREEN {
--    tag "$meta.id"
-+    tag "$meta.id | $meta2.database_name"
-     label 'process_medium'
- 
-     conda "${moduleDir}/environment.yml"
-     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
--        'https://depot.galaxyproject.org/singularity/fastq-screen:0.15.3--pl5321hdfd78af_0':
--        'biocontainers/fastq-screen:0.15.3--pl5321hdfd78af_0'}"
-+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fc/fc53eee7ca23c32220a9662fbb63c67769756544b6d74a1ee85cf439ea79a7ee/data' :
-+        'community.wave.seqera.io/library/fastq-screen_perl-gdgraph:5c1786a5d5bc1309'}"
- 
-     input:
--    tuple val(meta), path(reads)  // .fastq files
--    path database
-+    // NOTE for meta 2 and database [[database_name,  database_notes], database_path]
-+    tuple val(meta), path(reads), val(meta2), path(database)
- 
-     output:
-     tuple val(meta), path("*.txt")     , emit: txt
-@@ -24,13 +24,18 @@
-     script:
-     def prefix = task.ext.prefix ?: "${meta.id}"
-     def args = task.ext.args ?: ""
-+    // 'Database name','Genome path and basename','Notes'
-+    """
-+    echo "Writing config"
-+    echo "DATABASE    ${meta2.database_name}    ./${database}/genome    ${meta2.database_notes}" > fastq_screen.conf
-+    echo "Wrote config"
- 
--    """
--    fastq_screen --threads ${task.cpus} \\
--        --aligner bowtie2 \\
--        --conf ${database}/fastq_screen.conf \\
-+    fastq_screen \\
-+        --conf fastq_screen.conf \\
-+        --threads ${task.cpus} \\
-+        --aligner ${meta2.database_notes.toLowerCase()} \\
-         $reads \\
--        $args \\
-+        $args
- 
-     cat <<-END_VERSIONS > versions.yml
-     "${task.process}":
-
-'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap' is unchanged
-'modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml' is unchanged
-'modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config' is unchanged
-'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test' is unchanged
-************************************************************

From 6af9204497054d3acd4f59491f6ed35b3b57745b Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 7 Nov 2024 12:05:16 +0000
Subject: [PATCH 113/530] spacing

---
 workflows/seqinspector.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 54974dc7..fe8e99df 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -27,7 +27,7 @@ include { methodsDescriptionText        } from '../subworkflows/local/utils_nfco
 workflow SEQINSPECTOR {
 
     take:
-    ch_samplesheet // channel: samplesheet read in from --input
+    ch_samplesheet               // channel: samplesheet read in from --input
     ch_fastqscreen_databasesheet // channel: database sheet read in from --fastqscreen_database_sheet
 
     main:

From 2eba94f570c96c1571421e5f0ba09b2d2eed978a Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 7 Nov 2024 12:21:06 +0000
Subject: [PATCH 114/530] Revert remove diff dump, now I see why it should be
 here :)

---
 .../fastqscreen/fastqscreen-fastqscreen.diff  | 73 +++++++++++++++++++
 1 file changed, 73 insertions(+)
 create mode 100644 modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff

diff --git a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
new file mode 100644
index 00000000..e2f8a54d
--- /dev/null
+++ b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
@@ -0,0 +1,73 @@
+Changes in module 'nf-core/fastqscreen/fastqscreen'
+Changes in 'fastqscreen/fastqscreen/environment.yml':
+--- modules/nf-core/fastqscreen/fastqscreen/environment.yml
++++ modules/nf-core/fastqscreen/fastqscreen/environment.yml
+@@ -4,5 +4,11 @@
+   - conda-forge
+   - bioconda
+ dependencies:
+-  - "bioconda::fastq-screen=0.15.3"
++  - bioconda::fastq-screen=0.16.0
+   - bioconda::perl-gdgraph=1.54
++  # - gzip
++  # - SAMtools
++  # - bowtie
++  # - bowtie2
++  # - bwa
++  # - bismark
+
+'modules/nf-core/fastqscreen/fastqscreen/meta.yml' is unchanged
+Changes in 'fastqscreen/fastqscreen/main.nf':
+--- modules/nf-core/fastqscreen/fastqscreen/main.nf
++++ modules/nf-core/fastqscreen/fastqscreen/main.nf
+@@ -1,15 +1,15 @@
+ process FASTQSCREEN_FASTQSCREEN {
+-    tag "$meta.id"
++    tag "$meta.id | $meta2.database_name"
+     label 'process_medium'
+ 
+     conda "${moduleDir}/environment.yml"
+     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+-        'https://depot.galaxyproject.org/singularity/fastq-screen:0.15.3--pl5321hdfd78af_0':
+-        'biocontainers/fastq-screen:0.15.3--pl5321hdfd78af_0'}"
++        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fc/fc53eee7ca23c32220a9662fbb63c67769756544b6d74a1ee85cf439ea79a7ee/data' :
++        'community.wave.seqera.io/library/fastq-screen_perl-gdgraph:5c1786a5d5bc1309'}"
+ 
+     input:
+-    tuple val(meta), path(reads)  // .fastq files
+-    path database
++    // NOTE for meta 2 and database [[database_name,  database_notes], database_path]
++    tuple val(meta), path(reads), val(meta2), path(database)
+ 
+     output:
+     tuple val(meta), path("*.txt")     , emit: txt
+@@ -24,13 +24,18 @@
+     script:
+     def prefix = task.ext.prefix ?: "${meta.id}"
+     def args = task.ext.args ?: ""
++    // 'Database name','Genome path and basename','Notes'
++    """
++    echo "Writing config"
++    echo "DATABASE    ${meta2.database_name}    ./${database}/genome    ${meta2.database_notes}" > fastq_screen.conf
++    echo "Wrote config"
+ 
+-    """
+-    fastq_screen --threads ${task.cpus} \\
+-        --aligner bowtie2 \\
+-        --conf ${database}/fastq_screen.conf \\
++    fastq_screen \\
++        --conf fastq_screen.conf \\
++        --threads ${task.cpus} \\
++        --aligner ${meta2.database_notes.toLowerCase()} \\
+         $reads \\
+-        $args \\
++        $args
+ 
+     cat <<-END_VERSIONS > versions.yml
+     "${task.process}":
+
+'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test' is unchanged
+************************************************************

From 2166d7ca322c679e2739b9c9970dcf6f3116156a Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 7 Nov 2024 12:31:04 +0000
Subject: [PATCH 115/530] fix faulty params var name in test config

---
 conf/test.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/test.config b/conf/test.config
index c0324318..1a6f84b4 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -26,7 +26,7 @@ params {
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
     input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
-    database_sheet = "${projectDir}/assets/databasesheet.csv"
+    fastqscreen_database_sheet = "${projectDir}/assets/databasesheet.csv"
 
     // Genome references
     genome = 'R64-1-1'

From 315bde194b28dc7c4fa1f74816a063ec40a72523 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 7 Nov 2024 12:37:41 +0000
Subject: [PATCH 116/530] update snapshots for new multiqc citations

---
 tests/MiSeq.main.nf.test.snap                 |  8 ++++----
 tests/NovaSeq6000.main.nf.test.snap           | 16 ++++++++--------
 tests/NovaSeq6000.main_subsample.nf.test.snap | 16 ++++++++--------
 tests/PromethION.main.nf.test.snap            |  8 ++++----
 4 files changed, 24 insertions(+), 24 deletions(-)

diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index de0afa29..1dc646e5 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -1,14 +1,14 @@
 {
     "MiSeq data test": {
         "content": [
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
             "multiqc_general_stats.txt:md5,5b28a83b14cb2fe88d084d08900ebdbf"
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-10-30T09:08:29.692511055"
+        "timestamp": "2024-11-07T12:32:20.523618752"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index 62ccd4aa..823926fb 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -1,26 +1,26 @@
 {
     "NovaSeq6000 data test": {
         "content": [
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d",
             "multiqc_general_stats.txt:md5,25abe0f6a35eb4a3b056fc3cf5c13732",
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
             "multiqc_general_stats.txt:md5,90ee35137492b80aab36ef67f72d8921",
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
             "multiqc_general_stats.txt:md5,d62a2fc39e674d98783d408791803148",
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
             "multiqc_general_stats.txt:md5,2f09b8f199ac40cf67ba50843cebd29c",
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
             "multiqc_general_stats.txt:md5,6a1c16f068d7ba3a9225a17eb570ed9a"
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-10-30T09:09:57.158871165"
+        "timestamp": "2024-11-07T12:33:47.150820885"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index 651973b1..024fa662 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -1,26 +1,26 @@
 {
     "NovaSeq6000 data test sample size": {
         "content": [
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,aba942d1e6996b579f19798e5673f514",
             "multiqc_general_stats.txt:md5,ad1ec9c64cbdb1131a26aeb6de51e31c",
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8",
             "multiqc_general_stats.txt:md5,c73c8d10568a56f6534d280fff701e60",
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,ff996e1d3dc4a46e0c9535e54d51ccab",
             "multiqc_general_stats.txt:md5,834e1868b887171cfda72029bbbe2d3f",
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,3df36ecfe76b25b0c22dcda84bce2b3b",
             "multiqc_general_stats.txt:md5,274a001b007521970f14d68bd176e5be",
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,ce61b4ce4b1d76ec3f20de3bf0c9ec7f",
             "multiqc_general_stats.txt:md5,d476ad59458a035a329605d5284b6012"
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-10-30T09:37:46.182191597"
+        "timestamp": "2024-11-07T12:35:00.745830145"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index dfa4eb6f..24a77664 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -1,14 +1,14 @@
 {
     "PromethION data test": {
         "content": [
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,1a4b472e13cadc770832b0e20d1de7b0",
             "multiqc_general_stats.txt:md5,409cefc7f17f95d176ced6032bf8fb32"
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-10-30T09:12:03.048502046"
+        "timestamp": "2024-11-07T12:35:46.010641114"
     }
 }
\ No newline at end of file

From 05ef44ee4e32dad90306375e0a68bcdca7e1df07 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 7 Nov 2024 12:53:19 +0000
Subject: [PATCH 117/530] module tests of fastqscreen are dependent on
 non-installed modules, so try to limit the scope of nf-test to the tests/ dir

---
 .github/workflows/nf-test.yml | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index b0d7b8e8..3a2abcbd 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -5,9 +5,7 @@ on: [push, pull_request]
 jobs:
   test:
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        shard: [1, 2, 3, 4]
+
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -28,5 +26,5 @@ jobs:
           wget -qO- https://get.nf-test.com | bash
           sudo mv nf-test /usr/local/bin/
 
-      - name: Run Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }})
-        run: nf-test test --ci --shard ${{ matrix.shard }}/${{ strategy.job-total }} .
+      - name: Run Tests
+        run: nf-test test --ci tests

From 627ee46e97089cd350d3a4e141a2aae6661f9222 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 7 Nov 2024 13:34:52 +0000
Subject: [PATCH 118/530] Append changelog entry

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 299e0305..01d94016 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,7 +15,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#50](https://github.com/nf-core/seqinspector/pull/50) Add an optional subsampling step.
 - [#51](https://github.com/nf-core/seqinspector/pull/51) Add nf-test to CI.
 - [#63](https://github.com/nf-core/seqinspector/pull/63) Contribution guidelines added about displaying results for new tools
-- [#53](https://github.com/nf-core/seqinspector/pull/53) Add FastQ-Screen database multiplexing
+- [#53](https://github.com/nf-core/seqinspector/pull/53) Add FastQ-Screen database multiplexing and limit scope of nf-test in CI.
 
 ### `Fixed`
 

From e446bef33e22addeb32c33bb764b51cdd2e30bb0 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 7 Nov 2024 13:38:26 +0000
Subject: [PATCH 119/530] Check for fastQ Screen files in multiqc report in
 pipeline tests and update snapshots accordingly

---
 tests/MiSeq.main.nf.test                      | 1 +
 tests/MiSeq.main.nf.test.snap                 | 5 +++--
 tests/NovaSeq6000.main.nf.test                | 7 ++++++-
 tests/NovaSeq6000.main.nf.test.snap           | 9 +++++++--
 tests/NovaSeq6000.main_subsample.nf.test      | 5 +++++
 tests/NovaSeq6000.main_subsample.nf.test.snap | 9 +++++++--
 tests/PromethION.main.nf.test                 | 1 +
 tests/PromethION.main.nf.test.snap            | 5 +++--
 8 files changed, 33 insertions(+), 9 deletions(-)

diff --git a/tests/MiSeq.main.nf.test b/tests/MiSeq.main.nf.test
index 246a05a5..a1badfac 100644
--- a/tests/MiSeq.main.nf.test
+++ b/tests/MiSeq.main.nf.test
@@ -21,6 +21,7 @@ nextflow_pipeline {
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt"),
                     ).match()
                 }
             )
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 1dc646e5..0e8fec2e 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -3,12 +3,13 @@
         "content": [
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
-            "multiqc_general_stats.txt:md5,5b28a83b14cb2fe88d084d08900ebdbf"
+            "multiqc_general_stats.txt:md5,5b28a83b14cb2fe88d084d08900ebdbf",
+            "multiqc_fastq_screen.txt:md5,88473b5190a4ff3bbe5a1b5b92da2601"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-07T12:32:20.523618752"
+        "timestamp": "2024-11-07T13:33:59.180570696"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test b/tests/NovaSeq6000.main.nf.test
index e24637cd..06a5cb14 100644
--- a/tests/NovaSeq6000.main.nf.test
+++ b/tests/NovaSeq6000.main.nf.test
@@ -21,23 +21,28 @@ nextflow_pipeline {
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt"),
 
                     path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_fastq_screen.txt"),
 
                     path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt"),
 
                     path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_fastq_screen.txt"),
 
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt"),
-                    ).match()
+                                        path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt"),
+                                        ).match()
                 },
             )
         }
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index 823926fb..c22361f9 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -4,23 +4,28 @@
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d",
             "multiqc_general_stats.txt:md5,25abe0f6a35eb4a3b056fc3cf5c13732",
+            "multiqc_fastq_screen.txt:md5,836b01175da79f0de458df899b9751e1",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
             "multiqc_general_stats.txt:md5,90ee35137492b80aab36ef67f72d8921",
+            "multiqc_fastq_screen.txt:md5,fd72aaf00fd4fac3da4ef222608e0c32",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
             "multiqc_general_stats.txt:md5,d62a2fc39e674d98783d408791803148",
+            "multiqc_fastq_screen.txt:md5,301fe12a6c6ccd09904c4f759008d416",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
             "multiqc_general_stats.txt:md5,2f09b8f199ac40cf67ba50843cebd29c",
+            "multiqc_fastq_screen.txt:md5,045f5b7623f6abb99b7075734fdb0cf4",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
-            "multiqc_general_stats.txt:md5,6a1c16f068d7ba3a9225a17eb570ed9a"
+            "multiqc_general_stats.txt:md5,6a1c16f068d7ba3a9225a17eb570ed9a",
+            "multiqc_fastq_screen.txt:md5,ee786f054e356ee005ca33c7558866dc"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-07T12:33:47.150820885"
+        "timestamp": "2024-11-07T13:35:28.998292704"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main_subsample.nf.test b/tests/NovaSeq6000.main_subsample.nf.test
index fe2b0685..d006de37 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test
+++ b/tests/NovaSeq6000.main_subsample.nf.test
@@ -21,22 +21,27 @@ nextflow_pipeline {
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt"),
 
                     path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_fastq_screen.txt"),
 
                     path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt"),
 
                     path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_fastq_screen.txt"),
 
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt"),
                     ).match()
                 },
             )
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index 024fa662..b3407e2e 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -4,23 +4,28 @@
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,aba942d1e6996b579f19798e5673f514",
             "multiqc_general_stats.txt:md5,ad1ec9c64cbdb1131a26aeb6de51e31c",
+            "multiqc_fastq_screen.txt:md5,2730834c61a9e1349b357ef6a729ddd9",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8",
             "multiqc_general_stats.txt:md5,c73c8d10568a56f6534d280fff701e60",
+            "multiqc_fastq_screen.txt:md5,a2b7469ab6b81d2872214eeba32933f5",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,ff996e1d3dc4a46e0c9535e54d51ccab",
             "multiqc_general_stats.txt:md5,834e1868b887171cfda72029bbbe2d3f",
+            "multiqc_fastq_screen.txt:md5,956cb8876c334293186ea213c4c39c6e",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,3df36ecfe76b25b0c22dcda84bce2b3b",
             "multiqc_general_stats.txt:md5,274a001b007521970f14d68bd176e5be",
+            "multiqc_fastq_screen.txt:md5,81cedab716aa382d7b4db2e42b681cb2",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,ce61b4ce4b1d76ec3f20de3bf0c9ec7f",
-            "multiqc_general_stats.txt:md5,d476ad59458a035a329605d5284b6012"
+            "multiqc_general_stats.txt:md5,d476ad59458a035a329605d5284b6012",
+            "multiqc_fastq_screen.txt:md5,8bbb1968587dbf3139bac07991a225cb"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-07T12:35:00.745830145"
+        "timestamp": "2024-11-07T13:36:43.785887669"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test b/tests/PromethION.main.nf.test
index ad6fe6d0..126a58c1 100644
--- a/tests/PromethION.main.nf.test
+++ b/tests/PromethION.main.nf.test
@@ -21,6 +21,7 @@ nextflow_pipeline {
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt"),
                     ).match()
                 },
             )
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index 24a77664..17178fdd 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -3,12 +3,13 @@
         "content": [
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,1a4b472e13cadc770832b0e20d1de7b0",
-            "multiqc_general_stats.txt:md5,409cefc7f17f95d176ced6032bf8fb32"
+            "multiqc_general_stats.txt:md5,409cefc7f17f95d176ced6032bf8fb32",
+            "multiqc_fastq_screen.txt:md5,37efa56cefb899abf506cf7a7fba0d54"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-07T12:35:46.010641114"
+        "timestamp": "2024-11-07T13:37:39.008847194"
     }
 }
\ No newline at end of file

From b5b1214a085df82addd52afe4e61365a11119059 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 7 Nov 2024 13:54:40 +0000
Subject: [PATCH 120/530] fix indent

---
 tests/NovaSeq6000.main.nf.test | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/NovaSeq6000.main.nf.test b/tests/NovaSeq6000.main.nf.test
index 06a5cb14..e70a191c 100644
--- a/tests/NovaSeq6000.main.nf.test
+++ b/tests/NovaSeq6000.main.nf.test
@@ -41,8 +41,8 @@ nextflow_pipeline {
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt"),
-                                        path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt"),
-                                        ).match()
+                    path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt"),
+                    ).match()
                 },
             )
         }

From b67c0f227431e0768b02e39d3136651840d56b3c Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Thu, 14 Nov 2024 11:14:57 -0600
Subject: [PATCH 121/530] fix: Rename fastqscreen files so they're unique

---
 .../fastqscreen/fastqscreen-fastqscreen.diff       |  6 +++++-
 modules/nf-core/fastqscreen/fastqscreen/main.nf    |  4 ++++
 tests/MiSeq.main.nf.test.snap                      |  6 +++---
 tests/NovaSeq6000.main.nf.test.snap                | 14 +++++++-------
 tests/NovaSeq6000.main_subsample.nf.test.snap      | 14 +++++++-------
 tests/PromethION.main.nf.test.snap                 |  6 +++---
 6 files changed, 29 insertions(+), 21 deletions(-)

diff --git a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
index e2f8a54d..ad5b6fe0 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
+++ b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
@@ -41,7 +41,7 @@ Changes in 'fastqscreen/fastqscreen/main.nf':
  
      output:
      tuple val(meta), path("*.txt")     , emit: txt
-@@ -24,13 +24,18 @@
+@@ -24,13 +24,22 @@
      script:
      def prefix = task.ext.prefix ?: "${meta.id}"
      def args = task.ext.args ?: ""
@@ -62,6 +62,10 @@ Changes in 'fastqscreen/fastqscreen/main.nf':
          $reads \\
 -        $args \\
 +        $args
++
++    mv *_screen.txt ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.txt
++    mv *_screen.html ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.html
++    mv *_screen.png ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.png
  
      cat <<-END_VERSIONS > versions.yml
      "${task.process}":
diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index 5037db6a..c0f98b9e 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -37,6 +37,10 @@ process FASTQSCREEN_FASTQSCREEN {
         $reads \\
         $args
 
+    mv *_screen.txt ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.txt
+    mv *_screen.html ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.html
+    mv *_screen.png ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.png
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//')
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 0e8fec2e..9207f882 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -4,12 +4,12 @@
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
             "multiqc_general_stats.txt:md5,5b28a83b14cb2fe88d084d08900ebdbf",
-            "multiqc_fastq_screen.txt:md5,88473b5190a4ff3bbe5a1b5b92da2601"
+            "multiqc_fastq_screen.txt:md5,435d8c1ac6e237448c9ce38e853ac82e"
         ],
         "meta": {
-            "nf-test": "0.9.0",
+            "nf-test": "0.9.2",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-07T13:33:59.180570696"
+        "timestamp": "2024-11-14T11:21:34.348023"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index c22361f9..8b0f1366 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -4,28 +4,28 @@
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d",
             "multiqc_general_stats.txt:md5,25abe0f6a35eb4a3b056fc3cf5c13732",
-            "multiqc_fastq_screen.txt:md5,836b01175da79f0de458df899b9751e1",
+            "multiqc_fastq_screen.txt:md5,c7b24e20fd157128924384e52eb3405d",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
             "multiqc_general_stats.txt:md5,90ee35137492b80aab36ef67f72d8921",
-            "multiqc_fastq_screen.txt:md5,fd72aaf00fd4fac3da4ef222608e0c32",
+            "multiqc_fastq_screen.txt:md5,a1e15006994d06a47634ccf07a08df0f",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
             "multiqc_general_stats.txt:md5,d62a2fc39e674d98783d408791803148",
-            "multiqc_fastq_screen.txt:md5,301fe12a6c6ccd09904c4f759008d416",
+            "multiqc_fastq_screen.txt:md5,d4f1cc5396c4f719b1fcaab2470e7d7c",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
             "multiqc_general_stats.txt:md5,2f09b8f199ac40cf67ba50843cebd29c",
-            "multiqc_fastq_screen.txt:md5,045f5b7623f6abb99b7075734fdb0cf4",
+            "multiqc_fastq_screen.txt:md5,02246ddb4bf5373b157b45eab698cdc8",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
             "multiqc_general_stats.txt:md5,6a1c16f068d7ba3a9225a17eb570ed9a",
-            "multiqc_fastq_screen.txt:md5,ee786f054e356ee005ca33c7558866dc"
+            "multiqc_fastq_screen.txt:md5,483995ed26ba25b3217650840b2d82fa"
         ],
         "meta": {
-            "nf-test": "0.9.0",
+            "nf-test": "0.9.2",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-07T13:35:28.998292704"
+        "timestamp": "2024-11-14T11:22:20.902938"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index b3407e2e..da7ba9a4 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -4,28 +4,28 @@
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,aba942d1e6996b579f19798e5673f514",
             "multiqc_general_stats.txt:md5,ad1ec9c64cbdb1131a26aeb6de51e31c",
-            "multiqc_fastq_screen.txt:md5,2730834c61a9e1349b357ef6a729ddd9",
+            "multiqc_fastq_screen.txt:md5,c7b24e20fd157128924384e52eb3405d",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8",
             "multiqc_general_stats.txt:md5,c73c8d10568a56f6534d280fff701e60",
-            "multiqc_fastq_screen.txt:md5,a2b7469ab6b81d2872214eeba32933f5",
+            "multiqc_fastq_screen.txt:md5,a1e15006994d06a47634ccf07a08df0f",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,ff996e1d3dc4a46e0c9535e54d51ccab",
             "multiqc_general_stats.txt:md5,834e1868b887171cfda72029bbbe2d3f",
-            "multiqc_fastq_screen.txt:md5,956cb8876c334293186ea213c4c39c6e",
+            "multiqc_fastq_screen.txt:md5,d4f1cc5396c4f719b1fcaab2470e7d7c",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,3df36ecfe76b25b0c22dcda84bce2b3b",
             "multiqc_general_stats.txt:md5,274a001b007521970f14d68bd176e5be",
-            "multiqc_fastq_screen.txt:md5,81cedab716aa382d7b4db2e42b681cb2",
+            "multiqc_fastq_screen.txt:md5,02246ddb4bf5373b157b45eab698cdc8",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,ce61b4ce4b1d76ec3f20de3bf0c9ec7f",
             "multiqc_general_stats.txt:md5,d476ad59458a035a329605d5284b6012",
-            "multiqc_fastq_screen.txt:md5,8bbb1968587dbf3139bac07991a225cb"
+            "multiqc_fastq_screen.txt:md5,483995ed26ba25b3217650840b2d82fa"
         ],
         "meta": {
-            "nf-test": "0.9.0",
+            "nf-test": "0.9.2",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-07T13:36:43.785887669"
+        "timestamp": "2024-11-14T11:23:19.55095"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index 17178fdd..74c12f5d 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -4,12 +4,12 @@
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,1a4b472e13cadc770832b0e20d1de7b0",
             "multiqc_general_stats.txt:md5,409cefc7f17f95d176ced6032bf8fb32",
-            "multiqc_fastq_screen.txt:md5,37efa56cefb899abf506cf7a7fba0d54"
+            "multiqc_fastq_screen.txt:md5,2931dcec302d74c378b69a0831363224"
         ],
         "meta": {
-            "nf-test": "0.9.0",
+            "nf-test": "0.9.2",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-07T13:37:39.008847194"
+        "timestamp": "2024-11-14T11:23:42.382002"
     }
 }
\ No newline at end of file

From 554a67ae270b2699b53026b8f59e45ef0dfa4c64 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Thu, 14 Nov 2024 12:05:44 -0600
Subject: [PATCH 122/530] fix: collectFile fastqscreen rough draft

---
 workflows/seqinspector.nf | 24 +++++++++++++++++++++++-
 1 file changed, 23 insertions(+), 1 deletion(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 307b163f..d9996829 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -83,7 +83,29 @@ workflow SEQINSPECTOR {
     FASTQSCREEN_FASTQSCREEN (
         ch_samplesheet.combine(ch_databases)
     )
-    ch_multiqc_files = ch_multiqc_files.mix(FASTQSCREEN_FASTQSCREEN.out.txt)
+    // Group by sample
+    FASTQSCREEN_FASTQSCREEN.out.txt
+        .groupTuple(by: [0])
+        .collectFile(
+            keepHeader: true,
+            skip: 1,
+            newLine: false,
+            storeDir: "${params.outdir}/fastqscreen/",
+        )
+        { meta, file ->
+            filename = "${meta.id}_screen.txt"
+            [filename, file.text]
+        }
+        // TODO Add % Not hit
+        .map { path ->
+            meta = [
+                id:path.getSimpleName(),
+            ]
+            [meta, file(path)]
+        }
+        .set { ch_fastqscreen_clean }
+
+    ch_multiqc_files = ch_multiqc_files.mix(ch_fastqscreen_clean)
     ch_versions = ch_versions.mix(FASTQSCREEN_FASTQSCREEN.out.versions.first())
 
     //

From 73b79dff6574b3652b87040755da4aeaff2400a3 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Thu, 14 Nov 2024 12:10:07 -0600
Subject: [PATCH 123/530] chore: Lock down arity in fastqscreen

---
 .../fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff        | 2 +-
 modules/nf-core/fastqscreen/fastqscreen/main.nf                 | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
index ad5b6fe0..df84f5ad 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
+++ b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
@@ -37,7 +37,7 @@ Changes in 'fastqscreen/fastqscreen/main.nf':
 -    tuple val(meta), path(reads)  // .fastq files
 -    path database
 +    // NOTE for meta 2 and database [[database_name,  database_notes], database_path]
-+    tuple val(meta), path(reads), val(meta2), path(database)
++    tuple val(meta), path(reads, arity: '1..2'), val(meta2), path(database, arity: '1')
  
      output:
      tuple val(meta), path("*.txt")     , emit: txt
diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index c0f98b9e..fff1414b 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -9,7 +9,7 @@ process FASTQSCREEN_FASTQSCREEN {
 
     input:
     // NOTE for meta 2 and database [[database_name,  database_notes], database_path]
-    tuple val(meta), path(reads), val(meta2), path(database)
+    tuple val(meta), path(reads, arity: '1..2'), val(meta2), path(database, arity: '1')
 
     output:
     tuple val(meta), path("*.txt")     , emit: txt

From 58a778dc5f2067acd54460882894d27199f91297 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Thu, 14 Nov 2024 13:16:41 -0600
Subject: [PATCH 124/530] feat: Getting close to making the config on the head
 node

---
 .../nf-core/fastqscreen/fastqscreen/main.nf   | 20 +++++-----
 workflows/seqinspector.nf                     | 37 +++++++------------
 2 files changed, 23 insertions(+), 34 deletions(-)

diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index fff1414b..4f2bdf9a 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -1,5 +1,5 @@
 process FASTQSCREEN_FASTQSCREEN {
-    tag "$meta.id | $meta2.database_name"
+    tag "$meta.id"
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
@@ -8,8 +8,10 @@ process FASTQSCREEN_FASTQSCREEN {
         'community.wave.seqera.io/library/fastq-screen_perl-gdgraph:5c1786a5d5bc1309'}"
 
     input:
-    // NOTE for meta 2 and database [[database_name,  database_notes], database_path]
-    tuple val(meta), path(reads, arity: '1..2'), val(meta2), path(database, arity: '1')
+    tuple val(meta), path(reads, arity: '1..2')
+    path('fastq_screen.conf', arity: '1')
+    path(database, arity:'1..*', name: '*/*')
+
 
     output:
     tuple val(meta), path("*.txt")     , emit: txt
@@ -25,21 +27,17 @@ process FASTQSCREEN_FASTQSCREEN {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def args = task.ext.args ?: ""
     // 'Database name','Genome path and basename','Notes'
+    // FIXME? --aligner ${meta2.database_notes.toLowerCase()} \\
     """
-    echo "Writing config"
-    echo "DATABASE    ${meta2.database_name}    ./${database}/genome    ${meta2.database_notes}" > fastq_screen.conf
-    echo "Wrote config"
-
     fastq_screen \\
         --conf fastq_screen.conf \\
         --threads ${task.cpus} \\
-        --aligner ${meta2.database_notes.toLowerCase()} \\
         $reads \\
         $args
 
-    mv *_screen.txt ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.txt
-    mv *_screen.html ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.html
-    mv *_screen.png ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.png
+    mv *_screen.txt ${prefix}_screen.txt
+    mv *_screen.html ${prefix}_screen.html
+    mv *_screen.png ${prefix}_screen.png
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index d9996829..059bda7a 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -79,33 +79,24 @@ workflow SEQINSPECTOR {
     //
     ch_databases = Channel
         .fromList(samplesheetToList(ch_fastqscreen_databasesheet, "${projectDir}/assets/schema_database.json"))
-
-    FASTQSCREEN_FASTQSCREEN (
-        ch_samplesheet.combine(ch_databases)
-    )
-    // Group by sample
-    FASTQSCREEN_FASTQSCREEN.out.txt
-        .groupTuple(by: [0])
+    ch_fastqscreen_config = ch_databases
         .collectFile(
-            keepHeader: true,
-            skip: 1,
-            newLine: false,
+            newLine: true,
+            name: 'fastq_screen.conf',
             storeDir: "${params.outdir}/fastqscreen/",
         )
-        { meta, file ->
-            filename = "${meta.id}_screen.txt"
-            [filename, file.text]
-        }
-        // TODO Add % Not hit
-        .map { path ->
-            meta = [
-                id:path.getSimpleName(),
-            ]
-            [meta, file(path)]
-        }
-        .set { ch_fastqscreen_clean }
+    {
+        meta, db ->
+        "DATABASE    ${meta.database_name}    ./${db}/genome    ${meta.database_notes}"
+    }
+    ch_database_files = ch_databases.collect { meta, db -> db}
 
-    ch_multiqc_files = ch_multiqc_files.mix(ch_fastqscreen_clean)
+    FASTQSCREEN_FASTQSCREEN (
+        ch_samplesheet,
+        ch_fastqscreen_config,
+        ch_database_files,
+    )
+    ch_multiqc_files = ch_multiqc_files.mix(FASTQSCREEN_FASTQSCREEN.out.txt)
     ch_versions = ch_versions.mix(FASTQSCREEN_FASTQSCREEN.out.versions.first())
 
     //

From 4c597201836e99dc7d7f30bd8e94898f6fd82866 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 5 Dec 2024 11:57:04 +0000
Subject: [PATCH 125/530] make functional :')

---
 assets/databasesheet.csv                      |  6 ++--
 .../nf-core/fastqscreen/fastqscreen/main.nf   | 31 +++++++++----------
 workflows/seqinspector.nf                     | 26 +++++++---------
 3 files changed, 28 insertions(+), 35 deletions(-)

diff --git a/assets/databasesheet.csv b/assets/databasesheet.csv
index 150f8318..16d1a3e7 100644
--- a/assets/databasesheet.csv
+++ b/assets/databasesheet.csv
@@ -1,4 +1,4 @@
 name,index,aligner
-Ecoli,s3://ngi-igenomes/igenomes/Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/Bowtie2Index/,BOWTIE2
-PhiX,s3://ngi-igenomes/igenomes/PhiX/Illumina/RTA/Sequence/Bowtie2Index/,BOWTIE2
-Scerevisiae,s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/NCBI/build3.1/Sequence/Bowtie2Index/,BOWTIE2
+Ecoli,s3://ngi-igenomes/igenomes/Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/Bowtie2Index/,Bowtie2
+PhiX,s3://ngi-igenomes/igenomes/PhiX/Illumina/RTA/Sequence/Bowtie2Index/,Bowtie2
+Scerevisiae,s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/NCBI/build3.1/Sequence/Bowtie2Index/,Bowtie2
diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index 4f2bdf9a..6b0a04d4 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -9,9 +9,7 @@ process FASTQSCREEN_FASTQSCREEN {
 
     input:
     tuple val(meta), path(reads, arity: '1..2')
-    path('fastq_screen.conf', arity: '1')
-    path(database, arity:'1..*', name: '*/*')
-
+    tuple val(ref_names), path(ref_paths, name:"ref*"), val(ref_aligners)
 
     output:
     tuple val(meta), path("*.txt")     , emit: txt
@@ -26,9 +24,10 @@ process FASTQSCREEN_FASTQSCREEN {
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
     def args = task.ext.args ?: ""
-    // 'Database name','Genome path and basename','Notes'
-    // FIXME? --aligner ${meta2.database_notes.toLowerCase()} \\
+    def config_content = ref_names.withIndex().collect { name, i -> "DATABASE ${name} ./${ref_paths[i]}/genome ${ref_aligners[i]}" }.join('\n')
     """
+    echo '${config_content}' > fastq_screen.conf
+
     fastq_screen \\
         --conf fastq_screen.conf \\
         --threads ${task.cpus} \\
@@ -39,23 +38,21 @@ process FASTQSCREEN_FASTQSCREEN {
     mv *_screen.html ${prefix}_screen.html
     mv *_screen.png ${prefix}_screen.png
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//')
-    END_VERSIONS
+    fastq_screen_version=\$(fastq_screen --version 2>&1 | sed 's/^.*FastQ Screen v//; s/ .*\$//')
+    echo "\\\"${task.process}\\\":" > versions.yml
+    echo "    fastqscreen: \$fastq_screen_version" >> versions.yml
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch test_1_screen.html
-    touch test_1_screen.png
-    touch test_1_screen.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//')
-    END_VERSIONS
+    touch ${prefix}_screen.html
+    touch ${prefix}_screen.png
+    touch ${prefix}_screen.txt
+
+    fastq_screen_version=\$(fastq_screen --version 2>&1 | sed 's/^.*FastQ Screen v//; s/ .*\$//')
+    echo "\\\"${task.process}\\\":" > versions.yml
+    echo "    fastqscreen: \$fastq_screen_version" >> versions.yml
     """
 
 }
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 059bda7a..a66beced 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -77,24 +77,20 @@ workflow SEQINSPECTOR {
     //
     // MODULE: Run FastQ Screen
     //
-    ch_databases = Channel
-        .fromList(samplesheetToList(ch_fastqscreen_databasesheet, "${projectDir}/assets/schema_database.json"))
-    ch_fastqscreen_config = ch_databases
-        .collectFile(
-            newLine: true,
-            name: 'fastq_screen.conf',
-            storeDir: "${params.outdir}/fastqscreen/",
-        )
-    {
-        meta, db ->
-        "DATABASE    ${meta.database_name}    ./${db}/genome    ${meta.database_notes}"
-    }
-    ch_database_files = ch_databases.collect { meta, db -> db}
+
+    // Parse the reference info needed to create a FastQ Screen config file
+    // and transpose it into a tuple containing lists of names, index paths and aligners
+    ch_fastqscreen_refs = Channel
+        .fromPath("${projectDir}/assets/databasesheet.csv")
+        .splitCsv(header: true)
+        .map { row -> tuple(row.name, row.index, row.aligner) }
+        .toList()
+        .transpose()
+        .toList()
 
     FASTQSCREEN_FASTQSCREEN (
         ch_samplesheet,
-        ch_fastqscreen_config,
-        ch_database_files,
+        ch_fastqscreen_refs
     )
     ch_multiqc_files = ch_multiqc_files.mix(FASTQSCREEN_FASTQSCREEN.out.txt)
     ch_versions = ch_versions.mix(FASTQSCREEN_FASTQSCREEN.out.versions.first())

From b29ced7a2723b3859ee643885d135a67b477213d Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 5 Dec 2024 13:46:38 +0000
Subject: [PATCH 126/530] make input mounting more flexible by separating
 mounted dir path from basename of reference / index files therein

---
 assets/databasesheet.csv                        | 8 ++++----
 modules/nf-core/fastqscreen/fastqscreen/main.nf | 4 ++--
 workflows/seqinspector.nf                       | 2 +-
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/assets/databasesheet.csv b/assets/databasesheet.csv
index 16d1a3e7..31f93a16 100644
--- a/assets/databasesheet.csv
+++ b/assets/databasesheet.csv
@@ -1,4 +1,4 @@
-name,index,aligner
-Ecoli,s3://ngi-igenomes/igenomes/Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/Bowtie2Index/,Bowtie2
-PhiX,s3://ngi-igenomes/igenomes/PhiX/Illumina/RTA/Sequence/Bowtie2Index/,Bowtie2
-Scerevisiae,s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/NCBI/build3.1/Sequence/Bowtie2Index/,Bowtie2
+name,dir,basename,aligner
+Ecoli,s3://ngi-igenomes/igenomes/Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/Bowtie2Index/,genome,Bowtie2
+PhiX,s3://ngi-igenomes/igenomes/PhiX/Illumina/RTA/Sequence/Bowtie2Index/,genome,Bowtie2
+Scerevisiae,s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/NCBI/build3.1/Sequence/Bowtie2Index/,genome,Bowtie2
diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index 6b0a04d4..2eba8390 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -9,7 +9,7 @@ process FASTQSCREEN_FASTQSCREEN {
 
     input:
     tuple val(meta), path(reads, arity: '1..2')
-    tuple val(ref_names), path(ref_paths, name:"ref*"), val(ref_aligners)
+    tuple val(ref_names), path(ref_dirs, name:"ref*"), val(ref_basenames), val(ref_aligners)
 
     output:
     tuple val(meta), path("*.txt")     , emit: txt
@@ -24,7 +24,7 @@ process FASTQSCREEN_FASTQSCREEN {
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
     def args = task.ext.args ?: ""
-    def config_content = ref_names.withIndex().collect { name, i -> "DATABASE ${name} ./${ref_paths[i]}/genome ${ref_aligners[i]}" }.join('\n')
+    def config_content = ref_names.withIndex().collect { name, i -> "DATABASE ${name} ./${ref_dirs[i]}/${ref_basenames[i]} ${ref_aligners[i]}" }.join('\n')
     """
     echo '${config_content}' > fastq_screen.conf
 
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index a66beced..8536a877 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -83,7 +83,7 @@ workflow SEQINSPECTOR {
     ch_fastqscreen_refs = Channel
         .fromPath("${projectDir}/assets/databasesheet.csv")
         .splitCsv(header: true)
-        .map { row -> tuple(row.name, row.index, row.aligner) }
+        .map { row -> tuple(row.name, row.dir, row.basename, row.aligner) }
         .toList()
         .transpose()
         .toList()

From e8479b9e01ea3ea5eedbcfea4126b68734c8eb1d Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 5 Dec 2024 14:31:55 +0000
Subject: [PATCH 127/530] successfully use schema validation for fastqscreen
 reference .csv

---
 assets/databasesheet.csv    |  6 +++---
 assets/schema_database.json | 19 +++++++++++--------
 workflows/seqinspector.nf   |  8 +++++---
 3 files changed, 19 insertions(+), 14 deletions(-)

diff --git a/assets/databasesheet.csv b/assets/databasesheet.csv
index 31f93a16..59f0cdf6 100644
--- a/assets/databasesheet.csv
+++ b/assets/databasesheet.csv
@@ -1,4 +1,4 @@
 name,dir,basename,aligner
-Ecoli,s3://ngi-igenomes/igenomes/Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/Bowtie2Index/,genome,Bowtie2
-PhiX,s3://ngi-igenomes/igenomes/PhiX/Illumina/RTA/Sequence/Bowtie2Index/,genome,Bowtie2
-Scerevisiae,s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/NCBI/build3.1/Sequence/Bowtie2Index/,genome,Bowtie2
+Ecoli,s3://ngi-igenomes/igenomes/Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/Bowtie2Index/,genome,bowtie2
+PhiX,s3://ngi-igenomes/igenomes/PhiX/Illumina/RTA/Sequence/Bowtie2Index/,genome,bowtie2
+Scerevisiae,s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/NCBI/build3.1/Sequence/Bowtie2Index/,genome,bowtie2
diff --git a/assets/schema_database.json b/assets/schema_database.json
index e735ea42..4a796bbc 100644
--- a/assets/schema_database.json
+++ b/assets/schema_database.json
@@ -10,23 +10,26 @@
             "name": {
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "The database name for fastq screen",
-                "meta": ["database_name"]
+                "errorMessage": "The reference name as referred to by FastQ Screen."
             },
-            "index": {
+            "dir": {
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
                 "pattern": "^\\S+$",
-                "errorMessage": "Path to the aligner index"
+                "errorMessage": "Path to the dir containing the aligner reference and index. Can be remote."
+            },
+            "basename": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "The shared basename of the reference and index files contained in the dir."
             },
             "aligner": {
                 "type": "string",
-                "enum": ["BOWTIE", "BOWTIE2", "BWA", "MINIMAP2"],
-                "errorMessage": "Specify the aligner to use for the mapping. Valid arguments are 'bowtie', bowtie2' (default), 'bwa' or 'minimap2'.",
-                "meta": ["database_notes"]
+                "enum": ["bowtie", "bowtie2", "bwa", "minimap2"],
+                "errorMessage": "Specify the aligner to use for the mapping. Valid arguments are 'bowtie', bowtie2' (default), 'bwa' or 'minimap2'."
             }
         },
-        "required": ["name", "index", "aligner"]
+        "required": ["name", "dir", "basename", "aligner"]
     }
 }
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 8536a877..0d622cc3 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -81,9 +81,11 @@ workflow SEQINSPECTOR {
     // Parse the reference info needed to create a FastQ Screen config file
     // and transpose it into a tuple containing lists of names, index paths and aligners
     ch_fastqscreen_refs = Channel
-        .fromPath("${projectDir}/assets/databasesheet.csv")
-        .splitCsv(header: true)
-        .map { row -> tuple(row.name, row.dir, row.basename, row.aligner) }
+        .fromList(samplesheetToList(
+            "${projectDir}/assets/databasesheet.csv",
+            "${projectDir}/assets/schema_database.json"
+        ))
+        .map { row -> tuple(row[0], row[1], row[2], row[3]) }
         .toList()
         .transpose()
         .toList()

From d91ea7ea1dadbb07dec56c436ec1e50d196011fb Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 5 Dec 2024 14:42:57 +0000
Subject: [PATCH 128/530] remove redundant operator

---
 workflows/seqinspector.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 0d622cc3..4c745f71 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -85,7 +85,6 @@ workflow SEQINSPECTOR {
             "${projectDir}/assets/databasesheet.csv",
             "${projectDir}/assets/schema_database.json"
         ))
-        .map { row -> tuple(row[0], row[1], row[2], row[3]) }
         .toList()
         .transpose()
         .toList()

From 738993f92d4b02e9cc3429fe0217422fabe9ea60 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 5 Dec 2024 14:46:05 +0000
Subject: [PATCH 129/530] update comment

---
 workflows/seqinspector.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 4c745f71..b2b7f672 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -79,7 +79,7 @@ workflow SEQINSPECTOR {
     //
 
     // Parse the reference info needed to create a FastQ Screen config file
-    // and transpose it into a tuple containing lists of names, index paths and aligners
+    // and transpose it into a tuple containing lists for each property
     ch_fastqscreen_refs = Channel
         .fromList(samplesheetToList(
             "${projectDir}/assets/databasesheet.csv",

From f18c05c6d0c03b882f77d5c78327693f99660bc0 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 5 Dec 2024 14:59:48 +0000
Subject: [PATCH 130/530] switch to cleaner file and variable names, remove
 fastqscreen .csv as main workflow input

---
 ...tabasesheet.csv => example_fastq_screen_references.csv} | 0
 ...a_database.json => schema_fastq_screen_references.json} | 6 +++---
 conf/test.config                                           | 2 +-
 main.nf                                                    | 7 ++-----
 nextflow.config                                            | 2 +-
 nextflow_schema.json                                       | 6 +++---
 workflows/seqinspector.nf                                  | 6 +++---
 7 files changed, 13 insertions(+), 16 deletions(-)
 rename assets/{databasesheet.csv => example_fastq_screen_references.csv} (100%)
 rename assets/{schema_database.json => schema_fastq_screen_references.json} (89%)

diff --git a/assets/databasesheet.csv b/assets/example_fastq_screen_references.csv
similarity index 100%
rename from assets/databasesheet.csv
rename to assets/example_fastq_screen_references.csv
diff --git a/assets/schema_database.json b/assets/schema_fastq_screen_references.json
similarity index 89%
rename from assets/schema_database.json
rename to assets/schema_fastq_screen_references.json
index 4a796bbc..9a938d99 100644
--- a/assets/schema_database.json
+++ b/assets/schema_fastq_screen_references.json
@@ -1,8 +1,8 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "$id": "https://raw.githubusercontent.com/nf-core/seqinspector/master/assets/schema_database.json",
-    "title": "nf-core/seqinspector pipeline - params.fastqscreen_databasesheet schema",
-    "description": "Schema for the file provided with params.fastq_screen_databasesheet",
+    "$id": "https://raw.githubusercontent.com/nf-core/seqinspector/master/assets/schema_fastq_screen_references.json",
+    "title": "nf-core/seqinspector pipeline - params.fastq_screen_references schema",
+    "description": "Schema for the file provided with params.fastq_screen_references",
     "type": "array",
     "items": {
         "type": "object",
diff --git a/conf/test.config b/conf/test.config
index 1a6f84b4..0ebc405a 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -26,7 +26,7 @@ params {
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
     input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
-    fastqscreen_database_sheet = "${projectDir}/assets/databasesheet.csv"
+    fastq_screen_references = "${projectDir}/assets/example_fastq_screen_references.csv"
 
     // Genome references
     genome = 'R64-1-1'
diff --git a/main.nf b/main.nf
index cd4af962..85027a4b 100644
--- a/main.nf
+++ b/main.nf
@@ -44,7 +44,6 @@ workflow NFCORE_SEQINSPECTOR {
 
     take:
     samplesheet // channel: samplesheet read in from --input
-    database_sheet
 
     main:
 
@@ -52,8 +51,7 @@ workflow NFCORE_SEQINSPECTOR {
     // WORKFLOW: Run pipeline
     //
     SEQINSPECTOR (
-        samplesheet,
-        database_sheet,
+        samplesheet
     )
     emit:
     global_report   = SEQINSPECTOR.out.global_report    // channel: /path/to/multiqc_report.html
@@ -85,8 +83,7 @@ workflow {
     // WORKFLOW: Run main workflow
     //
     NFCORE_SEQINSPECTOR (
-        PIPELINE_INITIALISATION.out.samplesheet,
-        params.fastqscreen_database_sheet,
+        PIPELINE_INITIALISATION.out.samplesheet
     )
     //
     // SUBWORKFLOW: Run completion tasks
diff --git a/nextflow.config b/nextflow.config
index 9b9a8bd4..5b835a8b 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -20,7 +20,7 @@ params {
     igenomes_ignore            = false
 
     // Fastqscreen options
-    fastqscreen_database_sheet = './assets/databasesheet.csv'
+    fastq_screen_references    = './assets/example_fastq_screen_references.csv'
 
     // MultiQC options
     multiqc_config             = null
diff --git a/nextflow_schema.json b/nextflow_schema.json
index b320d2be..722d80bf 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -87,11 +87,11 @@
                     "hidden": true,
                     "default": "s3://ngi-igenomes/igenomes/"
                 },
-                "fastqscreen_database_sheet": {
+                "fastq_screen_references": {
                     "type": "string",
-                    "default": "./assets/databasesheet.csv",
+                    "default": "./assets/example_fastq_screen_references.csv",
                     "fa_icon": "fas fa-search",
-                    "description": "list of reference genomes (databases) to be mapped against in fastqscreen"
+                    "description": "A .csv of reference genomes to be mapped against by FastQ Screen"
                 }
             }
         },
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index b2b7f672..4afff158 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -29,7 +29,6 @@ workflow SEQINSPECTOR {
 
     take:
     ch_samplesheet               // channel: samplesheet read in from --input
-    ch_fastqscreen_databasesheet // channel: database sheet read in from --fastqscreen_database_sheet
 
     main:
 
@@ -80,10 +79,11 @@ workflow SEQINSPECTOR {
 
     // Parse the reference info needed to create a FastQ Screen config file
     // and transpose it into a tuple containing lists for each property
+
     ch_fastqscreen_refs = Channel
         .fromList(samplesheetToList(
-            "${projectDir}/assets/databasesheet.csv",
-            "${projectDir}/assets/schema_database.json"
+            "${projectDir}/assets/example_fastq_screen_references.csv",
+            "${projectDir}/assets/schema_fastq_screen_references.json"
         ))
         .toList()
         .transpose()

From 444e5af5a932daddc0d93bf4382813373972eab9 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 5 Dec 2024 15:11:32 +0000
Subject: [PATCH 131/530] update docs

---
 docs/output.md | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/docs/output.md b/docs/output.md
index a2706a8f..dc26159f 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -56,7 +56,16 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 [Fastqscreen](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/) allows you to set up a standard set of libraries against which all of your sequences can be searched. Your search libraries might contain the genomes of all of the organisms you work on, along with PhiX, Vectors or other contaminants commonly seen in sequencing experiments.
 
-It requires the supply of referenced (databases) in a config file. In order to parallelize the mapping of the different samples, in seqinspector, this a fastqscreen config file is generated for every sample/reference combination.
+It requires a `.csv` detailing:
+
+- the working name of the reference
+- the name of the aligner used to generate its index (which is also the aligner and index used by the tool)
+- the file basename of the reference and its index (e.g. the reference `genoma.fa` and its index `genome.bt2` have the basename `genome`)
+- the path to a dir where the reference and index files both reside.
+
+See `assets/example_fastq_screen_references.csv` for example.
+
+The `.csv` is provided as a pipeline parameter `fastq_screen_references`. The `.csv` is used to construct a `FastQ Screen` configuration file within the context of the process work directory in order to properly mount the references.
 
 ### SeqFu Stats
 

From 31405f4ca74497cb4647c24940e26b594b385985 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 5 Dec 2024 15:20:51 +0000
Subject: [PATCH 132/530] update snapshots

---
 tests/MiSeq.main.nf.test.snap                 |  8 ++++----
 tests/NovaSeq6000.main.nf.test.snap           | 16 ++++++++--------
 tests/NovaSeq6000.main_subsample.nf.test.snap | 16 ++++++++--------
 tests/PromethION.main.nf.test.snap            |  8 ++++----
 4 files changed, 24 insertions(+), 24 deletions(-)

diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 9207f882..af7022dd 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -4,12 +4,12 @@
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
             "multiqc_general_stats.txt:md5,5b28a83b14cb2fe88d084d08900ebdbf",
-            "multiqc_fastq_screen.txt:md5,435d8c1ac6e237448c9ce38e853ac82e"
+            "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607"
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-14T11:21:34.348023"
+        "timestamp": "2024-12-05T15:15:09.227024034"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index 8b0f1366..9b3826a5 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -4,28 +4,28 @@
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d",
             "multiqc_general_stats.txt:md5,25abe0f6a35eb4a3b056fc3cf5c13732",
-            "multiqc_fastq_screen.txt:md5,c7b24e20fd157128924384e52eb3405d",
+            "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
             "multiqc_general_stats.txt:md5,90ee35137492b80aab36ef67f72d8921",
-            "multiqc_fastq_screen.txt:md5,a1e15006994d06a47634ccf07a08df0f",
+            "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
             "multiqc_general_stats.txt:md5,d62a2fc39e674d98783d408791803148",
-            "multiqc_fastq_screen.txt:md5,d4f1cc5396c4f719b1fcaab2470e7d7c",
+            "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
             "multiqc_general_stats.txt:md5,2f09b8f199ac40cf67ba50843cebd29c",
-            "multiqc_fastq_screen.txt:md5,02246ddb4bf5373b157b45eab698cdc8",
+            "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
             "multiqc_general_stats.txt:md5,6a1c16f068d7ba3a9225a17eb570ed9a",
-            "multiqc_fastq_screen.txt:md5,483995ed26ba25b3217650840b2d82fa"
+            "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5"
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-14T11:22:20.902938"
+        "timestamp": "2024-12-05T15:16:34.893751981"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index da7ba9a4..3ba50465 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -4,28 +4,28 @@
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,aba942d1e6996b579f19798e5673f514",
             "multiqc_general_stats.txt:md5,ad1ec9c64cbdb1131a26aeb6de51e31c",
-            "multiqc_fastq_screen.txt:md5,c7b24e20fd157128924384e52eb3405d",
+            "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8",
             "multiqc_general_stats.txt:md5,c73c8d10568a56f6534d280fff701e60",
-            "multiqc_fastq_screen.txt:md5,a1e15006994d06a47634ccf07a08df0f",
+            "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,ff996e1d3dc4a46e0c9535e54d51ccab",
             "multiqc_general_stats.txt:md5,834e1868b887171cfda72029bbbe2d3f",
-            "multiqc_fastq_screen.txt:md5,d4f1cc5396c4f719b1fcaab2470e7d7c",
+            "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,3df36ecfe76b25b0c22dcda84bce2b3b",
             "multiqc_general_stats.txt:md5,274a001b007521970f14d68bd176e5be",
-            "multiqc_fastq_screen.txt:md5,02246ddb4bf5373b157b45eab698cdc8",
+            "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,ce61b4ce4b1d76ec3f20de3bf0c9ec7f",
             "multiqc_general_stats.txt:md5,d476ad59458a035a329605d5284b6012",
-            "multiqc_fastq_screen.txt:md5,483995ed26ba25b3217650840b2d82fa"
+            "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5"
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-14T11:23:19.55095"
+        "timestamp": "2024-12-05T15:17:50.525033752"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index 74c12f5d..7d0a6bfe 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -4,12 +4,12 @@
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,1a4b472e13cadc770832b0e20d1de7b0",
             "multiqc_general_stats.txt:md5,409cefc7f17f95d176ced6032bf8fb32",
-            "multiqc_fastq_screen.txt:md5,2931dcec302d74c378b69a0831363224"
+            "multiqc_fastq_screen.txt:md5,7c5d711e27c53d13c81644a1f2468dba"
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-14T11:23:42.382002"
+        "timestamp": "2024-12-05T15:18:25.176791779"
     }
 }
\ No newline at end of file

From 8cc8a352bc2b3ab2dcc8e83d114be60e0b37b1b2 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 5 Dec 2024 15:28:25 +0000
Subject: [PATCH 133/530] re-generate module patch

---
 .../fastqscreen/fastqscreen-fastqscreen.diff  | 62 ++++++++++++-------
 1 file changed, 41 insertions(+), 21 deletions(-)

diff --git a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
index df84f5ad..2fbd94b3 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
+++ b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
@@ -16,15 +16,10 @@ Changes in 'fastqscreen/fastqscreen/environment.yml':
 +  # - bwa
 +  # - bismark
 
-'modules/nf-core/fastqscreen/fastqscreen/meta.yml' is unchanged
 Changes in 'fastqscreen/fastqscreen/main.nf':
 --- modules/nf-core/fastqscreen/fastqscreen/main.nf
 +++ modules/nf-core/fastqscreen/fastqscreen/main.nf
-@@ -1,15 +1,15 @@
- process FASTQSCREEN_FASTQSCREEN {
--    tag "$meta.id"
-+    tag "$meta.id | $meta2.database_name"
-     label 'process_medium'
+@@ -4,12 +4,12 @@
  
      conda "${moduleDir}/environment.yml"
      container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -36,20 +31,18 @@ Changes in 'fastqscreen/fastqscreen/main.nf':
      input:
 -    tuple val(meta), path(reads)  // .fastq files
 -    path database
-+    // NOTE for meta 2 and database [[database_name,  database_notes], database_path]
-+    tuple val(meta), path(reads, arity: '1..2'), val(meta2), path(database, arity: '1')
++    tuple val(meta), path(reads, arity: '1..2')
++    tuple val(ref_names), path(ref_dirs, name:"ref*"), val(ref_basenames), val(ref_aligners)
  
      output:
      tuple val(meta), path("*.txt")     , emit: txt
-@@ -24,13 +24,22 @@
+@@ -24,31 +24,35 @@
      script:
      def prefix = task.ext.prefix ?: "${meta.id}"
      def args = task.ext.args ?: ""
-+    // 'Database name','Genome path and basename','Notes'
++    def config_content = ref_names.withIndex().collect { name, i -> "DATABASE ${name} ./${ref_dirs[i]}/${ref_basenames[i]} ${ref_aligners[i]}" }.join('\n')
 +    """
-+    echo "Writing config"
-+    echo "DATABASE    ${meta2.database_name}    ./${database}/genome    ${meta2.database_notes}" > fastq_screen.conf
-+    echo "Wrote config"
++    echo '${config_content}' > fastq_screen.conf
  
 -    """
 -    fastq_screen --threads ${task.cpus} \\
@@ -58,20 +51,47 @@ Changes in 'fastqscreen/fastqscreen/main.nf':
 +    fastq_screen \\
 +        --conf fastq_screen.conf \\
 +        --threads ${task.cpus} \\
-+        --aligner ${meta2.database_notes.toLowerCase()} \\
          $reads \\
 -        $args \\
 +        $args
+ 
+-    cat <<-END_VERSIONS > versions.yml
+-    "${task.process}":
+-        fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//')
+-    END_VERSIONS
++    mv *_screen.txt ${prefix}_screen.txt
++    mv *_screen.html ${prefix}_screen.html
++    mv *_screen.png ${prefix}_screen.png
 +
-+    mv *_screen.txt ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.txt
-+    mv *_screen.html ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.html
-+    mv *_screen.png ${prefix}_${meta2.database_name}_${meta2.database_notes}_screen.png
++    fastq_screen_version=\$(fastq_screen --version 2>&1 | sed 's/^.*FastQ Screen v//; s/ .*\$//')
++    echo "\\\"${task.process}\\\":" > versions.yml
++    echo "    fastqscreen: \$fastq_screen_version" >> versions.yml
+     """
+ 
+     stub:
+     def prefix = task.ext.prefix ?: "${meta.id}"
+     """
+-    touch test_1_screen.html
+-    touch test_1_screen.png
+-    touch test_1_screen.txt
++    touch ${prefix}_screen.html
++    touch ${prefix}_screen.png
++    touch ${prefix}_screen.txt
+ 
+-    cat <<-END_VERSIONS > versions.yml
+-    "${task.process}":
+-        fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//')
+-    END_VERSIONS
++    fastq_screen_version=\$(fastq_screen --version 2>&1 | sed 's/^.*FastQ Screen v//; s/ .*\$//')
++    echo "\\\"${task.process}\\\":" > versions.yml
++    echo "    fastqscreen: \$fastq_screen_version" >> versions.yml
+     """
  
-     cat <<-END_VERSIONS > versions.yml
-     "${task.process}":
+ }
 
+'modules/nf-core/fastqscreen/fastqscreen/meta.yml' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test' is unchanged
 'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap' is unchanged
-'modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml' is unchanged
 'modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config' is unchanged
-'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml' is unchanged
 ************************************************************

From 10387aa50877e52053f048aeab1d78f32c51776b Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 5 Dec 2024 15:50:17 +0000
Subject: [PATCH 134/530] try gha update

---
 .github/workflows/nf-test.yml | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index 3a2abcbd..233897ed 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -10,14 +10,8 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Set up JDK 11
-        uses: actions/setup-java@v2
-        with:
-          java-version: "11"
-          distribution: "adopt"
-
       - name: Setup Nextflow latest-edge
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: "latest-edge"
 

From 4a2c175ebbf272771f902938fb179009b355044c Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Thu, 12 Dec 2024 11:24:33 +0000
Subject: [PATCH 135/530] Template update for nf-core/tools version 3.1.0

---
 .github/CONTRIBUTING.md                       |  12 +-
 .github/workflows/awsfulltest.yml             |  21 +-
 .github/workflows/branch.yml                  |  18 +-
 .github/workflows/ci.yml                      |   2 +-
 .github/workflows/download_pipeline.yml       |   8 +-
 .github/workflows/fix-linting.yml             |   4 +-
 .github/workflows/linting.yml                 |  10 +-
 .github/workflows/linting_comment.yml         |   2 +-
 .github/workflows/release-announcements.yml   |   2 +-
 .../workflows/template_version_comment.yml    |   2 +-
 .gitpod.yml                                   |  11 +-
 .nf-core.yml                                  |  10 +-
 .vscode/settings.json                         |   3 +
 conf/base.config                              |   2 +-
 conf/modules.config                           |   1 +
 docs/usage.md                                 |  32 +-
 modules.json                                  |   8 +-
 modules/nf-core/fastqc/main.nf                |   2 +-
 modules/nf-core/fastqc/meta.yml               |   1 +
 nextflow.config                               |  45 ++-
 nextflow_schema.json                          |   6 +
 ro-crate-metadata.json                        | 311 ++++++++++++++++++
 .../main.nf                                   |   7 +-
 .../nf-core/utils_nextflow_pipeline/main.nf   |   2 +
 .../tests/main.workflow.nf.test               |  10 +-
 .../nf-core/utils_nfcore_pipeline/main.nf     |  89 ++---
 .../tests/main.function.nf.test               |  46 ++-
 .../tests/main.function.nf.test.snap          |  30 --
 .../utils_nfschema_plugin/tests/main.nf.test  |   4 +-
 workflows/seqinspector.nf                     |   2 +-
 30 files changed, 484 insertions(+), 219 deletions(-)
 create mode 100644 .vscode/settings.json
 create mode 100644 ro-crate-metadata.json

diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 4bcb559a..8efc2032 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -1,4 +1,4 @@
-# nf-core/seqinspector: Contributing Guidelines
+# `nf-core/seqinspector`: Contributing Guidelines
 
 Hi there!
 Many thanks for taking an interest in improving nf-core/seqinspector.
@@ -55,9 +55,9 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 :warning: Only in the unlikely and regretful event of a release happening with a bug.
 
-- On your own fork, make a new branch `patch` based on `upstream/master`.
+- On your own fork, make a new branch `patch` based on `upstream/main` or `upstream/master`.
 - Fix the bug, and bump version (X.Y.Z+1).
-- A PR should be made on `master` from patch to directly this particular bug.
+- Open a pull-request from `patch` to `main`/`master` with the changes.
 
 ## Getting help
 
@@ -65,13 +65,13 @@ For further information/help, please consult the [nf-core/seqinspector documenta
 
 ## Pipeline contribution conventions
 
-To make the nf-core/seqinspector code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
+To make the `nf-core/seqinspector` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
 
 ### Adding a new step
 
 If you wish to contribute a new step, please use the following coding standards:
 
-1. Define the corresponding input channel into your new process from the expected previous process channel
+1. Define the corresponding input channel into your new process from the expected previous process channel.
 2. Write the process block (see below).
 3. Define the output channel if needed (see below).
 4. Add any new parameters to `nextflow.config` with a default (see below).
@@ -84,7 +84,7 @@ If you wish to contribute a new step, please use the following coding standards:
 
 ### Default values
 
-Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
+Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`.
 
 Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`.
 
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 5fdd2769..311d3d07 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -1,11 +1,12 @@
 name: nf-core AWS full size tests
-# This workflow is triggered on PRs opened against the master branch.
+# This workflow is triggered on PRs opened against the main/master branch.
 # It can be additionally triggered manually with GitHub actions workflow dispatch button.
 # It runs the -profile 'test_full' on AWS batch
 
 on:
   pull_request:
     branches:
+      - main
       - master
   workflow_dispatch:
   pull_request_review:
@@ -18,18 +19,30 @@ jobs:
     if: github.repository == 'nf-core/seqinspector' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
-      - uses: octokit/request-action@v2.x
+      - name: Get PR reviews
+        uses: octokit/request-action@v2.x
+        if: github.event_name != 'workflow_dispatch'
         id: check_approvals
+        continue-on-error: true
         with:
-          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews
+          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      - id: test_variables
+
+      - name: Check for approvals
+        if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
+        run: |
+          echo "No review approvals found. At least 2 approvals are required to run this action automatically."
+          exit 1
+
+      - name: Check for enough approvals (>=2)
+        id: test_variables
         if: github.event_name != 'workflow_dispatch'
         run: |
           JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
           CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
           test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
+
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         # TODO nf-core: You can customise AWS full pipeline tests as required
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index 5a2fffda..ffe93094 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -1,15 +1,17 @@
 name: nf-core branch protection
-# This workflow is triggered on PRs to master branch on the repository
-# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
+# This workflow is triggered on PRs to `main`/`master` branch on the repository
+# It fails when someone tries to make a PR against the nf-core `main`/`master` branch instead of `dev`
 on:
   pull_request_target:
-    branches: [master]
+    branches:
+      - main
+      - master
 
 jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
+      # PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
         if: github.repository == 'nf-core/seqinspector'
         run: |
@@ -22,7 +24,7 @@ jobs:
         uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         with:
           message: |
-            ## This PR is against the `master` branch :x:
+            ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x:
 
             * Do not close this PR
             * Click _Edit_ and change the `base` to `dev`
@@ -32,9 +34,9 @@ jobs:
 
             Hi @${{ github.event.pull_request.user.login }},
 
-            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch.
-            The `master` branch on nf-core repositories should always contain code from the latest release.
-            Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
+            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) ${{github.event.pull_request.base.ref}} branch.
+            The ${{github.event.pull_request.base.ref}} branch on nf-core repositories should always contain code from the latest release.
+            Because of this, PRs to ${{github.event.pull_request.base.ref}} are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
 
             You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
             Note that even after this, the test will continue to show as failing until you push a new commit.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 81d03080..f6c58143 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -45,7 +45,7 @@ jobs:
             profile: "singularity"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 713dc3e7..2576cc0c 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -2,7 +2,7 @@ name: Test successful pipeline download with 'nf-core pipelines download'
 
 # Run the workflow when:
 #  - dispatched manually
-#  - when a PR is opened or reopened to master branch
+#  - when a PR is opened or reopened to main/master branch
 #  - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev.
 on:
   workflow_dispatch:
@@ -17,9 +17,11 @@ on:
       - edited
       - synchronize
     branches:
+      - main
       - master
   pull_request_target:
     branches:
+      - main
       - master
 
 env:
@@ -35,7 +37,7 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           architecture: "x64"
@@ -69,7 +71,7 @@ jobs:
           --outdir ./${{ env.REPOTITLE_LOWERCASE }} \
           --compress "none" \
           --container-system 'singularity' \
-          --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \
+          --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io/library/" \
           --container-cache-utilisation 'amend' \
           --download-configuration 'yes'
 
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 1984e17d..5adee083 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,7 +32,7 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index a502573c..dbd52d5a 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -14,10 +14,10 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
@@ -31,12 +31,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           architecture: "x64"
@@ -74,7 +74,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
+        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 42e519bf..0bed96d3 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6
+        uses: dawidd6/action-download-artifact@80620a5d27ce0ae443b965134db88467fc607b43 # v7
         with:
           workflow: linting.yml
           workflow_conclusion: completed
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index c6ba35df..450b1d5e 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -31,7 +31,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.10"
       - name: Install dependencies
diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml
index e8aafe44..537529bc 100644
--- a/.github/workflows/template_version_comment.yml
+++ b/.github/workflows/template_version_comment.yml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           ref: ${{ github.event.pull_request.head.sha }}
 
diff --git a/.gitpod.yml b/.gitpod.yml
index 46118637..83599f63 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -6,12 +6,5 @@ tasks:
       nextflow self-update
 
 vscode:
-  extensions: # based on nf-core.nf-core-extensionpack
-    #- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
-    - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
-    - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
-    - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
-    - nextflow.nextflow # Nextflow syntax highlighting
-    - oderwat.indent-rainbow # Highlight indentation level
-    - streetsidesoftware.code-spell-checker # Spelling checker for source code
-    - charliermarsh.ruff # Code linter Ruff
+  extensions:
+    - nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack
diff --git a/.nf-core.yml b/.nf-core.yml
index fb856008..e44eaad4 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,7 +1,7 @@
-bump_version: null
-lint: null
-nf_core_version: 3.0.2
-org_path: null
+lint:
+  files_unchanged:
+    - .github/CONTRIBUTING.md
+nf_core_version: 3.1.0
 repository_type: pipeline
 template:
   author: Adrien Coulier
@@ -11,6 +11,4 @@ template:
   name: seqinspector
   org: nf-core
   outdir: .
-  skip_features: null
   version: 1.0dev
-update: null
diff --git a/.vscode/settings.json b/.vscode/settings.json
new file mode 100644
index 00000000..a33b527c
--- /dev/null
+++ b/.vscode/settings.json
@@ -0,0 +1,3 @@
+{
+    "markdown.styles": ["public/vscode_markdown.css"]
+}
diff --git a/conf/base.config b/conf/base.config
index b8e828de..eb6fbee3 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -20,7 +20,7 @@ process {
     maxErrors     = '-1'
 
     // Process-specific resource requirements
-    // NOTE - Please try and re-use the labels below as much as possible.
+    // NOTE - Please try and reuse the labels below as much as possible.
     //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
     //        If possible, it would be nice to keep the same label naming convention when
     //        adding in your local modules too.
diff --git a/conf/modules.config b/conf/modules.config
index d266a387..d203d2b6 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -21,6 +21,7 @@ process {
     withName: FASTQC {
         ext.args = '--quiet'
     }
+
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
diff --git a/docs/usage.md b/docs/usage.md
index bbc141ef..b400728f 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -75,9 +75,8 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than
 
 Pipeline settings can be provided in a `yaml` or `json` file via `-params-file <file>`.
 
-:::warning
-Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
-:::
+> [!WARNING]
+> Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
 
 The above pipeline run specified with a params file in yaml format:
 
@@ -106,23 +105,21 @@ nextflow pull nf-core/seqinspector
 
 ### Reproducibility
 
-It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.
+It is a good idea to specify the pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.
 
 First, go to the [nf-core/seqinspector releases page](https://github.com/nf-core/seqinspector/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag.
 
 This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports.
 
-To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
+To further assist in reproducibility, you can use share and reuse [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
 
-:::tip
-If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
-:::
+> [!TIP]
+> If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
 
 ## Core Nextflow arguments
 
-:::note
-These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).
-:::
+> [!NOTE]
+> These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen)
 
 ### `-profile`
 
@@ -130,16 +127,15 @@ Use this parameter to choose a configuration profile. Profiles can give configur
 
 Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below.
 
-:::info
-We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
-:::
+> [!IMPORTANT]
+> We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
 
-The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to see if your system is available in these configs please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation).
+The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to check if your system is suported, please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation).
 
 Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important!
 They are loaded in sequence, so later profiles can overwrite earlier profiles.
 
-If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer enviroment.
+If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer environment.
 
 - `test`
   - A profile with a complete configuration for automated testing
@@ -175,13 +171,13 @@ Specify the path to a specific config file (this is a core Nextflow command). Se
 
 ### Resource requests
 
-Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher requests (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped.
+Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the pipeline steps, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher resources request (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped.
 
 To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website.
 
 ### Custom Containers
 
-In some cases you may wish to change which container or conda environment a step of the pipeline uses for a particular tool. By default nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However in some cases the pipeline specified version maybe out of date.
+In some cases, you may wish to change the container or conda environment used by a pipeline steps for a particular tool. By default, nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However, in some cases the pipeline specified version maybe out of date.
 
 To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website.
 
diff --git a/modules.json b/modules.json
index 8e632d50..5605d989 100644
--- a/modules.json
+++ b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "dc94b6ee04a05ddb9f7ae050712ff30a13149164",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
@@ -21,17 +21,17 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",
+                        "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba",
+                        "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c",
+                        "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index d8989f48..752c3a10 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -24,7 +24,7 @@ process FASTQC {
     // Make list of old name and new name pairs to use for renaming in the bash while loop
     def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
     def rename_to = old_new_pairs*.join(' ').join(' ')
-    def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
+    def renamed_files = old_new_pairs.collect{ _old_name, new_name -> new_name }.join(' ')
 
     // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory)
     // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
index 4827da7a..2b2e62b8 100644
--- a/modules/nf-core/fastqc/meta.yml
+++ b/modules/nf-core/fastqc/meta.yml
@@ -11,6 +11,7 @@ tools:
         FastQC gives general quality metrics about your reads.
         It provides information about the quality score distribution
         across your reads, the per base sequence content (%A/C/G/T).
+
         You get information about adapter contamination and other
         overrepresented sequences.
       homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
diff --git a/nextflow.config b/nextflow.config
index 1c1ca6b1..e588aee1 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -38,8 +38,7 @@ params {
     show_hidden                  = false
     version                      = false
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
-
-    // Config options
+    trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')// Config options
     config_profile_name        = null
     config_profile_description = null
 
@@ -153,6 +152,13 @@ profiles {
         executor.name           = 'local'
         executor.cpus           = 4
         executor.memory         = 8.GB
+        process {
+            resourceLimits = [
+                memory: 8.GB,
+                cpus  : 4,
+                time  : 1.h
+            ]
+        }
     }
     test      { includeConfig 'conf/test.config'      }
     test_full { includeConfig 'conf/test_full.config' }
@@ -201,30 +207,41 @@ set -C # No clobber - prevent output redirection from overwriting files.
 // Disable process selector warnings by default. Use debug profile to enable warnings.
 nextflow.enable.configProcessNamesValidation = false
 
-def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 timeline {
     enabled = true
-    file    = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/execution_timeline_${params.trace_report_suffix}.html"
 }
 report {
     enabled = true
-    file    = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/execution_report_${params.trace_report_suffix}.html"
 }
 trace {
     enabled = true
-    file    = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
+    file    = "${params.outdir}/pipeline_info/execution_trace_${params.trace_report_suffix}.txt"
 }
 dag {
     enabled = true
-    file    = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html"
 }
 
 manifest {
     name            = 'nf-core/seqinspector'
-    author          = """Adrien Coulier"""
+    author          = """Adrien Coulier""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead
+    contributors    = [
+        // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
+        [
+            name: 'Adrien Coulier',
+            affiliation: '',
+            email: '',
+            github: '',
+            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
+            orcid: ''
+        ],
+    ]
     homePage        = 'https://github.com/nf-core/seqinspector'
     description     = """Pipeline to QC your sequences"""
     mainScript      = 'main.nf'
+    defaultBranch   = 'master'
     nextflowVersion = '!>=24.04.2'
     version         = '1.0dev'
     doi             = ''
@@ -237,9 +254,10 @@ plugins {
 
 validation {
     defaultIgnoreParams = ["genomes"]
+    monochromeLogs = params.monochrome_logs
     help {
         enabled = true
-        command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
+        command = "nextflow run nf-core/seqinspector -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
         fullParameter = "help_full"
         showHiddenParameter = "show_hidden"
         beforeText = """
@@ -249,15 +267,15 @@ validation {
 \033[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \033[0;33m}  {\033[0m
 \033[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \033[0;32m\\`-._,-`-,\033[0m
                                         \033[0;32m`._,._,\'\033[0m
-\033[0;35m  ${manifest.name} ${manifest.version}\033[0m
+\033[0;35m  nf-core/seqinspector ${manifest.version}\033[0m
 -\033[2m----------------------------------------------------\033[0m-
 """
-        afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "  https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
+        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
 * The nf-core framework
     https://doi.org/10.1038/s41587-020-0439-x
 
 * Software dependencies
-    https://github.com/${manifest.name}/blob/master/CITATIONS.md
+    https://github.com/nf-core/seqinspector/blob/master/CITATIONS.md
 """
     }
     summary {
@@ -265,6 +283,3 @@ validation {
         afterText = validation.help.afterText
     }
 }
-
-// Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 88fd607b..2a598bf6 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -218,6 +218,12 @@
                     "description": "Base URL or local path to location of pipeline test dataset files",
                     "default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
                     "hidden": true
+                },
+                "trace_report_suffix": {
+                    "type": "string",
+                    "fa_icon": "far calendar",
+                    "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.",
+                    "hidden": true
                 }
             }
         }
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
new file mode 100644
index 00000000..24c84dc6
--- /dev/null
+++ b/ro-crate-metadata.json
@@ -0,0 +1,311 @@
+{
+    "@context": [
+        "https://w3id.org/ro/crate/1.1/context",
+        {
+            "GithubService": "https://w3id.org/ro/terms/test#GithubService",
+            "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService",
+            "PlanemoEngine": "https://w3id.org/ro/terms/test#PlanemoEngine",
+            "TestDefinition": "https://w3id.org/ro/terms/test#TestDefinition",
+            "TestInstance": "https://w3id.org/ro/terms/test#TestInstance",
+            "TestService": "https://w3id.org/ro/terms/test#TestService",
+            "TestSuite": "https://w3id.org/ro/terms/test#TestSuite",
+            "TravisService": "https://w3id.org/ro/terms/test#TravisService",
+            "definition": "https://w3id.org/ro/terms/test#definition",
+            "engineVersion": "https://w3id.org/ro/terms/test#engineVersion",
+            "instance": "https://w3id.org/ro/terms/test#instance",
+            "resource": "https://w3id.org/ro/terms/test#resource",
+            "runsOn": "https://w3id.org/ro/terms/test#runsOn"
+        }
+    ],
+    "@graph": [
+        {
+            "@id": "./",
+            "@type": "Dataset",
+            "creativeWorkStatus": "InProgress",
+            "datePublished": "2024-12-12T11:24:30+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by Adrien Coulier.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "hasPart": [
+                {
+                    "@id": "main.nf"
+                },
+                {
+                    "@id": "assets/"
+                },
+                {
+                    "@id": "conf/"
+                },
+                {
+                    "@id": "docs/"
+                },
+                {
+                    "@id": "docs/images/"
+                },
+                {
+                    "@id": "modules/"
+                },
+                {
+                    "@id": "modules/nf-core/"
+                },
+                {
+                    "@id": "workflows/"
+                },
+                {
+                    "@id": "subworkflows/"
+                },
+                {
+                    "@id": "nextflow.config"
+                },
+                {
+                    "@id": "README.md"
+                },
+                {
+                    "@id": "nextflow_schema.json"
+                },
+                {
+                    "@id": "CHANGELOG.md"
+                },
+                {
+                    "@id": "LICENSE"
+                },
+                {
+                    "@id": "CODE_OF_CONDUCT.md"
+                },
+                {
+                    "@id": "CITATIONS.md"
+                },
+                {
+                    "@id": "modules.json"
+                },
+                {
+                    "@id": "docs/usage.md"
+                },
+                {
+                    "@id": "docs/output.md"
+                },
+                {
+                    "@id": ".nf-core.yml"
+                },
+                {
+                    "@id": ".pre-commit-config.yaml"
+                },
+                {
+                    "@id": ".prettierignore"
+                }
+            ],
+            "isBasedOn": "https://github.com/nf-core/seqinspector",
+            "license": "MIT",
+            "mainEntity": {
+                "@id": "main.nf"
+            },
+            "mentions": [
+                {
+                    "@id": "#a2f9223f-7e69-4788-87c8-468ddf886506"
+                }
+            ],
+            "name": "nf-core/seqinspector"
+        },
+        {
+            "@id": "ro-crate-metadata.json",
+            "@type": "CreativeWork",
+            "about": {
+                "@id": "./"
+            },
+            "conformsTo": [
+                {
+                    "@id": "https://w3id.org/ro/crate/1.1"
+                },
+                {
+                    "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
+                }
+            ]
+        },
+        {
+            "@id": "main.nf",
+            "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
+            "creator": [
+                {
+                    "@id": "https://orcid.org/0000-0003-2702-1103"
+                }
+            ],
+            "dateCreated": "",
+            "dateModified": "2024-12-12T11:24:30Z",
+            "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
+            "keywords": ["nf-core", "nextflow", "genomics", "quality-control"],
+            "license": ["MIT"],
+            "maintainer": [
+                {
+                    "@id": "https://orcid.org/0000-0003-2702-1103"
+                }
+            ],
+            "name": ["nf-core/seqinspector"],
+            "programmingLanguage": {
+                "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow"
+            },
+            "sdPublisher": {
+                "@id": "https://nf-co.re/"
+            },
+            "url": ["https://github.com/nf-core/seqinspector", "https://nf-co.re/seqinspector/dev/"],
+            "version": ["1.0dev"]
+        },
+        {
+            "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow",
+            "@type": "ComputerLanguage",
+            "identifier": {
+                "@id": "https://www.nextflow.io/"
+            },
+            "name": "Nextflow",
+            "url": {
+                "@id": "https://www.nextflow.io/"
+            },
+            "version": "!>=24.04.2"
+        },
+        {
+            "@id": "#a2f9223f-7e69-4788-87c8-468ddf886506",
+            "@type": "TestSuite",
+            "instance": [
+                {
+                    "@id": "#4fd17b03-0bda-4f65-91a0-832482b15fe2"
+                }
+            ],
+            "mainEntity": {
+                "@id": "main.nf"
+            },
+            "name": "Test suite for nf-core/seqinspector"
+        },
+        {
+            "@id": "#4fd17b03-0bda-4f65-91a0-832482b15fe2",
+            "@type": "TestInstance",
+            "name": "GitHub Actions workflow for testing nf-core/seqinspector",
+            "resource": "repos/nf-core/seqinspector/actions/workflows/ci.yml",
+            "runsOn": {
+                "@id": "https://w3id.org/ro/terms/test#GithubService"
+            },
+            "url": "https://api.github.com"
+        },
+        {
+            "@id": "https://w3id.org/ro/terms/test#GithubService",
+            "@type": "TestService",
+            "name": "Github Actions",
+            "url": {
+                "@id": "https://github.com"
+            }
+        },
+        {
+            "@id": "assets/",
+            "@type": "Dataset",
+            "description": "Additional files"
+        },
+        {
+            "@id": "conf/",
+            "@type": "Dataset",
+            "description": "Configuration files"
+        },
+        {
+            "@id": "docs/",
+            "@type": "Dataset",
+            "description": "Markdown files for documenting the pipeline"
+        },
+        {
+            "@id": "docs/images/",
+            "@type": "Dataset",
+            "description": "Images for the documentation files"
+        },
+        {
+            "@id": "modules/",
+            "@type": "Dataset",
+            "description": "Modules used by the pipeline"
+        },
+        {
+            "@id": "modules/nf-core/",
+            "@type": "Dataset",
+            "description": "nf-core modules"
+        },
+        {
+            "@id": "workflows/",
+            "@type": "Dataset",
+            "description": "Main pipeline workflows to be executed in main.nf"
+        },
+        {
+            "@id": "subworkflows/",
+            "@type": "Dataset",
+            "description": "Smaller subworkflows"
+        },
+        {
+            "@id": "nextflow.config",
+            "@type": "File",
+            "description": "Main Nextflow configuration file"
+        },
+        {
+            "@id": "README.md",
+            "@type": "File",
+            "description": "Basic pipeline usage information"
+        },
+        {
+            "@id": "nextflow_schema.json",
+            "@type": "File",
+            "description": "JSON schema for pipeline parameter specification"
+        },
+        {
+            "@id": "CHANGELOG.md",
+            "@type": "File",
+            "description": "Information on changes made to the pipeline"
+        },
+        {
+            "@id": "LICENSE",
+            "@type": "File",
+            "description": "The license - should be MIT"
+        },
+        {
+            "@id": "CODE_OF_CONDUCT.md",
+            "@type": "File",
+            "description": "The nf-core code of conduct"
+        },
+        {
+            "@id": "CITATIONS.md",
+            "@type": "File",
+            "description": "Citations needed when using the pipeline"
+        },
+        {
+            "@id": "modules.json",
+            "@type": "File",
+            "description": "Version information for modules from nf-core/modules"
+        },
+        {
+            "@id": "docs/usage.md",
+            "@type": "File",
+            "description": "Usage documentation"
+        },
+        {
+            "@id": "docs/output.md",
+            "@type": "File",
+            "description": "Output documentation"
+        },
+        {
+            "@id": ".nf-core.yml",
+            "@type": "File",
+            "description": "nf-core configuration file, configuring template features and linting rules"
+        },
+        {
+            "@id": ".pre-commit-config.yaml",
+            "@type": "File",
+            "description": "Configuration file for pre-commit hooks"
+        },
+        {
+            "@id": ".prettierignore",
+            "@type": "File",
+            "description": "Ignore file for prettier"
+        },
+        {
+            "@id": "https://nf-co.re/",
+            "@type": "Organization",
+            "name": "nf-core",
+            "url": "https://nf-co.re/"
+        },
+        {
+            "@id": "https://orcid.org/0000-0003-2702-1103",
+            "@type": "Person",
+            "email": "adrien.coulier@medsci.uu.se",
+            "name": "Adrien Coulier"
+        }
+    ]
+}
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index 8384b833..20a5206f 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -116,7 +116,8 @@ workflow PIPELINE_COMPLETION {
 
     main:
     summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
-
+    def multiqc_reports = multiqc_report.toList()
+    
     //
     // Completion email and summary
     //
@@ -129,7 +130,7 @@ workflow PIPELINE_COMPLETION {
                 plaintext_email,
                 outdir,
                 monochrome_logs,
-                multiqc_report.toList()
+                multiqc_reports.getVal(),
             )
         }
 
@@ -225,7 +226,7 @@ def toolBibliographyText() {
 }
 
 def methodsDescriptionText(mqc_methods_yaml) {
-    // Convert  to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file
+    // Convert  to a named map so can be used as with familiar NXF ${workflow} variable syntax in the MultiQC YML file
     def meta = [:]
     meta.workflow = workflow.toMap()
     meta["manifest_map"] = workflow.manifest.toMap()
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index 0fcbf7b3..d6e593e8 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -92,10 +92,12 @@ def checkCondaChannels() {
         channels = config.channels
     }
     catch (NullPointerException e) {
+        log.debug(e)
         log.warn("Could not verify conda channel configuration.")
         return null
     }
     catch (IOException e) {
+        log.debug(e)
         log.warn("Could not verify conda channel configuration.")
         return null
     }
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
index ca964ce8..02dbf094 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
@@ -52,10 +52,12 @@ nextflow_workflow {
         }
 
         then {
-            assertAll(
-                { assert workflow.success },
-                { assert workflow.stdout.contains("nextflow_workflow v9.9.9") }
-            )
+            expect {
+                with(workflow) {
+                    assert success
+                    assert "nextflow_workflow v9.9.9" in stdout
+                }
+            }
         }
     }
 
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index 5cb7bafe..bfd25876 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -56,21 +56,6 @@ def checkProfileProvided(nextflow_cli_args) {
     }
 }
 
-//
-// Citation string for pipeline
-//
-def workflowCitation() {
-    def temp_doi_ref = ""
-    def manifest_doi = workflow.manifest.doi.tokenize(",")
-    // Handling multiple DOIs
-    // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
-    // Removing ` ` since the manifest.doi is a string and not a proper list
-    manifest_doi.each { doi_ref ->
-        temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
-    }
-    return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + "* The nf-core framework\n" + "  https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
-}
-
 //
 // Generate workflow version string
 //
@@ -150,33 +135,6 @@ def paramsSummaryMultiqc(summary_params) {
     return yaml_file_text
 }
 
-//
-// nf-core logo
-//
-def nfCoreLogo(monochrome_logs=true) {
-    def colors = logColours(monochrome_logs) as Map
-    String.format(
-        """\n
-        ${dashedLine(monochrome_logs)}
-                                                ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
-        ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
-        ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
-        ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
-                                                ${colors.green}`._,._,\'${colors.reset}
-        ${colors.purple}  ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset}
-        ${dashedLine(monochrome_logs)}
-        """.stripIndent()
-    )
-}
-
-//
-// Return dashed line
-//
-def dashedLine(monochrome_logs=true) {
-    def colors = logColours(monochrome_logs) as Map
-    return "-${colors.dim}----------------------------------------------------${colors.reset}-"
-}
-
 //
 // ANSII colours used for terminal logging
 //
@@ -245,28 +203,24 @@ def logColours(monochrome_logs=true) {
     return colorcodes
 }
 
-//
-// Attach the multiqc report to email
-//
-def attachMultiqcReport(multiqc_report) {
-    def mqc_report = null
-    try {
-        if (workflow.success) {
-            mqc_report = multiqc_report.getVal()
-            if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
-                if (mqc_report.size() > 1) {
-                    log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one")
-                }
-                mqc_report = mqc_report[0]
-            }
+// Return a single report from an object that may be a Path or List
+//
+def getSingleReport(multiqc_reports) {
+    if (multiqc_reports instanceof Path) {
+        return multiqc_reports
+    } else if (multiqc_reports instanceof List) {
+        if (multiqc_reports.size() == 0) {
+            log.warn("[${workflow.manifest.name}] No reports found from process 'MULTIQC'")
+            return null
+        } else if (multiqc_reports.size() == 1) {
+            return multiqc_reports.first()
+        } else {
+            log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one")
+            return multiqc_reports.first()
         }
+    } else {
+        return null
     }
-    catch (Exception all) {
-        if (multiqc_report) {
-            log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email")
-        }
-    }
-    return mqc_report
 }
 
 //
@@ -320,7 +274,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     email_fields['summary']      = summary << misc_fields
 
     // On success try attach the multiqc report
-    def mqc_report = attachMultiqcReport(multiqc_report)
+    def mqc_report = getSingleReport(multiqc_report)
 
     // Check if we are only sending emails on failure
     def email_address = email
@@ -340,7 +294,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     def email_html    = html_template.toString()
 
     // Render the sendmail template
-    def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit
+    def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as MemoryUnit
     def smail_fields           = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()]
     def sf                     = new File("${workflow.projectDir}/assets/sendmail_template.txt")
     def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
@@ -351,14 +305,17 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     if (email_address) {
         try {
             if (plaintext_email) {
-new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML')            }
+                new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML')
+            }
             // Try to send HTML e-mail using sendmail
             def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
             sendmail_tf.withWriter { w -> w << sendmail_html }
             ['sendmail', '-t'].execute() << sendmail_html
             log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-")
         }
-        catch (Exception all) {
+        catch (Exception msg) {
+            log.debug(msg.toString())
+            log.debug("Trying with mail instead of sendmail")
             // Catch failures and try with plaintext
             def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address]
             mail_cmd.execute() << email_html
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
index 1dc317f8..f117040c 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
@@ -41,26 +41,14 @@ nextflow_function {
         }
     }
 
-    test("Test Function workflowCitation") {
-
-        function "workflowCitation"
-
-        then {
-            assertAll(
-                { assert function.success },
-                { assert snapshot(function.result).match() }
-            )
-        }
-    }
-
-    test("Test Function nfCoreLogo") {
+    test("Test Function without logColours") {
 
-        function "nfCoreLogo"
+        function "logColours"
 
         when {
             function {
                 """
-                input[0] = false
+                input[0] = true
                 """
             }
         }
@@ -73,9 +61,8 @@ nextflow_function {
         }
     }
 
-    test("Test Function dashedLine") {
-
-        function "dashedLine"
+    test("Test Function with logColours") {
+        function "logColours"
 
         when {
             function {
@@ -93,14 +80,13 @@ nextflow_function {
         }
     }
 
-    test("Test Function without logColours") {
-
-        function "logColours"
+    test("Test Function getSingleReport with a single file") {
+        function "getSingleReport"
 
         when {
             function {
                 """
-                input[0] = true
+                input[0] = file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true)
                 """
             }
         }
@@ -108,18 +94,22 @@ nextflow_function {
         then {
             assertAll(
                 { assert function.success },
-                { assert snapshot(function.result).match() }
+                { assert function.result.contains("test.tsv") }
             )
         }
     }
 
-    test("Test Function with logColours") {
-        function "logColours"
+    test("Test Function getSingleReport with multiple files") {
+        function "getSingleReport"
 
         when {
             function {
                 """
-                input[0] = false
+                input[0] = [
+                    file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true),
+                    file(params.modules_testdata_base_path + '/generic/tsv/network.tsv', checkIfExists: true),
+                    file(params.modules_testdata_base_path + '/generic/tsv/expression.tsv', checkIfExists: true)
+                ]
                 """
             }
         }
@@ -127,7 +117,9 @@ nextflow_function {
         then {
             assertAll(
                 { assert function.success },
-                { assert snapshot(function.result).match() }
+                { assert function.result.contains("test.tsv") },
+                { assert !function.result.contains("network.tsv") },
+                { assert !function.result.contains("expression.tsv") }
             )
         }
     }
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
index 1037232c..02c67014 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
@@ -17,26 +17,6 @@
         },
         "timestamp": "2024-02-28T12:02:59.729647"
     },
-    "Test Function nfCoreLogo": {
-        "content": [
-            "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n                                        \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m        ___     __   __   __   ___     \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \u001b[0;33m}  {\u001b[0m\n\u001b[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \u001b[0;32m\\`-._,-`-,\u001b[0m\n                                        \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m  nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:03:10.562934"
-    },
-    "Test Function workflowCitation": {
-        "content": [
-            "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n  https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n  https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n  https://github.com/nextflow_workflow/blob/master/CITATIONS.md"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:03:07.019761"
-    },
     "Test Function without logColours": {
         "content": [
             {
@@ -95,16 +75,6 @@
         },
         "timestamp": "2024-02-28T12:03:17.969323"
     },
-    "Test Function dashedLine": {
-        "content": [
-            "-\u001b[2m----------------------------------------------------\u001b[0m-"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:03:14.366181"
-    },
     "Test Function with logColours": {
         "content": [
             {
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
index 842dc432..8fb30164 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
@@ -42,7 +42,7 @@ nextflow_workflow {
 
             params {
                 test_data   = ''
-                outdir      = 1
+                outdir      = null
             }
 
             workflow {
@@ -94,7 +94,7 @@ nextflow_workflow {
 
             params {
                 test_data   = ''
-                outdir      = 1
+                outdir      = null
             }
 
             workflow {
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 4a9df1ca..a009066f 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -39,7 +39,7 @@ workflow SEQINSPECTOR {
     softwareVersionsToYAML(ch_versions)
         .collectFile(
             storeDir: "${params.outdir}/pipeline_info",
-            name: 'nf_core_'  + 'pipeline_software_' +  'mqc_'  + 'versions.yml',
+            name: 'nf_core_'  +  'seqinspector_software_'  + 'mqc_'  + 'versions.yml',
             sort: true,
             newLine: true
         ).set { ch_collated_versions }

From 345a8c774da778c6776555123860927c0f702d40 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Fri, 13 Dec 2024 12:30:18 +0100
Subject: [PATCH 136/530] Fix pre-commit

---
 subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index 93d640e4..70994073 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -144,7 +144,7 @@ workflow PIPELINE_COMPLETION {
     main:
     summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
     def multiqc_reports = multiqc_report.toList()
-    
+
     //
     // Completion email and summary
     //

From f5edba1fd7544272b6bc98e54086685035d31a65 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Fri, 13 Dec 2024 12:57:06 +0100
Subject: [PATCH 137/530] Fix warning messages

---
 modules.json                                  | 10 +++
 modules/nf-core/bowtie2/build/environment.yml |  5 ++
 modules/nf-core/bowtie2/build/main.nf         | 42 +++++++++++
 modules/nf-core/bowtie2/build/meta.yml        | 49 +++++++++++++
 .../nf-core/bowtie2/build/tests/main.nf.test  | 31 ++++++++
 .../bowtie2/build/tests/main.nf.test.snap     | 45 ++++++++++++
 modules/nf-core/bowtie2/build/tests/tags.yml  |  2 +
 .../buildfromindex/environment.yml            |  7 ++
 .../fastqscreen/buildfromindex/main.nf        | 69 ++++++++++++++++++
 .../fastqscreen/buildfromindex/meta.yml       | 39 ++++++++++
 .../buildfromindex/tests/main.nf.test         | 71 +++++++++++++++++++
 .../buildfromindex/tests/main.nf.test.snap    | 71 +++++++++++++++++++
 .../fastqscreen/buildfromindex/tests/tags.yml |  2 +
 13 files changed, 443 insertions(+)
 create mode 100644 modules/nf-core/bowtie2/build/environment.yml
 create mode 100644 modules/nf-core/bowtie2/build/main.nf
 create mode 100644 modules/nf-core/bowtie2/build/meta.yml
 create mode 100644 modules/nf-core/bowtie2/build/tests/main.nf.test
 create mode 100644 modules/nf-core/bowtie2/build/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/bowtie2/build/tests/tags.yml
 create mode 100644 modules/nf-core/fastqscreen/buildfromindex/environment.yml
 create mode 100644 modules/nf-core/fastqscreen/buildfromindex/main.nf
 create mode 100644 modules/nf-core/fastqscreen/buildfromindex/meta.yml
 create mode 100644 modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test
 create mode 100644 modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/fastqscreen/buildfromindex/tests/tags.yml

diff --git a/modules.json b/modules.json
index 9864725e..01ae9110 100644
--- a/modules.json
+++ b/modules.json
@@ -5,11 +5,21 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
+                    "bowtie2/build": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296",
                         "installed_by": ["modules"]
                     },
+                    "fastqscreen/buildfromindex": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "fastqscreen/fastqscreen": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
diff --git a/modules/nf-core/bowtie2/build/environment.yml b/modules/nf-core/bowtie2/build/environment.yml
new file mode 100644
index 00000000..e590f7ce
--- /dev/null
+++ b/modules/nf-core/bowtie2/build/environment.yml
@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::bowtie2=2.5.2
diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf
new file mode 100644
index 00000000..9e2e0e5e
--- /dev/null
+++ b/modules/nf-core/bowtie2/build/main.nf
@@ -0,0 +1,42 @@
+process BOWTIE2_BUILD {
+    tag "$fasta"
+    label 'process_high'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bowtie2:2.5.2--py39h6fed5c7_0' :
+        'biocontainers/bowtie2:2.5.2--py39h6fed5c7_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path('bowtie2')    , emit: index
+    path "versions.yml"                 , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    mkdir bowtie2
+    bowtie2-build $args --threads $task.cpus $fasta bowtie2/${fasta.baseName}
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    mkdir bowtie2
+    touch bowtie2/${fasta.baseName}.{1..4}.bt2
+    touch bowtie2/${fasta.baseName}.rev.{1,2}.bt2
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/bowtie2/build/meta.yml b/modules/nf-core/bowtie2/build/meta.yml
new file mode 100644
index 00000000..2729a92e
--- /dev/null
+++ b/modules/nf-core/bowtie2/build/meta.yml
@@ -0,0 +1,49 @@
+name: bowtie2_build
+description: Builds bowtie index for reference genome
+keywords:
+  - build
+  - index
+  - fasta
+  - genome
+  - reference
+tools:
+  - bowtie2:
+      description: |
+        Bowtie 2 is an ultrafast and memory-efficient tool for aligning
+        sequencing reads to long reference sequences.
+      homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
+      documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
+      doi: 10.1038/nmeth.1923
+      licence: ["GPL-3.0-or-later"]
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'test', single_end:false ]
+    - fasta:
+        type: file
+        description: Input genome fasta file
+output:
+  - index:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing reference information
+            e.g. [ id:'test', single_end:false ]
+      - bowtie2:
+          type: file
+          description: Bowtie2 genome index files
+          pattern: "*.bt2"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@joseespinosa"
+  - "@drpatelh"
+maintainers:
+  - "@joseespinosa"
+  - "@drpatelh"
diff --git a/modules/nf-core/bowtie2/build/tests/main.nf.test b/modules/nf-core/bowtie2/build/tests/main.nf.test
new file mode 100644
index 00000000..16376025
--- /dev/null
+++ b/modules/nf-core/bowtie2/build/tests/main.nf.test
@@ -0,0 +1,31 @@
+nextflow_process {
+
+    name "Test Process BOWTIE2_BUILD"
+    script "modules/nf-core/bowtie2/build/main.nf"
+    process "BOWTIE2_BUILD"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bowtie2"
+    tag "bowtie2/build"
+
+    test("Should run without failures") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/bowtie2/build/tests/main.nf.test.snap b/modules/nf-core/bowtie2/build/tests/main.nf.test.snap
new file mode 100644
index 00000000..6875e021
--- /dev/null
+++ b/modules/nf-core/bowtie2/build/tests/main.nf.test.snap
@@ -0,0 +1,45 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "genome.1.bt2:md5,cbe3d0bbea55bc57c99b4bfa25b5fbdf",
+                            "genome.2.bt2:md5,47b153cd1319abc88dda532462651fcf",
+                            "genome.3.bt2:md5,4ed93abba181d8dfab2e303e33114777",
+                            "genome.4.bt2:md5,c25be5f8b0378abf7a58c8a880b87626",
+                            "genome.rev.1.bt2:md5,52be6950579598a990570fbcf5372184",
+                            "genome.rev.2.bt2:md5,e3b4ef343dea4dd571642010a7d09597"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,1df11e9b82891527271c889c880d3974"
+                ],
+                "index": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "genome.1.bt2:md5,cbe3d0bbea55bc57c99b4bfa25b5fbdf",
+                            "genome.2.bt2:md5,47b153cd1319abc88dda532462651fcf",
+                            "genome.3.bt2:md5,4ed93abba181d8dfab2e303e33114777",
+                            "genome.4.bt2:md5,c25be5f8b0378abf7a58c8a880b87626",
+                            "genome.rev.1.bt2:md5,52be6950579598a990570fbcf5372184",
+                            "genome.rev.2.bt2:md5,e3b4ef343dea4dd571642010a7d09597"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,1df11e9b82891527271c889c880d3974"
+                ]
+            }
+        ],
+        "timestamp": "2023-11-23T11:51:01.107681997"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bowtie2/build/tests/tags.yml b/modules/nf-core/bowtie2/build/tests/tags.yml
new file mode 100644
index 00000000..81aa61da
--- /dev/null
+++ b/modules/nf-core/bowtie2/build/tests/tags.yml
@@ -0,0 +1,2 @@
+bowtie2/build:
+  - modules/nf-core/bowtie2/build/**
diff --git a/modules/nf-core/fastqscreen/buildfromindex/environment.yml b/modules/nf-core/fastqscreen/buildfromindex/environment.yml
new file mode 100644
index 00000000..85764e0d
--- /dev/null
+++ b/modules/nf-core/fastqscreen/buildfromindex/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::fastq-screen=0.15.3"
diff --git a/modules/nf-core/fastqscreen/buildfromindex/main.nf b/modules/nf-core/fastqscreen/buildfromindex/main.nf
new file mode 100644
index 00000000..33840120
--- /dev/null
+++ b/modules/nf-core/fastqscreen/buildfromindex/main.nf
@@ -0,0 +1,69 @@
+process FASTQSCREEN_BUILDFROMINDEX {
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/fastq-screen:0.15.3--pl5321hdfd78af_0':
+        'biocontainers/fastq-screen:0.15.3--pl5321hdfd78af_0'}"
+
+    input:
+    val(genome_names)
+    path(indexes), stageAs: "dir*"
+
+    output:
+    path("FastQ_Screen_Genomes"), emit: database
+    path "versions.yml"         , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    dir = "FastQ_Screen_Genomes"
+    folder = indexes.collect { it.toString() }
+    database = [genome_names, folder].transpose()
+    copy_indexes = folder.collect { "cp -r ${it} $dir/${it}"}.join(" && ")
+
+    // Folder name and index (within folder) name could be different - use bash to look for index name
+    config = database
+        .collect { "########## ${it[0]} \nDATABASE ${it[0]} $dir/${it[1]}/${it[1] + '_to_be_replaced'}" }
+        .join("\n\n")
+        .replace("\n", "\\n")
+
+    """
+    mkdir $dir
+    $copy_indexes
+
+    echo "$config" > fastq_screen.conf
+    sed 's/\\\\n/\\n/g' fastq_screen.conf > $dir/fastq_screen.conf
+    echo "Replace folder name real index name"
+
+    for f in ${folder.join(' ')}
+    do
+        TO_REPLACE=\${f}_to_be_replaced
+
+        REPLACE_WITH=(\$f"/*.rev.1.bt2")
+        REPLACE_WITH=\$(basename \$REPLACE_WITH)
+        REPLACE_WITH=\${REPLACE_WITH%%.rev.1.bt2}
+
+        sed "s/\$TO_REPLACE/\$REPLACE_WITH/g" $dir/fastq_screen.conf > new_conf.conf
+        mv new_conf.conf $dir/fastq_screen.conf
+    done
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    dir = "FastQ_Screen_Genomes"
+    """
+    mkdir $dir
+    touch $dir/fastq_screen.conf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/fastqscreen/buildfromindex/meta.yml b/modules/nf-core/fastqscreen/buildfromindex/meta.yml
new file mode 100644
index 00000000..d92817fc
--- /dev/null
+++ b/modules/nf-core/fastqscreen/buildfromindex/meta.yml
@@ -0,0 +1,39 @@
+name: "fastqscreen_buildfromindex"
+description: Build fastq screen config file from bowtie index files
+keywords:
+  - build
+  - index
+  - genome
+  - reference
+tools:
+  - "fastqscreen":
+      description: "FastQ Screen allows you to screen a library of sequences in FastQ
+        format against a set of sequence databases so you can see if the composition
+        of the library matches with what you expect."
+      homepage: "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/"
+      documentation: "https://stevenwingett.github.io/FastQ-Screen/"
+      tool_dev_url: "https://github.com/StevenWingett/FastQ-Screen/archive/refs/tags/v0.15.3.zip"
+      doi: "10.5281/zenodo.5838377"
+      licence: ["GPL-3.0-or-later"]
+      identifier: ""
+input:
+  - - genome_names:
+        type: string
+        description: List of names for each index
+  - - indexes:
+        type: directory
+        description: Bowtie2 genome directories containing index files
+output:
+  - database:
+      - FastQ_Screen_Genomes:
+          type: directory
+          description: fastq screen database folder containing config file and index folders
+          pattern: "FastQ_Screen_Genomes"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@snesic"
+  - "@JPejovicApis"
diff --git a/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test b/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test
new file mode 100644
index 00000000..5357712a
--- /dev/null
+++ b/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test
@@ -0,0 +1,71 @@
+nextflow_process {
+
+    name "Test Process FASTQSCREEN_BUILDFROMINDEX"
+    script "../main.nf"
+    process "FASTQSCREEN_BUILDFROMINDEX"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "fastqscreen"
+    tag "fastqscreen/buildfromindex"
+    tag "bowtie2/build"
+
+    setup {
+
+        run("BOWTIE2_BUILD") {
+            script "../../../bowtie2/build/main.nf"
+            process {
+                """
+                input[0] =  Channel.from([
+                                    [[id: "sarscov2"], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)],
+                                    [[id: "human"]   , file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)]
+                            ])
+                """
+            }
+        }
+
+    }
+
+    test("sarscov2 - human") {
+
+        when {
+            process {
+                """
+                input[0] = BOWTIE2_BUILD.out.index.map{meta, index -> meta.id}.collect()
+                input[1] = BOWTIE2_BUILD.out.index.map{meta, index -> index}.collect()
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.database, process.out.versions).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - human - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = BOWTIE2_BUILD.out.index.map{meta, index -> meta.id}.collect()
+                input[1] = BOWTIE2_BUILD.out.index.map{meta, index -> index}.collect()
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test.snap b/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test.snap
new file mode 100644
index 00000000..0fe7d7d1
--- /dev/null
+++ b/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test.snap
@@ -0,0 +1,71 @@
+{
+    "database": {
+        "content": [
+            [
+                [
+                    [
+                        "genome.1.bt2:md5,cbe3d0bbea55bc57c99b4bfa25b5fbdf",
+                        "genome.2.bt2:md5,47b153cd1319abc88dda532462651fcf",
+                        "genome.3.bt2:md5,4ed93abba181d8dfab2e303e33114777",
+                        "genome.4.bt2:md5,c25be5f8b0378abf7a58c8a880b87626",
+                        "genome.rev.1.bt2:md5,52be6950579598a990570fbcf5372184",
+                        "genome.rev.2.bt2:md5,e3b4ef343dea4dd571642010a7d09597"
+                    ],
+                    [
+                        "genome.1.bt2:md5,2fbc8eeaf480f03b3a2362a782fa5755",
+                        "genome.2.bt2:md5,a5300e3cf590d4cd8bd5521cac6337d6",
+                        "genome.3.bt2:md5,d2a7a0e1c9891e847a15781c0695b84e",
+                        "genome.4.bt2:md5,a55dc4b09e3e00586de6963800c95b9a",
+                        "genome.rev.1.bt2:md5,93c07f7d04e5da6bf1322ad5f46ac806",
+                        "genome.rev.2.bt2:md5,c3fa30132c0c9b9bc7868059e8e23466"
+                    ],
+                    "fastq_screen.conf:md5,ca56e866c7006a46bdfe4e751e787265"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-01T20:37:34.647221"
+    },
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,c2bcf85b00046c72d5dccd2dba8ac35c"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-01T20:37:35.126085"
+    },
+    "sarscov2 - human - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "fastq_screen.conf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,c2bcf85b00046c72d5dccd2dba8ac35c"
+                ],
+                "database": [
+                    [
+                        "fastq_screen.conf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,c2bcf85b00046c72d5dccd2dba8ac35c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-01T20:39:14.913696"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/fastqscreen/buildfromindex/tests/tags.yml b/modules/nf-core/fastqscreen/buildfromindex/tests/tags.yml
new file mode 100644
index 00000000..9c98e870
--- /dev/null
+++ b/modules/nf-core/fastqscreen/buildfromindex/tests/tags.yml
@@ -0,0 +1,2 @@
+fastqscreen/buildfromindex:
+  - "modules/nf-core/fastqscreen/buildfromindex/**"

From 143ab30f867f65eb291a442e59b979c324e57e88 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Fri, 13 Dec 2024 13:12:05 +0100
Subject: [PATCH 138/530] Fix contributor field

---
 nextflow.config | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 46144693..bac5d198 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -230,15 +230,13 @@ dag {
 
 manifest {
     name            = 'nf-core/seqinspector'
-    author          = """Adrien Coulier""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead
     contributors    = [
-        // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
         [
-            name: 'Adrien Coulier',
+            name: 'National Genomics Infrastructure',
             affiliation: '',
             email: '',
-            github: '',
-            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
+            github: 'https://github.com/NationalGenomicsInfrastructure/',
+            contribution: ['author'], // List of contribution types ('author', 'maintainer' or 'contributor')
             orcid: ''
         ],
     ]

From 79e3b403f22e8bd72aa5757a0d0a5a6eb24cd7a3 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Fri, 13 Dec 2024 16:06:26 +0100
Subject: [PATCH 139/530] Include conf/modules.config again

---
 nextflow.config | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nextflow.config b/nextflow.config
index bac5d198..9ab822e8 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -57,6 +57,7 @@ params {
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
+includeConfig 'conf/modules.config'
 
 profiles {
     debug {

From 5177aa04713ced38b0db76049574b58776f3dc61 Mon Sep 17 00:00:00 2001
From: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 17 Dec 2024 16:24:12 +0000
Subject: [PATCH 140/530] Patch fastqscreen to handle multiple input FASTQ
 files

---
 modules.json                                  |  5 ++++
 .../fastqscreen/fastqscreen-fastqscreen.diff  | 24 +++++++++++++------
 .../nf-core/fastqscreen/fastqscreen/main.nf   | 16 ++++++++++---
 3 files changed, 35 insertions(+), 10 deletions(-)

diff --git a/modules.json b/modules.json
index 566d84ec..8f0fd8d5 100644
--- a/modules.json
+++ b/modules.json
@@ -16,6 +16,11 @@
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff"
                     },
+                    "fq/lint": {
+                        "branch": "master",
+                        "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc",
+                        "installed_by": ["modules"]
+                    },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
diff --git a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
index 2fbd94b3..beef4a99 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
+++ b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
@@ -16,6 +16,7 @@ Changes in 'fastqscreen/fastqscreen/environment.yml':
 +  # - bwa
 +  # - bismark
 
+'modules/nf-core/fastqscreen/fastqscreen/meta.yml' is unchanged
 Changes in 'fastqscreen/fastqscreen/main.nf':
 --- modules/nf-core/fastqscreen/fastqscreen/main.nf
 +++ modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -36,11 +37,21 @@ Changes in 'fastqscreen/fastqscreen/main.nf':
  
      output:
      tuple val(meta), path("*.txt")     , emit: txt
-@@ -24,31 +24,35 @@
+@@ -24,31 +24,45 @@
      script:
      def prefix = task.ext.prefix ?: "${meta.id}"
      def args = task.ext.args ?: ""
 +    def config_content = ref_names.withIndex().collect { name, i -> "DATABASE ${name} ./${ref_dirs[i]}/${ref_basenames[i]} ${ref_aligners[i]}" }.join('\n')
++    def num_reads     = reads instanceof List  ? reads.size() : 1
++    def mv_txt_cmd    = (num_reads == 1) ? 
++            "mv ${reads[0].simpleName}_screen.txt ${prefix}_screen.txt" : 
++            reads.collect { "mv ${it.simpleName}_screen.txt ${prefix}_${it.simpleName}_screen.txt" }.join(' && ')
++    def mv_html_cmd   = (num_reads == 1) ? 
++            "mv ${reads[0].simpleName}_screen.html ${prefix}_1_screen.html" : 
++            reads.collect { "mv ${it.simpleName}_screen.txt ${prefix}_${it.simpleName}_screen.txt" }.join(' && ')
++    def mv_png_cmd    = (num_reads == 1) ? 
++            "mv ${reads[0].simpleName}_screen.png ${prefix}_1_screen.png" : 
++            reads.collect { "mv ${it.simpleName}_screen.txt ${prefix}_${it.simpleName}_screen.txt" }.join(' && ')
 +    """
 +    echo '${config_content}' > fastq_screen.conf
  
@@ -59,9 +70,9 @@ Changes in 'fastqscreen/fastqscreen/main.nf':
 -    "${task.process}":
 -        fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//')
 -    END_VERSIONS
-+    mv *_screen.txt ${prefix}_screen.txt
-+    mv *_screen.html ${prefix}_screen.html
-+    mv *_screen.png ${prefix}_screen.png
++    $mv_txt_cmd
++    $mv_html_cmd
++    $mv_png_cmd
 +
 +    fastq_screen_version=\$(fastq_screen --version 2>&1 | sed 's/^.*FastQ Screen v//; s/ .*\$//')
 +    echo "\\\"${task.process}\\\":" > versions.yml
@@ -89,9 +100,8 @@ Changes in 'fastqscreen/fastqscreen/main.nf':
  
  }
 
-'modules/nf-core/fastqscreen/fastqscreen/meta.yml' is unchanged
-'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test' is unchanged
 'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap' is unchanged
-'modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config' is unchanged
 'modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test' is unchanged
 ************************************************************
diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index 2eba8390..9df8e27c 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -25,6 +25,16 @@ process FASTQSCREEN_FASTQSCREEN {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def args = task.ext.args ?: ""
     def config_content = ref_names.withIndex().collect { name, i -> "DATABASE ${name} ./${ref_dirs[i]}/${ref_basenames[i]} ${ref_aligners[i]}" }.join('\n')
+    def num_reads     = reads instanceof List  ? reads.size() : 1
+    def mv_txt_cmd    = (num_reads == 1) ? 
+            "mv ${reads[0].simpleName}_screen.txt ${prefix}_screen.txt" : 
+            reads.collect { "mv ${it.simpleName}_screen.txt ${prefix}_${it.simpleName}_screen.txt" }.join(' && ')
+    def mv_html_cmd   = (num_reads == 1) ? 
+            "mv ${reads[0].simpleName}_screen.html ${prefix}_1_screen.html" : 
+            reads.collect { "mv ${it.simpleName}_screen.txt ${prefix}_${it.simpleName}_screen.txt" }.join(' && ')
+    def mv_png_cmd    = (num_reads == 1) ? 
+            "mv ${reads[0].simpleName}_screen.png ${prefix}_1_screen.png" : 
+            reads.collect { "mv ${it.simpleName}_screen.txt ${prefix}_${it.simpleName}_screen.txt" }.join(' && ')
     """
     echo '${config_content}' > fastq_screen.conf
 
@@ -34,9 +44,9 @@ process FASTQSCREEN_FASTQSCREEN {
         $reads \\
         $args
 
-    mv *_screen.txt ${prefix}_screen.txt
-    mv *_screen.html ${prefix}_screen.html
-    mv *_screen.png ${prefix}_screen.png
+    $mv_txt_cmd
+    $mv_html_cmd
+    $mv_png_cmd
 
     fastq_screen_version=\$(fastq_screen --version 2>&1 | sed 's/^.*FastQ Screen v//; s/ .*\$//')
     echo "\\\"${task.process}\\\":" > versions.yml

From 2ac1413bc350e7206cac9ce9430c75b62414fd6f Mon Sep 17 00:00:00 2001
From: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 17 Dec 2024 16:43:39 +0000
Subject: [PATCH 141/530] docs: CHANGELOG

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a4b5e286..91ee0b7f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -20,6 +20,8 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 
 ### `Fixed`
 
+- [#71](https://github.com/nf-core/seqinspector/pull/71) FASTQSCREEN does not fail when multiple reads are provided.
+
 ### `Dependencies`
 
 ### `Deprecated`

From 4d7e7489b0dbbbf89140ec31affcc05971dfcbaa Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <89784800+kedhammar@users.noreply.github.com>
Date: Wed, 18 Dec 2024 14:10:30 +0100
Subject: [PATCH 142/530] Bugfix

The file extensions were a bit wonky. Likely due to hasty copy-pasty :)
---
 modules/nf-core/fastqscreen/fastqscreen/main.nf | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index 9df8e27c..ee6eeb2b 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -30,11 +30,11 @@ process FASTQSCREEN_FASTQSCREEN {
             "mv ${reads[0].simpleName}_screen.txt ${prefix}_screen.txt" : 
             reads.collect { "mv ${it.simpleName}_screen.txt ${prefix}_${it.simpleName}_screen.txt" }.join(' && ')
     def mv_html_cmd   = (num_reads == 1) ? 
-            "mv ${reads[0].simpleName}_screen.html ${prefix}_1_screen.html" : 
-            reads.collect { "mv ${it.simpleName}_screen.txt ${prefix}_${it.simpleName}_screen.txt" }.join(' && ')
+            "mv ${reads[0].simpleName}_screen.html ${prefix}_screen.html" : 
+            reads.collect { "mv ${it.simpleName}_screen.html ${prefix}_${it.simpleName}_screen.html" }.join(' && ')
     def mv_png_cmd    = (num_reads == 1) ? 
-            "mv ${reads[0].simpleName}_screen.png ${prefix}_1_screen.png" : 
-            reads.collect { "mv ${it.simpleName}_screen.txt ${prefix}_${it.simpleName}_screen.txt" }.join(' && ')
+            "mv ${reads[0].simpleName}_screen.png ${prefix}_screen.png" : 
+            reads.collect { "mv ${it.simpleName}_screen.png ${prefix}_${it.simpleName}_screen.png" }.join(' && ')
     """
     echo '${config_content}' > fastq_screen.conf
 

From 9d01fac45d37ee4b6a878e925c44485ed8ad7992 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <89784800+kedhammar@users.noreply.github.com>
Date: Wed, 18 Dec 2024 16:04:42 +0100
Subject: [PATCH 143/530] Use <meta.id>(_1|2)?_screen filenames and make DRYer

---
 .../nf-core/fastqscreen/fastqscreen/main.nf   | 23 ++++++++-----------
 1 file changed, 10 insertions(+), 13 deletions(-)

diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index ee6eeb2b..21012c1f 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -25,16 +25,15 @@ process FASTQSCREEN_FASTQSCREEN {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def args = task.ext.args ?: ""
     def config_content = ref_names.withIndex().collect { name, i -> "DATABASE ${name} ./${ref_dirs[i]}/${ref_basenames[i]} ${ref_aligners[i]}" }.join('\n')
-    def num_reads     = reads instanceof List  ? reads.size() : 1
-    def mv_txt_cmd    = (num_reads == 1) ? 
-            "mv ${reads[0].simpleName}_screen.txt ${prefix}_screen.txt" : 
-            reads.collect { "mv ${it.simpleName}_screen.txt ${prefix}_${it.simpleName}_screen.txt" }.join(' && ')
-    def mv_html_cmd   = (num_reads == 1) ? 
-            "mv ${reads[0].simpleName}_screen.html ${prefix}_screen.html" : 
-            reads.collect { "mv ${it.simpleName}_screen.html ${prefix}_${it.simpleName}_screen.html" }.join(' && ')
-    def mv_png_cmd    = (num_reads == 1) ? 
-            "mv ${reads[0].simpleName}_screen.png ${prefix}_screen.png" : 
-            reads.collect { "mv ${it.simpleName}_screen.png ${prefix}_${it.simpleName}_screen.png" }.join(' && ')
+
+    // Build mv commands to rename the output files. Dual reads will be appended with '_1' and '_2'
+    def num_reads = reads instanceof List  ? reads.size() : 1
+    def file_extensions = ['txt', 'html', 'png']
+    def mv_cmd = file_extensions.collect { ext ->
+        reads.withIndex().collect { read, i ->
+            "mv ${read.simpleName}_screen.${ext} ${prefix}${num_reads > 1 ? "_${i+1}" : ''}_screen.${ext}"
+        }.join(' && ')
+    }.join(' && ')
     """
     echo '${config_content}' > fastq_screen.conf
 
@@ -44,9 +43,7 @@ process FASTQSCREEN_FASTQSCREEN {
         $reads \\
         $args
 
-    $mv_txt_cmd
-    $mv_html_cmd
-    $mv_png_cmd
+    $mv_cmd
 
     fastq_screen_version=\$(fastq_screen --version 2>&1 | sed 's/^.*FastQ Screen v//; s/ .*\$//')
     echo "\\\"${task.process}\\\":" > versions.yml

From 3ae6a58d28dce71d91992ebbee7bc74831aa4991 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 19 Dec 2024 10:02:43 +0000
Subject: [PATCH 144/530] bump docs

---
 docs/output.md | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/docs/output.md b/docs/output.md
index dc26159f..3d3c3497 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -13,7 +13,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - [Seqtk](#seqtk) - Subsample a specific number of reads per sample
 - [FastQC](#fastqc) - Raw read QC
 - [SeqFu Stats](#seqfu_stats) - Statistics for FASTA or FASTQ files
-- [Fastqscreen](#fastqscreen) - mapping against a set of references for basic contamination QC
+- [FastQ Screen](#fastqscreen) - Mapping against a set of references for basic contamination QC
 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
@@ -42,21 +42,21 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
 
-### FASTQSCREEN
+### FastQ Screen
 
 <details markdown="1">
 <summary>Output files</summary>
 
 - `fastqscreen/`
-  - `*_screen.html`: Interactive graphical fastqscreen report which summaries the mapping of your sequences against each of your libraries.
-  - `*_screen.pdf`: Static graphical fastqscreen report which summaries the mapping of your sequences against each of your libraries.
-  - `*_screen.txt` : text based fastqscreen report which summaries the mapping of your sequences against each of your libraries.
+  - `*_screen.html`: Interactive graphical report.
+  - `*_screen.pdf`: Static graphical report.
+  - `*_screen.txt` : Text-based report.
 
 </details>
 
-[Fastqscreen](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/) allows you to set up a standard set of libraries against which all of your sequences can be searched. Your search libraries might contain the genomes of all of the organisms you work on, along with PhiX, Vectors or other contaminants commonly seen in sequencing experiments.
+[FastQ Screen](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/) allows you to set up a standard set of references against which all of your samples can be mapped. Your references might contain the genomes of all of the organisms you work on, along with PhiX, vectors or other contaminants commonly seen in sequencing experiments.
 
-It requires a `.csv` detailing:
+To use FastQ Screen, this pipeline requires a `.csv` detailing:
 
 - the working name of the reference
 - the name of the aligner used to generate its index (which is also the aligner and index used by the tool)
@@ -65,7 +65,7 @@ It requires a `.csv` detailing:
 
 See `assets/example_fastq_screen_references.csv` for example.
 
-The `.csv` is provided as a pipeline parameter `fastq_screen_references`. The `.csv` is used to construct a `FastQ Screen` configuration file within the context of the process work directory in order to properly mount the references.
+The `.csv` is provided as a pipeline parameter `fastq_screen_references` and is used to construct a `FastQ Screen` configuration file within the context of the process work directory in order to properly mount the references.
 
 ### SeqFu Stats
 

From 44aabfa264b148247acc3f5156b5ae7f5ef9c481 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 19 Dec 2024 10:11:53 +0000
Subject: [PATCH 145/530] bump module patch

---
 .../fastqscreen/fastqscreen-fastqscreen.diff  | 38 +++++++++----------
 1 file changed, 17 insertions(+), 21 deletions(-)

diff --git a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
index beef4a99..658d149b 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
+++ b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
@@ -1,4 +1,4 @@
-Changes in module 'nf-core/fastqscreen/fastqscreen'
+Changes in component 'nf-core/fastqscreen/fastqscreen'
 Changes in 'fastqscreen/fastqscreen/environment.yml':
 --- modules/nf-core/fastqscreen/fastqscreen/environment.yml
 +++ modules/nf-core/fastqscreen/fastqscreen/environment.yml
@@ -16,7 +16,6 @@ Changes in 'fastqscreen/fastqscreen/environment.yml':
 +  # - bwa
 +  # - bismark
 
-'modules/nf-core/fastqscreen/fastqscreen/meta.yml' is unchanged
 Changes in 'fastqscreen/fastqscreen/main.nf':
 --- modules/nf-core/fastqscreen/fastqscreen/main.nf
 +++ modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -37,28 +36,26 @@ Changes in 'fastqscreen/fastqscreen/main.nf':
  
      output:
      tuple val(meta), path("*.txt")     , emit: txt
-@@ -24,31 +24,45 @@
+@@ -24,31 +24,42 @@
      script:
      def prefix = task.ext.prefix ?: "${meta.id}"
      def args = task.ext.args ?: ""
 +    def config_content = ref_names.withIndex().collect { name, i -> "DATABASE ${name} ./${ref_dirs[i]}/${ref_basenames[i]} ${ref_aligners[i]}" }.join('\n')
-+    def num_reads     = reads instanceof List  ? reads.size() : 1
-+    def mv_txt_cmd    = (num_reads == 1) ? 
-+            "mv ${reads[0].simpleName}_screen.txt ${prefix}_screen.txt" : 
-+            reads.collect { "mv ${it.simpleName}_screen.txt ${prefix}_${it.simpleName}_screen.txt" }.join(' && ')
-+    def mv_html_cmd   = (num_reads == 1) ? 
-+            "mv ${reads[0].simpleName}_screen.html ${prefix}_1_screen.html" : 
-+            reads.collect { "mv ${it.simpleName}_screen.txt ${prefix}_${it.simpleName}_screen.txt" }.join(' && ')
-+    def mv_png_cmd    = (num_reads == 1) ? 
-+            "mv ${reads[0].simpleName}_screen.png ${prefix}_1_screen.png" : 
-+            reads.collect { "mv ${it.simpleName}_screen.txt ${prefix}_${it.simpleName}_screen.txt" }.join(' && ')
-+    """
-+    echo '${config_content}' > fastq_screen.conf
  
--    """
++    // Build mv commands to rename the output files. Dual reads will be appended with '_1' and '_2'
++    def num_reads = reads instanceof List  ? reads.size() : 1
++    def file_extensions = ['txt', 'html', 'png']
++    def mv_cmd = file_extensions.collect { ext ->
++        reads.withIndex().collect { read, i ->
++            "mv ${read.simpleName}_screen.${ext} ${prefix}${num_reads > 1 ? "_${i+1}" : ''}_screen.${ext}"
++        }.join(' && ')
++    }.join(' && ')
+     """
 -    fastq_screen --threads ${task.cpus} \\
 -        --aligner bowtie2 \\
 -        --conf ${database}/fastq_screen.conf \\
++    echo '${config_content}' > fastq_screen.conf
++
 +    fastq_screen \\
 +        --conf fastq_screen.conf \\
 +        --threads ${task.cpus} \\
@@ -70,9 +67,7 @@ Changes in 'fastqscreen/fastqscreen/main.nf':
 -    "${task.process}":
 -        fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//')
 -    END_VERSIONS
-+    $mv_txt_cmd
-+    $mv_html_cmd
-+    $mv_png_cmd
++    $mv_cmd
 +
 +    fastq_screen_version=\$(fastq_screen --version 2>&1 | sed 's/^.*FastQ Screen v//; s/ .*\$//')
 +    echo "\\\"${task.process}\\\":" > versions.yml
@@ -100,8 +95,9 @@ Changes in 'fastqscreen/fastqscreen/main.nf':
  
  }
 
+'modules/nf-core/fastqscreen/fastqscreen/meta.yml' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test' is unchanged
 'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap' is unchanged
-'modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml' is unchanged
 'modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config' is unchanged
-'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml' is unchanged
 ************************************************************

From 0730d896f6035aa1f935f510a0ce71927c32aaed Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 19 Dec 2024 10:20:39 +0000
Subject: [PATCH 146/530] nf-core tools lint autofixes

---
 .github/workflows/branch.yml          | 18 ++++++++++--------
 .github/workflows/linting.yml         | 10 +++++-----
 .github/workflows/linting_comment.yml |  2 +-
 3 files changed, 16 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index 5a2fffda..ffe93094 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -1,15 +1,17 @@
 name: nf-core branch protection
-# This workflow is triggered on PRs to master branch on the repository
-# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
+# This workflow is triggered on PRs to `main`/`master` branch on the repository
+# It fails when someone tries to make a PR against the nf-core `main`/`master` branch instead of `dev`
 on:
   pull_request_target:
-    branches: [master]
+    branches:
+      - main
+      - master
 
 jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
+      # PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
         if: github.repository == 'nf-core/seqinspector'
         run: |
@@ -22,7 +24,7 @@ jobs:
         uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         with:
           message: |
-            ## This PR is against the `master` branch :x:
+            ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x:
 
             * Do not close this PR
             * Click _Edit_ and change the `base` to `dev`
@@ -32,9 +34,9 @@ jobs:
 
             Hi @${{ github.event.pull_request.user.login }},
 
-            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch.
-            The `master` branch on nf-core repositories should always contain code from the latest release.
-            Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
+            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) ${{github.event.pull_request.base.ref}} branch.
+            The ${{github.event.pull_request.base.ref}} branch on nf-core repositories should always contain code from the latest release.
+            Because of this, PRs to ${{github.event.pull_request.base.ref}} are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
 
             You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
             Note that even after this, the test will continue to show as failing until you push a new commit.
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index a502573c..dbd52d5a 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -14,10 +14,10 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
@@ -31,12 +31,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           architecture: "x64"
@@ -74,7 +74,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
+        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 42e519bf..0bed96d3 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6
+        uses: dawidd6/action-download-artifact@80620a5d27ce0ae443b965134db88467fc607b43 # v7
         with:
           workflow: linting.yml
           workflow_conclusion: completed

From 8e68e65bcb89468f3a2356b2cf4f4fb3e17d015d Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 19 Dec 2024 11:13:08 +0000
Subject: [PATCH 147/530] remove fq/lint from modules.json, handled in separate
 PR

---
 modules.json | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/modules.json b/modules.json
index 82514096..01ae9110 100644
--- a/modules.json
+++ b/modules.json
@@ -26,11 +26,6 @@
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff"
                     },
-                    "fq/lint": {
-                        "branch": "master",
-                        "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc",
-                        "installed_by": ["modules"]
-                    },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",

From 965fe9d2ee19ab8ade23456b19c483dbacc45786 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 29 Oct 2024 10:11:24 +0100
Subject: [PATCH 148/530] Add skip tools parameter

---
 nextflow.config           |  1 +
 nextflow_schema.json      |  5 +++++
 workflows/seqinspector.nf | 29 +++++++++++++++++------------
 3 files changed, 23 insertions(+), 12 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 9ab822e8..924274c1 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -13,6 +13,7 @@ params {
     // Input options
     input                      = null
     sample_size                = 0
+    skip_tools                 = ''
     // References
     genome                     = null
     fasta                      = null
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 3f84164a..465b2a23 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -47,6 +47,11 @@
                     "type": "string",
                     "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
                     "fa_icon": "fas fa-file-signature"
+                },
+                "skip_tools": {
+                    "type": "string",
+                    "description": "Comma-separated string of tools to skip",
+                    "pattern": "^(fastqc|seqfu_stats)(,(fastqc|seqfu_stats))*$$"
                 }
             }
         },
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index edce5425..0888270e 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -31,6 +31,7 @@ workflow SEQINSPECTOR {
     ch_samplesheet               // channel: samplesheet read in from --input
 
     main:
+    skip_tools = params.skip_tools ? params.skip_tools.split(',') : []
 
     ch_versions            = Channel.empty()
     ch_multiqc_files       = Channel.empty()
@@ -55,23 +56,27 @@ workflow SEQINSPECTOR {
     //
     // MODULE: Run FastQC
     //
-    FASTQC (
-        ch_sample_sized.map {
-            meta, subsampled -> [meta, subsampled]
-        }
-    )
-    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip)
-    ch_versions = ch_versions.mix(FASTQC.out.versions.first())
+    if (!("fastqc" in skip_tools)) {
+        FASTQC (
+            ch_sample_sized.map {
+                meta, subsampled -> [meta, subsampled]
+            }
+        )
+        ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip)
+        ch_versions = ch_versions.mix(FASTQC.out.versions.first())
+    }
 
 
     //
     // Module: Run SeqFu stats
     //
-    SEQFU_STATS (
-        ch_samplesheet
-    )
-    ch_multiqc_files = ch_multiqc_files.mix(SEQFU_STATS.out.multiqc)
-    ch_versions = ch_versions.mix(SEQFU_STATS.out.versions.first())
+    if (!("seqfu_stats" in skip_tools)) {
+        SEQFU_STATS (
+            ch_samplesheet
+        )
+        ch_multiqc_files = ch_multiqc_files.mix(SEQFU_STATS.out.multiqc)
+        ch_versions = ch_versions.mix(SEQFU_STATS.out.versions.first())
+    }
 
     //
     // MODULE: Run FastQ Screen

From c89dc21d79f1c642927c3be853024bdda42437aa Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Fri, 22 Nov 2024 13:32:10 +0100
Subject: [PATCH 149/530] Add tests for skip_tools

---
 tests/MiSeq.main.nf.test      | 23 +++++++++++++++++++++++
 tests/MiSeq.main.nf.test.snap | 12 +++++++++++-
 2 files changed, 34 insertions(+), 1 deletion(-)

diff --git a/tests/MiSeq.main.nf.test b/tests/MiSeq.main.nf.test
index a1badfac..d5851898 100644
--- a/tests/MiSeq.main.nf.test
+++ b/tests/MiSeq.main.nf.test
@@ -27,4 +27,27 @@ nextflow_pipeline {
             )
         }
     }
+
+    test("Miseq data test (skip fastqc)") {
+        when {
+            config "./MiSeq.main.nf.test.config"
+            params {
+                outdir = "$outputDir"
+                skip_tools = "fastqc"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
+                    ).match()
+                },
+                {
+                  assert !path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt").exists()
+                }
+            )
+        }
+    }
 }
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index af7022dd..9d8026d0 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -10,6 +10,16 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-05T15:15:09.227024034"
+        "timestamp": "2024-12-13T16:10:21.816261"
+    },
+    "Miseq data test (skip fastqc)": {
+        "content": [
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-13T16:10:53.718831"
     }
 }
\ No newline at end of file

From 459b92df071a1bb55aca23102dbacee7273484ac Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Fri, 22 Nov 2024 13:52:03 +0100
Subject: [PATCH 150/530] Update docs

---
 docs/usage.md | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/docs/usage.md b/docs/usage.md
index 01211f28..c82131e1 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -98,6 +98,12 @@ Optionally, the `sample_size` parameter allows you to subset a random number of
 nextflow run nf-core/seqinspector --input ./samplesheet.csv --outdir ./results --sample_size 1000000 -profile docker
 ```
 
+### Skipping tools
+
+Some tools might not be compatible with your data. In this case it might be desired to skip some of them. This can be done easily by providing a comma-separated list of tools to be skipped with the `--skip_tools` parameter.
+
+In case you want to make this more permanent, it is recommended to specify this in a params file, or even in your own nextflow configuration file. The nextflow configuration file can also be use to customise tool arguments. See official [nexflow](https://www.nextflow.io/docs/latest/config.html) and [nf-core](https://nf-co.re/docs/usage/configuration) documentation for further details.
+
 ### Updating the pipeline
 
 When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline:

From 73db018cd21741a4dd0ac22a4075acc5afdb8b69 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Fri, 22 Nov 2024 14:19:48 +0100
Subject: [PATCH 151/530] Update CHANGELOG

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 91ee0b7f..6086d786 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 
 ### `Added`
 
+- [#68](https://github.com/nf-core/seqinspector/pull/68) Add tool selector
 - [#20](https://github.com/nf-core/seqinspector/pull/20) Use tags to generate group reports
 - [#13](https://github.com/nf-core/seqinspector/pull/13) Generate reports per run, per project and per lane.
 - [#49](https://github.com/nf-core/seqinspector/pull/49) Merge with template 3.0.2.

From abf8592a2b6a6f87d69571d55e6776ff6e939ea4 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Fri, 22 Nov 2024 14:21:45 +0100
Subject: [PATCH 152/530] Fixed linting

---
 tests/MiSeq.main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/MiSeq.main.nf.test b/tests/MiSeq.main.nf.test
index d5851898..0b584453 100644
--- a/tests/MiSeq.main.nf.test
+++ b/tests/MiSeq.main.nf.test
@@ -45,7 +45,7 @@ nextflow_pipeline {
                     ).match()
                 },
                 {
-                  assert !path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt").exists()
+                    assert !path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt").exists()
                 }
             )
         }

From 129da608d1f8e66854900a6274840a529bd15034 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Fri, 13 Dec 2024 16:16:17 +0100
Subject: [PATCH 153/530] Improve `skip_tools` regex pattern

---
 nextflow_schema.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 465b2a23..a0cbf942 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -51,7 +51,7 @@
                 "skip_tools": {
                     "type": "string",
                     "description": "Comma-separated string of tools to skip",
-                    "pattern": "^(fastqc|seqfu_stats)(,(fastqc|seqfu_stats))*$$"
+                    "pattern": "^((fastqc|fastqscreen|seqfu_stats|seqtk_sample)?,?)*(?<!,)$"
                 }
             }
         },

From 6e5c10393bbdd157b01bf374f4ce40f567dd71db Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Fri, 13 Dec 2024 16:16:52 +0100
Subject: [PATCH 154/530] Add option to skip fastqscreen and subsampling

---
 nextflow_schema.json      |  4 ++--
 workflows/seqinspector.nf | 36 +++++++++++++++++++-----------------
 2 files changed, 21 insertions(+), 19 deletions(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index a0cbf942..248660b7 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -25,9 +25,9 @@
                 },
                 "sample_size": {
                     "type": "integer",
-                    "default": 0,
                     "description": "Take this number of reads as a subset.",
-                    "help_text": "Choose the size of the subset or 0, if no subsampling shall be performed. Note that it refers to an absolute number."
+                    "help_text": "Choose the size of the subset or 0, if no subsampling shall be performed. Note that it refers to an absolute number.",
+                    "default": 0
                 },
                 "outdir": {
                     "type": "string",
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 0888270e..fc9b8f7f 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -41,7 +41,7 @@ workflow SEQINSPECTOR {
     //
     // MODULE: Run Seqtk sample to perform subsampling
     //
-    if (params.sample_size > 0 ) {
+    if (!("seqtk_sample" in skip_tools) && params.sample_size > 0) {
         ch_sample_sized = SEQTK_SAMPLE(
             ch_samplesheet.map {
                 meta, reads -> [meta, reads, params.sample_size]
@@ -49,7 +49,7 @@ workflow SEQINSPECTOR {
         ).reads
         ch_versions = ch_versions.mix(SEQTK_SAMPLE.out.versions.first())
     } else {
-        // No do subsample
+        // No subsampling
         ch_sample_sized = ch_samplesheet
     }
 
@@ -85,21 +85,23 @@ workflow SEQINSPECTOR {
     // Parse the reference info needed to create a FastQ Screen config file
     // and transpose it into a tuple containing lists for each property
 
-    ch_fastqscreen_refs = Channel
-        .fromList(samplesheetToList(
-            "${projectDir}/assets/example_fastq_screen_references.csv",
-            "${projectDir}/assets/schema_fastq_screen_references.json"
-        ))
-        .toList()
-        .transpose()
-        .toList()
-
-    FASTQSCREEN_FASTQSCREEN (
-        ch_samplesheet,
-        ch_fastqscreen_refs
-    )
-    ch_multiqc_files = ch_multiqc_files.mix(FASTQSCREEN_FASTQSCREEN.out.txt)
-    ch_versions = ch_versions.mix(FASTQSCREEN_FASTQSCREEN.out.versions.first())
+    if (!("fastqscreen" in skip_tools)) {
+        ch_fastqscreen_refs = Channel
+            .fromList(samplesheetToList(
+                "${projectDir}/assets/example_fastq_screen_references.csv",
+                "${projectDir}/assets/schema_fastq_screen_references.json"
+            ))
+            .toList()
+            .transpose()
+            .toList()
+
+        FASTQSCREEN_FASTQSCREEN (
+            ch_samplesheet,
+            ch_fastqscreen_refs
+        )
+        ch_multiqc_files = ch_multiqc_files.mix(FASTQSCREEN_FASTQSCREEN.out.txt)
+        ch_versions = ch_versions.mix(FASTQSCREEN_FASTQSCREEN.out.versions.first())
+    }
 
     //
     // Collate and save software versions

From f4722620d7569d50f8cbff70bfd4db37040d6aca Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Fri, 13 Dec 2024 16:19:30 +0100
Subject: [PATCH 155/530] Fix link to nf-core docs

---
 docs/usage.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/usage.md b/docs/usage.md
index c82131e1..2d84000e 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -102,7 +102,7 @@ nextflow run nf-core/seqinspector --input ./samplesheet.csv --outdir ./results -
 
 Some tools might not be compatible with your data. In this case it might be desired to skip some of them. This can be done easily by providing a comma-separated list of tools to be skipped with the `--skip_tools` parameter.
 
-In case you want to make this more permanent, it is recommended to specify this in a params file, or even in your own nextflow configuration file. The nextflow configuration file can also be use to customise tool arguments. See official [nexflow](https://www.nextflow.io/docs/latest/config.html) and [nf-core](https://nf-co.re/docs/usage/configuration) documentation for further details.
+In case you want to make this more permanent, it is recommended to specify this in a params file, or even in your own nextflow configuration file. The nextflow configuration file can also be use to customise tool arguments. See official [nexflow](https://www.nextflow.io/docs/latest/config.html) and [nf-core](https://nf-co.re/docs/usage/configuration#customising-tool-arguments) documentation for further details.
 
 ### Updating the pipeline
 

From 042de6a8856b6fc9f892a8bbb39eb6d7952d7c9d Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Wed, 15 Jan 2025 13:30:00 +0000
Subject: [PATCH 156/530] Template update for nf-core/tools version 3.1.2.dev0

---
 .editorconfig                                 |  4 ++
 .github/ISSUE_TEMPLATE/bug_report.yml         |  1 -
 .github/workflows/ci.yml                      |  2 +
 .github/workflows/download_pipeline.yml       | 51 ++++++++++++-------
 .nf-core.yml                                  |  2 +-
 .prettierignore                               |  1 +
 CITATIONS.md                                  |  4 +-
 LICENSE                                       |  2 +-
 README.md                                     | 15 ++----
 conf/test.config                              |  4 +-
 docs/output.md                                | 11 ++--
 docs/usage.md                                 |  2 +-
 nextflow.config                               |  3 ++
 ro-crate-metadata.json                        | 14 ++---
 .../main.nf                                   |  2 +-
 15 files changed, 62 insertions(+), 56 deletions(-)

diff --git a/.editorconfig b/.editorconfig
index 72dda289..6d9b74cc 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -31,3 +31,7 @@ indent_size = unset
 # ignore python and markdown
 [*.{py,md}]
 indent_style = unset
+
+# ignore ro-crate metadata files
+[**/ro-crate-metadata.json]
+insert_final_newline = unset
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index 5bcf7a88..6e640abf 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -9,7 +9,6 @@ body:
 
         - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
         - [nf-core/seqinspector pipeline documentation](https://nf-co.re/seqinspector/usage)
-
   - type: textarea
     id: description
     attributes:
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index f6c58143..d6fc106a 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -46,6 +46,8 @@ jobs:
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          fetch-depth: 0
 
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 2576cc0c..ab06316e 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -28,8 +28,23 @@ env:
   NXF_ANSI_LOG: false
 
 jobs:
+  configure:
+    runs-on: ubuntu-latest
+    outputs:
+      REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }}
+      REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }}
+      REPO_BRANCH: ${{ steps.get_repo_properties.outputs.REPO_BRANCH }}
+    steps:
+      - name: Get the repository name and current branch
+        id: get_repo_properties
+        run: |
+          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT"
+          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT"
+          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"
+
   download:
     runs-on: ubuntu-latest
+    needs: configure
     steps:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
@@ -52,12 +67,6 @@ jobs:
           python -m pip install --upgrade pip
           pip install git+https://github.com/nf-core/tools.git@dev
 
-      - name: Get the repository name and current branch set as environment variable
-        run: |
-          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV}
-          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
-          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}
-
       - name: Make a cache directory for the container images
         run: |
           mkdir -p ./singularity_container_images
@@ -66,9 +75,9 @@ jobs:
         env:
           NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
         run: |
-          nf-core pipelines download ${{ env.REPO_LOWERCASE }} \
-          --revision ${{ env.REPO_BRANCH }} \
-          --outdir ./${{ env.REPOTITLE_LOWERCASE }} \
+          nf-core pipelines download ${{ needs.configure.outputs.REPO_LOWERCASE }} \
+          --revision ${{ needs.configure.outputs.REPO_BRANCH }} \
+          --outdir ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} \
           --compress "none" \
           --container-system 'singularity' \
           --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io/library/" \
@@ -76,14 +85,17 @@ jobs:
           --download-configuration 'yes'
 
       - name: Inspect download
-        run: tree ./${{ env.REPOTITLE_LOWERCASE }}
+        run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}
+
+      - name: Inspect container images
+        run: tree ./singularity_container_images | tee ./container_initial
 
       - name: Count the downloaded number of container images
         id: count_initial
         run: |
           image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
           echo "Initial container image count: $image_count"
-          echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV}
+          echo "IMAGE_COUNT_INITIAL=$image_count" >> "$GITHUB_OUTPUT"
 
       - name: Run the downloaded pipeline (stub)
         id: stub_run_pipeline
@@ -91,30 +103,31 @@ jobs:
         env:
           NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
+        run: nextflow run ./${{needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
       - name: Run the downloaded pipeline (stub run not supported)
         id: run_pipeline
-        if: ${{ job.steps.stub_run_pipeline.status == failure() }}
+        if: ${{ steps.stub_run_pipeline.outcome == 'failure' }}
         env:
           NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
+        run: nextflow run ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -profile test,singularity --outdir ./results
 
       - name: Count the downloaded number of container images
         id: count_afterwards
         run: |
           image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
           echo "Post-pipeline run container image count: $image_count"
-          echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV}
+          echo "IMAGE_COUNT_AFTER=$image_count" >> "$GITHUB_OUTPUT"
 
       - name: Compare container image counts
         run: |
-          if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then
-            initial_count=${{ env.IMAGE_COUNT_INITIAL }}
-            final_count=${{ env.IMAGE_COUNT_AFTER }}
+          if [ "${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}" -ne "${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}" ]; then
+            initial_count=${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}
+            final_count=${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}
             difference=$((final_count - initial_count))
             echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!"
-            tree ./singularity_container_images
+            tree ./singularity_container_images > ./container_afterwards
+            diff ./container_initial ./container_afterwards
             exit 1
           else
             echo "The pipeline can be downloaded successfully!"
diff --git a/.nf-core.yml b/.nf-core.yml
index e44eaad4..7c9cb078 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,7 +1,7 @@
 lint:
   files_unchanged:
     - .github/CONTRIBUTING.md
-nf_core_version: 3.1.0
+nf_core_version: 3.1.2.dev0
 repository_type: pipeline
 template:
   author: Adrien Coulier
diff --git a/.prettierignore b/.prettierignore
index 437d763d..edd29f01 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -10,3 +10,4 @@ testing/
 testing*
 *.pyc
 bin/
+ro-crate-metadata.json
diff --git a/CITATIONS.md b/CITATIONS.md
index ecbfb16e..6cf38e0b 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -12,9 +12,7 @@
 
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
-> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
-
-- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
 > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
diff --git a/LICENSE b/LICENSE
index f3045f2f..3295b9f8 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) Adrien Coulier
+Copyright (c) The nf-core/seqinspector team
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
diff --git a/README.md b/README.md
index 2b5e2c85..70e63d69 100644
--- a/README.md
+++ b/README.md
@@ -3,9 +3,7 @@
     <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-seqinspector_logo_dark.png">
     <img alt="nf-core/seqinspector" src="docs/images/nf-core-seqinspector_logo_light.png">
   </picture>
-</h1>
-
-[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml)
+</h1>[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
@@ -29,15 +27,12 @@
 
 <!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
      workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->
-<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
-
-1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
 
 ## Usage
 
 > [!NOTE]
-> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
+> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow.Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
 
 <!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
      Explain what rows and columns represent. For instance (please edit as appropriate):
@@ -94,9 +89,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 ## Citations
 
 <!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
-<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
-
-<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
+<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) --><!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 
diff --git a/conf/test.config b/conf/test.config
index 1838ae52..c2d2fe62 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -25,8 +25,6 @@ params {
     // Input data
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input  = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
-
-    // Genome references
+    input  = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'// Genome references
     genome = 'R64-1-1'
 }
diff --git a/docs/output.md b/docs/output.md
index e8665e59..254cc7ee 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -12,8 +12,7 @@ The directories listed below will be created in the results directory after the
 
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
-- [FastQC](#fastqc) - Raw read QC
-- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
+- [FastQC](#fastqc) - Raw read QC- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
 ### FastQC
@@ -27,9 +26,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 </details>
 
-[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
-
-### MultiQC
+[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).### MultiQC
 
 <details markdown="1">
 <summary>Output files</summary>
@@ -43,9 +40,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 [MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.
 
-Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.
-
-### Pipeline information
+Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.### Pipeline information
 
 <details markdown="1">
 <summary>Output files</summary>
diff --git a/docs/usage.md b/docs/usage.md
index b400728f..4f3549a1 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -130,7 +130,7 @@ Several generic profiles are bundled with the pipeline which instruct the pipeli
 > [!IMPORTANT]
 > We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
 
-The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to check if your system is suported, please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation).
+The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to check if your system is supported, please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation).
 
 Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important!
 They are loaded in sequence, so later profiles can overwrite earlier profiles.
diff --git a/nextflow.config b/nextflow.config
index e588aee1..0d1889c7 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -283,3 +283,6 @@ validation {
         afterText = validation.help.afterText
     }
 }
+
+// Load modules.config for DSL2 module specific options
+includeConfig 'conf/modules.config'
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 24c84dc6..3d6459ec 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,8 +22,8 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2024-12-12T11:24:30+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by Adrien Coulier.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "datePublished": "2025-01-15T13:29:44+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow.Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by Adrien Coulier.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) --><!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
                     "@id": "main.nf"
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#a2f9223f-7e69-4788-87c8-468ddf886506"
+                    "@id": "#6c41c52a-aa1c-4300-8053-c8e4c2980384"
                 }
             ],
             "name": "nf-core/seqinspector"
@@ -128,7 +128,7 @@
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2024-12-12T11:24:30Z",
+            "dateModified": "2025-01-15T13:29:44Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": ["nf-core", "nextflow", "genomics", "quality-control"],
             "license": ["MIT"],
@@ -160,11 +160,11 @@
             "version": "!>=24.04.2"
         },
         {
-            "@id": "#a2f9223f-7e69-4788-87c8-468ddf886506",
+            "@id": "#6c41c52a-aa1c-4300-8053-c8e4c2980384",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#4fd17b03-0bda-4f65-91a0-832482b15fe2"
+                    "@id": "#8ac10261-0b1b-406e-a778-3ef7f7c89980"
                 }
             ],
             "mainEntity": {
@@ -173,7 +173,7 @@
             "name": "Test suite for nf-core/seqinspector"
         },
         {
-            "@id": "#4fd17b03-0bda-4f65-91a0-832482b15fe2",
+            "@id": "#8ac10261-0b1b-406e-a778-3ef7f7c89980",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/seqinspector",
             "resource": "repos/nf-core/seqinspector/actions/workflows/ci.yml",
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index 20a5206f..297dc0dc 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -117,7 +117,7 @@ workflow PIPELINE_COMPLETION {
     main:
     summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
     def multiqc_reports = multiqc_report.toList()
-    
+
     //
     // Completion email and summary
     //

From 260af87c7344389262a317f55754a797441c0be7 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Wed, 15 Jan 2025 15:32:11 +0100
Subject: [PATCH 157/530] Set nf_core version to 3.1.1

---
 .nf-core.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index 7c9cb078..4bf81e71 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,7 +1,7 @@
 lint:
   files_unchanged:
     - .github/CONTRIBUTING.md
-nf_core_version: 3.1.2.dev0
+nf_core_version: 3.1.1
 repository_type: pipeline
 template:
   author: Adrien Coulier

From bc4427b0b6b0203eb4ced530162de7fcafeddd46 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Wed, 15 Jan 2025 15:39:22 +0100
Subject: [PATCH 158/530] Remove double include of modules.config

---
 nextflow.config | 1 -
 1 file changed, 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 2703524a..3f726e02 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -57,7 +57,6 @@ params {
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
-includeConfig 'conf/modules.config'
 
 profiles {
     debug {

From 3d6ab8bb7884ac9eb4cc91128b01ddf07940199c Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Fri, 17 Jan 2025 13:47:28 +0100
Subject: [PATCH 159/530] Update CITATIONS.md
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
---
 CITATIONS.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/CITATIONS.md b/CITATIONS.md
index b1c06043..a8aaa88e 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -12,7 +12,9 @@
 
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
-> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
+
+- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
 - [SeqFu](https://telatin.github.io/seqfu2/)
 

From a8ca701b911a3654fc5d6db14029c1ef14cb23eb Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Fri, 17 Jan 2025 13:47:42 +0100
Subject: [PATCH 160/530] Update README.md
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
---
 README.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 238dc163..e884871d 100644
--- a/README.md
+++ b/README.md
@@ -3,7 +3,8 @@
     <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-seqinspector_logo_dark.png">
     <img alt="nf-core/seqinspector" src="docs/images/nf-core-seqinspector_logo_light.png">
   </picture>
-</h1>[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml)
+</h1>
+[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 

From da9bd1e88d731a4fbcbb959608414bd44a720fae Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Fri, 17 Jan 2025 13:48:33 +0100
Subject: [PATCH 161/530] Update README.md
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index e884871d..c60b7dfa 100644
--- a/README.md
+++ b/README.md
@@ -37,7 +37,7 @@
 ## Usage
 
 > [!NOTE]
-> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow.Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
+> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
 
 First, prepare a samplesheet with your input data that looks as follows:
 

From f85b7144feaa743516ef91f950b43dfb66c119dd Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Fri, 17 Jan 2025 13:48:58 +0100
Subject: [PATCH 162/530] Update docs/output.md
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
---
 docs/output.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/docs/output.md b/docs/output.md
index a9f505fb..3d3c3497 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -110,7 +110,9 @@ nf-core/seqinspector will generate the following MultiQC reports:
 
 [MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.
 
-Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.### Pipeline information
+Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.
+
+### Pipeline information
 
 <details markdown="1">
 <summary>Output files</summary>

From 605ec1e2f9daac0d38598f641600951fcbf89e15 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Mon, 20 Jan 2025 14:35:57 +0000
Subject: [PATCH 163/530] Template update for nf-core/tools version 3.1.2

---
 .nf-core.yml           |  2 +-
 CITATIONS.md           |  4 +++-
 README.md              | 10 +++++++---
 nextflow.config        |  2 +-
 ro-crate-metadata.json | 14 +++++++-------
 5 files changed, 19 insertions(+), 13 deletions(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index 7c9cb078..f2b91109 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,7 +1,7 @@
 lint:
   files_unchanged:
     - .github/CONTRIBUTING.md
-nf_core_version: 3.1.2.dev0
+nf_core_version: 3.1.2
 repository_type: pipeline
 template:
   author: Adrien Coulier
diff --git a/CITATIONS.md b/CITATIONS.md
index 6cf38e0b..ecbfb16e 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -12,7 +12,9 @@
 
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
-> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
+
+- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
 > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
diff --git a/README.md b/README.md
index 70e63d69..1c2cc4bc 100644
--- a/README.md
+++ b/README.md
@@ -3,7 +3,9 @@
     <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-seqinspector_logo_dark.png">
     <img alt="nf-core/seqinspector" src="docs/images/nf-core-seqinspector_logo_light.png">
   </picture>
-</h1>[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml)
+</h1>
+
+[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
@@ -32,7 +34,7 @@
 ## Usage
 
 > [!NOTE]
-> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow.Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
+> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
 
 <!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
      Explain what rows and columns represent. For instance (please edit as appropriate):
@@ -89,7 +91,9 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 ## Citations
 
 <!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
-<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) --><!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
+<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+
+<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 
diff --git a/nextflow.config b/nextflow.config
index 0d1889c7..d15031cf 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -249,7 +249,7 @@ manifest {
 
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 validation {
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 3d6459ec..6028e4fe 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,8 +22,8 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2025-01-15T13:29:44+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow.Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by Adrien Coulier.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) --><!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "datePublished": "2025-01-20T14:35:53+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by Adrien Coulier.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
                     "@id": "main.nf"
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#6c41c52a-aa1c-4300-8053-c8e4c2980384"
+                    "@id": "#5184a477-6d1e-4fff-9e1a-1b88129a2190"
                 }
             ],
             "name": "nf-core/seqinspector"
@@ -128,7 +128,7 @@
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2025-01-15T13:29:44Z",
+            "dateModified": "2025-01-20T14:35:53Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": ["nf-core", "nextflow", "genomics", "quality-control"],
             "license": ["MIT"],
@@ -160,11 +160,11 @@
             "version": "!>=24.04.2"
         },
         {
-            "@id": "#6c41c52a-aa1c-4300-8053-c8e4c2980384",
+            "@id": "#5184a477-6d1e-4fff-9e1a-1b88129a2190",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#8ac10261-0b1b-406e-a778-3ef7f7c89980"
+                    "@id": "#d8998226-48a8-47b9-bf40-5630f88b24cc"
                 }
             ],
             "mainEntity": {
@@ -173,7 +173,7 @@
             "name": "Test suite for nf-core/seqinspector"
         },
         {
-            "@id": "#8ac10261-0b1b-406e-a778-3ef7f7c89980",
+            "@id": "#d8998226-48a8-47b9-bf40-5630f88b24cc",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/seqinspector",
             "resource": "repos/nf-core/seqinspector/actions/workflows/ci.yml",

From de7c9edd89f56511b47dae83df019635b3e14ab2 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Mon, 27 Jan 2025 14:47:41 +0000
Subject: [PATCH 164/530] Template update for nf-core/tools version 3.2.0

---
 .github/workflows/linting_comment.yml         |  2 +-
 .github/workflows/release-announcements.yml   | 33 -------------------
 .nf-core.yml                                  |  2 +-
 .pre-commit-config.yaml                       |  2 +-
 docs/output.md                                | 11 +++++--
 modules.json                                  |  4 +--
 modules/nf-core/fastqc/main.nf                | 20 +++++------
 modules/nf-core/fastqc/tests/tags.yml         |  2 --
 modules/nf-core/multiqc/environment.yml       |  2 +-
 modules/nf-core/multiqc/main.nf               |  4 +--
 .../nf-core/multiqc/tests/main.nf.test.snap   | 24 +++++++-------
 nextflow.config                               | 16 ++++-----
 ro-crate-metadata.json                        | 12 +++----
 13 files changed, 52 insertions(+), 82 deletions(-)
 delete mode 100644 modules/nf-core/fastqc/tests/tags.yml

diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 0bed96d3..95b6b6af 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@80620a5d27ce0ae443b965134db88467fc607b43 # v7
+        uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8
         with:
           workflow: linting.yml
           workflow_conclusion: completed
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index 450b1d5e..76a9e67e 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -27,39 +27,6 @@ jobs:
 
             ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
 
-  send-tweet:
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
-        with:
-          python-version: "3.10"
-      - name: Install dependencies
-        run: pip install tweepy==4.14.0
-      - name: Send tweet
-        shell: python
-        run: |
-          import os
-          import tweepy
-
-          client = tweepy.Client(
-              access_token=os.getenv("TWITTER_ACCESS_TOKEN"),
-              access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"),
-              consumer_key=os.getenv("TWITTER_CONSUMER_KEY"),
-              consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"),
-          )
-          tweet = os.getenv("TWEET")
-          client.create_tweet(text=tweet)
-        env:
-          TWEET: |
-            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
-
-            Please see the changelog: ${{ github.event.release.html_url }}
-          TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }}
-          TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }}
-          TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }}
-          TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }}
-
   bsky-post:
     runs-on: ubuntu-latest
     steps:
diff --git a/.nf-core.yml b/.nf-core.yml
index f2b91109..c984b0c3 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,7 +1,7 @@
 lint:
   files_unchanged:
     - .github/CONTRIBUTING.md
-nf_core_version: 3.1.2
+nf_core_version: 3.2.0
 repository_type: pipeline
 template:
   author: Adrien Coulier
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 9e9f0e1c..1dec8650 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,7 +7,7 @@ repos:
           - prettier@3.2.5
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "3.0.3"
+    rev: "3.1.2"
     hooks:
       - id: editorconfig-checker
         alias: ec
diff --git a/docs/output.md b/docs/output.md
index 254cc7ee..e8665e59 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -12,7 +12,8 @@ The directories listed below will be created in the results directory after the
 
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
-- [FastQC](#fastqc) - Raw read QC- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
+- [FastQC](#fastqc) - Raw read QC
+- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
 ### FastQC
@@ -26,7 +27,9 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 </details>
 
-[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).### MultiQC
+[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
+
+### MultiQC
 
 <details markdown="1">
 <summary>Output files</summary>
@@ -40,7 +43,9 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 [MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.
 
-Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.### Pipeline information
+Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.
+
+### Pipeline information
 
 <details markdown="1">
 <summary>Output files</summary>
diff --git a/modules.json b/modules.json
index 5605d989..cc0aaa51 100644
--- a/modules.json
+++ b/modules.json
@@ -7,12 +7,12 @@
                 "nf-core": {
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "dc94b6ee04a05ddb9f7ae050712ff30a13149164",
+                        "git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
+                        "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad",
                         "installed_by": ["modules"]
                     }
                 }
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 752c3a10..033f4154 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -1,5 +1,5 @@
 process FASTQC {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
@@ -19,30 +19,30 @@ process FASTQC {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args          = task.ext.args ?: ''
+    def prefix        = task.ext.prefix ?: "${meta.id}"
     // Make list of old name and new name pairs to use for renaming in the bash while loop
     def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
-    def rename_to = old_new_pairs*.join(' ').join(' ')
+    def rename_to     = old_new_pairs*.join(' ').join(' ')
     def renamed_files = old_new_pairs.collect{ _old_name, new_name -> new_name }.join(' ')
 
     // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory)
     // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222
     // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label
-    def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus
+    def memory_in_mb = task.memory ? task.memory.toUnit('MB').toFloat() / task.cpus : null
     // FastQC memory value allowed range (100 - 10000)
     def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
 
     """
-    printf "%s %s\\n" $rename_to | while read old_name new_name; do
+    printf "%s %s\\n" ${rename_to} | while read old_name new_name; do
         [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
     done
 
     fastqc \\
-        $args \\
-        --threads $task.cpus \\
-        --memory $fastqc_memory \\
-        $renamed_files
+        ${args} \\
+        --threads ${task.cpus} \\
+        --memory ${fastqc_memory} \\
+        ${renamed_files}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/fastqc/tests/tags.yml b/modules/nf-core/fastqc/tests/tags.yml
deleted file mode 100644
index 7834294b..00000000
--- a/modules/nf-core/fastqc/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-fastqc:
-  - modules/nf-core/fastqc/**
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index 6f5b867b..a27122ce 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::multiqc=1.25.1
+  - bioconda::multiqc=1.27
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index cc0643e1..58d9313c 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,8 +3,8 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.27--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.27--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index 2fcbb5ff..7b7c1322 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
+                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-02T17:51:46.317523"
+        "timestamp": "2025-01-27T09:29:57.631982377"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
+                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-02T17:52:20.680978"
+        "timestamp": "2025-01-27T09:30:34.743726958"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
+                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-02T17:52:09.185842"
+        "timestamp": "2025-01-27T09:30:21.44383553"
     }
 }
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index d15031cf..c1d108ba 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -195,14 +195,14 @@ env {
 }
 
 // Set bash options
-process.shell = """\
-bash
-
-set -e # Exit if a tool returns a non-zero status/exit code
-set -u # Treat unset variables and parameters as an error
-set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
-set -C # No clobber - prevent output redirection from overwriting files.
-"""
+process.shell = [
+    "bash",
+    "-C",         // No clobber - prevent output redirection from overwriting files.
+    "-e",         // Exit if a tool returns a non-zero status/exit code
+    "-u",         // Treat unset variables and parameters as an error
+    "-o",         // Returns the status of the last command to exit..
+    "pipefail"    //   ..with a non-zero status or zero if all successfully execute
+]
 
 // Disable process selector warnings by default. Use debug profile to enable warnings.
 nextflow.enable.configProcessNamesValidation = false
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 6028e4fe..4d95888e 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,7 +22,7 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2025-01-20T14:35:53+00:00",
+            "datePublished": "2025-01-27T14:47:37+00:00",
             "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by Adrien Coulier.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#5184a477-6d1e-4fff-9e1a-1b88129a2190"
+                    "@id": "#9eab6b17-216a-48ea-bfa3-1b29feb0a808"
                 }
             ],
             "name": "nf-core/seqinspector"
@@ -128,7 +128,7 @@
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2025-01-20T14:35:53Z",
+            "dateModified": "2025-01-27T14:47:37Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": ["nf-core", "nextflow", "genomics", "quality-control"],
             "license": ["MIT"],
@@ -160,11 +160,11 @@
             "version": "!>=24.04.2"
         },
         {
-            "@id": "#5184a477-6d1e-4fff-9e1a-1b88129a2190",
+            "@id": "#9eab6b17-216a-48ea-bfa3-1b29feb0a808",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#d8998226-48a8-47b9-bf40-5630f88b24cc"
+                    "@id": "#bafa694e-20a0-4ba4-b6e4-b501d4c026aa"
                 }
             ],
             "mainEntity": {
@@ -173,7 +173,7 @@
             "name": "Test suite for nf-core/seqinspector"
         },
         {
-            "@id": "#d8998226-48a8-47b9-bf40-5630f88b24cc",
+            "@id": "#bafa694e-20a0-4ba4-b6e4-b501d4c026aa",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/seqinspector",
             "resource": "repos/nf-core/seqinspector/actions/workflows/ci.yml",

From 978b6785b6520fa81ec89e376dce98ccfe85c603 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Mon, 27 Jan 2025 16:15:49 +0000
Subject: [PATCH 165/530] Template update for nf-core/tools version 3.2.0

---
 ro-crate-metadata.json | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 4d95888e..7b22e103 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,7 +22,7 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2025-01-27T14:47:37+00:00",
+            "datePublished": "2025-01-27T16:15:35+00:00",
             "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by Adrien Coulier.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#9eab6b17-216a-48ea-bfa3-1b29feb0a808"
+                    "@id": "#d25cadcb-fa1a-425e-8f2d-e5d85d309c29"
                 }
             ],
             "name": "nf-core/seqinspector"
@@ -128,7 +128,7 @@
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2025-01-27T14:47:37Z",
+            "dateModified": "2025-01-27T16:15:35Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": ["nf-core", "nextflow", "genomics", "quality-control"],
             "license": ["MIT"],
@@ -160,11 +160,11 @@
             "version": "!>=24.04.2"
         },
         {
-            "@id": "#9eab6b17-216a-48ea-bfa3-1b29feb0a808",
+            "@id": "#d25cadcb-fa1a-425e-8f2d-e5d85d309c29",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#bafa694e-20a0-4ba4-b6e4-b501d4c026aa"
+                    "@id": "#ec706afc-83c1-4f5f-bb83-661e72cacb33"
                 }
             ],
             "mainEntity": {
@@ -173,7 +173,7 @@
             "name": "Test suite for nf-core/seqinspector"
         },
         {
-            "@id": "#bafa694e-20a0-4ba4-b6e4-b501d4c026aa",
+            "@id": "#ec706afc-83c1-4f5f-bb83-661e72cacb33",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/seqinspector",
             "resource": "repos/nf-core/seqinspector/actions/workflows/ci.yml",

From d1feaa11796a7e08168b8483fb8dc55cd16e49ae Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 7 Jan 2025 16:55:07 +0100
Subject: [PATCH 166/530] Set up nft-utils in tests

---
 nf-test.config                      |   3 +
 tests/.nftignore                    |  12 +
 tests/MiSeq.main.nf.test            |  90 +++-
 tests/MiSeq.main.nf.test.snap       | 225 +++++++++-
 tests/NovaSeq6000.main.nf.test      |  47 +--
 tests/NovaSeq6000.main.nf.test.snap | 610 +++++++++++++++++++++++++++-
 tests/PromethION.main.nf.test       |  27 +-
 tests/PromethION.main.nf.test.snap  | 141 ++++++-
 8 files changed, 1070 insertions(+), 85 deletions(-)
 create mode 100644 tests/.nftignore

diff --git a/nf-test.config b/nf-test.config
index 6969c085..d4d15358 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -5,4 +5,7 @@ config {
     configFile "tests/nextflow.config"
     profile "test,docker"
 
+    plugins {
+        load "nft-utils@0.0.3"
+    }
 }
diff --git a/tests/.nftignore b/tests/.nftignore
new file mode 100644
index 00000000..504be1c6
--- /dev/null
+++ b/tests/.nftignore
@@ -0,0 +1,12 @@
+.DS_Store
+multiqc/{global_report,group_reports/*}/multiqc_data/multiqc.log
+multiqc/{global_report,group_reports/*}/multiqc_data/multiqc_data.json
+multiqc/{global_report,group_reports/*}/multiqc_data/multiqc_general_stats.txt
+multiqc/{global_report,group_reports/*}/multiqc_data/multiqc_software_versions.txt
+multiqc/{global_report,group_reports/*}/multiqc_data/multiqc_sources.txt
+multiqc/{global_report,group_reports/*}/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
+multiqc/{global_report,group_reports/*}/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
+multiqc/{global_report,group_reports/*}/multiqc_report.html
+pipeline_info/*.{html,json,txt,yml}
+fastqscreen/*_screen.html
+fastqc/*_fastqc.zip
diff --git a/tests/MiSeq.main.nf.test b/tests/MiSeq.main.nf.test
index 0b584453..0ed7052a 100644
--- a/tests/MiSeq.main.nf.test
+++ b/tests/MiSeq.main.nf.test
@@ -15,15 +15,28 @@ nextflow_pipeline {
         }
 
         then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(
+                params.outdir,
+                relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']
+            )
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(
+                params.outdir,
+                ignoreFile: 'tests/.nftignore'
+            )
             assertAll(
-                { assert workflow.success },
+                { assert workflow.success},
                 { assert snapshot(
-                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt"),
-                    ).match()
-                }
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
+                    // All stable path names, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
             )
         }
     }
@@ -38,15 +51,64 @@ nextflow_pipeline {
         }
 
         then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(
+                params.outdir,
+                relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']
+            )
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(
+                params.outdir,
+                ignoreFile: 'tests/.nftignore'
+            )
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
+                    // All stable path names, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+
+    test("Miseq data test (skip all tools)") {
+        when {
+            config "./MiSeq.main.nf.test.config"
+            params {
+                outdir = "$outputDir"
+                skip_tools = "fastqc,fastqscreen,seqfu_stats,seqtk_sample"
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(
+                params.outdir,
+                relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']
+            )
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(
+                params.outdir,
+                ignoreFile: 'tests/.nftignore'
+            )
             assertAll(
-                { assert workflow.success },
+                { assert workflow.success},
                 { assert snapshot(
-                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
-                    ).match()
-                },
-                {
-                    assert !path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt").exists()
-                }
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
+                    // All stable path names, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
             )
         }
     }
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 9d8026d0..66996292 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -1,25 +1,232 @@
 {
     "MiSeq data test": {
         "content": [
-            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-            "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
-            "multiqc_general_stats.txt:md5,5b28a83b14cb2fe88d084d08900ebdbf",
-            "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607"
+            4,
+            {
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "FASTQSCREEN_FASTQSCREEN": {
+                    "fastqscreen": "0.16.0"
+                },
+                "SEQFU_STATS": {
+                    "seqfu": "1.20.3"
+                },
+                "Workflow": {
+                    "nf-core/seqinspector": "v1.0dev"
+                }
+            },
+            [
+                "fastqc",
+                "fastqc/SAMPLE_SINGLE_END_1_fastqc.html",
+                "fastqc/SAMPLE_SINGLE_END_1_fastqc.zip",
+                "fastqscreen",
+                "fastqscreen/SAMPLE_SINGLE_END_1_screen.html",
+                "fastqscreen/SAMPLE_SINGLE_END_1_screen.png",
+                "fastqscreen/SAMPLE_SINGLE_END_1_screen.txt",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc_SAMPLE_SINGLE_END_1.txt",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_plots",
+                "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/SAMPLE_SINGLE_END_1.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/SAMPLE_SINGLE_END_1.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
+                "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/SAMPLE_SINGLE_END_1.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/global_report/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "seqfu_stats",
+                "seqfu_stats/SAMPLE_SINGLE_END_1.tsv",
+                "seqfu_stats/SAMPLE_SINGLE_END_1_mqc.txt"
+            ],
+            [
+                "SAMPLE_SINGLE_END_1_fastqc.html:md5,a299e4a9a0b5aa289d6a325b71f915ce",
+                "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
+                "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
+                "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
+                "fastqc-status-check-heatmap.txt:md5,8f98652c377741c974e485652a19f37f",
+                "fastqc_overrepresented_sequences_plot.txt:md5,cdc7479933cae03e0043ae794f81c304",
+                "fastqc_per_base_n_content_plot.txt:md5,dd8d6976dc5ea8cf67d9fa2c3be9e24b",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,5f9a98d3068aab17f26731ae0615f41a",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,1de1333bb959189dcf8230706f60dbfc",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,62f140bfa52d462c9c499dfdabc35476",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,5fda43eb9b7c60cf6b4348f734a94b26",
+                "fastqc_sequence_counts_plot.txt:md5,00cd6842465f7aa9ae75434e175946a6",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,c3befe0812d2f1c23d5e75e6fccf0622",
+                "multiqc_SAMPLE_SINGLE_END_1.txt:md5,8e6989a2392f599a09a5c3edf8119702",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607",
+                "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
+                "SAMPLE_SINGLE_END_1.tsv:md5,f65c868e562291647d539090698ba5eb",
+                "SAMPLE_SINGLE_END_1_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
+            ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.10.2"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-13T16:10:21.816261"
+        "timestamp": "2025-02-03T16:39:35.285693"
+    },
+    "Miseq data test (skip all tools)": {
+        "content": [
+            1,
+            {
+                "Workflow": {
+                    "nf-core/seqinspector": "v1.0dev"
+                }
+            },
+            [
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"
+            ],
+            [
+                "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-07T13:49:22.707398"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
-            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a"
+            3,
+            {
+                "FASTQSCREEN_FASTQSCREEN": {
+                    "fastqscreen": "0.16.0"
+                },
+                "SEQFU_STATS": {
+                    "seqfu": "1.20.3"
+                },
+                "Workflow": {
+                    "nf-core/seqinspector": "v1.0dev"
+                }
+            },
+            [
+                "fastqscreen",
+                "fastqscreen/SAMPLE_SINGLE_END_1_screen.html",
+                "fastqscreen/SAMPLE_SINGLE_END_1_screen.png",
+                "fastqscreen/SAMPLE_SINGLE_END_1_screen.txt",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc_SAMPLE_SINGLE_END_1.txt",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_plots",
+                "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/SAMPLE_SINGLE_END_1.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/SAMPLE_SINGLE_END_1.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/SAMPLE_SINGLE_END_1.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "seqfu_stats",
+                "seqfu_stats/SAMPLE_SINGLE_END_1.tsv",
+                "seqfu_stats/SAMPLE_SINGLE_END_1_mqc.txt"
+            ],
+            [
+                "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
+                "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
+                "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
+                "multiqc_SAMPLE_SINGLE_END_1.txt:md5,8e6989a2392f599a09a5c3edf8119702",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607",
+                "SAMPLE_SINGLE_END_1.tsv:md5,f65c868e562291647d539090698ba5eb",
+                "SAMPLE_SINGLE_END_1_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
+            ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.10.2"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-13T16:10:53.718831"
+        "timestamp": "2025-02-03T16:40:27.8664"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test b/tests/NovaSeq6000.main.nf.test
index e70a191c..8eea81f7 100644
--- a/tests/NovaSeq6000.main.nf.test
+++ b/tests/NovaSeq6000.main.nf.test
@@ -15,35 +15,28 @@ nextflow_pipeline {
         }
 
         then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(
+                params.outdir,
+                relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']
+            )
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(
+                params.outdir,
+                ignoreFile: 'tests/.nftignore'
+            )
             assertAll(
-                { assert workflow.success },
+                { assert workflow.success},
                 { assert snapshot(
-                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt"),
-
-                    path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_fastq_screen.txt"),
-
-                    path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt"),
-
-                    path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_fastq_screen.txt"),
-
-                    path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt"),
-                    ).match()
-                },
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
+                    // All stable path names, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
             )
         }
     }
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index 9b3826a5..0a9ab878 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -1,31 +1,597 @@
 {
     "NovaSeq6000 data test": {
         "content": [
-            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-            "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d",
-            "multiqc_general_stats.txt:md5,25abe0f6a35eb4a3b056fc3cf5c13732",
-            "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
-            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-            "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
-            "multiqc_general_stats.txt:md5,90ee35137492b80aab36ef67f72d8921",
-            "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
-            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-            "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
-            "multiqc_general_stats.txt:md5,d62a2fc39e674d98783d408791803148",
-            "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
-            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-            "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
-            "multiqc_general_stats.txt:md5,2f09b8f199ac40cf67ba50843cebd29c",
-            "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
-            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-            "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
-            "multiqc_general_stats.txt:md5,6a1c16f068d7ba3a9225a17eb570ed9a",
-            "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5"
+            20,
+            {
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "FASTQSCREEN_FASTQSCREEN": {
+                    "fastqscreen": "0.16.0"
+                },
+                "SEQFU_STATS": {
+                    "seqfu": "1.20.3"
+                },
+                "Workflow": {
+                    "nf-core/seqinspector": "v1.0dev"
+                }
+            },
+            [
+                "fastqc",
+                "fastqc/Sample1_1_fastqc.html",
+                "fastqc/Sample1_1_fastqc.zip",
+                "fastqc/Sample23_3_fastqc.html",
+                "fastqc/Sample23_3_fastqc.zip",
+                "fastqc/SampleA_2_fastqc.html",
+                "fastqc/SampleA_2_fastqc.zip",
+                "fastqc/Undetermined_5_fastqc.html",
+                "fastqc/Undetermined_5_fastqc.zip",
+                "fastqc/sampletest_4_fastqc.html",
+                "fastqc/sampletest_4_fastqc.zip",
+                "fastqscreen",
+                "fastqscreen/Sample1_1_screen.html",
+                "fastqscreen/Sample1_1_screen.png",
+                "fastqscreen/Sample1_1_screen.txt",
+                "fastqscreen/Sample23_3_screen.html",
+                "fastqscreen/Sample23_3_screen.png",
+                "fastqscreen/Sample23_3_screen.txt",
+                "fastqscreen/SampleA_2_screen.html",
+                "fastqscreen/SampleA_2_screen.png",
+                "fastqscreen/SampleA_2_screen.txt",
+                "fastqscreen/Undetermined_5_screen.html",
+                "fastqscreen/Undetermined_5_screen.png",
+                "fastqscreen/Undetermined_5_screen.txt",
+                "fastqscreen/sampletest_4_screen.html",
+                "fastqscreen/sampletest_4_screen.png",
+                "fastqscreen/sampletest_4_screen.txt",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc_Sample1_1.txt",
+                "multiqc/global_report/multiqc_data/multiqc_Sample23_3.txt",
+                "multiqc/global_report/multiqc_data/multiqc_SampleA_2.txt",
+                "multiqc/global_report/multiqc_data/multiqc_Undetermined_5.txt",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sampletest_4.txt",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_plots",
+                "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/Sample1_1.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/Sample23_3.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/SampleA_2.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/Undetermined_5.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/sampletest_4.pdf",
+                "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/Sample1_1.png",
+                "multiqc/global_report/multiqc_plots/png/Sample23_3.png",
+                "multiqc/global_report/multiqc_plots/png/SampleA_2.png",
+                "multiqc/global_report/multiqc_plots/png/Undetermined_5.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
+                "multiqc/global_report/multiqc_plots/png/sampletest_4.png",
+                "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/Sample1_1.svg",
+                "multiqc/global_report/multiqc_plots/svg/Sample23_3.svg",
+                "multiqc/global_report/multiqc_plots/svg/SampleA_2.svg",
+                "multiqc/global_report/multiqc_plots/svg/Undetermined_5.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
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+                "multiqc/group_reports/test/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc.log",
+                "multiqc/group_reports/test/multiqc_data/multiqc_Sample23_3.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_Undetermined_5.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_citations.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_data.json",
+                "multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_sampletest_4.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/test/multiqc_plots",
+                "multiqc/group_reports/test/multiqc_plots/pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/Sample23_3.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/Undetermined_5.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/sampletest_4.pdf",
+                "multiqc/group_reports/test/multiqc_plots/png",
+                "multiqc/group_reports/test/multiqc_plots/png/Sample23_3.png",
+                "multiqc/group_reports/test/multiqc_plots/png/Undetermined_5.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/test/multiqc_plots/png/general_stats_table.png",
+                "multiqc/group_reports/test/multiqc_plots/png/sampletest_4.png",
+                "multiqc/group_reports/test/multiqc_plots/svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/Sample23_3.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/Undetermined_5.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/sampletest_4.svg",
+                "multiqc/group_reports/test/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "seqfu_stats",
+                "seqfu_stats/Sample1_1.tsv",
+                "seqfu_stats/Sample1_1_mqc.txt",
+                "seqfu_stats/Sample23_3.tsv",
+                "seqfu_stats/Sample23_3_mqc.txt",
+                "seqfu_stats/SampleA_2.tsv",
+                "seqfu_stats/SampleA_2_mqc.txt",
+                "seqfu_stats/Undetermined_5.tsv",
+                "seqfu_stats/Undetermined_5_mqc.txt",
+                "seqfu_stats/sampletest_4.tsv",
+                "seqfu_stats/sampletest_4_mqc.txt"
+            ],
+            [
+                "Sample1_1_fastqc.html:md5,358c1d6e7ea23b531312d88b51f525fa",
+                "Sample23_3_fastqc.html:md5,5b2b55815c667515184d1591fc57249b",
+                "SampleA_2_fastqc.html:md5,ecc7ab9529216dac84acc864bde7c839",
+                "Undetermined_5_fastqc.html:md5,ec71c3ad29df3c70411777b0bcbddd61",
+                "sampletest_4_fastqc.html:md5,62fc1e99df0da04e3dd5e17fa608a763",
+                "Sample1_1_screen.png:md5,562256290643b51e4374c2225a15f463",
+                "Sample1_1_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "Sample23_3_screen.png:md5,6bb2caf67b9b2ed25d3d5f32c343e9ab",
+                "Sample23_3_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "SampleA_2_screen.png:md5,b2c3e95e034f5c038754bf108537de0e",
+                "SampleA_2_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "Undetermined_5_screen.png:md5,fc5d53f8876dfae3d1a781fa512ea1db",
+                "Undetermined_5_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "sampletest_4_screen.png:md5,1fb60070e8f4b70de0c1b3786b54f27e",
+                "sampletest_4_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "fastq_screen_plot.txt:md5,562b783630f698c3220c951b73b87027",
+                "fastqc-status-check-heatmap.txt:md5,6cd55dc80642c78b5e0d71821b83fe2e",
+                "fastqc_overrepresented_sequences_plot.txt:md5,37fd53c396d047467fbd38c5c4a0c4ba",
+                "fastqc_per_base_n_content_plot.txt:md5,75aee7627205c6513389d7a52e7a383b",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,2a60a8518caad855e842cf70a8037dad",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,1325b4b3971f7d4d544d9e252abf47b9",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,ef663c12746dfb88f7297b891756fadd",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,5a224c4e837ba42c16b724289bb1bf32",
+                "fastqc_sequence_counts_plot.txt:md5,20364b3b979bc99ae375a2dffcaf1cc1",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,7f33f3d0e2eb3405eb6456acbd18dfd4",
+                "fastqc_sequence_length_distribution_plot.txt:md5,9472fb38f57150d55fb9e4995aaeeb90",
+                "multiqc_Sample1_1.txt:md5,000ff826a01fcae9fe0bf43fa11df1dc",
+                "multiqc_Sample23_3.txt:md5,b5434520fa5be5c98be5ed164a464d23",
+                "multiqc_SampleA_2.txt:md5,3ce1aacaff46ea0df3fbbb07da9dba6a",
+                "multiqc_Undetermined_5.txt:md5,9dffb6858b809b9bb97ca450158abb6c",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
+                "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d",
+                "multiqc_sampletest_4.txt:md5,ded2705a3247b72dffb5367bcb5f95b8",
+                "fastq_screen_plot.txt:md5,c25d34568f10f131156294d31fbfa994",
+                "fastqc-status-check-heatmap.txt:md5,67afbf7ec626c4fc7a28b4922352bc84",
+                "fastqc_overrepresented_sequences_plot.txt:md5,0356d007eaf807f7b63714b438b11289",
+                "fastqc_per_base_n_content_plot.txt:md5,4c5bfb1594b391f3e36a9e1223b43a94",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,6251cde1646484446499252bd15c58a2",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,f645e38916efafd07d4c2c3d5c7cd051",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,a9d3152a43988e39fae4a75faa3a5aa4",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,aef487a8b267a14a92be64b0b01d9b5c",
+                "fastqc_sequence_counts_plot.txt:md5,5021496dd00366d08064804bbb5192e3",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,e37e8e4584f0157a5fa0d53b4834e836",
+                "fastqc_sequence_length_distribution_plot.txt:md5,393cc090200a5151561efb1ed5280b89",
+                "multiqc_Sample1_1.txt:md5,000ff826a01fcae9fe0bf43fa11df1dc",
+                "multiqc_SampleA_2.txt:md5,3ce1aacaff46ea0df3fbbb07da9dba6a",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
+                "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
+                "fastq_screen_plot.txt:md5,44fca6453b0a3d0590271bd7a31cc740",
+                "fastqc-status-check-heatmap.txt:md5,b6872d9dbaa3cce396d48dc137076e53",
+                "fastqc_overrepresented_sequences_plot.txt:md5,eac8d0fd31c614d8d0f56bd54ee8c78c",
+                "fastqc_per_base_n_content_plot.txt:md5,b7b249afe807ca2321e6dd839961795c",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,3bca5f0121d27b0777a40a4ab44e2abc",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,ee29af5517a8c6f872adbaccea4ff2f8",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,3eaf12f9267c10e4e457a2bb9bdc70ea",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,1818e0b917e45a583740f2cbb0638f8d",
+                "fastqc_sequence_counts_plot.txt:md5,0c4863a5475a2444cd00b053eb8941b1",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,a7a050f827a4f821117efd8d25668c51",
+                "fastqc_sequence_length_distribution_plot.txt:md5,9c0761008be04d8ccf4c0e16acc6348c",
+                "multiqc_Sample23_3.txt:md5,b5434520fa5be5c98be5ed164a464d23",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
+                "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
+                "fastq_screen_plot.txt:md5,5f748d33a7a396547fe8c260b728aa06",
+                "fastqc-status-check-heatmap.txt:md5,08228a8f3d6f11b174b98626bb22bda1",
+                "fastqc_overrepresented_sequences_plot.txt:md5,3434dfb79f150e2e584e85866983ba01",
+                "fastqc_per_base_n_content_plot.txt:md5,e371981072ec99d11c6adb5a4034808c",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,bf83d019eaaeb1ca659ff28cfb2bdfea",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,3f40b8ee69d3eaefe657cc5ed622cc8b",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,86b61d09437a96448e1325e6be834048",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,9f7307469b112bd054f8ee0cc2cf4d65",
+                "fastqc_sequence_counts_plot.txt:md5,f0c693cc281a6e61ba219bab04f59a47",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,8c2aa91358fd4a2e946cbcc1f312f9b6",
+                "fastqc_sequence_length_distribution_plot.txt:md5,875ebcd6726bb9d36ffa64265e5071d0",
+                "multiqc_Sample1_1.txt:md5,000ff826a01fcae9fe0bf43fa11df1dc",
+                "multiqc_Sample23_3.txt:md5,b5434520fa5be5c98be5ed164a464d23",
+                "multiqc_SampleA_2.txt:md5,3ce1aacaff46ea0df3fbbb07da9dba6a",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
+                "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
+                "fastq_screen_plot.txt:md5,8622e1dbd0fe62520af6096207b9775d",
+                "fastqc-status-check-heatmap.txt:md5,2a66f5d61b9eb579555905cd5954b04c",
+                "fastqc_overrepresented_sequences_plot.txt:md5,e0b5bfc4b64d37611b51c939e61196fa",
+                "fastqc_per_base_n_content_plot.txt:md5,1380831484d1b069a2fd4a20437118bf",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,12585cf6b03db684a5ebd959f51e77e7",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a1464399e84711454499d27e98ed942b",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,026d11e7b49a49ac7bac85f376760305",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,4d646b20970d09d846947b87961efe7e",
+                "fastqc_sequence_counts_plot.txt:md5,057fb961863b325fe875d3a7879cb888",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,3b86c9d8625c439376102f3286c7bba7",
+                "fastqc_sequence_length_distribution_plot.txt:md5,6296c9ddbf8ba8e12053149d057fd7b2",
+                "multiqc_Sample23_3.txt:md5,b5434520fa5be5c98be5ed164a464d23",
+                "multiqc_Undetermined_5.txt:md5,9dffb6858b809b9bb97ca450158abb6c",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5",
+                "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
+                "multiqc_sampletest_4.txt:md5,ded2705a3247b72dffb5367bcb5f95b8",
+                "Sample1_1.tsv:md5,269fabf8435defcd327aa69a050b7869",
+                "Sample1_1_mqc.txt:md5,a354b0ed16b9cf84aa88f501d7740fd6",
+                "Sample23_3.tsv:md5,6fdadbeeefccbf957f880d6852bf9676",
+                "Sample23_3_mqc.txt:md5,e94269e3efc8b8192d7ac9c15ea2aa99",
+                "SampleA_2.tsv:md5,b980ed694a05825fcf7c8b5b73888eb3",
+                "SampleA_2_mqc.txt:md5,1d4b0e918644cf553108b7ccf77b4a01",
+                "Undetermined_5.tsv:md5,b4458d41df4dee9321da03f4d4672aae",
+                "Undetermined_5_mqc.txt:md5,0c869488cb61d2f87758c621bded212b",
+                "sampletest_4.tsv:md5,db3179b0c41a09e6317a5a5c0852f476",
+                "sampletest_4_mqc.txt:md5,590b97cc48268629204f59007bae7ad7"
+            ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.10.2"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-05T15:16:34.893751981"
+        "timestamp": "2025-02-03T16:42:55.549005"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test b/tests/PromethION.main.nf.test
index 126a58c1..5cb291ef 100644
--- a/tests/PromethION.main.nf.test
+++ b/tests/PromethION.main.nf.test
@@ -15,15 +15,28 @@ nextflow_pipeline {
         }
 
         then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(
+                params.outdir,
+                relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']
+            )
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(
+                params.outdir,
+                ignoreFile: 'tests/.nftignore'
+            )
             assertAll(
-                { assert workflow.success },
+                { assert workflow.success},
                 { assert snapshot(
-                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt"),
-                    ).match()
-                },
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
+                    // All stable path names, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
             )
         }
     }
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index 7d0a6bfe..6e3f39c1 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -1,15 +1,144 @@
 {
     "PromethION data test": {
         "content": [
-            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-            "multiqc_fastqc.txt:md5,1a4b472e13cadc770832b0e20d1de7b0",
-            "multiqc_general_stats.txt:md5,409cefc7f17f95d176ced6032bf8fb32",
-            "multiqc_fastq_screen.txt:md5,7c5d711e27c53d13c81644a1f2468dba"
+            4,
+            {
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "FASTQSCREEN_FASTQSCREEN": {
+                    "fastqscreen": "0.16.0"
+                },
+                "SEQFU_STATS": {
+                    "seqfu": "1.20.3"
+                },
+                "Workflow": {
+                    "nf-core/seqinspector": "v1.0dev"
+                }
+            },
+            [
+                "fastqc",
+                "fastqc/hg001_1_fastqc.html",
+                "fastqc/hg001_1_fastqc.zip",
+                "fastqscreen",
+                "fastqscreen/hg001_1_screen.html",
+                "fastqscreen/hg001_1_screen.png",
+                "fastqscreen/hg001_1_screen.txt",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/global_report/multiqc_data/fastqc_adapter_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_hg001_1.txt",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_plots",
+                "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/hg001_1.pdf",
+                "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_adapter_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
+                "multiqc/global_report/multiqc_plots/png/hg001_1.png",
+                "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/hg001_1.svg",
+                "multiqc/global_report/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "seqfu_stats",
+                "seqfu_stats/hg001_1.tsv",
+                "seqfu_stats/hg001_1_mqc.txt"
+            ],
+            [
+                "hg001_1_fastqc.html:md5,e1c944e38d02d26a2220fdb0ead48114",
+                "hg001_1_screen.png:md5,b9c58e388f18ad11f4c2e29e9b573a5e",
+                "hg001_1_screen.txt:md5,8e53ea043d658a130f4b8ca455e2ba9b",
+                "fastq_screen_plot.txt:md5,3023b86477fecf6d46d8fc60d82cc53a",
+                "fastqc-status-check-heatmap.txt:md5,825668e94de27356f0a112beb758e416",
+                "fastqc_adapter_content_plot.txt:md5,1fa991080c20755e5e729a5eeab960e5",
+                "fastqc_overrepresented_sequences_plot.txt:md5,e810a3d3eba0ba83b122763505f511a7",
+                "fastqc_per_base_n_content_plot.txt:md5,cbdb64298ff839665e8c8c8e89896e87",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,4962950bc3ce77169ac510d64cb769c6",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,e62273533304be59dab5f13afef93b3e",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,3d49290a15406cb5dac1460c02729f0f",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,7cc10d1bc92ca09431a506c38d911228",
+                "fastqc_sequence_counts_plot.txt:md5,0425d7298c24df6158d5bf7aca1d4190",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,9111d942c7eed5af0e9ccb8c42db8505",
+                "fastqc_sequence_length_distribution_plot.txt:md5,04adfcd0125ebcc3e3bb631f1956c812",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,7c5d711e27c53d13c81644a1f2468dba",
+                "multiqc_fastqc.txt:md5,1a4b472e13cadc770832b0e20d1de7b0",
+                "multiqc_hg001_1.txt:md5,9595d608ff5709f2bdec8cb1016416c0",
+                "hg001_1.tsv:md5,b133752c897afbb4d8721b911fa117d4",
+                "hg001_1_mqc.txt:md5,6285f582c03faa70e8dcb3503e5db728"
+            ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.10.2"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-05T15:18:25.176791779"
+        "timestamp": "2025-02-03T16:45:47.047432"
     }
 }
\ No newline at end of file

From c4ecdd3a3285c18e722028f91a4bd061c7bcac49 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 4 Feb 2025 10:13:05 +0100
Subject: [PATCH 167/530] Exclude fastqc/*_fastqc.html files

---
 tests/.nftignore                    | 2 +-
 tests/MiSeq.main.nf.test.snap       | 3 +--
 tests/NovaSeq6000.main.nf.test.snap | 7 +------
 tests/PromethION.main.nf.test.snap  | 3 +--
 4 files changed, 4 insertions(+), 11 deletions(-)

diff --git a/tests/.nftignore b/tests/.nftignore
index 504be1c6..ded3eac7 100644
--- a/tests/.nftignore
+++ b/tests/.nftignore
@@ -9,4 +9,4 @@ multiqc/{global_report,group_reports/*}/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,p
 multiqc/{global_report,group_reports/*}/multiqc_report.html
 pipeline_info/*.{html,json,txt,yml}
 fastqscreen/*_screen.html
-fastqc/*_fastqc.zip
+fastqc/*_fastqc.{html,zip}
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 66996292..71bf40cc 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -104,7 +104,6 @@
                 "seqfu_stats/SAMPLE_SINGLE_END_1_mqc.txt"
             ],
             [
-                "SAMPLE_SINGLE_END_1_fastqc.html:md5,a299e4a9a0b5aa289d6a325b71f915ce",
                 "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
                 "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
                 "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
@@ -129,7 +128,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-02-03T16:39:35.285693"
+        "timestamp": "2025-02-04T10:07:47.514983"
     },
     "Miseq data test (skip all tools)": {
         "content": [
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index 0a9ab878..6838297d 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -477,11 +477,6 @@
                 "seqfu_stats/sampletest_4_mqc.txt"
             ],
             [
-                "Sample1_1_fastqc.html:md5,358c1d6e7ea23b531312d88b51f525fa",
-                "Sample23_3_fastqc.html:md5,5b2b55815c667515184d1591fc57249b",
-                "SampleA_2_fastqc.html:md5,ecc7ab9529216dac84acc864bde7c839",
-                "Undetermined_5_fastqc.html:md5,ec71c3ad29df3c70411777b0bcbddd61",
-                "sampletest_4_fastqc.html:md5,62fc1e99df0da04e3dd5e17fa608a763",
                 "Sample1_1_screen.png:md5,562256290643b51e4374c2225a15f463",
                 "Sample1_1_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
                 "Sample23_3_screen.png:md5,6bb2caf67b9b2ed25d3d5f32c343e9ab",
@@ -592,6 +587,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-02-03T16:42:55.549005"
+        "timestamp": "2025-02-04T10:10:13.268943"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index 6e3f39c1..c256a372 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -112,7 +112,6 @@
                 "seqfu_stats/hg001_1_mqc.txt"
             ],
             [
-                "hg001_1_fastqc.html:md5,e1c944e38d02d26a2220fdb0ead48114",
                 "hg001_1_screen.png:md5,b9c58e388f18ad11f4c2e29e9b573a5e",
                 "hg001_1_screen.txt:md5,8e53ea043d658a130f4b8ca455e2ba9b",
                 "fastq_screen_plot.txt:md5,3023b86477fecf6d46d8fc60d82cc53a",
@@ -139,6 +138,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-02-03T16:45:47.047432"
+        "timestamp": "2025-02-04T10:12:21.446251"
     }
 }
\ No newline at end of file

From 4f242c3c5f98d9a71eb8647fa4a81ae88811ba18 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 4 Feb 2025 10:42:25 +0100
Subject: [PATCH 168/530] Update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6086d786..3ea1be05 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 
 ### `Added`
 
+- [#75](https://github.com/nf-core/seqinspector/pull/75) Set up nft-utils
 - [#68](https://github.com/nf-core/seqinspector/pull/68) Add tool selector
 - [#20](https://github.com/nf-core/seqinspector/pull/20) Use tags to generate group reports
 - [#13](https://github.com/nf-core/seqinspector/pull/13) Generate reports per run, per project and per lane.

From 726d931808a896f11c6c46119aaa6e37c964401c Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Mon, 17 Mar 2025 17:09:51 +0100
Subject: [PATCH 169/530] use parameter-supplied fastqscreen reference instead
 of hardcoded example

---
 workflows/seqinspector.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 4afff158..910ac3c7 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -82,7 +82,7 @@ workflow SEQINSPECTOR {
 
     ch_fastqscreen_refs = Channel
         .fromList(samplesheetToList(
-            "${projectDir}/assets/example_fastq_screen_references.csv",
+            params.fastq_screen_references,
             "${projectDir}/assets/schema_fastq_screen_references.json"
         ))
         .toList()

From 38325e7c5ffb8f0f541c0198a4118aa5a5b090d5 Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Mon, 17 Mar 2025 17:15:42 +0100
Subject: [PATCH 170/530] typo

---
 workflows/seqinspector.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 1a6b6dc0..9488cea0 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -88,7 +88,7 @@ workflow SEQINSPECTOR {
     if (!("fastqscreen" in skip_tools)) {
         ch_fastqscreen_refs = Channel
             .fromList(samplesheetToList(
-                params.fastq_screen_references.csv,
+                params.fastq_screen_references,
                 "${projectDir}/assets/schema_fastq_screen_references.json"
             ))
             .toList()

From 99bd09ab4d74efbfee1a064a936c045d4fb2260b Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Tue, 18 Mar 2025 11:26:25 +0100
Subject: [PATCH 171/530] add assertions

---
 workflows/seqinspector.nf | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 9488cea0..45c77681 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -86,6 +86,10 @@ workflow SEQINSPECTOR {
     // and transpose it into a tuple containing lists for each property
 
     if (!("fastqscreen" in skip_tools)) {
+
+        assert params.fastq_screen_references; "params.fastq_screen_references is not defined, either supply it or skip running FastQ Screen"
+        assert file(params.fastq_screen_references).exists(); "params.fastq_screen_references does not exist, either supply it or skip running FastQ Screen"
+
         ch_fastqscreen_refs = Channel
             .fromList(samplesheetToList(
                 params.fastq_screen_references,

From 56cbcd308de1c134db905ce1a0d26feb93f311c6 Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Tue, 18 Mar 2025 11:34:02 +0100
Subject: [PATCH 172/530] Revert "add assertions"

This reverts commit 99bd09ab4d74efbfee1a064a936c045d4fb2260b.
---
 workflows/seqinspector.nf | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 45c77681..9488cea0 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -86,10 +86,6 @@ workflow SEQINSPECTOR {
     // and transpose it into a tuple containing lists for each property
 
     if (!("fastqscreen" in skip_tools)) {
-
-        assert params.fastq_screen_references; "params.fastq_screen_references is not defined, either supply it or skip running FastQ Screen"
-        assert file(params.fastq_screen_references).exists(); "params.fastq_screen_references does not exist, either supply it or skip running FastQ Screen"
-
         ch_fastqscreen_refs = Channel
             .fromList(samplesheetToList(
                 params.fastq_screen_references,

From 8446f5891ebc3849ff34107437924353626bcdc0 Mon Sep 17 00:00:00 2001
From: Mac <mac@employee-17-200.eduroam.muni.cz>
Date: Mon, 24 Mar 2025 16:06:42 +0100
Subject: [PATCH 173/530] Added missing citations to citation tool

---
 .../main.nf                                   | 32 +++++++++----------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index 70994073..31405ac2 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -229,27 +229,27 @@ def genomeExistsError() {
 // Generate methods description for MultiQC
 //
 def toolCitationText() {
-    // TODO nf-core: Optionally add in-text citation tools to this list.
-    // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "",
-    // Uncomment function in methodsDescriptionText to render in MultiQC report
     def citation_text = [
-            "Tools used in the workflow included:",
-            "FastQC (Andrews 2010),",
-            "MultiQC (Ewels et al. 2016)",
-            "."
-        ].join(' ').trim()
+        "Tools used in the workflow included:",
+        "FastQC (Andrews 2010),",
+        "MultiQC (Ewels et al. 2016),",
+        "FastQ Screen (Wingett & Andrews 2018)",
+        params.sample_size > 0 ? "Seqtk (Li 2021)," : "",
+        "SeqFu (Telatin et al. 2021),",
+        "."
+    ].join(' ').trim()
 
     return citation_text
 }
 
 def toolBibliographyText() {
-    // TODO nf-core: Optionally add bibliographic entries to this list.
-    // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "<li>Author (2023) Pub name, Journal, DOI</li>" : "",
-    // Uncomment function in methodsDescriptionText to render in MultiQC report
     def reference_text = [
-            "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).</li>",
-            "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>"
-        ].join(' ').trim()
+        "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.</li>",
+        "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics, 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>",
+        "<li>Wingett SW, Andrews S. FastQ Screen: A tool for multi-genome mapping and quality control. F1000Res. 2018 Aug 24 [revised 2018 Jan 1];7:1338. doi: 10.12688/f1000research.15931.2. eCollection</li>",
+        params.sample_size > 0 ? "<li>Li, H. SeqTk. Available online: https://github.com/lh3/seqtk (accessed on 6 May 2021)</li>" : "",
+        "<li>Telatin, A.; Fariselli, P.; Birolo, G. SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files. Bioengineering 2021, 8, 59. https://doi.org/10.3390/bioengineering8050059</li>"
+    ].join(' ').trim()
 
     return reference_text
 }
@@ -279,8 +279,8 @@ def methodsDescriptionText(mqc_methods_yaml) {
     meta["tool_bibliography"] = ""
 
     // TODO nf-core: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
-    // meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
-    // meta["tool_bibliography"] = toolBibliographyText()
+    meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
+    meta["tool_bibliography"] = toolBibliographyText()
 
 
     def methods_text = mqc_methods_yaml.text

From 6cab526998bcf94971997c8135cb78ee35b9b6d1 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Mon, 24 Mar 2025 16:55:45 +0000
Subject: [PATCH 174/530] wip, need container with pyyaml

---
 modules/local/rundirparser/environment.yml    |  7 ++
 modules/local/rundirparser/main.nf            | 69 ++++++++++++++++++
 modules/local/rundirparser/meta.yml           | 68 +++++++++++++++++
 modules/local/rundirparser/rundirparser.py    | 27 +++++++
 modules/local/rundirparser/tests/main.nf.test | 73 +++++++++++++++++++
 workflows/seqinspector.nf                     | 14 ++++
 6 files changed, 258 insertions(+)
 create mode 100644 modules/local/rundirparser/environment.yml
 create mode 100644 modules/local/rundirparser/main.nf
 create mode 100644 modules/local/rundirparser/meta.yml
 create mode 100644 modules/local/rundirparser/rundirparser.py
 create mode 100644 modules/local/rundirparser/tests/main.nf.test

diff --git a/modules/local/rundirparser/environment.yml b/modules/local/rundirparser/environment.yml
new file mode 100644
index 00000000..4b3c9d37
--- /dev/null
+++ b/modules/local/rundirparser/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "YOUR-TOOL-HERE"
diff --git a/modules/local/rundirparser/main.nf b/modules/local/rundirparser/main.nf
new file mode 100644
index 00000000..751640c1
--- /dev/null
+++ b/modules/local/rundirparser/main.nf
@@ -0,0 +1,69 @@
+// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
+//               https://github.com/nf-core/modules/tree/master/modules/nf-core/
+//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
+//               https://nf-co.re/join
+// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
+//               All other parameters MUST be provided using the "task.ext" directive, see here:
+//               https://www.nextflow.io/docs/latest/process.html#ext
+//               where "task.ext" is a string.
+//               Any parameters that need to be evaluated in the context of a particular sample
+//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
+// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
+//               unless there is a run-time, storage advantage in implementing in this way
+//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
+//                 bwa mem | samtools view -B -T ref.fasta
+// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
+//               list (`[]`) instead of a file can be used to work around this issue.
+
+process RUNDIRPARSER {
+    tag "$rundir.baseName"
+    label 'process_single'
+
+    // TODO nf-core: List required Conda package(s).
+    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
+    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
+    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
+    conda "python=3.12"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/python:3.12' :
+        'python:3.12' }"
+
+    input:
+    path(rundir)
+    path(parser_script)
+
+    output:
+    path("*_mqc.yaml"), emit: yaml
+    path "versions.yml", emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${rundir.baseName}"
+    """
+    python ${parser_script} ${rundir}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        rundirparser: \$(python --version |& sed '1!d ; s/Python //')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${rundir.baseName}"
+    // TODO nf-core: A stub section should mimic the execution of the original module as best as possible
+    //               Have a look at the following examples:
+    //               Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63
+    //               Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54
+    """
+    touch rundir_metadata.yml
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        rundirparser: "stub_version"
+    END_VERSIONS
+    """
+}
diff --git a/modules/local/rundirparser/meta.yml b/modules/local/rundirparser/meta.yml
new file mode 100644
index 00000000..7027a80d
--- /dev/null
+++ b/modules/local/rundirparser/meta.yml
@@ -0,0 +1,68 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "rundirparser"
+## TODO nf-core: Add a description of the module and list keywords
+description: write your description here
+keywords:
+  - sort
+  - example
+  - genomics
+tools:
+  - "rundirparser":
+      ## TODO nf-core: Add a description and other details for the software below
+      description: ""
+      homepage: ""
+      documentation: ""
+      tool_dev_url: ""
+      doi: ""
+      licence:
+      identifier:
+
+## TODO nf-core: Add a description of all of the variables used as input
+input:
+  # Only when we have meta
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+
+    ## TODO nf-core: Delete / customise this example input
+    - bam:
+        type: file
+        description: Sorted BAM/CRAM/SAM file
+        pattern: "*.{bam,cram,sam}"
+        ontologies:
+          - edam: "http://edamontology.org/format_25722"
+          - edam: "http://edamontology.org/format_2573"
+          - edam: "http://edamontology.org/format_3462"
+
+## TODO nf-core: Add a description of all of the variables used as output
+output:
+  - bam:
+      #Only when we have meta
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      ## TODO nf-core: Delete / customise this example output
+      - "*.bam":
+          type: file
+          description: Sorted BAM/CRAM/SAM file
+          pattern: "*.{bam,cram,sam}"
+          ontologies:
+            - edam: "http://edamontology.org/format_25722"
+            - edam: "http://edamontology.org/format_2573"
+            - edam: "http://edamontology.org/format_3462"
+
+  - versions:
+      - "versions.yml":
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+
+authors:
+  - "@kedhammar"
+maintainers:
+  - "@kedhammar"
diff --git a/modules/local/rundirparser/rundirparser.py b/modules/local/rundirparser/rundirparser.py
new file mode 100644
index 00000000..f5056cdc
--- /dev/null
+++ b/modules/local/rundirparser/rundirparser.py
@@ -0,0 +1,27 @@
+# rundirparser.py
+import sys
+import yaml
+
+
+def parse_rundir(rundir):
+    # Dummy implementation, replace with actual logic
+    return_dict = {
+        "rundir": rundir,
+        "samples": [
+            {"sample_id": "SAMPLE_1", "metric_1": 10, "metric_2": 20},
+            {"sample_id": "SAMPLE_2", "metric_1": 15, "metric_2": 25},
+            {"sample_id": "SAMPLE_3", "metric_1": 20, "metric_2": 30},
+        ],
+    }
+    return return_dict
+
+
+def main():
+    rundir = sys.argv[1]
+    metadata = parse_rundir(rundir)
+    with open(f"{rundir}_mqc.yml", "w") as outfile:
+        yaml.dump(metadata, outfile, default_flow_style=False)
+
+
+if __name__ == "__main__":
+    main()
diff --git a/modules/local/rundirparser/tests/main.nf.test b/modules/local/rundirparser/tests/main.nf.test
new file mode 100644
index 00000000..c1e8440f
--- /dev/null
+++ b/modules/local/rundirparser/tests/main.nf.test
@@ -0,0 +1,73 @@
+// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
+// nf-core modules test rundirparser
+nextflow_process {
+
+    name "Test Process RUNDIRPARSER"
+    script "../main.nf"
+    process "RUNDIRPARSER"
+
+    tag "modules"
+    tag "modules_"
+    tag "rundirparser"
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used
+    test("sarscov2 - bam") {
+
+        // TODO nf-core: If you are created a test for a chained module
+        // (the module requires running more than one process to generate the required output)
+        // add the 'setup' method here.
+        // You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules).
+
+        when {
+            process {
+                """
+                // TODO nf-core: define inputs of the process here. Example:
+                
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+                //TODO nf-core: Add all required assertions to verify the test output.
+                // See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples.
+            )
+        }
+
+    }
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
+    test("sarscov2 - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                // TODO nf-core: define inputs of the process here. Example:
+                
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+                //TODO nf-core: Add all required assertions to verify the test output.
+            )
+        }
+
+    }
+
+}
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 9488cea0..dade2511 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -10,6 +10,7 @@ include { SEQTK_SAMPLE                  } from '../modules/nf-core/seqtk/sample/
 include { FASTQC                        } from '../modules/nf-core/fastqc/main'
 include { SEQFU_STATS                   } from '../modules/nf-core/seqfu/stats'
 include { FASTQSCREEN_FASTQSCREEN       } from '../modules/nf-core/fastqscreen/fastqscreen/main'
+include { RUNDIRPARSER                  } from '../modules/local/rundirparser/main'
 
 include { MULTIQC as MULTIQC_GLOBAL     } from '../modules/nf-core/multiqc/main'
 include { MULTIQC as MULTIQC_PER_TAG    } from '../modules/nf-core/multiqc/main'
@@ -38,6 +39,19 @@ workflow SEQINSPECTOR {
     ch_multiqc_extra_files = Channel.empty()
     ch_multiqc_reports     = Channel.empty()
 
+    //
+    // MODULE: Parse rundir info
+    //
+    if (!("rundirparser" in skip_tools)) {
+
+        ch_rundir = ch_samplesheet
+            .map { meta, _reads -> meta.rundir }
+            .distinct()
+            .view()
+
+        RUNDIRPARSER(ch_rundir, "${projectDir}/modules/local/rundirparser/rundirparser.py")
+    }
+
     //
     // MODULE: Run Seqtk sample to perform subsampling
     //

From d3cd57c7515d3c066ec4b4a96ad0952d721d2034 Mon Sep 17 00:00:00 2001
From: Patricie34 <patricie.johnova@email.cz>
Date: Tue, 25 Mar 2025 09:34:38 +0100
Subject: [PATCH 175/530] TODOs removed

---
 .../local/utils_nfcore_seqinspector_pipeline/main.nf         | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index 31405ac2..708d73fb 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -275,14 +275,9 @@ def methodsDescriptionText(mqc_methods_yaml) {
     meta["nodoi_text"] = meta.manifest_map.doi ? "" : "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
 
     // Tool references
-    meta["tool_citations"] = ""
-    meta["tool_bibliography"] = ""
-
-    // TODO nf-core: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
     meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
     meta["tool_bibliography"] = toolBibliographyText()
 
-
     def methods_text = mqc_methods_yaml.text
 
     def engine =  new groovy.text.SimpleTemplateEngine()

From 146e950edba850136cdfe23c9ed3a667b56b7854 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Tue, 25 Mar 2025 08:40:27 +0000
Subject: [PATCH 176/530] fix conda env and functional containers

---
 modules/local/rundirparser/environment.yml | 6 +++---
 modules/local/rundirparser/main.nf         | 8 ++++----
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/modules/local/rundirparser/environment.yml b/modules/local/rundirparser/environment.yml
index 4b3c9d37..046f88d8 100644
--- a/modules/local/rundirparser/environment.yml
+++ b/modules/local/rundirparser/environment.yml
@@ -1,7 +1,7 @@
----
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "YOUR-TOOL-HERE"
+  - pip
+  - pip:
+      - PyYAML==6.0.2
diff --git a/modules/local/rundirparser/main.nf b/modules/local/rundirparser/main.nf
index 751640c1..81a1fe41 100644
--- a/modules/local/rundirparser/main.nf
+++ b/modules/local/rundirparser/main.nf
@@ -23,17 +23,17 @@ process RUNDIRPARSER {
     //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
     //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
     // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
-    conda "python=3.12"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/python:3.12' :
-        'python:3.12' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ad/ad2bcce70756f81c07c7e2ffd9b66213bf48ace786466395ac3a402840df2ffb/data' :
+        'community.wave.seqera.io/library/pip_pyyaml:c2ecf27a7f63796e' }"
 
     input:
     path(rundir)
     path(parser_script)
 
     output:
-    path("*_mqc.yaml"), emit: yaml
+    path("*_mqc.yml"), emit: yaml
     path "versions.yml", emit: versions
 
     when:

From 55857245ef5011d452cb0a00677a545dda0b6a06 Mon Sep 17 00:00:00 2001
From: Patricie34 <patricie.johnova@email.cz>
Date: Tue, 25 Mar 2025 09:59:45 +0100
Subject: [PATCH 177/530] CHANGELOG.md updated

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3ea1be05..530200b3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -19,6 +19,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#51](https://github.com/nf-core/seqinspector/pull/51) Add nf-test to CI.
 - [#63](https://github.com/nf-core/seqinspector/pull/63) Contribution guidelines added about displaying results for new tools
 - [#53](https://github.com/nf-core/seqinspector/pull/53) Add FastQ-Screen database multiplexing and limit scope of nf-test in CI.
+- [#96](https://github.com/nf-core/seqinspector/pull/96) Added missing citations to citation tool
 
 ### `Fixed`
 

From ffc0c6793e6e95caee9ef20654d809d3207ad3db Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Tue, 25 Mar 2025 09:47:30 +0000
Subject: [PATCH 178/530] spacing

---
 modules/nf-core/seqfu/stats/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/seqfu/stats/main.nf b/modules/nf-core/seqfu/stats/main.nf
index 0f8bb3e2..2ea8e439 100644
--- a/modules/nf-core/seqfu/stats/main.nf
+++ b/modules/nf-core/seqfu/stats/main.nf
@@ -14,7 +14,7 @@ process SEQFU_STATS {
 
     output:
     tuple val(meta), path("*.tsv")    ,  emit: stats
-    tuple val(meta), path("*_mqc.txt"), emit: multiqc
+    tuple val(meta), path("*_mqc.txt"),  emit: multiqc
     path "versions.yml"               ,  emit: versions
 
     when:

From 2feea05c214f0294b9362a62dc8a8029bc5f19c0 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Tue, 25 Mar 2025 09:47:54 +0000
Subject: [PATCH 179/530] channel magic to refactor meta on rundir-level

---
 modules/local/rundirparser/main.nf |  6 +++---
 workflows/seqinspector.nf          | 17 ++++++++++++++---
 2 files changed, 17 insertions(+), 6 deletions(-)

diff --git a/modules/local/rundirparser/main.nf b/modules/local/rundirparser/main.nf
index 81a1fe41..de31d5e1 100644
--- a/modules/local/rundirparser/main.nf
+++ b/modules/local/rundirparser/main.nf
@@ -29,12 +29,12 @@ process RUNDIRPARSER {
         'community.wave.seqera.io/library/pip_pyyaml:c2ecf27a7f63796e' }"
 
     input:
-    path(rundir)
+    tuple val(joint_meta), path(rundir)
     path(parser_script)
 
     output:
-    path("*_mqc.yml"), emit: yaml
-    path "versions.yml", emit: versions
+    tuple val(joint_meta), path("*_mqc.yml"), emit: multiqc
+    path "versions.yml",                      emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index dade2511..5f3e4e6a 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -45,11 +45,22 @@ workflow SEQINSPECTOR {
     if (!("rundirparser" in skip_tools)) {
 
         ch_rundir = ch_samplesheet
-            .map { meta, _reads -> meta.rundir }
-            .distinct()
-            .view()
+            // Group by rundir to merge tags from samples with the same rundir
+            .map { meta, _reads -> [meta.rundir, meta] }
+            .groupTuple()
+            // Create a new meta object with merged tags for each unique rundir
+            .map { rundir, metas ->
+                // Collect all tags across all samples with this rundir
+                def all_tags = metas.collect { it.tags }.flatten().unique()
+                // Create a new meta object with the merged tags
+                def new_meta = [tags: all_tags]
+                // Return the new structure
+                [new_meta, rundir]
+            }
 
         RUNDIRPARSER(ch_rundir, "${projectDir}/modules/local/rundirparser/rundirparser.py")
+        ch_multiqc_files = ch_multiqc_files.mix(RUNDIRPARSER.out.multiqc.first())
+        ch_versions = ch_versions.mix(RUNDIRPARSER.out.versions.first())
     }
 
     //

From 59770b4b784f08a240603bbd967734106404805e Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Tue, 25 Mar 2025 10:02:12 +0000
Subject: [PATCH 180/530] update process versioning and stubs

---
 modules/local/rundirparser/main.nf | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/modules/local/rundirparser/main.nf b/modules/local/rundirparser/main.nf
index de31d5e1..3d6ea9ee 100644
--- a/modules/local/rundirparser/main.nf
+++ b/modules/local/rundirparser/main.nf
@@ -47,7 +47,8 @@ process RUNDIRPARSER {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        rundirparser: \$(python --version |& sed '1!d ; s/Python //')
+        Python: \$(python --version |& sed '1!d ; s/Python //')
+        PyYAML: \$(python -c "import yaml; print(yaml.__version__)")
     END_VERSIONS
     """
 
@@ -59,11 +60,12 @@ process RUNDIRPARSER {
     //               Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63
     //               Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54
     """
-    touch rundir_metadata.yml
+    touch rundir_mqc.yml
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        rundirparser: "stub_version"
+        Python: stub_version
+        PyYAML: stub_version
     END_VERSIONS
     """
 }

From 48f5fee280bffcc43e1e9995c6dc4d8e92cc5b26 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Tue, 25 Mar 2025 11:11:32 +0000
Subject: [PATCH 181/530] remove todo:s, make process agnostic to mqc file
 extensions

---
 modules/local/rundirparser/main.nf | 27 +++------------------------
 1 file changed, 3 insertions(+), 24 deletions(-)

diff --git a/modules/local/rundirparser/main.nf b/modules/local/rundirparser/main.nf
index 3d6ea9ee..3c9206aa 100644
--- a/modules/local/rundirparser/main.nf
+++ b/modules/local/rundirparser/main.nf
@@ -1,28 +1,7 @@
-// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
-//               https://github.com/nf-core/modules/tree/master/modules/nf-core/
-//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
-//               https://nf-co.re/join
-// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
-//               All other parameters MUST be provided using the "task.ext" directive, see here:
-//               https://www.nextflow.io/docs/latest/process.html#ext
-//               where "task.ext" is a string.
-//               Any parameters that need to be evaluated in the context of a particular sample
-//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
-// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
-//               unless there is a run-time, storage advantage in implementing in this way
-//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
-//                 bwa mem | samtools view -B -T ref.fasta
-// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
-//               list (`[]`) instead of a file can be used to work around this issue.
-
 process RUNDIRPARSER {
     tag "$rundir.baseName"
     label 'process_single'
 
-    // TODO nf-core: List required Conda package(s).
-    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
-    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ad/ad2bcce70756f81c07c7e2ffd9b66213bf48ace786466395ac3a402840df2ffb/data' :
@@ -33,8 +12,8 @@ process RUNDIRPARSER {
     path(parser_script)
 
     output:
-    tuple val(joint_meta), path("*_mqc.yml"), emit: multiqc
-    path "versions.yml",                      emit: versions
+    tuple val(joint_meta), path("*_mqc.*"), emit: multiqc
+    path "versions.yml",                    emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -60,7 +39,7 @@ process RUNDIRPARSER {
     //               Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63
     //               Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54
     """
-    touch rundir_mqc.yml
+    touch rundir_mqc.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From 812a939ee2c5e79058e00ff34342dfffa83c8b01 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Tue, 25 Mar 2025 11:11:56 +0000
Subject: [PATCH 182/530] generate _mqc.txt dummy file with table from rundir
 keys

---
 modules/local/rundirparser/rundirparser.py | 60 +++++++++++++++++-----
 1 file changed, 48 insertions(+), 12 deletions(-)

diff --git a/modules/local/rundirparser/rundirparser.py b/modules/local/rundirparser/rundirparser.py
index f5056cdc..0820d4e4 100644
--- a/modules/local/rundirparser/rundirparser.py
+++ b/modules/local/rundirparser/rundirparser.py
@@ -5,22 +5,58 @@
 
 def parse_rundir(rundir):
     # Dummy implementation, replace with actual logic
-    return_dict = {
-        "rundir": rundir,
-        "samples": [
-            {"sample_id": "SAMPLE_1", "metric_1": 10, "metric_2": 20},
-            {"sample_id": "SAMPLE_2", "metric_1": 15, "metric_2": 25},
-            {"sample_id": "SAMPLE_3", "metric_1": 20, "metric_2": 30},
-        ],
-    }
-    return return_dict
+
+    yml_contents = """# plot_type: 'table'
+# section_name: 'rundir stats'
+# description: 'dummy rundir stats'
+# pconfig:
+#     namespace: 'Cust Data'
+# headers:
+#     col1:
+#         title: '#Seqs'
+#         description: 'Number of sequences'
+#         format: '{:,.0f}'
+#     col2:
+#         title: 'Total bp'
+#         description: 'Total size of the dataset'
+#     col3:
+#         title: 'Avg'
+#         description: 'Average sequence length'
+#     col4:
+#         title: 'N50'
+#         description: '50% of the sequences are longer than this size'
+#     col5:
+#         title: 'N75'
+#         description: '75% of the sequences are longer than this size'
+#     col6:
+#         title: 'N90'
+#         description: '90% of the sequences are longer than this size'
+#     col7:
+#         title: 'Min'
+#         description: 'Length of the shortest sequence'
+#     col8:
+#         title: 'Max'
+#         description: 'Length of the longest sequence'
+#     col9:
+#         title: 'auN'
+#         description: 'Area under the Nx curve'
+#     col10:
+#         title: 'GC'
+#         description: 'Relative GC content (excluding Ns)'
+"""
+    tsv_contents = f"""Sample	col1	col2	col3	col4	col5	col6	col7	col8	col9	col10
+{rundir}	10	147806	14780.6000000	22507	16573	15322	22801.9181765	344	33340	NaN
+"""
+
+    contents = yml_contents + tsv_contents
+
+    with open(f"{rundir}_mqc.txt", "w") as f:
+        f.write(contents)
 
 
 def main():
     rundir = sys.argv[1]
-    metadata = parse_rundir(rundir)
-    with open(f"{rundir}_mqc.yml", "w") as outfile:
-        yaml.dump(metadata, outfile, default_flow_style=False)
+    parse_rundir(rundir)
 
 
 if __name__ == "__main__":

From ec32f5ac25767f1104e47d15c0d4dfdb51f698d3 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Tue, 25 Mar 2025 11:12:19 +0000
Subject: [PATCH 183/530] clean up formatting and underscore unused variables

---
 workflows/seqinspector.nf | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 5f3e4e6a..c26f9a98 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -150,14 +150,14 @@ workflow SEQINSPECTOR {
         Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
         Channel.empty()
 
-    summary_params                        = paramsSummaryMap(
+    summary_params = paramsSummaryMap(
         workflow, parameters_schema: "nextflow_schema.json")
-    ch_workflow_summary                   = Channel.value(
+    ch_workflow_summary = Channel.value(
         paramsSummaryMultiqc(summary_params))
     ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
         file(params.multiqc_methods_description, checkIfExists: true) :
         file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
-    ch_methods_description                = Channel.value(
+    ch_methods_description = Channel.value(
         methodsDescriptionText(ch_multiqc_custom_methods_description))
 
     ch_multiqc_extra_files = ch_multiqc_extra_files.mix(
@@ -172,7 +172,7 @@ workflow SEQINSPECTOR {
 
     MULTIQC_GLOBAL (
         ch_multiqc_files
-            .map { meta, file -> file }
+            .map { _meta, file -> file }
             .mix(ch_multiqc_extra_files)
             .collect(),
         ch_multiqc_config.toList(),
@@ -183,7 +183,7 @@ workflow SEQINSPECTOR {
     )
 
     ch_tags = ch_multiqc_files
-        .map { meta, sample -> meta.tags }
+        .map { meta, _sample -> meta.tags }
         .flatten()
         .unique()
 
@@ -193,13 +193,13 @@ workflow SEQINSPECTOR {
     // Group samples by tag
     tagged_mqc_files = ch_tags
         .combine(ch_multiqc_files)
-        .filter { sample_tag, meta, sample -> sample_tag in meta.tags }
-        .map { sample_tag, meta, sample -> [sample_tag, sample] }
+        .filter { sample_tag, meta, _sample -> sample_tag in meta.tags }
+        .map { sample_tag, _meta, sample -> [sample_tag, sample] }
         .mix(multiqc_extra_files_per_tag)
         .groupTuple()
         .tap { mqc_by_tag }
         .collectFile {
-            sample_tag, samples ->
+            sample_tag, _samples ->
             def prefix_tag = "[TAG:${sample_tag}]"
             [
                 "${prefix_tag}_multiqc_extra_config.yml",
@@ -212,7 +212,7 @@ workflow SEQINSPECTOR {
         }
         .map { file -> [ (file =~ /\[TAG:(.+)\]/)[0][1], file ] }
         .join(mqc_by_tag)
-        .multiMap { sample_tag, config, samples ->
+        .multiMap { _sample_tag, config, samples ->
             samples_per_tag: samples
             config: config
         }

From b88519f1ac994492651fd03a5bc7d5f134623b17 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 25 Mar 2025 10:34:40 +0100
Subject: [PATCH 184/530] Add test with paired end reads

---
 tests/MiSeq_PairedEnd.main.nf.test        |  43 ++++++
 tests/MiSeq_PairedEnd.main.nf.test.config |   7 +
 tests/MiSeq_PairedEnd.main.nf.test.snap   | 163 ++++++++++++++++++++++
 3 files changed, 213 insertions(+)
 create mode 100644 tests/MiSeq_PairedEnd.main.nf.test
 create mode 100644 tests/MiSeq_PairedEnd.main.nf.test.config
 create mode 100644 tests/MiSeq_PairedEnd.main.nf.test.snap

diff --git a/tests/MiSeq_PairedEnd.main.nf.test b/tests/MiSeq_PairedEnd.main.nf.test
new file mode 100644
index 00000000..df708c99
--- /dev/null
+++ b/tests/MiSeq_PairedEnd.main.nf.test
@@ -0,0 +1,43 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf on MiSeq data"
+    script "../main.nf"
+    tag "seqinspector"
+    tag "PIPELINE"
+
+    test("MiSeq data test") {
+
+        when {
+            config "./MiSeq_PairedEnd.main.nf.test.config"
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(
+                params.outdir,
+                relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']
+            )
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(
+                params.outdir,
+                ignoreFile: 'tests/.nftignore'
+            )
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
+                    // All stable path names, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.config b/tests/MiSeq_PairedEnd.main.nf.test.config
new file mode 100644
index 00000000..279ac0e4
--- /dev/null
+++ b/tests/MiSeq_PairedEnd.main.nf.test.config
@@ -0,0 +1,7 @@
+// Load the basic test config
+includeConfig 'nextflow.config'
+
+// Load the correct samplesheet for that test
+params {
+    input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/Miseq_PairedEnd/samplesheet.csv'
+}
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
new file mode 100644
index 00000000..caa96b30
--- /dev/null
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -0,0 +1,163 @@
+{
+    "MiSeq data test": {
+        "content": [
+            7,
+            {
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "FASTQSCREEN_FASTQSCREEN": {
+                    "fastqscreen": "0.16.0"
+                },
+                "SEQFU_STATS": {
+                    "seqfu": "1.20.3"
+                },
+                "Workflow": {
+                    "nf-core/seqinspector": "v1.0dev"
+                }
+            },
+            [
+                "fastqc",
+                "fastqc/SAMPLE_PAIRED_END_1_1_1_fastqc.html",
+                "fastqc/SAMPLE_PAIRED_END_1_1_1_fastqc.zip",
+                "fastqc/SAMPLE_PAIRED_END_1_1_2_fastqc.html",
+                "fastqc/SAMPLE_PAIRED_END_1_1_2_fastqc.zip",
+                "fastqc/SAMPLE_PAIRED_END_2_2_1_fastqc.html",
+                "fastqc/SAMPLE_PAIRED_END_2_2_1_fastqc.zip",
+                "fastqc/SAMPLE_PAIRED_END_2_2_2_fastqc.html",
+                "fastqc/SAMPLE_PAIRED_END_2_2_2_fastqc.zip",
+                "fastqscreen",
+                "fastqscreen/SAMPLE_PAIRED_END_1_1_1_screen.html",
+                "fastqscreen/SAMPLE_PAIRED_END_1_1_1_screen.png",
+                "fastqscreen/SAMPLE_PAIRED_END_1_1_1_screen.txt",
+                "fastqscreen/SAMPLE_PAIRED_END_1_1_2_screen.html",
+                "fastqscreen/SAMPLE_PAIRED_END_1_1_2_screen.png",
+                "fastqscreen/SAMPLE_PAIRED_END_1_1_2_screen.txt",
+                "fastqscreen/SAMPLE_PAIRED_END_2_2_1_screen.html",
+                "fastqscreen/SAMPLE_PAIRED_END_2_2_1_screen.png",
+                "fastqscreen/SAMPLE_PAIRED_END_2_2_1_screen.txt",
+                "fastqscreen/SAMPLE_PAIRED_END_2_2_2_screen.html",
+                "fastqscreen/SAMPLE_PAIRED_END_2_2_2_screen.png",
+                "fastqscreen/SAMPLE_PAIRED_END_2_2_2_screen.txt",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/global_report/multiqc_data/fastqc_adapter_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc_SAMPLE_PAIRED_END_1_1.txt",
+                "multiqc/global_report/multiqc_data/multiqc_SAMPLE_PAIRED_END_2_2.txt",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_plots",
+                "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/SAMPLE_PAIRED_END_1_1.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/SAMPLE_PAIRED_END_2_2.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/SAMPLE_PAIRED_END_1_1.png",
+                "multiqc/global_report/multiqc_plots/png/SAMPLE_PAIRED_END_2_2.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_adapter_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
+                "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/SAMPLE_PAIRED_END_1_1.svg",
+                "multiqc/global_report/multiqc_plots/svg/SAMPLE_PAIRED_END_2_2.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/global_report/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "seqfu_stats",
+                "seqfu_stats/SAMPLE_PAIRED_END_1_1.tsv",
+                "seqfu_stats/SAMPLE_PAIRED_END_1_1_mqc.txt",
+                "seqfu_stats/SAMPLE_PAIRED_END_2_2.tsv",
+                "seqfu_stats/SAMPLE_PAIRED_END_2_2_mqc.txt"
+            ],
+            [
+                "SAMPLE_PAIRED_END_1_1_1_screen.png:md5,f52ddd0e65f23f68dd8d58d5453417db",
+                "SAMPLE_PAIRED_END_1_1_1_screen.txt:md5,921b08eeb461a2aa1bd42bba53900f70",
+                "SAMPLE_PAIRED_END_1_1_2_screen.png:md5,908f4fceea8aa546106efdaa7ca78f7d",
+                "SAMPLE_PAIRED_END_1_1_2_screen.txt:md5,e9ea5789e356f666de27ba658704e80d",
+                "SAMPLE_PAIRED_END_2_2_1_screen.png:md5,48d546767ed2a34a1eda59d97dd00c18",
+                "SAMPLE_PAIRED_END_2_2_1_screen.txt:md5,a5b047f495d01bf9dcb0ae516d3c7fc3",
+                "SAMPLE_PAIRED_END_2_2_2_screen.png:md5,e3684b17339d16e6fb64ace7593cc388",
+                "SAMPLE_PAIRED_END_2_2_2_screen.txt:md5,fc95e5058e764596d5da182cbc0614cf",
+                "fastq_screen_plot.txt:md5,642264b93871c724aaa5d38b91c752dd",
+                "fastqc-status-check-heatmap.txt:md5,8e29ad6b23e03267c33bd9ed3385a44b",
+                "fastqc_adapter_content_plot.txt:md5,46fbd727a4996a3f0310d0423c628445",
+                "fastqc_per_base_n_content_plot.txt:md5,4eca1ef40d4d3d318b82e68e9fa3c589",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,218757a51c3de79a39a704c979df03da",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a4035ac9f0a0c07574130758b06630d7",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,637b937e023c84115ec06b529cc8ec1b",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,47d60153a430e2b8da51655704c2b31b",
+                "fastqc_sequence_counts_plot.txt:md5,10737092a3473fba81fbe49555512b2b",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,6412f57686de02e1f1c3751a7ca2be8b",
+                "multiqc_SAMPLE_PAIRED_END_1_1.txt:md5,f6a5c7426b2c70dba8566b1f27d27fbf",
+                "multiqc_SAMPLE_PAIRED_END_2_2.txt:md5,f531e01892d985ca20fc4924dec7b9f2",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,5ef00028497d3271c9f0ea9a961db1e5",
+                "multiqc_fastqc.txt:md5,bc499ad273fd1c887056c31b82544984",
+                "SAMPLE_PAIRED_END_1_1.tsv:md5,bbd911ff3fa43212dfd4c5a5872dbdb6",
+                "SAMPLE_PAIRED_END_1_1_mqc.txt:md5,cd60f746b6749cc66213d031af1b931c",
+                "SAMPLE_PAIRED_END_2_2.tsv:md5,152566a128dd657da33465b4966b5799",
+                "SAMPLE_PAIRED_END_2_2_mqc.txt:md5,8a3296956e094e3a95e28431e6009c40"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-03-25T10:33:30.467558"
+    }
+}
\ No newline at end of file

From 506f19d1f98cf7a01315cddffc37183ec6e6a882 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 25 Mar 2025 12:02:28 +0100
Subject: [PATCH 185/530] Fix group reports for paired reads

---
 tests/MiSeq_PairedEnd.main.nf.test.snap | 96 ++++++++++++++++++++++++-
 workflows/seqinspector.nf               |  2 +-
 2 files changed, 95 insertions(+), 3 deletions(-)

diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index caa96b30..028a96be 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "MiSeq data test": {
         "content": [
-            7,
+            8,
             {
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -116,6 +116,83 @@
                 "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
                 "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
                 "multiqc/global_report/multiqc_report.html",
+                "multiqc/group_reports",
+                "multiqc/group_reports/Bpacificus",
+                "multiqc/group_reports/Bpacificus/multiqc_data",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_adapter_content_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc.log",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_SAMPLE_PAIRED_END_1_1.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_SAMPLE_PAIRED_END_2_2.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_citations.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_data.json",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_plots",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/SAMPLE_PAIRED_END_1_1.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/SAMPLE_PAIRED_END_2_2.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/SAMPLE_PAIRED_END_1_1.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/SAMPLE_PAIRED_END_2_2.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_adapter_content_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/general_stats_table.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/SAMPLE_PAIRED_END_1_1.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/SAMPLE_PAIRED_END_2_2.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "seqfu_stats",
@@ -148,6 +225,21 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,5ef00028497d3271c9f0ea9a961db1e5",
                 "multiqc_fastqc.txt:md5,bc499ad273fd1c887056c31b82544984",
+                "fastq_screen_plot.txt:md5,642264b93871c724aaa5d38b91c752dd",
+                "fastqc-status-check-heatmap.txt:md5,8e29ad6b23e03267c33bd9ed3385a44b",
+                "fastqc_adapter_content_plot.txt:md5,46fbd727a4996a3f0310d0423c628445",
+                "fastqc_per_base_n_content_plot.txt:md5,4eca1ef40d4d3d318b82e68e9fa3c589",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,218757a51c3de79a39a704c979df03da",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a4035ac9f0a0c07574130758b06630d7",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,637b937e023c84115ec06b529cc8ec1b",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,47d60153a430e2b8da51655704c2b31b",
+                "fastqc_sequence_counts_plot.txt:md5,10737092a3473fba81fbe49555512b2b",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,6412f57686de02e1f1c3751a7ca2be8b",
+                "multiqc_SAMPLE_PAIRED_END_1_1.txt:md5,f6a5c7426b2c70dba8566b1f27d27fbf",
+                "multiqc_SAMPLE_PAIRED_END_2_2.txt:md5,f531e01892d985ca20fc4924dec7b9f2",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,5ef00028497d3271c9f0ea9a961db1e5",
+                "multiqc_fastqc.txt:md5,bc499ad273fd1c887056c31b82544984",
                 "SAMPLE_PAIRED_END_1_1.tsv:md5,bbd911ff3fa43212dfd4c5a5872dbdb6",
                 "SAMPLE_PAIRED_END_1_1_mqc.txt:md5,cd60f746b6749cc66213d031af1b931c",
                 "SAMPLE_PAIRED_END_2_2.tsv:md5,152566a128dd657da33465b4966b5799",
@@ -158,6 +250,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-03-25T10:33:30.467558"
+        "timestamp": "2025-03-25T12:00:04.338174"
     }
 }
\ No newline at end of file
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 9488cea0..bd936fa9 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -188,7 +188,7 @@ workflow SEQINSPECTOR {
         .map { file -> [ (file =~ /\[TAG:(.+)\]/)[0][1], file ] }
         .join(mqc_by_tag)
         .multiMap { sample_tag, config, samples ->
-            samples_per_tag: samples
+            samples_per_tag: samples.flatten()
             config: config
         }
 

From 04f445bada2627b12263ae187ab3c4887e032557 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 25 Mar 2025 12:19:16 +0100
Subject: [PATCH 186/530] Update Changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 530200b3..562cb4cf 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -24,6 +24,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 ### `Fixed`
 
 - [#71](https://github.com/nf-core/seqinspector/pull/71) FASTQSCREEN does not fail when multiple reads are provided.
+- [#99](https://github.com/nf-core/seqinspector/pull/99) Fix group reports for paired reads
 
 ### `Dependencies`
 

From 7b75818f0b9ff2b973cb195326f4098cc72c92e6 Mon Sep 17 00:00:00 2001
From: Franziska Bonath <41994400+FranBonath@users.noreply.github.com>
Date: Tue, 25 Mar 2025 12:48:56 +0100
Subject: [PATCH 187/530] add official seqinspector hex logos

---
 .../nfcore-seqinspector-logo-hex-dark.png     | Bin 0 -> 15346 bytes
 .../nfcore-seqinspector-logo-hex-dark.svg     | 224 +++++++++++++++
 .../nfcore-seqinspector-logo-hex-light.png    | Bin 0 -> 15477 bytes
 .../nfcore-seqinspector-logo-hex-light.svg    | 255 ++++++++++++++++++
 4 files changed, 479 insertions(+)
 create mode 100644 docs/images/nfcore-seqinspector-logo-hex-dark.png
 create mode 100644 docs/images/nfcore-seqinspector-logo-hex-dark.svg
 create mode 100644 docs/images/nfcore-seqinspector-logo-hex-light.png
 create mode 100644 docs/images/nfcore-seqinspector-logo-hex-light.svg

diff --git a/docs/images/nfcore-seqinspector-logo-hex-dark.png b/docs/images/nfcore-seqinspector-logo-hex-dark.png
new file mode 100644
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From 57592513006172fb4c504be4e650612401596fa1 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Tue, 25 Mar 2025 11:52:45 +0000
Subject: [PATCH 188/530] use module binary instead of supplying script as
 process input

---
 modules/local/rundirparser/main.nf                             | 3 +--
 .../local/rundirparser/{ => resources/usr/bin}/rundirparser.py | 2 +-
 nextflow.config                                                | 3 +++
 workflows/seqinspector.nf                                      | 2 +-
 4 files changed, 6 insertions(+), 4 deletions(-)
 rename modules/local/rundirparser/{ => resources/usr/bin}/rundirparser.py (98%)
 mode change 100644 => 100755

diff --git a/modules/local/rundirparser/main.nf b/modules/local/rundirparser/main.nf
index 3c9206aa..86591fb9 100644
--- a/modules/local/rundirparser/main.nf
+++ b/modules/local/rundirparser/main.nf
@@ -9,7 +9,6 @@ process RUNDIRPARSER {
 
     input:
     tuple val(joint_meta), path(rundir)
-    path(parser_script)
 
     output:
     tuple val(joint_meta), path("*_mqc.*"), emit: multiqc
@@ -22,7 +21,7 @@ process RUNDIRPARSER {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${rundir.baseName}"
     """
-    python ${parser_script} ${rundir}
+    rundirparser.py ${rundir}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/rundirparser/rundirparser.py b/modules/local/rundirparser/resources/usr/bin/rundirparser.py
old mode 100644
new mode 100755
similarity index 98%
rename from modules/local/rundirparser/rundirparser.py
rename to modules/local/rundirparser/resources/usr/bin/rundirparser.py
index 0820d4e4..6a965f9f
--- a/modules/local/rundirparser/rundirparser.py
+++ b/modules/local/rundirparser/resources/usr/bin/rundirparser.py
@@ -1,4 +1,4 @@
-# rundirparser.py
+#!/usr/bin/env python
 import sys
 import yaml
 
diff --git a/nextflow.config b/nextflow.config
index bb1cb279..caefca9f 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -6,6 +6,9 @@
 ----------------------------------------------------------------------------------------
 */
 
+// Enable use of module binaries for e.g. module specific Python scripts
+nextflow.enable.moduleBinaries = true
+
 // Global default params, used in configs
 params {
 
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index c26f9a98..ea26529e 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -58,7 +58,7 @@ workflow SEQINSPECTOR {
                 [new_meta, rundir]
             }
 
-        RUNDIRPARSER(ch_rundir, "${projectDir}/modules/local/rundirparser/rundirparser.py")
+        RUNDIRPARSER( ch_rundir )
         ch_multiqc_files = ch_multiqc_files.mix(RUNDIRPARSER.out.multiqc.first())
         ch_versions = ch_versions.mix(RUNDIRPARSER.out.versions.first())
     }

From 7e32710f47e132113b97bdaa4bd568e07b930f7a Mon Sep 17 00:00:00 2001
From: Karthik Nair <karthik.nair1194@gmail.com>
Date: Tue, 25 Mar 2025 14:56:42 +0100
Subject: [PATCH 189/530] Configure full-tests

Co-authored-by: Adrien Coulier <adrien.coulier@medsci.uu.se>
---
 .github/workflows/awsfulltest.yml | 3 ---
 conf/test_full.config             | 5 ++---
 2 files changed, 2 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 311d3d07..4e9a944b 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -45,9 +45,6 @@ jobs:
 
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
-        # TODO nf-core: You can customise AWS full pipeline tests as required
-        # Add full size test data (but still relatively small datasets for few samples)
-        # on the `test_full.config` test runs with only one set of parameters
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
diff --git a/conf/test_full.config b/conf/test_full.config
index 53b22883..65f0a532 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -10,14 +10,13 @@
 ----------------------------------------------------------------------------------------
 */
 
+
 params {
     config_profile_name        = 'Full test profile'
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
-    // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
-    // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
+    input = params.pipelines_testdata_base_path + 'seqinspector/full_tests/SampleSheet.csv'
 
     // Genome references
     genome = 'R64-1-1'

From c9b337d221dff157e751f9820ac388c1b319ebf2 Mon Sep 17 00:00:00 2001
From: Karthik Nair <karthik.nair1194@gmail.com>
Date: Tue, 25 Mar 2025 15:08:08 +0100
Subject: [PATCH 190/530] Update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 562cb4cf..0062af4a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -20,6 +20,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#63](https://github.com/nf-core/seqinspector/pull/63) Contribution guidelines added about displaying results for new tools
 - [#53](https://github.com/nf-core/seqinspector/pull/53) Add FastQ-Screen database multiplexing and limit scope of nf-test in CI.
 - [#96](https://github.com/nf-core/seqinspector/pull/96) Added missing citations to citation tool
+- [#103](https://github.com/nf-core/seqinspector/pull/103) Configure full-tests
 
 ### `Fixed`
 

From 6e7f1ee198ccc82c4b4d750f381762a40723687a Mon Sep 17 00:00:00 2001
From: FranBonath <franziska.bonath@scilifelab.se>
Date: Tue, 25 Mar 2025 15:13:27 +0100
Subject: [PATCH 191/530] improve logos

---
 .../nfcore-seqinspector-logo-hex-dark.png     | Bin 15346 -> 15347 bytes
 .../nfcore-seqinspector-logo-hex-dark.svg     | 153 +++++++-------
 .../nfcore-seqinspector-logo-hex-light.png    | Bin 15477 -> 15551 bytes
 .../nfcore-seqinspector-logo-hex-light.svg    | 188 +++++++++---------
 4 files changed, 173 insertions(+), 168 deletions(-)

diff --git a/docs/images/nfcore-seqinspector-logo-hex-dark.png b/docs/images/nfcore-seqinspector-logo-hex-dark.png
index 666736b731d55d487a309cf533e568751fd8c59e..d92e0d09e60b0276288f368a049814ef8d221d4f 100644
GIT binary patch
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-                 id="text53-6-5-0-7-1-3"
+            </g>
+            <text
+               id="text53-6-5-0-7-1-3"
+               x="-125.72501"
+               y="349.245"
+               font-size="209.87"
+               font-weight="bold"
+               style="font-weight:700;font-size:209.87px;font-family:'Maven Pro'"><tspan
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-                 id="text69-63-6-5-3-9-5"
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+               id="text69-63-6-5-3-9-5"
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+                 id="tspan71-9-2-9-5-4-6"
                  x="182.517"
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+            <path
+               id="path67-8-7-8-1-0-1"
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From 9327c9d128f60b9f315afc9c4beee1b0028c6371 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Tue, 25 Mar 2025 14:23:10 +0000
Subject: [PATCH 192/530] add all multiqc files to channel, not just first

---
 workflows/seqinspector.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index ea26529e..d0af8142 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -59,7 +59,7 @@ workflow SEQINSPECTOR {
             }
 
         RUNDIRPARSER( ch_rundir )
-        ch_multiqc_files = ch_multiqc_files.mix(RUNDIRPARSER.out.multiqc.first())
+        ch_multiqc_files = ch_multiqc_files.mix(RUNDIRPARSER.out.multiqc)
         ch_versions = ch_versions.mix(RUNDIRPARSER.out.versions.first())
     }
 

From 84f98e3c6176179d948bb2afe2b4a317f25e3260 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Tue, 25 Mar 2025 15:02:34 +0000
Subject: [PATCH 193/530] extend suffix to differentiate from other _mqc files

---
 modules/local/rundirparser/main.nf                           | 2 +-
 modules/local/rundirparser/resources/usr/bin/rundirparser.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/local/rundirparser/main.nf b/modules/local/rundirparser/main.nf
index 86591fb9..8c18b8a1 100644
--- a/modules/local/rundirparser/main.nf
+++ b/modules/local/rundirparser/main.nf
@@ -11,7 +11,7 @@ process RUNDIRPARSER {
     tuple val(joint_meta), path(rundir)
 
     output:
-    tuple val(joint_meta), path("*_mqc.*"), emit: multiqc
+    tuple val(joint_meta), path("*_rundir_mqc.*"), emit: multiqc
     path "versions.yml",                    emit: versions
 
     when:
diff --git a/modules/local/rundirparser/resources/usr/bin/rundirparser.py b/modules/local/rundirparser/resources/usr/bin/rundirparser.py
index 6a965f9f..9e08887f 100755
--- a/modules/local/rundirparser/resources/usr/bin/rundirparser.py
+++ b/modules/local/rundirparser/resources/usr/bin/rundirparser.py
@@ -50,7 +50,7 @@ def parse_rundir(rundir):
 
     contents = yml_contents + tsv_contents
 
-    with open(f"{rundir}_mqc.txt", "w") as f:
+    with open(f"{rundir}_rundir_mqc.txt", "w") as f:
         f.write(contents)
 
 

From 0b9efcb9f92836b0e85389f1dd16ee807c1aebdd Mon Sep 17 00:00:00 2001
From: nelnk861 <nelly.nkonge@uu.se>
Date: Wed, 26 Mar 2025 09:47:12 +0100
Subject: [PATCH 194/530] Put SeqFU-stats section reports together

Co-authored-by: Adrien Coulier <adrien.coulier@medsci.uu.se>
Co-authored-by: Karthik Nair <karthik.nair@medsci.uu.se>"
---
 workflows/seqinspector.nf | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 9488cea0..e05a2c89 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -73,6 +73,9 @@ workflow SEQINSPECTOR {
     if (!("seqfu_stats" in skip_tools)) {
         SEQFU_STATS (
             ch_samplesheet
+            .map { meta, reads ->               
+                [[id:"global", tags: meta.tags], reads] 
+            }
         )
         ch_multiqc_files = ch_multiqc_files.mix(SEQFU_STATS.out.multiqc)
         ch_versions = ch_versions.mix(SEQFU_STATS.out.versions.first())

From 19e8e0bbe8bc4c2f3c8dffc70cf1263bcfee07f8 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Wed, 26 Mar 2025 08:49:46 +0000
Subject: [PATCH 195/530] give mqc outputs the same name so they will be merged
 automatically in the multiqc report generation, make function take output
 name as cmd parameter

---
 modules/local/rundirparser/main.nf               | 16 ++++++----------
 .../resources/usr/bin/rundirparser.py            |  7 ++++---
 2 files changed, 10 insertions(+), 13 deletions(-)

diff --git a/modules/local/rundirparser/main.nf b/modules/local/rundirparser/main.nf
index 8c18b8a1..fe123234 100644
--- a/modules/local/rundirparser/main.nf
+++ b/modules/local/rundirparser/main.nf
@@ -11,17 +11,17 @@ process RUNDIRPARSER {
     tuple val(joint_meta), path(rundir)
 
     output:
-    tuple val(joint_meta), path("*_rundir_mqc.*"), emit: multiqc
+    tuple val(joint_meta), path("*_mqc.*"), emit: multiqc
     path "versions.yml",                    emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${rundir.baseName}"
+    // def args = task.ext.args ?: ''
+    // def prefix = task.ext.prefix ?: "${rundir.baseName}"
     """
-    rundirparser.py ${rundir}
+    rundirparser.py ${rundir} ${moduleDir.baseName}_mqc.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -31,12 +31,8 @@ process RUNDIRPARSER {
     """
 
     stub:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${rundir.baseName}"
-    // TODO nf-core: A stub section should mimic the execution of the original module as best as possible
-    //               Have a look at the following examples:
-    //               Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63
-    //               Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54
+    // def args = task.ext.args ?: ''
+    // def prefix = task.ext.prefix ?: "${rundir.baseName}"
     """
     touch rundir_mqc.txt
 
diff --git a/modules/local/rundirparser/resources/usr/bin/rundirparser.py b/modules/local/rundirparser/resources/usr/bin/rundirparser.py
index 9e08887f..68e91df0 100755
--- a/modules/local/rundirparser/resources/usr/bin/rundirparser.py
+++ b/modules/local/rundirparser/resources/usr/bin/rundirparser.py
@@ -3,7 +3,7 @@
 import yaml
 
 
-def parse_rundir(rundir):
+def parse_rundir(rundir, outname):
     # Dummy implementation, replace with actual logic
 
     yml_contents = """# plot_type: 'table'
@@ -50,13 +50,14 @@ def parse_rundir(rundir):
 
     contents = yml_contents + tsv_contents
 
-    with open(f"{rundir}_rundir_mqc.txt", "w") as f:
+    with open(outname, "w") as f:
         f.write(contents)
 
 
 def main():
     rundir = sys.argv[1]
-    parse_rundir(rundir)
+    outname = sys.argv[2]
+    parse_rundir(rundir, outname)
 
 
 if __name__ == "__main__":

From 218901d0bde775b13c99b6b57df458848ca4e504 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Wed, 26 Mar 2025 09:07:48 +0000
Subject: [PATCH 196/530] actually, let the script differentiate between seq
 platforms and name the outfile accordingly, for proper downstream grouping

---
 modules/local/rundirparser/main.nf                 |  2 +-
 .../rundirparser/resources/usr/bin/rundirparser.py | 14 +++++++++++---
 2 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/modules/local/rundirparser/main.nf b/modules/local/rundirparser/main.nf
index fe123234..bc96977c 100644
--- a/modules/local/rundirparser/main.nf
+++ b/modules/local/rundirparser/main.nf
@@ -21,7 +21,7 @@ process RUNDIRPARSER {
     // def args = task.ext.args ?: ''
     // def prefix = task.ext.prefix ?: "${rundir.baseName}"
     """
-    rundirparser.py ${rundir} ${moduleDir.baseName}_mqc.txt
+    rundirparser.py ${rundir}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/rundirparser/resources/usr/bin/rundirparser.py b/modules/local/rundirparser/resources/usr/bin/rundirparser.py
index 68e91df0..b8db68df 100755
--- a/modules/local/rundirparser/resources/usr/bin/rundirparser.py
+++ b/modules/local/rundirparser/resources/usr/bin/rundirparser.py
@@ -3,9 +3,11 @@
 import yaml
 
 
-def parse_rundir(rundir, outname):
+def parse_rundir(rundir):
     # Dummy implementation, replace with actual logic
 
+    sequencing_platform = None
+
     yml_contents = """# plot_type: 'table'
 # section_name: 'rundir stats'
 # description: 'dummy rundir stats'
@@ -50,14 +52,20 @@ def parse_rundir(rundir, outname):
 
     contents = yml_contents + tsv_contents
 
+    """
+    File names should be unique between sequencing platforms, but otherwise identical
+    so multiple rundirs of the same platform will be written to the same table
+    in the MultiQC report.
+    """
+    outname = f"{sequencing_platform or 'rundirparser'}_mqc.txt"
+
     with open(outname, "w") as f:
         f.write(contents)
 
 
 def main():
     rundir = sys.argv[1]
-    outname = sys.argv[2]
-    parse_rundir(rundir, outname)
+    parse_rundir(rundir)
 
 
 if __name__ == "__main__":

From 29f2af493853be56c940da04f4fe1647ce7bf3d8 Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Wed, 26 Mar 2025 10:36:55 +0100
Subject: [PATCH 197/530] editorconfig

---
 modules/local/rundirparser/tests/main.nf.test | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/local/rundirparser/tests/main.nf.test b/modules/local/rundirparser/tests/main.nf.test
index c1e8440f..0dc321de 100644
--- a/modules/local/rundirparser/tests/main.nf.test
+++ b/modules/local/rundirparser/tests/main.nf.test
@@ -22,7 +22,7 @@ nextflow_process {
             process {
                 """
                 // TODO nf-core: define inputs of the process here. Example:
-                
+
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
@@ -51,7 +51,7 @@ nextflow_process {
             process {
                 """
                 // TODO nf-core: define inputs of the process here. Example:
-                
+
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),

From 79b91124302c915bec5590549417af90977320c6 Mon Sep 17 00:00:00 2001
From: Patricie34 <patricie.johnova@email.cz>
Date: Wed, 26 Mar 2025 10:50:35 +0100
Subject: [PATCH 198/530] Test data validated, TODO removed

---
 conf/test.config | 2 --
 1 file changed, 2 deletions(-)

diff --git a/conf/test.config b/conf/test.config
index 0ebc405a..1b222be6 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -23,8 +23,6 @@ params {
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Input data
-    // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
-    // TODO nf-core: Give any required params for the test so that command line flags are not needed
     input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
     fastq_screen_references = "${projectDir}/assets/example_fastq_screen_references.csv"
 

From fc9373bb3e6caa7a583f85c9bebdbd9e1b9e9ac5 Mon Sep 17 00:00:00 2001
From: Patricie34 <patricie.johnova@email.cz>
Date: Wed, 26 Mar 2025 11:02:45 +0100
Subject: [PATCH 199/530] CHANGELOG.md updated

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0062af4a..b06aa3ca 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -21,6 +21,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#53](https://github.com/nf-core/seqinspector/pull/53) Add FastQ-Screen database multiplexing and limit scope of nf-test in CI.
 - [#96](https://github.com/nf-core/seqinspector/pull/96) Added missing citations to citation tool
 - [#103](https://github.com/nf-core/seqinspector/pull/103) Configure full-tests
+- [#94](https://github.com/nf-core/seqinspector/issues/94) Test data validation
 
 ### `Fixed`
 

From 5976a05046dd1aae75e1fae61a7f920c4b0b358b Mon Sep 17 00:00:00 2001
From: Patricie34 <patricie.johnova@email.cz>
Date: Wed, 26 Mar 2025 12:29:06 +0100
Subject: [PATCH 200/530] List of default steps in README.md

---
 README.md | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 6cf36dcc..3582178e 100644
--- a/README.md
+++ b/README.md
@@ -29,11 +29,12 @@
 
 <!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
      workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->
-<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
 
 1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))
 2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-3. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+3. Sequence statistics ([`SeqFu Stats`](https://github.com/telatin/seqfu2))
+4. Contamination QC ([`FastQ Screen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/))
+5. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
 
 ## Usage
 

From c6e0d7b58cf074961a7e022d1a0b5d3bf54824c4 Mon Sep 17 00:00:00 2001
From: Patricie34 <patricie.johnova@email.cz>
Date: Wed, 26 Mar 2025 12:30:32 +0100
Subject: [PATCH 201/530] CHANGELOG.md update

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b06aa3ca..65627095 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -22,6 +22,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#96](https://github.com/nf-core/seqinspector/pull/96) Added missing citations to citation tool
 - [#103](https://github.com/nf-core/seqinspector/pull/103) Configure full-tests
 - [#94](https://github.com/nf-core/seqinspector/issues/94) Test data validation
+- [#86](https://github.com/nf-core/seqinspector/issues/86) Update lists of default steps in the pipeline
 
 ### `Fixed`
 

From b038d2e4fd9f56ec2c6df8a4cdc33b0075be5c32 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Wed, 26 Mar 2025 13:16:25 +0100
Subject: [PATCH 202/530] Fix tests

Co-authored-by: nelnk861 <nelly.nkonge@uu.se>
Co-authored-by: kedhammar <alfred.kedhammar@scilifelab.se>
---
 conf/modules.config                     |   2 +-
 tests/MiSeq.main.nf.test                |   4 +-
 tests/MiSeq.main.nf.test.snap           | 108 +++++++++---------
 tests/MiSeq_PairedEnd.main.nf.test      |   4 +-
 tests/MiSeq_PairedEnd.main.nf.test.snap |  50 ++++-----
 tests/NovaSeq6000.main.nf.test.snap     | 139 ++++++++----------------
 tests/PromethION.main.nf.test.snap      |  22 ++--
 workflows/seqinspector.nf               |   4 +-
 8 files changed, 139 insertions(+), 194 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 4a653ed0..5a0b7ccd 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -31,7 +31,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/seqfu_stats" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.sample_id}_$filename" }
         ]
     }
 
diff --git a/tests/MiSeq.main.nf.test b/tests/MiSeq.main.nf.test
index 0ed7052a..439715c1 100644
--- a/tests/MiSeq.main.nf.test
+++ b/tests/MiSeq.main.nf.test
@@ -1,11 +1,11 @@
 nextflow_pipeline {
 
-    name "Test Workflow main.nf on MiSeq data"
+    name "Test Workflow main.nf on MiSeq data with single end reads"
     script "../main.nf"
     tag "seqinspector"
     tag "PIPELINE"
 
-    test("MiSeq data test") {
+    test("MiSeq data test (single end reads)") {
 
         when {
             config "./MiSeq.main.nf.test.config"
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 71bf40cc..beee2404 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -1,5 +1,36 @@
 {
-    "MiSeq data test": {
+    "Miseq data test (skip all tools)": {
+        "content": [
+            1,
+            {
+                "Workflow": {
+                    "nf-core/seqinspector": "v1.0dev"
+                }
+            },
+            [
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"
+            ],
+            [
+                "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-07T13:49:22.707398"
+    },
+    "MiSeq data test (single end reads)": {
         "content": [
             4,
             {
@@ -39,17 +70,16 @@
                 "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
                 "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
                 "multiqc/global_report/multiqc_data/multiqc.log",
-                "multiqc/global_report/multiqc_data/multiqc_SAMPLE_SINGLE_END_1.txt",
                 "multiqc/global_report/multiqc_data/multiqc_citations.txt",
                 "multiqc/global_report/multiqc_data/multiqc_data.json",
                 "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
-                "multiqc/global_report/multiqc_plots/pdf/SAMPLE_SINGLE_END_1.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
@@ -64,8 +94,8 @@
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
-                "multiqc/global_report/multiqc_plots/png/SAMPLE_SINGLE_END_1.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
@@ -80,8 +110,8 @@
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
-                "multiqc/global_report/multiqc_plots/svg/SAMPLE_SINGLE_END_1.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
@@ -96,12 +126,13 @@
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
                 "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "seqfu_stats",
-                "seqfu_stats/SAMPLE_SINGLE_END_1.tsv",
-                "seqfu_stats/SAMPLE_SINGLE_END_1_mqc.txt"
+                "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu.tsv",
+                "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu_mqc.txt"
             ],
             [
                 "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
@@ -116,50 +147,19 @@
                 "fastqc_per_sequence_quality_scores_plot.txt:md5,5fda43eb9b7c60cf6b4348f734a94b26",
                 "fastqc_sequence_counts_plot.txt:md5,00cd6842465f7aa9ae75434e175946a6",
                 "fastqc_sequence_duplication_levels_plot.txt:md5,c3befe0812d2f1c23d5e75e6fccf0622",
-                "multiqc_SAMPLE_SINGLE_END_1.txt:md5,8e6989a2392f599a09a5c3edf8119702",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607",
                 "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
-                "SAMPLE_SINGLE_END_1.tsv:md5,f65c868e562291647d539090698ba5eb",
-                "SAMPLE_SINGLE_END_1_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.3"
-        },
-        "timestamp": "2025-02-04T10:07:47.514983"
-    },
-    "Miseq data test (skip all tools)": {
-        "content": [
-            1,
-            {
-                "Workflow": {
-                    "nf-core/seqinspector": "v1.0dev"
-                }
-            },
-            [
-                "multiqc",
-                "multiqc/global_report",
-                "multiqc/global_report/multiqc_data",
-                "multiqc/global_report/multiqc_data/multiqc.log",
-                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
-                "multiqc/global_report/multiqc_data/multiqc_data.json",
-                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
-                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
-                "multiqc/global_report/multiqc_report.html",
-                "pipeline_info",
-                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"
-            ],
-            [
-                "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
+                "multiqc_seqfu.txt:md5,8e6989a2392f599a09a5c3edf8119702",
+                "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,f65c868e562291647d539090698ba5eb",
+                "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.10.3"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-07T13:49:22.707398"
+        "timestamp": "2025-03-26T13:00:21.042755"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
@@ -185,47 +185,47 @@
                 "multiqc/global_report/multiqc_data",
                 "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
                 "multiqc/global_report/multiqc_data/multiqc.log",
-                "multiqc/global_report/multiqc_data/multiqc_SAMPLE_SINGLE_END_1.txt",
                 "multiqc/global_report/multiqc_data/multiqc_citations.txt",
                 "multiqc/global_report/multiqc_data/multiqc_data.json",
                 "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
-                "multiqc/global_report/multiqc_plots/pdf/SAMPLE_SINGLE_END_1.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
-                "multiqc/global_report/multiqc_plots/png/SAMPLE_SINGLE_END_1.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
-                "multiqc/global_report/multiqc_plots/svg/SAMPLE_SINGLE_END_1.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "seqfu_stats",
-                "seqfu_stats/SAMPLE_SINGLE_END_1.tsv",
-                "seqfu_stats/SAMPLE_SINGLE_END_1_mqc.txt"
+                "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu.tsv",
+                "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu_mqc.txt"
             ],
             [
                 "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
                 "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
                 "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
-                "multiqc_SAMPLE_SINGLE_END_1.txt:md5,8e6989a2392f599a09a5c3edf8119702",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607",
-                "SAMPLE_SINGLE_END_1.tsv:md5,f65c868e562291647d539090698ba5eb",
-                "SAMPLE_SINGLE_END_1_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
+                "multiqc_seqfu.txt:md5,8e6989a2392f599a09a5c3edf8119702",
+                "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,f65c868e562291647d539090698ba5eb",
+                "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.10.3"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-02-03T16:40:27.8664"
+        "timestamp": "2025-03-26T13:00:53.07934"
     }
 }
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.main.nf.test b/tests/MiSeq_PairedEnd.main.nf.test
index df708c99..92807e95 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test
+++ b/tests/MiSeq_PairedEnd.main.nf.test
@@ -1,11 +1,11 @@
 nextflow_pipeline {
 
-    name "Test Workflow main.nf on MiSeq data"
+    name "Test Workflow main.nf on MiSeq data with paired end reads"
     script "../main.nf"
     tag "seqinspector"
     tag "PIPELINE"
 
-    test("MiSeq data test") {
+    test("MiSeq data test (paired end reads)") {
 
         when {
             config "./MiSeq_PairedEnd.main.nf.test.config"
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index 028a96be..6a5c6992 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "MiSeq data test": {
+    "MiSeq data test (paired end reads)": {
         "content": [
             8,
             {
@@ -54,19 +54,16 @@
                 "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
                 "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
                 "multiqc/global_report/multiqc_data/multiqc.log",
-                "multiqc/global_report/multiqc_data/multiqc_SAMPLE_PAIRED_END_1_1.txt",
-                "multiqc/global_report/multiqc_data/multiqc_SAMPLE_PAIRED_END_2_2.txt",
                 "multiqc/global_report/multiqc_data/multiqc_citations.txt",
                 "multiqc/global_report/multiqc_data/multiqc_data.json",
                 "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
-                "multiqc/global_report/multiqc_plots/pdf/SAMPLE_PAIRED_END_1_1.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/SAMPLE_PAIRED_END_2_2.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
@@ -81,9 +78,8 @@
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
-                "multiqc/global_report/multiqc_plots/png/SAMPLE_PAIRED_END_1_1.png",
-                "multiqc/global_report/multiqc_plots/png/SAMPLE_PAIRED_END_2_2.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
@@ -98,9 +94,8 @@
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
-                "multiqc/global_report/multiqc_plots/svg/SAMPLE_PAIRED_END_1_1.svg",
-                "multiqc/global_report/multiqc_plots/svg/SAMPLE_PAIRED_END_2_2.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
@@ -115,6 +110,7 @@
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
                 "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "multiqc/group_reports",
                 "multiqc/group_reports/Bpacificus",
@@ -131,19 +127,16 @@
                 "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc.log",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_SAMPLE_PAIRED_END_1_1.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_SAMPLE_PAIRED_END_2_2.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_citations.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_data.json",
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_plots",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/SAMPLE_PAIRED_END_1_1.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/SAMPLE_PAIRED_END_2_2.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
@@ -158,9 +151,8 @@
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/SAMPLE_PAIRED_END_1_1.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/SAMPLE_PAIRED_END_2_2.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-pct.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc-status-check-heatmap.png",
@@ -175,9 +167,8 @@
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/general_stats_table.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/SAMPLE_PAIRED_END_1_1.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/SAMPLE_PAIRED_END_2_2.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-pct.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
@@ -192,14 +183,15 @@
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "seqfu_stats",
-                "seqfu_stats/SAMPLE_PAIRED_END_1_1.tsv",
-                "seqfu_stats/SAMPLE_PAIRED_END_1_1_mqc.txt",
-                "seqfu_stats/SAMPLE_PAIRED_END_2_2.tsv",
-                "seqfu_stats/SAMPLE_PAIRED_END_2_2_mqc.txt"
+                "seqfu_stats/SAMPLE_PAIRED_END_1_1_seqfu.tsv",
+                "seqfu_stats/SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt",
+                "seqfu_stats/SAMPLE_PAIRED_END_2_2_seqfu.tsv",
+                "seqfu_stats/SAMPLE_PAIRED_END_2_2_seqfu_mqc.txt"
             ],
             [
                 "SAMPLE_PAIRED_END_1_1_1_screen.png:md5,f52ddd0e65f23f68dd8d58d5453417db",
@@ -220,11 +212,10 @@
                 "fastqc_per_sequence_quality_scores_plot.txt:md5,47d60153a430e2b8da51655704c2b31b",
                 "fastqc_sequence_counts_plot.txt:md5,10737092a3473fba81fbe49555512b2b",
                 "fastqc_sequence_duplication_levels_plot.txt:md5,6412f57686de02e1f1c3751a7ca2be8b",
-                "multiqc_SAMPLE_PAIRED_END_1_1.txt:md5,f6a5c7426b2c70dba8566b1f27d27fbf",
-                "multiqc_SAMPLE_PAIRED_END_2_2.txt:md5,f531e01892d985ca20fc4924dec7b9f2",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,5ef00028497d3271c9f0ea9a961db1e5",
                 "multiqc_fastqc.txt:md5,bc499ad273fd1c887056c31b82544984",
+                "multiqc_seqfu.txt:md5,1f1e063e4a509a26cee167c3b20389c0",
                 "fastq_screen_plot.txt:md5,642264b93871c724aaa5d38b91c752dd",
                 "fastqc-status-check-heatmap.txt:md5,8e29ad6b23e03267c33bd9ed3385a44b",
                 "fastqc_adapter_content_plot.txt:md5,46fbd727a4996a3f0310d0423c628445",
@@ -235,21 +226,20 @@
                 "fastqc_per_sequence_quality_scores_plot.txt:md5,47d60153a430e2b8da51655704c2b31b",
                 "fastqc_sequence_counts_plot.txt:md5,10737092a3473fba81fbe49555512b2b",
                 "fastqc_sequence_duplication_levels_plot.txt:md5,6412f57686de02e1f1c3751a7ca2be8b",
-                "multiqc_SAMPLE_PAIRED_END_1_1.txt:md5,f6a5c7426b2c70dba8566b1f27d27fbf",
-                "multiqc_SAMPLE_PAIRED_END_2_2.txt:md5,f531e01892d985ca20fc4924dec7b9f2",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,5ef00028497d3271c9f0ea9a961db1e5",
                 "multiqc_fastqc.txt:md5,bc499ad273fd1c887056c31b82544984",
-                "SAMPLE_PAIRED_END_1_1.tsv:md5,bbd911ff3fa43212dfd4c5a5872dbdb6",
-                "SAMPLE_PAIRED_END_1_1_mqc.txt:md5,cd60f746b6749cc66213d031af1b931c",
-                "SAMPLE_PAIRED_END_2_2.tsv:md5,152566a128dd657da33465b4966b5799",
-                "SAMPLE_PAIRED_END_2_2_mqc.txt:md5,8a3296956e094e3a95e28431e6009c40"
+                "multiqc_seqfu.txt:md5,1f1e063e4a509a26cee167c3b20389c0",
+                "SAMPLE_PAIRED_END_1_1_seqfu.tsv:md5,bbd911ff3fa43212dfd4c5a5872dbdb6",
+                "SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt:md5,cd60f746b6749cc66213d031af1b931c",
+                "SAMPLE_PAIRED_END_2_2_seqfu.tsv:md5,152566a128dd657da33465b4966b5799",
+                "SAMPLE_PAIRED_END_2_2_seqfu_mqc.txt:md5,8a3296956e094e3a95e28431e6009c40"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-03-25T12:00:04.338174"
+        "timestamp": "2025-03-26T13:02:05.27761"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index 6838297d..fa851d95 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -60,24 +60,16 @@
                 "multiqc/global_report/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
                 "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
                 "multiqc/global_report/multiqc_data/multiqc.log",
-                "multiqc/global_report/multiqc_data/multiqc_Sample1_1.txt",
-                "multiqc/global_report/multiqc_data/multiqc_Sample23_3.txt",
-                "multiqc/global_report/multiqc_data/multiqc_SampleA_2.txt",
-                "multiqc/global_report/multiqc_data/multiqc_Undetermined_5.txt",
                 "multiqc/global_report/multiqc_data/multiqc_citations.txt",
                 "multiqc/global_report/multiqc_data/multiqc_data.json",
                 "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/global_report/multiqc_data/multiqc_sampletest_4.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
-                "multiqc/global_report/multiqc_plots/pdf/Sample1_1.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/Sample23_3.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/SampleA_2.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/Undetermined_5.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
@@ -93,12 +85,8 @@
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/sampletest_4.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
-                "multiqc/global_report/multiqc_plots/png/Sample1_1.png",
-                "multiqc/global_report/multiqc_plots/png/Sample23_3.png",
-                "multiqc/global_report/multiqc_plots/png/SampleA_2.png",
-                "multiqc/global_report/multiqc_plots/png/Undetermined_5.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
@@ -114,12 +102,8 @@
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
-                "multiqc/global_report/multiqc_plots/png/sampletest_4.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
-                "multiqc/global_report/multiqc_plots/svg/Sample1_1.svg",
-                "multiqc/global_report/multiqc_plots/svg/Sample23_3.svg",
-                "multiqc/global_report/multiqc_plots/svg/SampleA_2.svg",
-                "multiqc/global_report/multiqc_plots/svg/Undetermined_5.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
@@ -135,7 +119,7 @@
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
                 "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
-                "multiqc/global_report/multiqc_plots/svg/sampletest_4.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "multiqc/group_reports",
                 "multiqc/group_reports/group1",
@@ -153,19 +137,16 @@
                 "multiqc/group_reports/group1/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
                 "multiqc/group_reports/group1/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc.log",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_Sample1_1.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_SampleA_2.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_citations.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_data.json",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/group1/multiqc_plots",
                 "multiqc/group_reports/group1/multiqc_plots/pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/Sample1_1.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/SampleA_2.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
@@ -181,9 +162,8 @@
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/png",
-                "multiqc/group_reports/group1/multiqc_plots/png/Sample1_1.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/SampleA_2.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-pct.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc-status-check-heatmap.png",
@@ -199,9 +179,8 @@
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/general_stats_table.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/group1/multiqc_plots/svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/Sample1_1.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/SampleA_2.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-pct.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
@@ -217,6 +196,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/group1/multiqc_report.html",
                 "multiqc/group_reports/group2",
                 "multiqc/group_reports/group2/multiqc_data",
@@ -233,17 +213,16 @@
                 "multiqc/group_reports/group2/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
                 "multiqc/group_reports/group2/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc.log",
-                "multiqc/group_reports/group2/multiqc_data/multiqc_Sample23_3.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_citations.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_data.json",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/group2/multiqc_plots",
                 "multiqc/group_reports/group2/multiqc_plots/pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/Sample23_3.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
@@ -259,8 +238,8 @@
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/png",
-                "multiqc/group_reports/group2/multiqc_plots/png/Sample23_3.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-pct.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc-status-check-heatmap.png",
@@ -276,8 +255,8 @@
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/general_stats_table.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/group2/multiqc_plots/svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/Sample23_3.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-pct.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
@@ -293,6 +272,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/group2/multiqc_report.html",
                 "multiqc/group_reports/lane1",
                 "multiqc/group_reports/lane1/multiqc_data",
@@ -309,21 +289,16 @@
                 "multiqc/group_reports/lane1/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
                 "multiqc/group_reports/lane1/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc.log",
-                "multiqc/group_reports/lane1/multiqc_data/multiqc_Sample1_1.txt",
-                "multiqc/group_reports/lane1/multiqc_data/multiqc_Sample23_3.txt",
-                "multiqc/group_reports/lane1/multiqc_data/multiqc_SampleA_2.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_citations.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_data.json",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/lane1/multiqc_plots",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/Sample1_1.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/Sample23_3.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/SampleA_2.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
@@ -339,10 +314,8 @@
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/Sample1_1.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/Sample23_3.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/SampleA_2.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-pct.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc-status-check-heatmap.png",
@@ -358,10 +331,8 @@
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/general_stats_table.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/lane1/multiqc_plots/svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/Sample1_1.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/Sample23_3.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/SampleA_2.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-pct.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
@@ -377,6 +348,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/lane1/multiqc_report.html",
                 "multiqc/group_reports/test",
                 "multiqc/group_reports/test/multiqc_data",
@@ -393,20 +365,16 @@
                 "multiqc/group_reports/test/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
                 "multiqc/group_reports/test/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc.log",
-                "multiqc/group_reports/test/multiqc_data/multiqc_Sample23_3.txt",
-                "multiqc/group_reports/test/multiqc_data/multiqc_Undetermined_5.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_citations.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_data.json",
                 "multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/group_reports/test/multiqc_data/multiqc_sampletest_4.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/test/multiqc_plots",
                 "multiqc/group_reports/test/multiqc_plots/pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/Sample23_3.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/Undetermined_5.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
@@ -422,10 +390,8 @@
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/general_stats_table.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/sampletest_4.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/test/multiqc_plots/png",
-                "multiqc/group_reports/test/multiqc_plots/png/Sample23_3.png",
-                "multiqc/group_reports/test/multiqc_plots/png/Undetermined_5.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-pct.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc-status-check-heatmap.png",
@@ -441,10 +407,8 @@
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/group_reports/test/multiqc_plots/png/general_stats_table.png",
-                "multiqc/group_reports/test/multiqc_plots/png/sampletest_4.png",
+                "multiqc/group_reports/test/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/test/multiqc_plots/svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/Sample23_3.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/Undetermined_5.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-pct.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
@@ -460,21 +424,21 @@
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/general_stats_table.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/sampletest_4.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/test/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "seqfu_stats",
-                "seqfu_stats/Sample1_1.tsv",
-                "seqfu_stats/Sample1_1_mqc.txt",
-                "seqfu_stats/Sample23_3.tsv",
-                "seqfu_stats/Sample23_3_mqc.txt",
-                "seqfu_stats/SampleA_2.tsv",
-                "seqfu_stats/SampleA_2_mqc.txt",
-                "seqfu_stats/Undetermined_5.tsv",
-                "seqfu_stats/Undetermined_5_mqc.txt",
-                "seqfu_stats/sampletest_4.tsv",
-                "seqfu_stats/sampletest_4_mqc.txt"
+                "seqfu_stats/Sample1_1_seqfu.tsv",
+                "seqfu_stats/Sample1_1_seqfu_mqc.txt",
+                "seqfu_stats/Sample23_3_seqfu.tsv",
+                "seqfu_stats/Sample23_3_seqfu_mqc.txt",
+                "seqfu_stats/SampleA_2_seqfu.tsv",
+                "seqfu_stats/SampleA_2_seqfu_mqc.txt",
+                "seqfu_stats/Undetermined_5_seqfu.tsv",
+                "seqfu_stats/Undetermined_5_seqfu_mqc.txt",
+                "seqfu_stats/sampletest_4_seqfu.tsv",
+                "seqfu_stats/sampletest_4_seqfu_mqc.txt"
             ],
             [
                 "Sample1_1_screen.png:md5,562256290643b51e4374c2225a15f463",
@@ -498,14 +462,10 @@
                 "fastqc_sequence_counts_plot.txt:md5,20364b3b979bc99ae375a2dffcaf1cc1",
                 "fastqc_sequence_duplication_levels_plot.txt:md5,7f33f3d0e2eb3405eb6456acbd18dfd4",
                 "fastqc_sequence_length_distribution_plot.txt:md5,9472fb38f57150d55fb9e4995aaeeb90",
-                "multiqc_Sample1_1.txt:md5,000ff826a01fcae9fe0bf43fa11df1dc",
-                "multiqc_Sample23_3.txt:md5,b5434520fa5be5c98be5ed164a464d23",
-                "multiqc_SampleA_2.txt:md5,3ce1aacaff46ea0df3fbbb07da9dba6a",
-                "multiqc_Undetermined_5.txt:md5,9dffb6858b809b9bb97ca450158abb6c",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
                 "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d",
-                "multiqc_sampletest_4.txt:md5,ded2705a3247b72dffb5367bcb5f95b8",
+                "multiqc_seqfu.txt:md5,5b54a49079169985795537d83d58bdd9",
                 "fastq_screen_plot.txt:md5,c25d34568f10f131156294d31fbfa994",
                 "fastqc-status-check-heatmap.txt:md5,67afbf7ec626c4fc7a28b4922352bc84",
                 "fastqc_overrepresented_sequences_plot.txt:md5,0356d007eaf807f7b63714b438b11289",
@@ -517,11 +477,10 @@
                 "fastqc_sequence_counts_plot.txt:md5,5021496dd00366d08064804bbb5192e3",
                 "fastqc_sequence_duplication_levels_plot.txt:md5,e37e8e4584f0157a5fa0d53b4834e836",
                 "fastqc_sequence_length_distribution_plot.txt:md5,393cc090200a5151561efb1ed5280b89",
-                "multiqc_Sample1_1.txt:md5,000ff826a01fcae9fe0bf43fa11df1dc",
-                "multiqc_SampleA_2.txt:md5,3ce1aacaff46ea0df3fbbb07da9dba6a",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
                 "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
+                "multiqc_seqfu.txt:md5,5579172a6f8ac09a5ffcb3ce6a99590e",
                 "fastq_screen_plot.txt:md5,44fca6453b0a3d0590271bd7a31cc740",
                 "fastqc-status-check-heatmap.txt:md5,b6872d9dbaa3cce396d48dc137076e53",
                 "fastqc_overrepresented_sequences_plot.txt:md5,eac8d0fd31c614d8d0f56bd54ee8c78c",
@@ -533,10 +492,10 @@
                 "fastqc_sequence_counts_plot.txt:md5,0c4863a5475a2444cd00b053eb8941b1",
                 "fastqc_sequence_duplication_levels_plot.txt:md5,a7a050f827a4f821117efd8d25668c51",
                 "fastqc_sequence_length_distribution_plot.txt:md5,9c0761008be04d8ccf4c0e16acc6348c",
-                "multiqc_Sample23_3.txt:md5,b5434520fa5be5c98be5ed164a464d23",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
                 "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
+                "multiqc_seqfu.txt:md5,b5434520fa5be5c98be5ed164a464d23",
                 "fastq_screen_plot.txt:md5,5f748d33a7a396547fe8c260b728aa06",
                 "fastqc-status-check-heatmap.txt:md5,08228a8f3d6f11b174b98626bb22bda1",
                 "fastqc_overrepresented_sequences_plot.txt:md5,3434dfb79f150e2e584e85866983ba01",
@@ -548,12 +507,10 @@
                 "fastqc_sequence_counts_plot.txt:md5,f0c693cc281a6e61ba219bab04f59a47",
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                 "fastqc_sequence_length_distribution_plot.txt:md5,875ebcd6726bb9d36ffa64265e5071d0",
-                "multiqc_Sample1_1.txt:md5,000ff826a01fcae9fe0bf43fa11df1dc",
-                "multiqc_Sample23_3.txt:md5,b5434520fa5be5c98be5ed164a464d23",
-                "multiqc_SampleA_2.txt:md5,3ce1aacaff46ea0df3fbbb07da9dba6a",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
                 "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
+                "multiqc_seqfu.txt:md5,e2e092852c011abe5ad75cdcd68b9383",
                 "fastq_screen_plot.txt:md5,8622e1dbd0fe62520af6096207b9775d",
                 "fastqc-status-check-heatmap.txt:md5,2a66f5d61b9eb579555905cd5954b04c",
                 "fastqc_overrepresented_sequences_plot.txt:md5,e0b5bfc4b64d37611b51c939e61196fa",
@@ -565,28 +522,26 @@
                 "fastqc_sequence_counts_plot.txt:md5,057fb961863b325fe875d3a7879cb888",
                 "fastqc_sequence_duplication_levels_plot.txt:md5,3b86c9d8625c439376102f3286c7bba7",
                 "fastqc_sequence_length_distribution_plot.txt:md5,6296c9ddbf8ba8e12053149d057fd7b2",
-                "multiqc_Sample23_3.txt:md5,b5434520fa5be5c98be5ed164a464d23",
-                "multiqc_Undetermined_5.txt:md5,9dffb6858b809b9bb97ca450158abb6c",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5",
                 "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
-                "multiqc_sampletest_4.txt:md5,ded2705a3247b72dffb5367bcb5f95b8",
-                "Sample1_1.tsv:md5,269fabf8435defcd327aa69a050b7869",
-                "Sample1_1_mqc.txt:md5,a354b0ed16b9cf84aa88f501d7740fd6",
-                "Sample23_3.tsv:md5,6fdadbeeefccbf957f880d6852bf9676",
-                "Sample23_3_mqc.txt:md5,e94269e3efc8b8192d7ac9c15ea2aa99",
-                "SampleA_2.tsv:md5,b980ed694a05825fcf7c8b5b73888eb3",
-                "SampleA_2_mqc.txt:md5,1d4b0e918644cf553108b7ccf77b4a01",
-                "Undetermined_5.tsv:md5,b4458d41df4dee9321da03f4d4672aae",
-                "Undetermined_5_mqc.txt:md5,0c869488cb61d2f87758c621bded212b",
-                "sampletest_4.tsv:md5,db3179b0c41a09e6317a5a5c0852f476",
-                "sampletest_4_mqc.txt:md5,590b97cc48268629204f59007bae7ad7"
+                "multiqc_seqfu.txt:md5,a1a0b9a0dde0c1c4fe184d44c675dcde",
+                "Sample1_1_seqfu.tsv:md5,269fabf8435defcd327aa69a050b7869",
+                "Sample1_1_seqfu_mqc.txt:md5,a354b0ed16b9cf84aa88f501d7740fd6",
+                "Sample23_3_seqfu.tsv:md5,6fdadbeeefccbf957f880d6852bf9676",
+                "Sample23_3_seqfu_mqc.txt:md5,e94269e3efc8b8192d7ac9c15ea2aa99",
+                "SampleA_2_seqfu.tsv:md5,b980ed694a05825fcf7c8b5b73888eb3",
+                "SampleA_2_seqfu_mqc.txt:md5,1d4b0e918644cf553108b7ccf77b4a01",
+                "Undetermined_5_seqfu.tsv:md5,b4458d41df4dee9321da03f4d4672aae",
+                "Undetermined_5_seqfu_mqc.txt:md5,0c869488cb61d2f87758c621bded212b",
+                "sampletest_4_seqfu.tsv:md5,db3179b0c41a09e6317a5a5c0852f476",
+                "sampletest_4_seqfu_mqc.txt:md5,590b97cc48268629204f59007bae7ad7"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.10.3"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-02-04T10:10:13.268943"
+        "timestamp": "2025-03-26T13:03:47.460854"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index c256a372..27a9c143 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -46,7 +46,7 @@
                 "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/global_report/multiqc_data/multiqc_hg001_1.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_plots",
@@ -67,7 +67,7 @@
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/hg001_1.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
@@ -85,7 +85,7 @@
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
-                "multiqc/global_report/multiqc_plots/png/hg001_1.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
@@ -103,13 +103,13 @@
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
                 "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
-                "multiqc/global_report/multiqc_plots/svg/hg001_1.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "seqfu_stats",
-                "seqfu_stats/hg001_1.tsv",
-                "seqfu_stats/hg001_1_mqc.txt"
+                "seqfu_stats/hg001_1_seqfu.tsv",
+                "seqfu_stats/hg001_1_seqfu_mqc.txt"
             ],
             [
                 "hg001_1_screen.png:md5,b9c58e388f18ad11f4c2e29e9b573a5e",
@@ -129,15 +129,15 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,7c5d711e27c53d13c81644a1f2468dba",
                 "multiqc_fastqc.txt:md5,1a4b472e13cadc770832b0e20d1de7b0",
-                "multiqc_hg001_1.txt:md5,9595d608ff5709f2bdec8cb1016416c0",
-                "hg001_1.tsv:md5,b133752c897afbb4d8721b911fa117d4",
-                "hg001_1_mqc.txt:md5,6285f582c03faa70e8dcb3503e5db728"
+                "multiqc_seqfu.txt:md5,9595d608ff5709f2bdec8cb1016416c0",
+                "hg001_1_seqfu.tsv:md5,b133752c897afbb4d8721b911fa117d4",
+                "hg001_1_seqfu_mqc.txt:md5,6285f582c03faa70e8dcb3503e5db728"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.10.3"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-02-04T10:12:21.446251"
+        "timestamp": "2025-03-26T13:05:53.896824"
     }
 }
\ No newline at end of file
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 76cdfade..22d37c30 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -73,8 +73,8 @@ workflow SEQINSPECTOR {
     if (!("seqfu_stats" in skip_tools)) {
         SEQFU_STATS (
             ch_samplesheet
-            .map { meta, reads ->               
-                [[id:"global", tags: meta.tags], reads] 
+            .map { meta, reads ->
+                [[id: "seqfu", sample_id: meta.id, tags: meta.tags], reads]
             }
         )
         ch_multiqc_files = ch_multiqc_files.mix(SEQFU_STATS.out.multiqc)

From cdaf5e93a0e9b99448088a00510c2ab4bd076d53 Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Wed, 26 Mar 2025 12:26:12 +0000
Subject: [PATCH 203/530] Update schema to accept tar file or directory

---
 assets/schema_input.json | 26 ++++++++++++++++++--------
 1 file changed, 18 insertions(+), 8 deletions(-)

diff --git a/assets/schema_input.json b/assets/schema_input.json
index 97ec6177..c879c73b 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -17,21 +17,31 @@
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
-                "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
+                "pattern": "\\.f(ast)?q\\.gz$",
+                "errorMessage": "FastQ files for read 1 must be provided and must have extension '.fq.gz' or '.fastq.gz'"
             },
             "fastq_2": {
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
-                "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
+                "pattern": "\\.f(ast)?q\\.gz$",
+                "errorMessage": "FastQ files for read 2 are optional and must have extension '.fq.gz' or '.fastq.gz' if provided"
             },
             "rundir": {
-                "type": "string",
-                "format": "path",
-                "exists": true,
-                "errorMessage": "Run directory must be a path",
+                "oneOf": [
+                    {
+                        "type": "string",
+                        "format": "file-path",
+                        "exists": true,
+                        "pattern": "\\.tar\\.gz$"
+                    },
+                    {
+                        "type": "string",
+                        "format": "directory-path",
+                        "exists": true
+                    }
+                ],
+                "errorMessage": "Run directory must be a path or tar directory",
                 "meta": ["rundir"]
             },
             "tags": {

From 0c672a1c5597d3eb60164c3898b4deb09db4800c Mon Sep 17 00:00:00 2001
From: Patricie34 <patricie.johnova@email.cz>
Date: Wed, 26 Mar 2025 13:54:02 +0100
Subject: [PATCH 204/530] Pipeline description in README.md

---
 CHANGELOG.md | 1 +
 README.md    | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 65627095..eb520fff 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -23,6 +23,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#103](https://github.com/nf-core/seqinspector/pull/103) Configure full-tests
 - [#94](https://github.com/nf-core/seqinspector/issues/94) Test data validation
 - [#86](https://github.com/nf-core/seqinspector/issues/86) Update lists of default steps in the pipeline
+- [#84](https://github.com/nf-core/seqinspector/issues/84) Short summary of seqinspector in README.md
 
 ### `Fixed`
 
diff --git a/README.md b/README.md
index 3582178e..29e031d6 100644
--- a/README.md
+++ b/README.md
@@ -19,7 +19,7 @@
 
 ## Introduction
 
-**nf-core/seqinspector** is a bioinformatics pipeline that ...
+**nf-core/seqinspector** is a bioinformatics pipeline that that processes raw sequencing data to provide comprehensive quality control and exploratory analysis. It performs subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants. The pipeline generates detailed reports with flexible output options, ranging from individual sample analyses to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments.
 
 <!-- TODO nf-core:
    Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the

From a46710da79b1ccc5ef22b9586980004a3308c4fd Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Wed, 26 Mar 2025 13:57:15 +0100
Subject: [PATCH 205/530] Update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0062af4a..b5e69f0a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -26,6 +26,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 
 - [#71](https://github.com/nf-core/seqinspector/pull/71) FASTQSCREEN does not fail when multiple reads are provided.
 - [#99](https://github.com/nf-core/seqinspector/pull/99) Fix group reports for paired reads
+- [#107](https://github.com/nf-core/seqinspector/pull/107)  Put SeqFU-stats section reports together
 
 ### `Dependencies`
 

From 2a5968a655f8d90d62a4bf2f897f247b0b3804e2 Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Wed, 26 Mar 2025 12:58:24 +0000
Subject: [PATCH 206/530] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0062af4a..3aafaf08 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -21,6 +21,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#53](https://github.com/nf-core/seqinspector/pull/53) Add FastQ-Screen database multiplexing and limit scope of nf-test in CI.
 - [#96](https://github.com/nf-core/seqinspector/pull/96) Added missing citations to citation tool
 - [#103](https://github.com/nf-core/seqinspector/pull/103) Configure full-tests
+- [#110](https://github.com/nf-core/seqinspector/pull/110) Update input schema to accept either tar file or directory as rundir, and fastq messages and patterns.
 
 ### `Fixed`
 

From 201bfc69e405b1ad02c038144b14461a61ec55b9 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Wed, 26 Mar 2025 13:59:28 +0100
Subject: [PATCH 207/530] Lint changelog

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b5e69f0a..6be536bf 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -26,7 +26,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 
 - [#71](https://github.com/nf-core/seqinspector/pull/71) FASTQSCREEN does not fail when multiple reads are provided.
 - [#99](https://github.com/nf-core/seqinspector/pull/99) Fix group reports for paired reads
-- [#107](https://github.com/nf-core/seqinspector/pull/107)  Put SeqFU-stats section reports together
+- [#107](https://github.com/nf-core/seqinspector/pull/107) Put SeqFU-stats section reports together
 
 ### `Dependencies`
 

From efacb54a0e4191965c30eb4e2da268a1d2e8aba2 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Wed, 26 Mar 2025 13:16:28 +0000
Subject: [PATCH 208/530] fix quotes and make rundirparser publish results with
 individual names for test consistency

---
 conf/modules.config | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 4a653ed0..60e78950 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -18,11 +18,11 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
-    withName: SEQTK_SAMPLE {
+    withName: 'SEQTK_SAMPLE' {
         ext.args = '-s100'
     }
 
-    withName: FASTQC {
+    withName: 'FASTQC' {
         ext.args = '--quiet'
     }
 
@@ -35,6 +35,14 @@ process {
         ]
     }
 
+    withName: 'RUNDIRPARSER' {
+        publishDir = [
+            path: { "${params.outdir}/rundirparser" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : "${dir_meta.dirname}_$filename" }
+        ]
+    }
+
     withName: 'MULTIQC_GLOBAL' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [

From c0b451daeaf5bbc66ff4ac683b53b2a61ba9e162 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Wed, 26 Mar 2025 13:17:09 +0000
Subject: [PATCH 209/530] clean up meta object names

---
 modules/local/rundirparser/main.nf | 10 +++-------
 workflows/seqinspector.nf          |  4 ++--
 2 files changed, 5 insertions(+), 9 deletions(-)

diff --git a/modules/local/rundirparser/main.nf b/modules/local/rundirparser/main.nf
index bc96977c..95d97190 100644
--- a/modules/local/rundirparser/main.nf
+++ b/modules/local/rundirparser/main.nf
@@ -1,5 +1,5 @@
 process RUNDIRPARSER {
-    tag "$rundir.baseName"
+    tag "$rundir.simpleName"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
@@ -8,18 +8,16 @@ process RUNDIRPARSER {
         'community.wave.seqera.io/library/pip_pyyaml:c2ecf27a7f63796e' }"
 
     input:
-    tuple val(joint_meta), path(rundir)
+    tuple val(dir_meta), path(rundir)
 
     output:
-    tuple val(joint_meta), path("*_mqc.*"), emit: multiqc
+    tuple val(dir_meta), path("*_mqc.*"), emit: multiqc
     path "versions.yml",                    emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    // def args = task.ext.args ?: ''
-    // def prefix = task.ext.prefix ?: "${rundir.baseName}"
     """
     rundirparser.py ${rundir}
 
@@ -31,8 +29,6 @@ process RUNDIRPARSER {
     """
 
     stub:
-    // def args = task.ext.args ?: ''
-    // def prefix = task.ext.prefix ?: "${rundir.baseName}"
     """
     touch rundir_mqc.txt
 
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 9f94c11e..ff922396 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -53,9 +53,9 @@ workflow SEQINSPECTOR {
                 // Collect all tags across all samples with this rundir
                 def all_tags = metas.collect { it.tags }.flatten().unique()
                 // Create a new meta object with the merged tags
-                def new_meta = [tags: all_tags]
+                def dir_meta = [tags: all_tags, dirname: rundir.simpleName]
                 // Return the new structure
-                [new_meta, rundir]
+                [dir_meta, rundir]
             }
 
         RUNDIRPARSER( ch_rundir )

From f1ab7d60845cb6fed4146b598591d80b51e55295 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Wed, 26 Mar 2025 13:37:21 +0000
Subject: [PATCH 210/530] docs and formatting

---
 conf/modules.config                |  3 +++
 modules/local/rundirparser/main.nf |  2 +-
 workflows/seqinspector.nf          | 17 ++++++++++++-----
 3 files changed, 16 insertions(+), 6 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 60e78950..9327925f 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -39,6 +39,9 @@ process {
         publishDir = [
             path: { "${params.outdir}/rundirparser" },
             mode: params.publish_dir_mode,
+            // The process _mqc.txt outputs should have identical names for the same sequencing platforms
+            // in order to be grouped together in the MultiQC report, but here we need to enforce uniqueness
+            // to avoid overwriting results in the publishDir.
             saveAs: { filename -> filename.equals('versions.yml') ? null : "${dir_meta.dirname}_$filename" }
         ]
     }
diff --git a/modules/local/rundirparser/main.nf b/modules/local/rundirparser/main.nf
index 95d97190..335acef2 100644
--- a/modules/local/rundirparser/main.nf
+++ b/modules/local/rundirparser/main.nf
@@ -12,7 +12,7 @@ process RUNDIRPARSER {
 
     output:
     tuple val(dir_meta), path("*_mqc.*"), emit: multiqc
-    path "versions.yml",                    emit: versions
+    path "versions.yml",                  emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index ff922396..0472ab3f 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -44,21 +44,28 @@ workflow SEQINSPECTOR {
     //
     if (!("rundirparser" in skip_tools)) {
 
+        // From samplesheet channel serving (sampleMetaObj, sampleReadsPath) tuples:
+        // --> Create new rundir channel serving (rundirMetaObj, rundirPath) tuples
         ch_rundir = ch_samplesheet
-            // Group by rundir to merge tags from samples with the same rundir
+            // Group by rundir
             .map { meta, _reads -> [meta.rundir, meta] }
             .groupTuple()
-            // Create a new meta object with merged tags for each unique rundir
+            // From all meta objects associated with a given rundir...
             .map { rundir, metas ->
-                // Collect all tags across all samples with this rundir
+                // Collect all unique tags into a list
                 def all_tags = metas.collect { it.tags }.flatten().unique()
-                // Create a new meta object with the merged tags
+                // Create a new meta object whose attributes are...
+                //  1. tags: The list of merged tags, used for grouping MultiQC reports
+                //  2. dirname: The simple name of the rundir, used for setting unique output names in publishDir
                 def dir_meta = [tags: all_tags, dirname: rundir.simpleName]
-                // Return the new structure
+                // Return the new structure, to...
+                //  1. Feed into rundir specific processes
+                //  2. Mix with the ch_multiqc_files channel downstream
                 [dir_meta, rundir]
             }
 
         RUNDIRPARSER( ch_rundir )
+
         ch_multiqc_files = ch_multiqc_files.mix(RUNDIRPARSER.out.multiqc)
         ch_versions = ch_versions.mix(RUNDIRPARSER.out.versions.first())
     }

From 3c0ca0855ca539b64bf89746560594a0fdc2694e Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Wed, 26 Mar 2025 14:09:08 +0000
Subject: [PATCH 211/530] updates to fit incoming template conventions

---
 .github/actions/get-shards/action.yml |  69 ++++++++++++
 .github/actions/nf-test/action.yml    | 117 ++++++++++++++++++++
 .github/workflows/ci.yml              |  87 ---------------
 .github/workflows/nf-test.yml         | 150 +++++++++++++++++++++++---
 nf-test.config                        |  19 +++-
 5 files changed, 338 insertions(+), 104 deletions(-)
 create mode 100644 .github/actions/get-shards/action.yml
 create mode 100644 .github/actions/nf-test/action.yml
 delete mode 100644 .github/workflows/ci.yml

diff --git a/.github/actions/get-shards/action.yml b/.github/actions/get-shards/action.yml
new file mode 100644
index 00000000..34085279
--- /dev/null
+++ b/.github/actions/get-shards/action.yml
@@ -0,0 +1,69 @@
+name: "Get number of shards"
+description: "Get the number of nf-test shards for the current CI job"
+inputs:
+  max_shards:
+    description: "Maximum number of shards allowed"
+    required: true
+  paths:
+    description: "Component paths to test"
+    required: false
+  tags:
+    description: "Tags to pass as argument for nf-test --tag parameter"
+    required: false
+outputs:
+  shard:
+    description: "Array of shard numbers"
+    value: ${{ steps.shards.outputs.shard }}
+  total_shards:
+    description: "Total number of shards"
+    value: ${{ steps.shards.outputs.total_shards }}
+runs:
+  using: "composite"
+  steps:
+    - name: Install nf-test
+      uses: nf-core/setup-nf-test@v1
+      with:
+        version: ${{ env.NFT_VER }}
+    - name: Get number of shards
+      id: shards
+      shell: bash
+      run: |
+        # Run nf-test with dynamic parameter
+        nftest_output=$(nf-test test \
+          --profile +docker \
+          $(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \
+          --dry-run \
+          --ci \
+          --changed-since HEAD^) || {
+            echo "nf-test command failed with exit code $?"
+            echo "Full output: $nftest_output"
+            exit 1
+        }
+        echo "nf-test dry-run output: $nftest_output"
+
+        # Default values for shard and total_shards
+        shard="[]"
+        total_shards=0
+
+        # Check if there are related tests
+        if echo "$nftest_output" | grep -q 'No tests to execute'; then
+          echo "No related tests found."
+        else
+          # Extract the number of related tests
+          number_of_shards=$(echo "$nftest_output" | sed -n 's|.*Executed \([0-9]*\) tests.*|\1|p')
+          if [[ -n "$number_of_shards" && "$number_of_shards" -gt 0 ]]; then
+            shards_to_run=$(( $number_of_shards < ${{ inputs.max_shards }} ? $number_of_shards : ${{ inputs.max_shards }} ))
+            shard=$(seq 1 "$shards_to_run" | jq -R . | jq -c -s .)
+            total_shards="$shards_to_run"
+          else
+            echo "Unexpected output format. Falling back to default values."
+          fi
+        fi
+
+        # Write to GitHub Actions outputs
+        echo "shard=$shard" >> $GITHUB_OUTPUT
+        echo "total_shards=$total_shards" >> $GITHUB_OUTPUT
+
+        # Debugging output
+        echo "Final shard array: $shard"
+        echo "Total number of shards: $total_shards"
diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml
new file mode 100644
index 00000000..7e53c879
--- /dev/null
+++ b/.github/actions/nf-test/action.yml
@@ -0,0 +1,117 @@
+name: "nf-test Action"
+description: "Runs nf-test with common setup steps"
+inputs:
+  profile:
+    description: "Profile to use"
+    required: true
+  shard:
+    description: "Shard number for this CI job"
+    required: true
+  total_shards:
+    description: "Total number of test shards(NOT the total number of matrix jobs)"
+    required: true
+  paths:
+    description: "Test paths"
+    required: true
+  tags:
+    description: "Tags to pass as argument for nf-test --tag parameter"
+    required: false
+runs:
+  using: "composite"
+  steps:
+    - name: Setup Nextflow
+      uses: nf-core/setup-nextflow@v2
+      with:
+        version: "${{ env.NXF_VERSION }}"
+
+    - name: Set up Python
+      uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
+      with:
+        python-version: "3.11"
+
+    - name: Install nf-test
+      uses: nf-core/setup-nf-test@v1
+      with:
+        version: "${{ env.NFT_VER }}"
+
+    - name: Setup apptainer
+      if: contains(inputs.profile, 'singularity')
+      uses: eWaterCycle/setup-apptainer@main
+
+    - name: Set up Singularity
+      if: contains(inputs.profile, 'singularity')
+      shell: bash
+      run: |
+        mkdir -p $NXF_SINGULARITY_CACHEDIR
+        mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+
+    - name: Conda setup
+      if: contains(inputs.profile, 'conda')
+      uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3
+      with:
+        auto-update-conda: true
+        conda-solver: libmamba
+        conda-remove-defaults: true
+
+    - name: Install pdiff
+      shell: bash
+      run: |
+        python -m pip install pdiff
+
+      # TODO Skip failing conda tests and document their failures
+      # https://github.com/nf-core/modules/issues/7017
+    - name: Run nf-test
+      shell: bash
+      env:
+        NFT_DIFF: ${{ env.NFT_DIFF }}
+        NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
+        NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
+      run: |
+        nf-test test \
+          --profile=+${{ inputs.profile }} \
+          $(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \
+          --ci \
+          --changed-since HEAD^ \
+          --verbose \
+          --tap=test.tap \
+          --shard ${{ inputs.shard }}/${{ inputs.total_shards }}
+
+          # Save the absolute path of the test.tap file to the output
+          echo "tap_file_path=$(realpath test.tap)" >> $GITHUB_OUTPUT
+
+    - name: Generate test summary
+      if: always()
+      shell: bash
+      run: |
+        # Add header if it doesn't exist (using a token file to track this)
+        if [ ! -f ".summary_header" ]; then
+          echo "# 🚀 nf-test results" >> $GITHUB_STEP_SUMMARY
+          echo "" >> $GITHUB_STEP_SUMMARY
+          echo "| Status | Test Name | Profile | Shard |" >> $GITHUB_STEP_SUMMARY
+          echo "|:------:|-----------|---------|-------|" >> $GITHUB_STEP_SUMMARY
+          touch .summary_header
+        fi
+
+        if [ -f test.tap ]; then
+          while IFS= read -r line; do
+            if [[ $line =~ ^ok ]]; then
+              test_name="${line#ok }"
+              # Remove the test number from the beginning
+              test_name="${test_name#* }"
+              echo "| ✅ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
+            elif [[ $line =~ ^not\ ok ]]; then
+              test_name="${line#not ok }"
+              # Remove the test number from the beginning
+              test_name="${test_name#* }"
+              echo "| ❌ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
+            fi
+          done < test.tap
+        else
+          echo "| ⚠️ | No test results found | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
+        fi
+
+    - name: Clean up
+      if: always()
+      shell: bash
+      run: |
+        sudo rm -rf /home/ubuntu/tests/
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
deleted file mode 100644
index d6fc106a..00000000
--- a/.github/workflows/ci.yml
+++ /dev/null
@@ -1,87 +0,0 @@
-name: nf-core CI
-# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
-on:
-  push:
-    branches:
-      - dev
-  pull_request:
-  release:
-    types: [published]
-  workflow_dispatch:
-
-env:
-  NXF_ANSI_LOG: false
-  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
-  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
-
-concurrency:
-  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
-  cancel-in-progress: true
-
-jobs:
-  test:
-    name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/seqinspector') }}"
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        NXF_VER:
-          - "24.04.2"
-          - "latest-everything"
-        profile:
-          - "conda"
-          - "docker"
-          - "singularity"
-        test_name:
-          - "test"
-        isMaster:
-          - ${{ github.base_ref == 'master' }}
-        # Exclude conda and singularity on dev
-        exclude:
-          - isMaster: false
-            profile: "conda"
-          - isMaster: false
-            profile: "singularity"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
-        with:
-          fetch-depth: 0
-
-      - name: Set up Nextflow
-        uses: nf-core/setup-nextflow@v2
-        with:
-          version: "${{ matrix.NXF_VER }}"
-
-      - name: Set up Apptainer
-        if: matrix.profile == 'singularity'
-        uses: eWaterCycle/setup-apptainer@main
-
-      - name: Set up Singularity
-        if: matrix.profile == 'singularity'
-        run: |
-          mkdir -p $NXF_SINGULARITY_CACHEDIR
-          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
-
-      - name: Set up Miniconda
-        if: matrix.profile == 'conda'
-        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
-        with:
-          miniconda-version: "latest"
-          auto-update-conda: true
-          conda-solver: libmamba
-          channels: conda-forge,bioconda
-
-      - name: Set up Conda
-        if: matrix.profile == 'conda'
-        run: |
-          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
-          echo $(realpath python) >> $GITHUB_PATH
-
-      - name: Clean up Disk space
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
-
-      - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index 233897ed..4715b740 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -1,24 +1,146 @@
-name: nf-test
+name: Run nf-test
+on:
+  push:
+    paths-ignore:
+      - "docs/**"
+      - "**/meta.yml"
+      - "**/*.md"
+      - "**/*.png"
+      - "**/*.svg"
+  pull_request:
+    paths-ignore:
+      - "docs/**"
+      - "**/meta.yml"
+      - "**/*.md"
+      - "**/*.png"
+      - "**/*.svg"
+  release:
+    types: [published]
+  workflow_dispatch:
+    inputs:
+      runners:
+        description: "Runners to test on"
+        type: choice
+        options:
+          - "ubuntu-latest"
+          - "self-hosted"
+        default: "ubuntu-latest"
 
-on: [push, pull_request]
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  NFT_DIFF: "pdiff"
+  NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
+  NFT_VER: "0.9.2"
+  NFT_WORKDIR: "~"
+  NXF_ANSI_LOG: false
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
 
 jobs:
-  test:
-    runs-on: ubuntu-latest
+  nf-test-changes:
+    name: nf-test-changes
+    runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
+    outputs:
+      shard: ${{ steps.set-shards.outputs.shard }}
+      total_shards: ${{ steps.set-shards.outputs.total_shards }}
+    steps:
+      - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner
+        run: |
+          ls -la ./
+          rm -rf ./* || true
+          rm -rf ./.??* || true
+          ls -la ./
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          fetch-depth: 0
+
+      - name: get number of shards
+        id: set-shards
+        uses: ./.github/actions/get-shards
+        env:
+          NFT_VER: ${{ env.NFT_VER }}
+        with:
+          max_shards: 7
+
+      - name: debug
+        run: |
+          echo ${{ steps.set-shards.outputs.shard }}
+          echo ${{ steps.set-shards.outputs.total_shards }}
+
+  nf-test:
+    runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
+    name: "${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/${{ needs.nf-test-changes.outputs.total_shards }}"
+    needs: [nf-test-changes]
+    if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }}
+    strategy:
+      fail-fast: false
+      matrix:
+        shard: ${{ fromJson(needs.nf-test-changes.outputs.shard) }}
+        profile: [conda, docker, singularity]
+        isMain:
+          - ${{ github.base_ref == 'master' || github.base_ref == 'main' }}
+        # Exclude conda and singularity on dev
+        exclude:
+          - isMain: false
+            profile: "conda"
+          - isMain: false
+            profile: "singularity"
+        NXF_VER:
+          - "24.10.2"
+          - "latest-everything"
+    env:
+      NXF_ANSI_LOG: false
+      TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
 
     steps:
-      - name: Checkout
-        uses: actions/checkout@v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          fetch-depth: 0
 
-      - name: Setup Nextflow latest-edge
-        uses: nf-core/setup-nextflow@v2
+      - name: Run nf-test
+        uses: ./.github/actions/nf-test
+        env:
+          NFT_DIFF: ${{ env.NFT_DIFF }}
+          NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
+          NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
         with:
-          version: "latest-edge"
+          profile: ${{ matrix.profile }}
+          shard: ${{ matrix.shard }}
+          total_shards: ${{ env.TOTAL_SHARDS }}
+  confirm-pass:
+    runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
+    needs: [nf-test]
+    if: always()
+    steps:
+      - name: One or more tests failed
+        if: ${{ contains(needs.*.result, 'failure') }}
+        run: exit 1
 
-      - name: Install nf-test
+      - name: One or more tests cancelled
+        if: ${{ contains(needs.*.result, 'cancelled') }}
+        run: exit 1
+
+      - name: All tests ok
+        if: ${{ contains(needs.*.result, 'success') }}
+        run: exit 0
+
+      - name: debug-print
+        if: always()
         run: |
-          wget -qO- https://get.nf-test.com | bash
-          sudo mv nf-test /usr/local/bin/
+          echo "::group::DEBUG: `needs` Contents"
+          echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}"
+          echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
+          echo "::endgroup::"
 
-      - name: Run Tests
-        run: nf-test test --ci tests
+      - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner
+        if: always()
+        run: |
+          ls -la ./
+          rm -rf ./* || true
+          rm -rf ./.??* || true
+          ls -la ./
diff --git a/nf-test.config b/nf-test.config
index d4d15358..889df760 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -1,10 +1,23 @@
 config {
+    // location for all nf-test tests
+    testsDir "."
 
-    testsDir "tests"
-    workDir ".nf-test"
+    // nf-test directory including temporary files for each test
+    workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"
+
+    // location of an optional nextflow.config file specific for executing tests
     configFile "tests/nextflow.config"
-    profile "test,docker"
 
+    // ignore tests coming from the nf-core/modules repo
+    ignore 'modules/nf-core/**/*', 'subworkflows/nf-core/**/*'
+
+    // run all test with defined profile(s) from the main nextflow.config
+    profile "test"
+
+    // list of filenames or patterns that should be trigger a full test run
+    triggers 'nextflow.config', 'nf-test.config', 'conf/test.config', 'tests/nextflow.config', 'tests/.nftignore'
+
+    // load the necessary plugins
     plugins {
         load "nft-utils@0.0.3"
     }

From 0b262caa3301170fae413bbdf6b942803b5a6c32 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Patricie=20Skal=C3=A1kov=C3=A1?=
 <158295213+Patricie34@users.noreply.github.com>
Date: Wed, 26 Mar 2025 15:13:31 +0100
Subject: [PATCH 212/530] Update README.md
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Matilda Åslin <matilda.aslin@medsci.uu.se>
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 29e031d6..3c4f9a36 100644
--- a/README.md
+++ b/README.md
@@ -19,7 +19,7 @@
 
 ## Introduction
 
-**nf-core/seqinspector** is a bioinformatics pipeline that that processes raw sequencing data to provide comprehensive quality control and exploratory analysis. It performs subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants. The pipeline generates detailed reports with flexible output options, ranging from individual sample analyses to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments.
+**nf-core/seqinspector** is a bioinformatics pipeline that that processes raw sequencedata (FASTQ) to provide comprehensive quality control. It can perform subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants. The pipeline generates detailed MultiQC reports with flexible output options, ranging from individual sample reports to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments.
 
 <!-- TODO nf-core:
    Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the

From 36ce4309301d991868a14b9a4b2d9579c45111c8 Mon Sep 17 00:00:00 2001
From: nelnk861 <nelly.nkonge@uu.se>
Date: Wed, 26 Mar 2025 14:06:00 +0100
Subject: [PATCH 213/530] Making fastq_screen_references value to use baseDir

---
 .nf-core.yml         | 3 +++
 CHANGELOG.md         | 1 +
 nextflow.config      | 2 +-
 nextflow_schema.json | 2 +-
 4 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index c984b0c3..9ee14341 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,6 +1,9 @@
 lint:
   files_unchanged:
     - .github/CONTRIBUTING.md
+  nextflow_config:
+    - config_defaults:
+        - params.fastq_screen_references
 nf_core_version: 3.2.0
 repository_type: pipeline
 template:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index d7eea135..dfa1685a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -28,6 +28,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#71](https://github.com/nf-core/seqinspector/pull/71) FASTQSCREEN does not fail when multiple reads are provided.
 - [#99](https://github.com/nf-core/seqinspector/pull/99) Fix group reports for paired reads
 - [#107](https://github.com/nf-core/seqinspector/pull/107) Put SeqFU-stats section reports together
+- [#112](https://github.com/nf-core/seqinspector/pull/112) Making fastq_screen_references value to use parentDir
 
 ### `Dependencies`
 
diff --git a/nextflow.config b/nextflow.config
index bb1cb279..f9db2601 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -21,7 +21,7 @@ params {
     igenomes_ignore            = false
 
     // Fastqscreen options
-    fastq_screen_references    = './assets/example_fastq_screen_references.csv'
+    fastq_screen_references    = "${projectDir}/assets/example_fastq_screen_references.csv"
 
     // MultiQC options
     multiqc_config             = null
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 248660b7..f00c0bb5 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -94,7 +94,7 @@
                 },
                 "fastq_screen_references": {
                     "type": "string",
-                    "default": "./assets/example_fastq_screen_references.csv",
+                    "default": "${projectDir}/assets/example_fastq_screen_references.csv",
                     "fa_icon": "fas fa-search",
                     "description": "A .csv of reference genomes to be mapped against by FastQ Screen"
                 }

From 3228f8c30f93859041b56e9ad19c64c8ac1ea1d4 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Wed, 26 Mar 2025 14:52:31 +0000
Subject: [PATCH 214/530] ignore lint for missing ci.yml

---
 .nf-core.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.nf-core.yml b/.nf-core.yml
index c984b0c3..83c25d23 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,6 +1,9 @@
 lint:
+  actions_ci: false
   files_unchanged:
     - .github/CONTRIBUTING.md
+  files_exist:
+    - .github/workflows/ci.yml
 nf_core_version: 3.2.0
 repository_type: pipeline
 template:

From 9a9b5d117a9778e6bdca41385fc1e5c89df43b4d Mon Sep 17 00:00:00 2001
From: matrulda <matilda.aslin@medsci.uu.se>
Date: Wed, 26 Mar 2025 16:53:08 +0100
Subject: [PATCH 215/530] Add parse_illumina.py

---
 modules/local/rundirparser/main.nf            |  6 +-
 .../resources/usr/bin/parse_illumina.py       | 95 +++++++++++++++++++
 2 files changed, 99 insertions(+), 2 deletions(-)
 create mode 100755 modules/local/rundirparser/resources/usr/bin/parse_illumina.py

diff --git a/modules/local/rundirparser/main.nf b/modules/local/rundirparser/main.nf
index 335acef2..c702e57b 100644
--- a/modules/local/rundirparser/main.nf
+++ b/modules/local/rundirparser/main.nf
@@ -4,8 +4,8 @@ process RUNDIRPARSER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ad/ad2bcce70756f81c07c7e2ffd9b66213bf48ace786466395ac3a402840df2ffb/data' :
-        'community.wave.seqera.io/library/pip_pyyaml:c2ecf27a7f63796e' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/41/412df2cdcf04e0a12971ba61b12cacaa5a49705442afe99ad96668bebbb8f880/data' :
+        'community.wave.seqera.io/library/pip_pyyaml_xmltodict:a4e48bd1ab4b6a53' }"
 
     input:
     tuple val(dir_meta), path(rundir)
@@ -19,7 +19,9 @@ process RUNDIRPARSER {
 
     script:
     """
+    # TODO: check what kind of seq platfrom to decide which script to use
     rundirparser.py ${rundir}
+    parse_illumina.py ${rundir}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/rundirparser/resources/usr/bin/parse_illumina.py b/modules/local/rundirparser/resources/usr/bin/parse_illumina.py
new file mode 100755
index 00000000..5d210aba
--- /dev/null
+++ b/modules/local/rundirparser/resources/usr/bin/parse_illumina.py
@@ -0,0 +1,95 @@
+#!/usr/bin/env python3
+
+import os
+import yaml
+import sys
+from datetime import datetime
+from pathlib import Path
+import xmltodict
+
+
+def read_run_parameters(directory):
+    alt_1 = directory / "runParameters.xml"
+    alt_2 = directory / "RunParameters.xml"
+    if alt_1.exists():
+        with open(alt_1) as f:
+            return xmltodict.parse(f.read())
+    elif alt_2.exists():
+        with open(alt_2) as f:
+            return xmltodict.parse(f.read())
+    else:
+        raise Exception("[Rr]unParameters.xml not found!")
+
+
+def find(d, tag):
+    if isinstance(d, dict):
+        if tag in d:
+            yield d[tag]
+        for k, v in d.items():
+            if isinstance(v, dict):
+                yield from find(v, tag)
+            if isinstance(v, list):
+                for i in v:
+                    yield from find(i, tag)
+
+
+def construct_data(run_parameters):
+    run_parameters_tags = {
+        "RunId": "Run ID",
+        "RunID": "Run ID",
+        "InstrumentType": "Instrument type",
+        "ApplicationName": "Control software",
+        "Application": "Control software",
+        "ApplicationVersion": "Control software version",
+        "SystemSuiteVersion": "Control software version",
+        "Flowcell": "Flowcell type",
+        "FlowCellMode": "Flowcell type",
+        "ReagentKitVersion": "Reagent kit version",
+        "RTAVersion": "RTA Version",
+        "RtaVersion": "RTA Version",
+    }
+    data = {}
+    for k, v in run_parameters_tags.items():
+        for key, value in run_parameters_tags.items():
+            info = list(find(run_parameters, key))
+            if info:
+                data[value] = info[0]
+        return data
+
+
+def construct_multiqc_yaml(directory):
+
+    directory_name = directory.name
+    run_parameters = read_run_parameters(directory)
+
+    data = construct_data(run_parameters)
+
+    #TODO: MultiQC currently ignores the data in this yaml RUDE
+    metadata = {
+        "custom_data": {
+            "my_data_type": {
+                "id": "mqc_seq_metadata",
+                "section_name": "Sequencing instrument metadata",
+                "description": directory_name,
+                "plot_type": "table",
+                "pconfig": {
+                    "id": 'custom_table',
+                    "title": 'Custom Table',
+                    "no_headers": "true",
+                    },
+                "data": data,
+            }
+        }
+    }
+
+    return metadata
+
+
+if __name__ == "__main__":
+    rundir_path = Path(sys.argv[1])
+    output_file = "illumina_mqc.yml"
+
+    multiqc_yaml = construct_multiqc_yaml(rundir_path)
+
+    with open(output_file, "w") as f:
+        yaml.dump(multiqc_yaml, f)

From 22a10e41762c70305c5c4aeccd6cd628cfd7d66f Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Thu, 27 Mar 2025 08:45:41 +0100
Subject: [PATCH 216/530] Update MultiQC to 1.28

Fixes #102
---
 modules.json                                   |  2 +-
 modules/nf-core/multiqc/environment.yml        |  4 +++-
 modules/nf-core/multiqc/main.nf                |  4 ++--
 .../nf-core/multiqc/tests/main.nf.test.snap    | 18 +++++++++---------
 modules/nf-core/multiqc/tests/tags.yml         |  2 --
 5 files changed, 15 insertions(+), 15 deletions(-)
 delete mode 100644 modules/nf-core/multiqc/tests/tags.yml

diff --git a/modules.json b/modules.json
index 28c9108c..71b4bbe5 100644
--- a/modules.json
+++ b/modules.json
@@ -28,7 +28,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad",
+                        "git_sha": "7b50cb7be890e4b28cffb82e438cc6a8d7805d3f",
                         "installed_by": ["modules"]
                     },
                     "seqfu/stats": {
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index a27122ce..d430da5f 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -1,5 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::multiqc=1.27
+  - bioconda::multiqc=1.28
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 58d9313c..f3b57047 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,8 +3,8 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.27--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.27--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.28--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.28--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index 7b7c1322..26d74307 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
+                "versions.yml:md5,b05075d2d2b4f485c0d627a5c8e475b2"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.0",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-27T09:29:57.631982377"
+        "timestamp": "2025-03-26T16:05:18.927925"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
+                "versions.yml:md5,b05075d2d2b4f485c0d627a5c8e475b2"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.0",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-27T09:30:34.743726958"
+        "timestamp": "2025-03-26T16:05:55.639955"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
+                "versions.yml:md5,b05075d2d2b4f485c0d627a5c8e475b2"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.0",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-27T09:30:21.44383553"
+        "timestamp": "2025-03-26T16:05:44.067369"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml
deleted file mode 100644
index bea6c0d3..00000000
--- a/modules/nf-core/multiqc/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-multiqc:
-  - modules/nf-core/multiqc/**

From 307943b98c6986f00ad105de9ef865c9f49c3139 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Thu, 27 Mar 2025 08:49:16 +0100
Subject: [PATCH 217/530] Update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index dfa1685a..08808a27 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -31,5 +31,6 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#112](https://github.com/nf-core/seqinspector/pull/112) Making fastq_screen_references value to use parentDir
 
 ### `Dependencies`
+- [#116](https://github.com/nf-core/seqinspector/pull/116) Update MultiQC to 1.28
 
 ### `Deprecated`

From 133664b1ea95d2b2d1d192fbeadf74c5d70c8f76 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Thu, 27 Mar 2025 08:50:41 +0100
Subject: [PATCH 218/530] Lint changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 08808a27..03788ac6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -31,6 +31,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#112](https://github.com/nf-core/seqinspector/pull/112) Making fastq_screen_references value to use parentDir
 
 ### `Dependencies`
+
 - [#116](https://github.com/nf-core/seqinspector/pull/116) Update MultiQC to 1.28
 
 ### `Deprecated`

From 2471b5ade6cb3b6e2ed385a58ba5066f815f11b3 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Thu, 27 Mar 2025 09:40:35 +0100
Subject: [PATCH 219/530] Update snapshots

---
 tests/MiSeq_PairedEnd.main.nf.test.snap | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index 6a5c6992..877fc5e0 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -52,7 +52,6 @@
                 "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
                 "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
                 "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
                 "multiqc/global_report/multiqc_data/multiqc.log",
                 "multiqc/global_report/multiqc_data/multiqc_citations.txt",
                 "multiqc/global_report/multiqc_data/multiqc_data.json",
@@ -76,7 +75,6 @@
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
@@ -92,7 +90,6 @@
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
                 "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
@@ -108,7 +105,6 @@
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
                 "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
                 "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
@@ -125,7 +121,6 @@
                 "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_sequence_counts_plot.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc.log",
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_citations.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_data.json",
@@ -149,7 +144,6 @@
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/general_stats_table.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png",
@@ -165,7 +159,6 @@
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/general_stats_table.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg",
@@ -181,7 +174,6 @@
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/general_stats_table.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_report.html",
@@ -240,6 +232,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-03-26T13:02:05.27761"
+        "timestamp": "2025-03-27T09:01:13.732951"
     }
 }
\ No newline at end of file

From 19d19cf1e8af5b5f214b7b68f6ae6e59fb5f3a33 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Wed, 2 Apr 2025 11:55:25 +0000
Subject: [PATCH 220/530] bump changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 03788ac6..fc243f3c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 
 ### `Added`
 
+- [#114](https://github.com/nf-core/seqinspector/pull/114/) Update CI
 - [#75](https://github.com/nf-core/seqinspector/pull/75) Set up nft-utils
 - [#68](https://github.com/nf-core/seqinspector/pull/68) Add tool selector
 - [#20](https://github.com/nf-core/seqinspector/pull/20) Use tags to generate group reports

From 309dfbc73e45248faa146e060c4006a1f92df86a Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Wed, 30 Apr 2025 12:28:44 +0000
Subject: [PATCH 221/530] Template update for nf-core/tools version 3.2.1

---
 .github/workflows/awsfulltest.yml | 41 ++++++++-----------------------
 .github/workflows/ci.yml          |  1 +
 .nf-core.yml                      |  8 +++++-
 nextflow.config                   |  2 +-
 ro-crate-metadata.json            | 12 ++++-----
 5 files changed, 25 insertions(+), 39 deletions(-)

diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 311d3d07..d5895dcc 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -4,44 +4,23 @@ name: nf-core AWS full size tests
 # It runs the -profile 'test_full' on AWS batch
 
 on:
-  pull_request:
-    branches:
-      - main
-      - master
   workflow_dispatch:
   pull_request_review:
     types: [submitted]
+  release:
+    types: [published]
 
 jobs:
   run-platform:
     name: Run AWS full tests
-    # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered
-    if: github.repository == 'nf-core/seqinspector' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
+    # run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered
+    if: github.repository == 'nf-core/seqinspector' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
-      - name: Get PR reviews
-        uses: octokit/request-action@v2.x
-        if: github.event_name != 'workflow_dispatch'
-        id: check_approvals
-        continue-on-error: true
-        with:
-          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Check for approvals
-        if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
-        run: |
-          echo "No review approvals found. At least 2 approvals are required to run this action automatically."
-          exit 1
-
-      - name: Check for enough approvals (>=2)
-        id: test_variables
-        if: github.event_name != 'workflow_dispatch'
+      - name: Set revision variable
+        id: revision
         run: |
-          JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
-          CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
-          test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
+          echo "revision=${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT"
 
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
@@ -52,12 +31,12 @@ jobs:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
-          revision: ${{ github.sha }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/seqinspector/work-${{ github.sha }}
+          revision: ${{ steps.revision.outputs.revision }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/seqinspector/work-${{ steps.revision.outputs.revision }}
           parameters: |
             {
               "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/seqinspector/results-${{ github.sha }}"
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/seqinspector/results-${{ steps.revision.outputs.revision }}"
             }
           profiles: test_full
 
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d6fc106a..47013c89 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -83,5 +83,6 @@ jobs:
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
       - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
+        continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results
diff --git a/.nf-core.yml b/.nf-core.yml
index c984b0c3..edec93e2 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,7 +1,13 @@
 lint:
+  actions_ci: false
+  files_exist:
+    - .github/workflows/ci.yml
   files_unchanged:
     - .github/CONTRIBUTING.md
-nf_core_version: 3.2.0
+  nextflow_config:
+    - config_defaults:
+        - params.fastq_screen_references
+nf_core_version: 3.2.1
 repository_type: pipeline
 template:
   author: Adrien Coulier
diff --git a/nextflow.config b/nextflow.config
index c1d108ba..f8cf02b6 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -249,7 +249,7 @@ manifest {
 
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-schema@2.2.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 validation {
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 7b22e103..47ed62dd 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,7 +22,7 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2025-01-27T16:15:35+00:00",
+            "datePublished": "2025-04-30T12:28:35+00:00",
             "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by Adrien Coulier.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#d25cadcb-fa1a-425e-8f2d-e5d85d309c29"
+                    "@id": "#3922d80d-b4bb-45e2-bfbe-319f044d5183"
                 }
             ],
             "name": "nf-core/seqinspector"
@@ -128,7 +128,7 @@
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2025-01-27T16:15:35Z",
+            "dateModified": "2025-04-30T12:28:35Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": ["nf-core", "nextflow", "genomics", "quality-control"],
             "license": ["MIT"],
@@ -160,11 +160,11 @@
             "version": "!>=24.04.2"
         },
         {
-            "@id": "#d25cadcb-fa1a-425e-8f2d-e5d85d309c29",
+            "@id": "#3922d80d-b4bb-45e2-bfbe-319f044d5183",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#ec706afc-83c1-4f5f-bb83-661e72cacb33"
+                    "@id": "#c221c6fd-141e-46a2-9917-cc5f1f223bba"
                 }
             ],
             "mainEntity": {
@@ -173,7 +173,7 @@
             "name": "Test suite for nf-core/seqinspector"
         },
         {
-            "@id": "#ec706afc-83c1-4f5f-bb83-661e72cacb33",
+            "@id": "#c221c6fd-141e-46a2-9917-cc5f1f223bba",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/seqinspector",
             "resource": "repos/nf-core/seqinspector/actions/workflows/ci.yml",

From 23d6b11ac6d42cd6928cd6c1e6ee143903747db2 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Tue, 3 Jun 2025 11:02:19 +0000
Subject: [PATCH 222/530] Template update for nf-core/tools version 3.3.1

---
 .editorconfig                                 |  37 -----
 .github/CONTRIBUTING.md                       |   2 +-
 .github/actions/get-shards/action.yml         |  69 +++++++++
 .github/actions/nf-test/action.yml            | 113 ++++++++++++++
 .github/workflows/awsfulltest.yml             |   4 +-
 .github/workflows/awstest.yml                 |   2 +-
 .github/workflows/ci.yml                      |  88 -----------
 .github/workflows/clean-up.yml                |   2 +-
 .github/workflows/download_pipeline.yml       |  20 +--
 .../{fix-linting.yml => fix_linting.yml}      |   4 +-
 .github/workflows/linting.yml                 |  15 +-
 .github/workflows/linting_comment.yml         |   4 +-
 .github/workflows/nf-test.yml                 | 142 ++++++++++++++++++
 .github/workflows/release-announcements.yml   |   2 +-
 ...mment.yml => template-version-comment.yml} |   2 +-
 .nf-core.yml                                  |   3 +-
 .pre-commit-config.yaml                       |  26 +++-
 .prettierrc.yml                               |   5 +
 README.md                                     |   7 +-
 conf/base.config                              |   5 +-
 nextflow.config                               |  17 ++-
 nf-test.config                                |  24 +++
 ro-crate-metadata.json                        |  16 +-
 .../main.nf                                   |   1 -
 tests/.nftignore                              |  10 ++
 tests/default.nf.test                         |  35 +++++
 tests/nextflow.config                         |  12 ++
 27 files changed, 487 insertions(+), 180 deletions(-)
 delete mode 100644 .editorconfig
 create mode 100644 .github/actions/get-shards/action.yml
 create mode 100644 .github/actions/nf-test/action.yml
 delete mode 100644 .github/workflows/ci.yml
 rename .github/workflows/{fix-linting.yml => fix_linting.yml} (96%)
 create mode 100644 .github/workflows/nf-test.yml
 rename .github/workflows/{template_version_comment.yml => template-version-comment.yml} (95%)
 create mode 100644 nf-test.config
 create mode 100644 tests/.nftignore
 create mode 100644 tests/default.nf.test
 create mode 100644 tests/nextflow.config

diff --git a/.editorconfig b/.editorconfig
deleted file mode 100644
index 6d9b74cc..00000000
--- a/.editorconfig
+++ /dev/null
@@ -1,37 +0,0 @@
-root = true
-
-[*]
-charset = utf-8
-end_of_line = lf
-insert_final_newline = true
-trim_trailing_whitespace = true
-indent_size = 4
-indent_style = space
-
-[*.{md,yml,yaml,html,css,scss,js}]
-indent_size = 2
-
-# These files are edited and tested upstream in nf-core/modules
-[/modules/nf-core/**]
-charset = unset
-end_of_line = unset
-insert_final_newline = unset
-trim_trailing_whitespace = unset
-indent_style = unset
-[/subworkflows/nf-core/**]
-charset = unset
-end_of_line = unset
-insert_final_newline = unset
-trim_trailing_whitespace = unset
-indent_style = unset
-
-[/assets/email*]
-indent_size = unset
-
-# ignore python and markdown
-[*.{py,md}]
-indent_style = unset
-
-# ignore ro-crate metadata files
-[**/ro-crate-metadata.json]
-insert_final_newline = unset
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 8efc2032..f4d9ad91 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -78,7 +78,7 @@ If you wish to contribute a new step, please use the following coding standards:
 5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool).
 6. Add sanity checks and validation for all relevant parameters.
 7. Perform local tests to validate that the new code works as expected.
-8. If applicable, add a new test command in `.github/workflow/ci.yml`.
+8. If applicable, add a new test in the `tests` directory.
 9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
 10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
 
diff --git a/.github/actions/get-shards/action.yml b/.github/actions/get-shards/action.yml
new file mode 100644
index 00000000..34085279
--- /dev/null
+++ b/.github/actions/get-shards/action.yml
@@ -0,0 +1,69 @@
+name: "Get number of shards"
+description: "Get the number of nf-test shards for the current CI job"
+inputs:
+  max_shards:
+    description: "Maximum number of shards allowed"
+    required: true
+  paths:
+    description: "Component paths to test"
+    required: false
+  tags:
+    description: "Tags to pass as argument for nf-test --tag parameter"
+    required: false
+outputs:
+  shard:
+    description: "Array of shard numbers"
+    value: ${{ steps.shards.outputs.shard }}
+  total_shards:
+    description: "Total number of shards"
+    value: ${{ steps.shards.outputs.total_shards }}
+runs:
+  using: "composite"
+  steps:
+    - name: Install nf-test
+      uses: nf-core/setup-nf-test@v1
+      with:
+        version: ${{ env.NFT_VER }}
+    - name: Get number of shards
+      id: shards
+      shell: bash
+      run: |
+        # Run nf-test with dynamic parameter
+        nftest_output=$(nf-test test \
+          --profile +docker \
+          $(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \
+          --dry-run \
+          --ci \
+          --changed-since HEAD^) || {
+            echo "nf-test command failed with exit code $?"
+            echo "Full output: $nftest_output"
+            exit 1
+        }
+        echo "nf-test dry-run output: $nftest_output"
+
+        # Default values for shard and total_shards
+        shard="[]"
+        total_shards=0
+
+        # Check if there are related tests
+        if echo "$nftest_output" | grep -q 'No tests to execute'; then
+          echo "No related tests found."
+        else
+          # Extract the number of related tests
+          number_of_shards=$(echo "$nftest_output" | sed -n 's|.*Executed \([0-9]*\) tests.*|\1|p')
+          if [[ -n "$number_of_shards" && "$number_of_shards" -gt 0 ]]; then
+            shards_to_run=$(( $number_of_shards < ${{ inputs.max_shards }} ? $number_of_shards : ${{ inputs.max_shards }} ))
+            shard=$(seq 1 "$shards_to_run" | jq -R . | jq -c -s .)
+            total_shards="$shards_to_run"
+          else
+            echo "Unexpected output format. Falling back to default values."
+          fi
+        fi
+
+        # Write to GitHub Actions outputs
+        echo "shard=$shard" >> $GITHUB_OUTPUT
+        echo "total_shards=$total_shards" >> $GITHUB_OUTPUT
+
+        # Debugging output
+        echo "Final shard array: $shard"
+        echo "Total number of shards: $total_shards"
diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml
new file mode 100644
index 00000000..243e7823
--- /dev/null
+++ b/.github/actions/nf-test/action.yml
@@ -0,0 +1,113 @@
+name: "nf-test Action"
+description: "Runs nf-test with common setup steps"
+inputs:
+  profile:
+    description: "Profile to use"
+    required: true
+  shard:
+    description: "Shard number for this CI job"
+    required: true
+  total_shards:
+    description: "Total number of test shards(NOT the total number of matrix jobs)"
+    required: true
+  paths:
+    description: "Test paths"
+    required: true
+  tags:
+    description: "Tags to pass as argument for nf-test --tag parameter"
+    required: false
+runs:
+  using: "composite"
+  steps:
+    - name: Setup Nextflow
+      uses: nf-core/setup-nextflow@v2
+      with:
+        version: "${{ env.NXF_VERSION }}"
+
+    - name: Set up Python
+      uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      with:
+        python-version: "3.13"
+
+    - name: Install nf-test
+      uses: nf-core/setup-nf-test@v1
+      with:
+        version: "${{ env.NFT_VER }}"
+        install-pdiff: true
+
+    - name: Setup apptainer
+      if: contains(inputs.profile, 'singularity')
+      uses: eWaterCycle/setup-apptainer@main
+
+    - name: Set up Singularity
+      if: contains(inputs.profile, 'singularity')
+      shell: bash
+      run: |
+        mkdir -p $NXF_SINGULARITY_CACHEDIR
+        mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+
+    - name: Conda setup
+      if: contains(inputs.profile, 'conda')
+      uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3
+      with:
+        auto-update-conda: true
+        conda-solver: libmamba
+        conda-remove-defaults: true
+
+      # TODO Skip failing conda tests and document their failures
+      # https://github.com/nf-core/modules/issues/7017
+    - name: Run nf-test
+      shell: bash
+      env:
+        NFT_DIFF: ${{ env.NFT_DIFF }}
+        NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
+        NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
+      run: |
+        nf-test test \
+          --profile=+${{ inputs.profile }} \
+          $(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \
+          --ci \
+          --changed-since HEAD^ \
+          --verbose \
+          --tap=test.tap \
+          --shard ${{ inputs.shard }}/${{ inputs.total_shards }}
+
+          # Save the absolute path of the test.tap file to the output
+          echo "tap_file_path=$(realpath test.tap)" >> $GITHUB_OUTPUT
+
+    - name: Generate test summary
+      if: always()
+      shell: bash
+      run: |
+        # Add header if it doesn't exist (using a token file to track this)
+        if [ ! -f ".summary_header" ]; then
+          echo "# 🚀 nf-test results" >> $GITHUB_STEP_SUMMARY
+          echo "" >> $GITHUB_STEP_SUMMARY
+          echo "| Status | Test Name | Profile | Shard |" >> $GITHUB_STEP_SUMMARY
+          echo "|:------:|-----------|---------|-------|" >> $GITHUB_STEP_SUMMARY
+          touch .summary_header
+        fi
+
+        if [ -f test.tap ]; then
+          while IFS= read -r line; do
+            if [[ $line =~ ^ok ]]; then
+              test_name="${line#ok }"
+              # Remove the test number from the beginning
+              test_name="${test_name#* }"
+              echo "| ✅ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
+            elif [[ $line =~ ^not\ ok ]]; then
+              test_name="${line#not ok }"
+              # Remove the test number from the beginning
+              test_name="${test_name#* }"
+              echo "| ❌ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
+            fi
+          done < test.tap
+        else
+          echo "| ⚠️ | No test results found | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
+        fi
+
+    - name: Clean up
+      if: always()
+      shell: bash
+      run: |
+        sudo rm -rf /home/ubuntu/tests/
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index d5895dcc..f8125112 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -14,7 +14,7 @@ jobs:
   run-platform:
     name: Run AWS full tests
     # run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered
-    if: github.repository == 'nf-core/seqinspector' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch'
+    if: github.repository == 'nf-core/seqinspector' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch' || github.event_name == 'release'
     runs-on: ubuntu-latest
     steps:
       - name: Set revision variable
@@ -40,7 +40,7 @@ jobs:
             }
           profiles: test_full
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
         with:
           name: Seqera Platform debug log file
           path: |
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index eef6f2c3..c6867673 100644
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@@ -25,7 +25,7 @@ jobs:
             }
           profiles: test
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
         with:
           name: Seqera Platform debug log file
           path: |
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
deleted file mode 100644
index 47013c89..00000000
--- a/.github/workflows/ci.yml
+++ /dev/null
@@ -1,88 +0,0 @@
-name: nf-core CI
-# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
-on:
-  push:
-    branches:
-      - dev
-  pull_request:
-  release:
-    types: [published]
-  workflow_dispatch:
-
-env:
-  NXF_ANSI_LOG: false
-  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
-  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
-
-concurrency:
-  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
-  cancel-in-progress: true
-
-jobs:
-  test:
-    name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/seqinspector') }}"
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        NXF_VER:
-          - "24.04.2"
-          - "latest-everything"
-        profile:
-          - "conda"
-          - "docker"
-          - "singularity"
-        test_name:
-          - "test"
-        isMaster:
-          - ${{ github.base_ref == 'master' }}
-        # Exclude conda and singularity on dev
-        exclude:
-          - isMaster: false
-            profile: "conda"
-          - isMaster: false
-            profile: "singularity"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
-        with:
-          fetch-depth: 0
-
-      - name: Set up Nextflow
-        uses: nf-core/setup-nextflow@v2
-        with:
-          version: "${{ matrix.NXF_VER }}"
-
-      - name: Set up Apptainer
-        if: matrix.profile == 'singularity'
-        uses: eWaterCycle/setup-apptainer@main
-
-      - name: Set up Singularity
-        if: matrix.profile == 'singularity'
-        run: |
-          mkdir -p $NXF_SINGULARITY_CACHEDIR
-          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
-
-      - name: Set up Miniconda
-        if: matrix.profile == 'conda'
-        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
-        with:
-          miniconda-version: "latest"
-          auto-update-conda: true
-          conda-solver: libmamba
-          channels: conda-forge,bioconda
-
-      - name: Set up Conda
-        if: matrix.profile == 'conda'
-        run: |
-          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
-          echo $(realpath python) >> $GITHUB_PATH
-
-      - name: Clean up Disk space
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
-
-      - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
-        continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results
diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
index 0b6b1f27..ac030fd5 100644
--- a/.github/workflows/clean-up.yml
+++ b/.github/workflows/clean-up.yml
@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9
+      - uses: actions/stale@5bef64f19d7facfb25b37b414482c7164d639639 # v9
         with:
           stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
           stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index ab06316e..999bcc38 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -12,14 +12,6 @@ on:
         required: true
         default: "dev"
   pull_request:
-    types:
-      - opened
-      - edited
-      - synchronize
-    branches:
-      - main
-      - master
-  pull_request_target:
     branches:
       - main
       - master
@@ -52,9 +44,9 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
           architecture: "x64"
 
       - name: Setup Apptainer
@@ -120,6 +112,7 @@ jobs:
           echo "IMAGE_COUNT_AFTER=$image_count" >> "$GITHUB_OUTPUT"
 
       - name: Compare container image counts
+        id: count_comparison
         run: |
           if [ "${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}" -ne "${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}" ]; then
             initial_count=${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}
@@ -132,3 +125,10 @@ jobs:
           else
             echo "The pipeline can be downloaded successfully!"
           fi
+
+      - name: Upload Nextflow logfile for debugging purposes
+        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        with:
+          name: nextflow_logfile.txt
+          path: .nextflow.log*
+          include-hidden-files: true
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix_linting.yml
similarity index 96%
rename from .github/workflows/fix-linting.yml
rename to .github/workflows/fix_linting.yml
index 5adee083..2e4ae888 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix_linting.yml
@@ -32,9 +32,9 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Install pre-commit
         run: pip install pre-commit
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index dbd52d5a..f2d7d1dd 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -3,9 +3,6 @@ name: nf-core linting
 # It runs the `nf-core pipelines lint` and markdown lint tests to ensure
 # that the code meets the nf-core guidelines.
 on:
-  push:
-    branches:
-      - dev
   pull_request:
   release:
     types: [published]
@@ -17,9 +14,9 @@ jobs:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -36,13 +33,13 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
           architecture: "x64"
 
       - name: read .nf-core.yml
-        uses: pietrobolcato/action-read-yaml@1.1.0
+        uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
         id: read_yml
         with:
           config: ${{ github.workspace }}/.nf-core.yml
@@ -74,7 +71,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
+        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 95b6b6af..7e8050fb 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8
+        uses: dawidd6/action-download-artifact@4c1e823582f43b179e2cbb49c3eade4e41f992e2 # v10
         with:
           workflow: linting.yml
           workflow_conclusion: completed
@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2
+        uses: marocchino/sticky-pull-request-comment@52423e01640425a022ef5fd42c6fb5f633a02728 # v2
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
new file mode 100644
index 00000000..f03aea0c
--- /dev/null
+++ b/.github/workflows/nf-test.yml
@@ -0,0 +1,142 @@
+name: Run nf-test
+on:
+  push:
+    paths-ignore:
+      - "docs/**"
+      - "**/meta.yml"
+      - "**/*.md"
+      - "**/*.png"
+      - "**/*.svg"
+  pull_request:
+    paths-ignore:
+      - "docs/**"
+      - "**/meta.yml"
+      - "**/*.md"
+      - "**/*.png"
+      - "**/*.svg"
+  release:
+    types: [published]
+  workflow_dispatch:
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  NFT_VER: "0.9.2"
+  NFT_WORKDIR: "~"
+  NXF_ANSI_LOG: false
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
+
+jobs:
+  nf-test-changes:
+    name: nf-test-changes
+    runs-on: # use self-hosted runners
+      - runs-on=$-nf-test-changes
+      - runner=4cpu-linux-x64
+    outputs:
+      shard: ${{ steps.set-shards.outputs.shard }}
+      total_shards: ${{ steps.set-shards.outputs.total_shards }}
+    steps:
+      - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner
+        run: |
+          ls -la ./
+          rm -rf ./* || true
+          rm -rf ./.??* || true
+          ls -la ./
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          fetch-depth: 0
+
+      - name: get number of shards
+        id: set-shards
+        uses: ./.github/actions/get-shards
+        env:
+          NFT_VER: ${{ env.NFT_VER }}
+        with:
+          max_shards: 7
+
+      - name: debug
+        run: |
+          echo ${{ steps.set-shards.outputs.shard }}
+          echo ${{ steps.set-shards.outputs.total_shards }}
+
+  nf-test:
+    name: "${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/${{ needs.nf-test-changes.outputs.total_shards }}"
+    needs: [nf-test-changes]
+    if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }}
+    runs-on: # use self-hosted runners
+      - runs-on=$-nf-test
+      - runner=4cpu-linux-x64
+    strategy:
+      fail-fast: false
+      matrix:
+        shard: ${{ fromJson(needs.nf-test-changes.outputs.shard) }}
+        profile: [conda, docker, singularity]
+        isMain:
+          - ${{ github.base_ref == 'master' || github.base_ref == 'main' }}
+        # Exclude conda and singularity on dev
+        exclude:
+          - isMain: false
+            profile: "conda"
+          - isMain: false
+            profile: "singularity"
+        NXF_VER:
+          - "24.04.2"
+          - "latest-everything"
+    env:
+      NXF_ANSI_LOG: false
+      TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
+
+    steps:
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          fetch-depth: 0
+
+      - name: Run nf-test
+        uses: ./.github/actions/nf-test
+        env:
+          NFT_DIFF: ${{ env.NFT_DIFF }}
+          NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
+          NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
+        with:
+          profile: ${{ matrix.profile }}
+          shard: ${{ matrix.shard }}
+          total_shards: ${{ env.TOTAL_SHARDS }}
+  confirm-pass:
+    needs: [nf-test]
+    if: always()
+    runs-on: # use self-hosted runners
+      - runs-on=$-confirm-pass
+      - runner=2cpu-linux-x64
+    steps:
+      - name: One or more tests failed
+        if: ${{ contains(needs.*.result, 'failure') }}
+        run: exit 1
+
+      - name: One or more tests cancelled
+        if: ${{ contains(needs.*.result, 'cancelled') }}
+        run: exit 1
+
+      - name: All tests ok
+        if: ${{ contains(needs.*.result, 'success') }}
+        run: exit 0
+
+      - name: debug-print
+        if: always()
+        run: |
+          echo "::group::DEBUG: `needs` Contents"
+          echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}"
+          echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
+          echo "::endgroup::"
+
+      - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner
+        if: always()
+        run: |
+          ls -la ./
+          rm -rf ./* || true
+          rm -rf ./.??* || true
+          ls -la ./
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index 76a9e67e..4abaf484 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -30,7 +30,7 @@ jobs:
   bsky-post:
     runs-on: ubuntu-latest
     steps:
-      - uses: zentered/bluesky-post-action@80dbe0a7697de18c15ad22f4619919ceb5ccf597 # v0.1.0
+      - uses: zentered/bluesky-post-action@4aa83560bb3eac05dbad1e5f221ee339118abdd2 # v0.2.0
         with:
           post: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template-version-comment.yml
similarity index 95%
rename from .github/workflows/template_version_comment.yml
rename to .github/workflows/template-version-comment.yml
index 537529bc..beb5c77f 100644
--- a/.github/workflows/template_version_comment.yml
+++ b/.github/workflows/template-version-comment.yml
@@ -14,7 +14,7 @@ jobs:
           ref: ${{ github.event.pull_request.head.sha }}
 
       - name: Read template version from .nf-core.yml
-        uses: nichmor/minimal-read-yaml@v0.0.2
+        uses: nichmor/minimal-read-yaml@1f7205277e25e156e1f63815781db80a6d490b8f # v0.0.2
         id: read_yml
         with:
           config: ${{ github.workspace }}/.nf-core.yml
diff --git a/.nf-core.yml b/.nf-core.yml
index edec93e2..a13ab5f1 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,5 +1,4 @@
 lint:
-  actions_ci: false
   files_exist:
     - .github/workflows/ci.yml
   files_unchanged:
@@ -7,7 +6,7 @@ lint:
   nextflow_config:
     - config_defaults:
         - params.fastq_screen_references
-nf_core_version: 3.2.1
+nf_core_version: 3.3.1
 repository_type: pipeline
 template:
   author: Adrien Coulier
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 1dec8650..9d0b248d 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -4,10 +4,24 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.2.5
-
-  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "3.1.2"
+          - prettier@3.5.0
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
     hooks:
-      - id: editorconfig-checker
-        alias: ec
+      - id: trailing-whitespace
+        args: [--markdown-linebreak-ext=md]
+        exclude: |
+          (?x)^(
+              .*ro-crate-metadata.json$|
+              modules/nf-core/.*|
+              subworkflows/nf-core/.*|
+              .*\.snap$
+          )$
+      - id: end-of-file-fixer
+        exclude: |
+          (?x)^(
+              .*ro-crate-metadata.json$|
+              modules/nf-core/.*|
+              subworkflows/nf-core/.*|
+              .*\.snap$
+          )$
diff --git a/.prettierrc.yml b/.prettierrc.yml
index c81f9a76..07dbd8bb 100644
--- a/.prettierrc.yml
+++ b/.prettierrc.yml
@@ -1 +1,6 @@
 printWidth: 120
+tabWidth: 4
+overrides:
+  - files: "*.{md,yml,yaml,html,css,scss,js,cff}"
+    options:
+      tabWidth: 2
diff --git a/README.md b/README.md
index 1c2cc4bc..58cae795 100644
--- a/README.md
+++ b/README.md
@@ -9,13 +9,14 @@
 [![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.04.2-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
+[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.1)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
 [![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)
 
-[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
+[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
 
 ## Introduction
 
@@ -28,7 +29,7 @@
 -->
 
 <!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
-     workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->
+     workflows use the "tube map" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples.   -->
 <!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
 
 ## Usage
diff --git a/conf/base.config b/conf/base.config
index eb6fbee3..29b4ddcc 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -15,7 +15,7 @@ process {
     memory = { 6.GB   * task.attempt }
     time   = { 4.h    * task.attempt }
 
-    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
+    errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' }
     maxRetries    = 1
     maxErrors     = '-1'
 
@@ -59,4 +59,7 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
+    withLabel: process_gpu {
+        ext.use_gpu = { workflow.profile.contains('gpu') }
+    }
 }
diff --git a/nextflow.config b/nextflow.config
index f8cf02b6..2a130599 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -160,16 +160,25 @@ profiles {
             ]
         }
     }
+    gpu {
+        docker.runOptions       = '-u $(id -u):$(id -g) --gpus all'
+        apptainer.runOptions    = '--nv'
+        singularity.runOptions  = '--nv'
+    }
     test      { includeConfig 'conf/test.config'      }
     test_full { includeConfig 'conf/test_full.config' }
 }
 
-// Load nf-core custom profiles from different Institutions
-includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
+// Load nf-core custom profiles from different institutions
+
+// If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included.
+// Load nf-core/seqinspector custom profiles from different institutions.
+includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
+
 
 // Load nf-core/seqinspector custom profiles from different institutions.
 // TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
-// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/seqinspector.config" : "/dev/null"
+// includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/seqinspector.config" : "/dev/null"
 
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
 // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
@@ -249,7 +258,7 @@ manifest {
 
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.2.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 validation {
diff --git a/nf-test.config b/nf-test.config
new file mode 100644
index 00000000..889df760
--- /dev/null
+++ b/nf-test.config
@@ -0,0 +1,24 @@
+config {
+    // location for all nf-test tests
+    testsDir "."
+
+    // nf-test directory including temporary files for each test
+    workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"
+
+    // location of an optional nextflow.config file specific for executing tests
+    configFile "tests/nextflow.config"
+
+    // ignore tests coming from the nf-core/modules repo
+    ignore 'modules/nf-core/**/*', 'subworkflows/nf-core/**/*'
+
+    // run all test with defined profile(s) from the main nextflow.config
+    profile "test"
+
+    // list of filenames or patterns that should be trigger a full test run
+    triggers 'nextflow.config', 'nf-test.config', 'conf/test.config', 'tests/nextflow.config', 'tests/.nftignore'
+
+    // load the necessary plugins
+    plugins {
+        load "nft-utils@0.0.3"
+    }
+}
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 47ed62dd..93443814 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,8 +22,8 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2025-04-30T12:28:35+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by Adrien Coulier.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "datePublished": "2025-06-03T11:02:14+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.04.2-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by Adrien Coulier.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
                     "@id": "main.nf"
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#3922d80d-b4bb-45e2-bfbe-319f044d5183"
+                    "@id": "#391b6670-7ba3-43a3-8911-62f797d852f6"
                 }
             ],
             "name": "nf-core/seqinspector"
@@ -128,7 +128,7 @@
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2025-04-30T12:28:35Z",
+            "dateModified": "2025-06-03T11:02:14Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": ["nf-core", "nextflow", "genomics", "quality-control"],
             "license": ["MIT"],
@@ -160,11 +160,11 @@
             "version": "!>=24.04.2"
         },
         {
-            "@id": "#3922d80d-b4bb-45e2-bfbe-319f044d5183",
+            "@id": "#391b6670-7ba3-43a3-8911-62f797d852f6",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#c221c6fd-141e-46a2-9917-cc5f1f223bba"
+                    "@id": "#7c992a78-479f-434b-9046-8a50507c617c"
                 }
             ],
             "mainEntity": {
@@ -173,10 +173,10 @@
             "name": "Test suite for nf-core/seqinspector"
         },
         {
-            "@id": "#c221c6fd-141e-46a2-9917-cc5f1f223bba",
+            "@id": "#7c992a78-479f-434b-9046-8a50507c617c",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/seqinspector",
-            "resource": "repos/nf-core/seqinspector/actions/workflows/ci.yml",
+            "resource": "repos/nf-core/seqinspector/actions/workflows/nf-test.yml",
             "runsOn": {
                 "@id": "https://w3id.org/ro/terms/test#GithubService"
             },
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index 297dc0dc..7de849fc 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -261,4 +261,3 @@ def methodsDescriptionText(mqc_methods_yaml) {
 
     return description_html.toString()
 }
-
diff --git a/tests/.nftignore b/tests/.nftignore
new file mode 100644
index 00000000..c10bc1f1
--- /dev/null
+++ b/tests/.nftignore
@@ -0,0 +1,10 @@
+.DS_Store
+multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
+multiqc/multiqc_data/multiqc.log
+multiqc/multiqc_data/multiqc_data.json
+multiqc/multiqc_data/multiqc_sources.txt
+multiqc/multiqc_data/multiqc_software_versions.txt
+multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
+multiqc/multiqc_report.html
+fastqc/*_fastqc.{html,zip}
+pipeline_info/*.{html,json,txt,yml}
diff --git a/tests/default.nf.test b/tests/default.nf.test
new file mode 100644
index 00000000..32014888
--- /dev/null
+++ b/tests/default.nf.test
@@ -0,0 +1,35 @@
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../main.nf"
+    tag "pipeline"
+
+    test("-profile test") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/tests/nextflow.config b/tests/nextflow.config
new file mode 100644
index 00000000..362d5403
--- /dev/null
+++ b/tests/nextflow.config
@@ -0,0 +1,12 @@
+/*
+========================================================================================
+    Nextflow config file for running nf-test tests
+========================================================================================
+*/
+
+// TODO nf-core: Specify any additional parameters here
+// Or any resources requirements
+params.modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+params.pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/seqinspector'
+
+aws.client.anonymous = true // fixes S3 access issues on self-hosted runners

From 0fe7d3f155dd81724103c4d401154636df66f47a Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Tue, 8 Jul 2025 11:39:26 +0000
Subject: [PATCH 223/530] Template update for nf-core/tools version 3.3.2

---
 .github/actions/nf-test/action.yml            |   4 -
 .github/workflows/linting.yml                 |   2 +-
 .github/workflows/linting_comment.yml         |   2 +-
 .github/workflows/nf-test.yml                 |  45 +++----
 .github/workflows/release-announcements.yml   |   2 +-
 .nf-core.yml                                  |   2 +-
 .pre-commit-config.yaml                       |   2 +-
 README.md                                     |   6 +-
 assets/schema_input.json                      |   4 +-
 conf/base.config                              |   1 +
 modules.json                                  |   4 +-
 modules/nf-core/fastqc/environment.yml        |   2 +
 modules/nf-core/fastqc/main.nf                |   2 +-
 modules/nf-core/fastqc/meta.yml               |  23 ++--
 modules/nf-core/multiqc/environment.yml       |   4 +-
 modules/nf-core/multiqc/main.nf               |   4 +-
 modules/nf-core/multiqc/meta.yml              | 110 ++++++++++--------
 .../nf-core/multiqc/tests/main.nf.test.snap   |  18 +--
 nextflow.config                               |   5 +-
 nf-test.config                                |   2 +-
 ro-crate-metadata.json                        |  16 +--
 .../tests/nextflow.config                     |   2 +-
 tests/.nftignore                              |   1 +
 tests/nextflow.config                         |   6 +-
 24 files changed, 146 insertions(+), 123 deletions(-)

diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml
index 243e7823..bf44d961 100644
--- a/.github/actions/nf-test/action.yml
+++ b/.github/actions/nf-test/action.yml
@@ -54,13 +54,9 @@ runs:
         conda-solver: libmamba
         conda-remove-defaults: true
 
-      # TODO Skip failing conda tests and document their failures
-      # https://github.com/nf-core/modules/issues/7017
     - name: Run nf-test
       shell: bash
       env:
-        NFT_DIFF: ${{ env.NFT_DIFF }}
-        NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
         NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
       run: |
         nf-test test \
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index f2d7d1dd..8b0f88c3 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -13,7 +13,7 @@ jobs:
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
-      - name: Set up Python 3.12
+      - name: Set up Python 3.13
         uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
           python-version: "3.13"
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 7e8050fb..d43797d9 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@4c1e823582f43b179e2cbb49c3eade4e41f992e2 # v10
+        uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11
         with:
           workflow: linting.yml
           workflow_conclusion: completed
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index f03aea0c..e7b58449 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -1,12 +1,5 @@
 name: Run nf-test
 on:
-  push:
-    paths-ignore:
-      - "docs/**"
-      - "**/meta.yml"
-      - "**/*.md"
-      - "**/*.png"
-      - "**/*.svg"
   pull_request:
     paths-ignore:
       - "docs/**"
@@ -35,7 +28,7 @@ jobs:
   nf-test-changes:
     name: nf-test-changes
     runs-on: # use self-hosted runners
-      - runs-on=$-nf-test-changes
+      - runs-on=${{ github.run_id }}-nf-test-changes
       - runner=4cpu-linux-x64
     outputs:
       shard: ${{ steps.set-shards.outputs.shard }}
@@ -69,7 +62,7 @@ jobs:
     needs: [nf-test-changes]
     if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }}
     runs-on: # use self-hosted runners
-      - runs-on=$-nf-test
+      - runs-on=${{ github.run_id }}-nf-test
       - runner=4cpu-linux-x64
     strategy:
       fail-fast: false
@@ -85,7 +78,7 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "24.04.2"
+          - "24.10.5"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false
@@ -97,23 +90,39 @@ jobs:
           fetch-depth: 0
 
       - name: Run nf-test
+        id: run_nf_test
         uses: ./.github/actions/nf-test
+        continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
         env:
-          NFT_DIFF: ${{ env.NFT_DIFF }}
-          NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
           NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
         with:
           profile: ${{ matrix.profile }}
           shard: ${{ matrix.shard }}
           total_shards: ${{ env.TOTAL_SHARDS }}
+
+      - name: Report test status
+        if: ${{ always() }}
+        run: |
+          if [[ "${{ steps.run_nf_test.outcome }}" == "failure" ]]; then
+            echo "::error::Test with ${{ matrix.NXF_VER }} failed"
+            # Add to workflow summary
+            echo "## ❌ Test failed: ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }}" >> $GITHUB_STEP_SUMMARY
+            if [[ "${{ matrix.NXF_VER }}" == "latest-everything" ]]; then
+              echo "::warning::Test with latest-everything failed but will not cause workflow failure. Please check if the error is expected or if it needs fixing."
+            fi
+            if [[ "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
+              exit 1
+            fi
+          fi
+
   confirm-pass:
     needs: [nf-test]
     if: always()
     runs-on: # use self-hosted runners
-      - runs-on=$-confirm-pass
+      - runs-on=${{ github.run_id }}-confirm-pass
       - runner=2cpu-linux-x64
     steps:
-      - name: One or more tests failed
+      - name: One or more tests failed (excluding latest-everything)
         if: ${{ contains(needs.*.result, 'failure') }}
         run: exit 1
 
@@ -132,11 +141,3 @@ jobs:
           echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}"
           echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
           echo "::endgroup::"
-
-      - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner
-        if: always()
-        run: |
-          ls -la ./
-          rm -rf ./* || true
-          rm -rf ./.??* || true
-          ls -la ./
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index 4abaf484..0f732495 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -30,7 +30,7 @@ jobs:
   bsky-post:
     runs-on: ubuntu-latest
     steps:
-      - uses: zentered/bluesky-post-action@4aa83560bb3eac05dbad1e5f221ee339118abdd2 # v0.2.0
+      - uses: zentered/bluesky-post-action@6461056ea355ea43b977e149f7bf76aaa572e5e8 # v0.3.0
         with:
           post: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
diff --git a/.nf-core.yml b/.nf-core.yml
index a13ab5f1..02240c94 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -6,7 +6,7 @@ lint:
   nextflow_config:
     - config_defaults:
         - params.fastq_screen_references
-nf_core_version: 3.3.1
+nf_core_version: 3.3.2
 repository_type: pipeline
 template:
   author: Adrien Coulier
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 9d0b248d..bb41beec 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -4,7 +4,7 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.5.0
+          - prettier@3.6.2
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:
diff --git a/README.md b/README.md
index 58cae795..174f6ba9 100644
--- a/README.md
+++ b/README.md
@@ -5,12 +5,12 @@
   </picture>
 </h1>
 
-[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml)
+[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.04.2-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
-[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.1)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
+[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
diff --git a/assets/schema_input.json b/assets/schema_input.json
index d7d48374..1e5d47b9 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -17,14 +17,14 @@
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
+                "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.f(ast)?q\\.gz$",
                 "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
             },
             "fastq_2": {
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
+                "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.f(ast)?q\\.gz$",
                 "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
             }
         },
diff --git a/conf/base.config b/conf/base.config
index 29b4ddcc..84739da8 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -61,5 +61,6 @@ process {
     }
     withLabel: process_gpu {
         ext.use_gpu = { workflow.profile.contains('gpu') }
+        accelerator = { workflow.profile.contains('gpu') ? 1 : null }
     }
 }
diff --git a/modules.json b/modules.json
index cc0aaa51..b25c6ad5 100644
--- a/modules.json
+++ b/modules.json
@@ -7,12 +7,12 @@
                 "nf-core": {
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["modules"]
                     }
                 }
diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml
index 691d4c76..f9f54ee9 100644
--- a/modules/nf-core/fastqc/environment.yml
+++ b/modules/nf-core/fastqc/environment.yml
@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 033f4154..23e16634 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -29,7 +29,7 @@ process FASTQC {
     // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory)
     // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222
     // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label
-    def memory_in_mb = task.memory ? task.memory.toUnit('MB').toFloat() / task.cpus : null
+    def memory_in_mb = task.memory ? task.memory.toUnit('MB') / task.cpus : null
     // FastQC memory value allowed range (100 - 10000)
     def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
 
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
index 2b2e62b8..c8d9d025 100644
--- a/modules/nf-core/fastqc/meta.yml
+++ b/modules/nf-core/fastqc/meta.yml
@@ -29,9 +29,10 @@ input:
         description: |
           List of input FastQ files of size 1 and 2 for single-end and paired-end data,
           respectively.
+        ontologies: []
 output:
-  - html:
-      - meta:
+  html:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -40,8 +41,9 @@ output:
           type: file
           description: FastQC report
           pattern: "*_{fastqc.html}"
-  - zip:
-      - meta:
+          ontologies: []
+  zip:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -50,11 +52,14 @@ output:
           type: file
           description: FastQC report archive
           pattern: "*_{fastqc.zip}"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@drpatelh"
   - "@grst"
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index a27122ce..812fc4c5 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -1,5 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::multiqc=1.27
+  - bioconda::multiqc=1.29
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 58d9313c..0ac3c369 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,8 +3,8 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.27--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.27--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.29--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.29--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index b16c1879..ce30eb73 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -15,57 +15,71 @@ tools:
       licence: ["GPL-3.0-or-later"]
       identifier: biotools:multiqc
 input:
-  - - multiqc_files:
-        type: file
-        description: |
-          List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
-  - - multiqc_config:
-        type: file
-        description: Optional config yml for MultiQC
-        pattern: "*.{yml,yaml}"
-  - - extra_multiqc_config:
-        type: file
-        description: Second optional config yml for MultiQC. Will override common sections
-          in multiqc_config.
-        pattern: "*.{yml,yaml}"
-  - - multiqc_logo:
+  - multiqc_files:
+      type: file
+      description: |
+        List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
+      ontologies: []
+  - multiqc_config:
+      type: file
+      description: Optional config yml for MultiQC
+      pattern: "*.{yml,yaml}"
+      ontologies:
+        - edam: http://edamontology.org/format_3750 # YAML
+  - extra_multiqc_config:
+      type: file
+      description: Second optional config yml for MultiQC. Will override common sections
+        in multiqc_config.
+      pattern: "*.{yml,yaml}"
+      ontologies:
+        - edam: http://edamontology.org/format_3750 # YAML
+  - multiqc_logo:
+      type: file
+      description: Optional logo file for MultiQC
+      pattern: "*.{png}"
+      ontologies: []
+  - replace_names:
+      type: file
+      description: |
+        Optional two-column sample renaming file. First column a set of
+        patterns, second column a set of corresponding replacements. Passed via
+        MultiQC's `--replace-names` option.
+      pattern: "*.{tsv}"
+      ontologies:
+        - edam: http://edamontology.org/format_3475 # TSV
+  - sample_names:
+      type: file
+      description: |
+        Optional TSV file with headers, passed to the MultiQC --sample_names
+        argument.
+      pattern: "*.{tsv}"
+      ontologies:
+        - edam: http://edamontology.org/format_3475 # TSV
+output:
+  report:
+    - "*multiqc_report.html":
         type: file
-        description: Optional logo file for MultiQC
-        pattern: "*.{png}"
-  - - replace_names:
+        description: MultiQC report file
+        pattern: "multiqc_report.html"
+        ontologies: []
+  data:
+    - "*_data":
+        type: directory
+        description: MultiQC data dir
+        pattern: "multiqc_data"
+  plots:
+    - "*_plots":
         type: file
-        description: |
-          Optional two-column sample renaming file. First column a set of
-          patterns, second column a set of corresponding replacements. Passed via
-          MultiQC's `--replace-names` option.
-        pattern: "*.{tsv}"
-  - - sample_names:
+        description: Plots created by MultiQC
+        pattern: "*_data"
+        ontologies: []
+  versions:
+    - versions.yml:
         type: file
-        description: |
-          Optional TSV file with headers, passed to the MultiQC --sample_names
-          argument.
-        pattern: "*.{tsv}"
-output:
-  - report:
-      - "*multiqc_report.html":
-          type: file
-          description: MultiQC report file
-          pattern: "multiqc_report.html"
-  - data:
-      - "*_data":
-          type: directory
-          description: MultiQC data dir
-          pattern: "multiqc_data"
-  - plots:
-      - "*_plots":
-          type: file
-          description: Plots created by MultiQC
-          pattern: "*_data"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@abhi18av"
   - "@bunop"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index 7b7c1322..88e90571 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
+                "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-01-27T09:29:57.631982377"
+        "timestamp": "2025-05-22T11:50:41.182332996"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
+                "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-01-27T09:30:34.743726958"
+        "timestamp": "2025-05-22T11:51:22.448739369"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
+                "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-01-27T09:30:21.44383553"
+        "timestamp": "2025-05-22T11:51:06.198928424"
     }
 }
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index 2a130599..7341b0a4 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -235,7 +235,6 @@ dag {
 
 manifest {
     name            = 'nf-core/seqinspector'
-    author          = """Adrien Coulier""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead
     contributors    = [
         // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
         [
@@ -251,14 +250,14 @@ manifest {
     description     = """Pipeline to QC your sequences"""
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
-    nextflowVersion = '!>=24.04.2'
+    nextflowVersion = '!>=24.10.5'
     version         = '1.0dev'
     doi             = ''
 }
 
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-schema@2.4.2' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 validation {
diff --git a/nf-test.config b/nf-test.config
index 889df760..3a1fff59 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -9,7 +9,7 @@ config {
     configFile "tests/nextflow.config"
 
     // ignore tests coming from the nf-core/modules repo
-    ignore 'modules/nf-core/**/*', 'subworkflows/nf-core/**/*'
+    ignore 'modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*'
 
     // run all test with defined profile(s) from the main nextflow.config
     profile "test"
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 93443814..bfba1da6 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,8 +22,8 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2025-06-03T11:02:14+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.04.2-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by Adrien Coulier.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "datePublished": "2025-07-08T11:39:22+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by Adrien Coulier.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
                     "@id": "main.nf"
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#391b6670-7ba3-43a3-8911-62f797d852f6"
+                    "@id": "#6e4028f7-2677-4b95-a287-5774a381ff36"
                 }
             ],
             "name": "nf-core/seqinspector"
@@ -128,7 +128,7 @@
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2025-06-03T11:02:14Z",
+            "dateModified": "2025-07-08T11:39:22Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": ["nf-core", "nextflow", "genomics", "quality-control"],
             "license": ["MIT"],
@@ -157,14 +157,14 @@
             "url": {
                 "@id": "https://www.nextflow.io/"
             },
-            "version": "!>=24.04.2"
+            "version": "!>=24.10.5"
         },
         {
-            "@id": "#391b6670-7ba3-43a3-8911-62f797d852f6",
+            "@id": "#6e4028f7-2677-4b95-a287-5774a381ff36",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#7c992a78-479f-434b-9046-8a50507c617c"
+                    "@id": "#73c03619-5e44-4c7a-9db2-e6b4a69852e5"
                 }
             ],
             "mainEntity": {
@@ -173,7 +173,7 @@
             "name": "Test suite for nf-core/seqinspector"
         },
         {
-            "@id": "#7c992a78-479f-434b-9046-8a50507c617c",
+            "@id": "#73c03619-5e44-4c7a-9db2-e6b4a69852e5",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/seqinspector",
             "resource": "repos/nf-core/seqinspector/actions/workflows/nf-test.yml",
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
index 0907ac58..09ef842a 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
@@ -1,5 +1,5 @@
 plugins {
-    id "nf-schema@2.1.0"
+    id "nf-schema@2.4.2"
 }
 
 validation {
diff --git a/tests/.nftignore b/tests/.nftignore
index c10bc1f1..158c83c5 100644
--- a/tests/.nftignore
+++ b/tests/.nftignore
@@ -1,5 +1,6 @@
 .DS_Store
 multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
+multiqc/multiqc_data/BETA-multiqc.parquet
 multiqc/multiqc_data/multiqc.log
 multiqc/multiqc_data/multiqc_data.json
 multiqc/multiqc_data/multiqc_sources.txt
diff --git a/tests/nextflow.config b/tests/nextflow.config
index 362d5403..eb96bc81 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -6,7 +6,9 @@
 
 // TODO nf-core: Specify any additional parameters here
 // Or any resources requirements
-params.modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
-params.pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/seqinspector'
+params {
+    modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/seqinspector'
+}
 
 aws.client.anonymous = true // fixes S3 access issues on self-hosted runners

From d4c1612e00a315c05aa44043aa0d837c88939d66 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pontus=20H=C3=B6jer?= <pontushojer@gmail.com>
Date: Wed, 9 Jul 2025 14:58:25 +0000
Subject: [PATCH 224/530] group paired samples in tables (fix #105)

---
 assets/multiqc_config.yml | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index e960d07e..e12f6a65 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -13,3 +13,11 @@ report_section_order:
 export_plots: true
 
 disable_version_detection: true
+
+table_sample_merge:
+  "Read1":
+    - type: regex
+      pattern: "_1$"
+  "Read2":
+    - type: regex
+      pattern: "_2$"

From 2e7299239b20e53a6528a3441917ec93affb7621 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pontus=20H=C3=B6jer?= <pontushojer@gmail.com>
Date: Wed, 9 Jul 2025 14:59:11 +0000
Subject: [PATCH 225/530] remove suffix added by fastqscreen

---
 assets/multiqc_config.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index e12f6a65..f05c55ee 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -14,6 +14,9 @@ export_plots: true
 
 disable_version_detection: true
 
+fn_clean_trim:
+ - "_screen" # Added by FastqScreen
+
 table_sample_merge:
   "Read1":
     - type: regex

From 8660037062643053047ed2a1f477fa294ddaf48b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pontus=20H=C3=B6jer?= <pontushojer@gmail.com>
Date: Wed, 9 Jul 2025 14:59:42 +0000
Subject: [PATCH 226/530] use sample name for prefix

---
 conf/modules.config | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/conf/modules.config b/conf/modules.config
index 5a0b7ccd..07e939d7 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -20,14 +20,21 @@ process {
 
     withName: SEQTK_SAMPLE {
         ext.args = '-s100'
+        ext.prefix = { "${meta.sample}" }
     }
 
     withName: FASTQC {
         ext.args = '--quiet'
+        ext.prefix = { "${meta.sample}" }
+    }
+
+    withName: 'FASTQSCREEN_FASTQSCREEN' {
+        ext.prefix = { "${meta.sample}" }
     }
 
     withName: 'SEQFU_STATS' {
         ext.args   = ''
+        ext.prefix = { "${meta.sample}" }
         publishDir = [
             path: { "${params.outdir}/seqfu_stats" },
             mode: params.publish_dir_mode,

From 96a3eb56a567b06e20573d189827fc8c8324e55b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pontus=20H=C3=B6jer?= <pontushojer@gmail.com>
Date: Fri, 8 Aug 2025 14:42:18 +0200
Subject: [PATCH 227/530] revert 8660037062643053047ed2a1f477fa294ddaf48b and
 update sample name index to have leading zeros

---
 conf/modules.config                           |   7 -
 .../main.nf                                   |   8 +-
 tests/MiSeq.main.nf.test.snap                 | 106 +++----
 tests/MiSeq_PairedEnd.main.nf.test.snap       | 146 ++++-----
 tests/NovaSeq6000.main.nf.test.snap           | 296 +++++++++---------
 tests/NovaSeq6000.main_subsample.nf.test.snap |  36 +--
 tests/PromethION.main.nf.test.snap            |  66 ++--
 7 files changed, 331 insertions(+), 334 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 07e939d7..5a0b7ccd 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -20,21 +20,14 @@ process {
 
     withName: SEQTK_SAMPLE {
         ext.args = '-s100'
-        ext.prefix = { "${meta.sample}" }
     }
 
     withName: FASTQC {
         ext.args = '--quiet'
-        ext.prefix = { "${meta.sample}" }
-    }
-
-    withName: 'FASTQSCREEN_FASTQSCREEN' {
-        ext.prefix = { "${meta.sample}" }
     }
 
     withName: 'SEQFU_STATS' {
         ext.args   = ''
-        ext.prefix = { "${meta.sample}" }
         publishDir = [
             path: { "${params.outdir}/seqfu_stats" },
             mode: params.publish_dir_mode,
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index 708d73fb..1242dee8 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -71,7 +71,9 @@ workflow PIPELINE_INITIALISATION {
     //
     // Create channel from input file provided through params.input
     //
-
+    nr_samples = Channel.fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
+        .toList().size()
+        
     Channel
         .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
         .toList()
@@ -79,7 +81,9 @@ workflow PIPELINE_INITIALISATION {
         .map {
             meta, fastq_1, fastq_2, idx ->
                 def tags = meta.tags ? meta.tags.tokenize(":") : []
-                def updated_meta = meta + [ id:"${meta.sample}_${idx}", tags:tags ]
+                def pad_positions = [nr_samples.length(), 2].max()
+                def zero_padded_idx = idx.padLeft(pad_positions, "0")
+                def updated_meta = meta + [ id:"${meta.sample}_${zero_padded_idx}", tags:tags ]
                 if (!fastq_2) {
                     return [
                         updated_meta.id,
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index beee2404..49c8b18b 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -25,10 +25,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-01-07T13:49:22.707398"
+        "timestamp": "2025-08-08T14:30:16.385321"
     },
     "MiSeq data test (single end reads)": {
         "content": [
@@ -49,12 +49,12 @@
             },
             [
                 "fastqc",
-                "fastqc/SAMPLE_SINGLE_END_1_fastqc.html",
-                "fastqc/SAMPLE_SINGLE_END_1_fastqc.zip",
+                "fastqc/SAMPLE_SINGLE_END_01_fastqc.html",
+                "fastqc/SAMPLE_SINGLE_END_01_fastqc.zip",
                 "fastqscreen",
-                "fastqscreen/SAMPLE_SINGLE_END_1_screen.html",
-                "fastqscreen/SAMPLE_SINGLE_END_1_screen.png",
-                "fastqscreen/SAMPLE_SINGLE_END_1_screen.txt",
+                "fastqscreen/SAMPLE_SINGLE_END_01_screen.html",
+                "fastqscreen/SAMPLE_SINGLE_END_01_screen.png",
+                "fastqscreen/SAMPLE_SINGLE_END_01_screen.txt",
                 "multiqc",
                 "multiqc/global_report",
                 "multiqc/global_report/multiqc_data",
@@ -75,7 +75,7 @@
                 "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu_mqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_plots",
@@ -94,7 +94,7 @@
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu_mqc.pdf",
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
@@ -110,7 +110,7 @@
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu_mqc.png",
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
@@ -126,40 +126,40 @@
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
                 "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
-                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu_mqc.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "seqfu_stats",
-                "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu.tsv",
-                "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu_mqc.txt"
+                "seqfu_stats/SAMPLE_SINGLE_END_01_seqfu.tsv",
+                "seqfu_stats/SAMPLE_SINGLE_END_01_seqfu_mqc.txt"
             ],
             [
-                "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
-                "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
-                "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
-                "fastqc-status-check-heatmap.txt:md5,8f98652c377741c974e485652a19f37f",
-                "fastqc_overrepresented_sequences_plot.txt:md5,cdc7479933cae03e0043ae794f81c304",
-                "fastqc_per_base_n_content_plot.txt:md5,dd8d6976dc5ea8cf67d9fa2c3be9e24b",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,5f9a98d3068aab17f26731ae0615f41a",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,1de1333bb959189dcf8230706f60dbfc",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,62f140bfa52d462c9c499dfdabc35476",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,5fda43eb9b7c60cf6b4348f734a94b26",
-                "fastqc_sequence_counts_plot.txt:md5,00cd6842465f7aa9ae75434e175946a6",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,c3befe0812d2f1c23d5e75e6fccf0622",
+                "SAMPLE_SINGLE_END_01_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
+                "SAMPLE_SINGLE_END_01_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
+                "fastq_screen_plot.txt:md5,9cf2d21a5f14a4d580976f86211e6911",
+                "fastqc-status-check-heatmap.txt:md5,a46613c90e9f4d18bdc0ec1ef9ab203e",
+                "fastqc_overrepresented_sequences_plot.txt:md5,51964511b46bdeedffb6fce3b027ca65",
+                "fastqc_per_base_n_content_plot.txt:md5,50b87e15b2481a0666912092bf37f6c4",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,c165c8d0054f648e35a1e98a2c650077",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,6e8a40154ed6d405713369507624cd6f",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,ddd618369eb3f9aee12cf1622dc6a94c",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,650faba9f5a438239e54f8ddb45b1fb5",
+                "fastqc_sequence_counts_plot.txt:md5,5cc97c72190127df57148848f5708a9d",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,cb9119cb01a0c4aba3ccbb686cb6281b",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607",
-                "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
-                "multiqc_seqfu.txt:md5,8e6989a2392f599a09a5c3edf8119702",
-                "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,f65c868e562291647d539090698ba5eb",
-                "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
+                "multiqc_fastq_screen.txt:md5,8f2a8b76c7e8dcf78ba77b68b1203621",
+                "multiqc_fastqc.txt:md5,f439bb0427d95c1b8fccb60f61acf76c",
+                "multiqc_seqfu_mqc.txt:md5,8e6989a2392f599a09a5c3edf8119702",
+                "SAMPLE_SINGLE_END_01_seqfu.tsv:md5,f65c868e562291647d539090698ba5eb",
+                "SAMPLE_SINGLE_END_01_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-03-26T13:00:21.042755"
+        "timestamp": "2025-08-08T14:29:09.170736"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
@@ -177,9 +177,9 @@
             },
             [
                 "fastqscreen",
-                "fastqscreen/SAMPLE_SINGLE_END_1_screen.html",
-                "fastqscreen/SAMPLE_SINGLE_END_1_screen.png",
-                "fastqscreen/SAMPLE_SINGLE_END_1_screen.txt",
+                "fastqscreen/SAMPLE_SINGLE_END_01_screen.html",
+                "fastqscreen/SAMPLE_SINGLE_END_01_screen.png",
+                "fastqscreen/SAMPLE_SINGLE_END_01_screen.txt",
                 "multiqc",
                 "multiqc/global_report",
                 "multiqc/global_report/multiqc_data",
@@ -188,44 +188,44 @@
                 "multiqc/global_report/multiqc_data/multiqc_citations.txt",
                 "multiqc/global_report/multiqc_data/multiqc_data.json",
                 "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
-                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu_mqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu_mqc.pdf",
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu_mqc.png",
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu_mqc.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "seqfu_stats",
-                "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu.tsv",
-                "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu_mqc.txt"
+                "seqfu_stats/SAMPLE_SINGLE_END_01_seqfu.tsv",
+                "seqfu_stats/SAMPLE_SINGLE_END_01_seqfu_mqc.txt"
             ],
             [
-                "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
-                "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
-                "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
+                "SAMPLE_SINGLE_END_01_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
+                "SAMPLE_SINGLE_END_01_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
+                "fastq_screen_plot.txt:md5,9cf2d21a5f14a4d580976f86211e6911",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607",
-                "multiqc_seqfu.txt:md5,8e6989a2392f599a09a5c3edf8119702",
-                "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,f65c868e562291647d539090698ba5eb",
-                "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
+                "multiqc_fastq_screen.txt:md5,8f2a8b76c7e8dcf78ba77b68b1203621",
+                "multiqc_seqfu_mqc.txt:md5,8e6989a2392f599a09a5c3edf8119702",
+                "SAMPLE_SINGLE_END_01_seqfu.tsv:md5,f65c868e562291647d539090698ba5eb",
+                "SAMPLE_SINGLE_END_01_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-03-26T13:00:53.07934"
+        "timestamp": "2025-08-08T14:29:52.271216"
     }
 }
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index 877fc5e0..8332a3a9 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -18,27 +18,27 @@
             },
             [
                 "fastqc",
-                "fastqc/SAMPLE_PAIRED_END_1_1_1_fastqc.html",
-                "fastqc/SAMPLE_PAIRED_END_1_1_1_fastqc.zip",
-                "fastqc/SAMPLE_PAIRED_END_1_1_2_fastqc.html",
-                "fastqc/SAMPLE_PAIRED_END_1_1_2_fastqc.zip",
-                "fastqc/SAMPLE_PAIRED_END_2_2_1_fastqc.html",
-                "fastqc/SAMPLE_PAIRED_END_2_2_1_fastqc.zip",
-                "fastqc/SAMPLE_PAIRED_END_2_2_2_fastqc.html",
-                "fastqc/SAMPLE_PAIRED_END_2_2_2_fastqc.zip",
+                "fastqc/SAMPLE_PAIRED_END_1_01_1_fastqc.html",
+                "fastqc/SAMPLE_PAIRED_END_1_01_1_fastqc.zip",
+                "fastqc/SAMPLE_PAIRED_END_1_01_2_fastqc.html",
+                "fastqc/SAMPLE_PAIRED_END_1_01_2_fastqc.zip",
+                "fastqc/SAMPLE_PAIRED_END_2_02_1_fastqc.html",
+                "fastqc/SAMPLE_PAIRED_END_2_02_1_fastqc.zip",
+                "fastqc/SAMPLE_PAIRED_END_2_02_2_fastqc.html",
+                "fastqc/SAMPLE_PAIRED_END_2_02_2_fastqc.zip",
                 "fastqscreen",
-                "fastqscreen/SAMPLE_PAIRED_END_1_1_1_screen.html",
-                "fastqscreen/SAMPLE_PAIRED_END_1_1_1_screen.png",
-                "fastqscreen/SAMPLE_PAIRED_END_1_1_1_screen.txt",
-                "fastqscreen/SAMPLE_PAIRED_END_1_1_2_screen.html",
-                "fastqscreen/SAMPLE_PAIRED_END_1_1_2_screen.png",
-                "fastqscreen/SAMPLE_PAIRED_END_1_1_2_screen.txt",
-                "fastqscreen/SAMPLE_PAIRED_END_2_2_1_screen.html",
-                "fastqscreen/SAMPLE_PAIRED_END_2_2_1_screen.png",
-                "fastqscreen/SAMPLE_PAIRED_END_2_2_1_screen.txt",
-                "fastqscreen/SAMPLE_PAIRED_END_2_2_2_screen.html",
-                "fastqscreen/SAMPLE_PAIRED_END_2_2_2_screen.png",
-                "fastqscreen/SAMPLE_PAIRED_END_2_2_2_screen.txt",
+                "fastqscreen/SAMPLE_PAIRED_END_1_01_1_screen.html",
+                "fastqscreen/SAMPLE_PAIRED_END_1_01_1_screen.png",
+                "fastqscreen/SAMPLE_PAIRED_END_1_01_1_screen.txt",
+                "fastqscreen/SAMPLE_PAIRED_END_1_01_2_screen.html",
+                "fastqscreen/SAMPLE_PAIRED_END_1_01_2_screen.png",
+                "fastqscreen/SAMPLE_PAIRED_END_1_01_2_screen.txt",
+                "fastqscreen/SAMPLE_PAIRED_END_2_02_1_screen.html",
+                "fastqscreen/SAMPLE_PAIRED_END_2_02_1_screen.png",
+                "fastqscreen/SAMPLE_PAIRED_END_2_02_1_screen.txt",
+                "fastqscreen/SAMPLE_PAIRED_END_2_02_2_screen.html",
+                "fastqscreen/SAMPLE_PAIRED_END_2_02_2_screen.png",
+                "fastqscreen/SAMPLE_PAIRED_END_2_02_2_screen.txt",
                 "multiqc",
                 "multiqc/global_report",
                 "multiqc/global_report/multiqc_data",
@@ -58,7 +58,7 @@
                 "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu_mqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_plots",
@@ -76,7 +76,7 @@
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu_mqc.pdf",
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
@@ -91,7 +91,7 @@
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu_mqc.png",
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
@@ -106,7 +106,7 @@
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
-                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu_mqc.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "multiqc/group_reports",
                 "multiqc/group_reports/Bpacificus",
@@ -127,7 +127,7 @@
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_seqfu_mqc.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_plots",
@@ -145,7 +145,7 @@
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/general_stats_table.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/seqfu_mqc.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-pct.png",
@@ -160,7 +160,7 @@
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/general_stats_table.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/seqfu.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/seqfu_mqc.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-pct.svg",
@@ -175,63 +175,63 @@
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/general_stats_table.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/seqfu.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/seqfu_mqc.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "seqfu_stats",
-                "seqfu_stats/SAMPLE_PAIRED_END_1_1_seqfu.tsv",
-                "seqfu_stats/SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt",
-                "seqfu_stats/SAMPLE_PAIRED_END_2_2_seqfu.tsv",
-                "seqfu_stats/SAMPLE_PAIRED_END_2_2_seqfu_mqc.txt"
+                "seqfu_stats/SAMPLE_PAIRED_END_1_01_seqfu.tsv",
+                "seqfu_stats/SAMPLE_PAIRED_END_1_01_seqfu_mqc.txt",
+                "seqfu_stats/SAMPLE_PAIRED_END_2_02_seqfu.tsv",
+                "seqfu_stats/SAMPLE_PAIRED_END_2_02_seqfu_mqc.txt"
             ],
             [
-                "SAMPLE_PAIRED_END_1_1_1_screen.png:md5,f52ddd0e65f23f68dd8d58d5453417db",
-                "SAMPLE_PAIRED_END_1_1_1_screen.txt:md5,921b08eeb461a2aa1bd42bba53900f70",
-                "SAMPLE_PAIRED_END_1_1_2_screen.png:md5,908f4fceea8aa546106efdaa7ca78f7d",
-                "SAMPLE_PAIRED_END_1_1_2_screen.txt:md5,e9ea5789e356f666de27ba658704e80d",
-                "SAMPLE_PAIRED_END_2_2_1_screen.png:md5,48d546767ed2a34a1eda59d97dd00c18",
-                "SAMPLE_PAIRED_END_2_2_1_screen.txt:md5,a5b047f495d01bf9dcb0ae516d3c7fc3",
-                "SAMPLE_PAIRED_END_2_2_2_screen.png:md5,e3684b17339d16e6fb64ace7593cc388",
-                "SAMPLE_PAIRED_END_2_2_2_screen.txt:md5,fc95e5058e764596d5da182cbc0614cf",
-                "fastq_screen_plot.txt:md5,642264b93871c724aaa5d38b91c752dd",
-                "fastqc-status-check-heatmap.txt:md5,8e29ad6b23e03267c33bd9ed3385a44b",
-                "fastqc_adapter_content_plot.txt:md5,46fbd727a4996a3f0310d0423c628445",
-                "fastqc_per_base_n_content_plot.txt:md5,4eca1ef40d4d3d318b82e68e9fa3c589",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,218757a51c3de79a39a704c979df03da",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a4035ac9f0a0c07574130758b06630d7",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,637b937e023c84115ec06b529cc8ec1b",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,47d60153a430e2b8da51655704c2b31b",
-                "fastqc_sequence_counts_plot.txt:md5,10737092a3473fba81fbe49555512b2b",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,6412f57686de02e1f1c3751a7ca2be8b",
+                "SAMPLE_PAIRED_END_1_01_1_screen.png:md5,f52ddd0e65f23f68dd8d58d5453417db",
+                "SAMPLE_PAIRED_END_1_01_1_screen.txt:md5,921b08eeb461a2aa1bd42bba53900f70",
+                "SAMPLE_PAIRED_END_1_01_2_screen.png:md5,908f4fceea8aa546106efdaa7ca78f7d",
+                "SAMPLE_PAIRED_END_1_01_2_screen.txt:md5,e9ea5789e356f666de27ba658704e80d",
+                "SAMPLE_PAIRED_END_2_02_1_screen.png:md5,48d546767ed2a34a1eda59d97dd00c18",
+                "SAMPLE_PAIRED_END_2_02_1_screen.txt:md5,a5b047f495d01bf9dcb0ae516d3c7fc3",
+                "SAMPLE_PAIRED_END_2_02_2_screen.png:md5,e3684b17339d16e6fb64ace7593cc388",
+                "SAMPLE_PAIRED_END_2_02_2_screen.txt:md5,fc95e5058e764596d5da182cbc0614cf",
+                "fastq_screen_plot.txt:md5,8b6d13f6101915666011fd2fff5ec53e",
+                "fastqc-status-check-heatmap.txt:md5,7fefe7407f92bab2ed60be6666d4fc45",
+                "fastqc_adapter_content_plot.txt:md5,3d344b2770dd05f0e7d0ebfdc2a0ce4e",
+                "fastqc_per_base_n_content_plot.txt:md5,b77864a0b0a491421dc4a95d05c848ca",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,f91f89151b14226cd0bd73a96c2d6171",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,c7a24ad5160c608246197ae5147bcd18",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,a7ceffbada63f8d71d5a6c8c3d78d7cd",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,a2291e048ef2a2e9bd42e17e5be5796a",
+                "fastqc_sequence_counts_plot.txt:md5,890786853f7701c3a2c80794cca56056",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,6e70e5e67c41ca26c702d4a6a47bc75e",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,5ef00028497d3271c9f0ea9a961db1e5",
-                "multiqc_fastqc.txt:md5,bc499ad273fd1c887056c31b82544984",
-                "multiqc_seqfu.txt:md5,1f1e063e4a509a26cee167c3b20389c0",
-                "fastq_screen_plot.txt:md5,642264b93871c724aaa5d38b91c752dd",
-                "fastqc-status-check-heatmap.txt:md5,8e29ad6b23e03267c33bd9ed3385a44b",
-                "fastqc_adapter_content_plot.txt:md5,46fbd727a4996a3f0310d0423c628445",
-                "fastqc_per_base_n_content_plot.txt:md5,4eca1ef40d4d3d318b82e68e9fa3c589",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,218757a51c3de79a39a704c979df03da",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a4035ac9f0a0c07574130758b06630d7",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,637b937e023c84115ec06b529cc8ec1b",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,47d60153a430e2b8da51655704c2b31b",
-                "fastqc_sequence_counts_plot.txt:md5,10737092a3473fba81fbe49555512b2b",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,6412f57686de02e1f1c3751a7ca2be8b",
+                "multiqc_fastq_screen.txt:md5,b5cc85fc598d1fa162ea3c7ef8272b20",
+                "multiqc_fastqc.txt:md5,369cba29e5b1d9fdb385bff8681e8461",
+                "multiqc_seqfu_mqc.txt:md5,1f1e063e4a509a26cee167c3b20389c0",
+                "fastq_screen_plot.txt:md5,8b6d13f6101915666011fd2fff5ec53e",
+                "fastqc-status-check-heatmap.txt:md5,7fefe7407f92bab2ed60be6666d4fc45",
+                "fastqc_adapter_content_plot.txt:md5,3d344b2770dd05f0e7d0ebfdc2a0ce4e",
+                "fastqc_per_base_n_content_plot.txt:md5,b77864a0b0a491421dc4a95d05c848ca",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,f91f89151b14226cd0bd73a96c2d6171",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,c7a24ad5160c608246197ae5147bcd18",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,a7ceffbada63f8d71d5a6c8c3d78d7cd",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,a2291e048ef2a2e9bd42e17e5be5796a",
+                "fastqc_sequence_counts_plot.txt:md5,890786853f7701c3a2c80794cca56056",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,6e70e5e67c41ca26c702d4a6a47bc75e",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,5ef00028497d3271c9f0ea9a961db1e5",
-                "multiqc_fastqc.txt:md5,bc499ad273fd1c887056c31b82544984",
-                "multiqc_seqfu.txt:md5,1f1e063e4a509a26cee167c3b20389c0",
-                "SAMPLE_PAIRED_END_1_1_seqfu.tsv:md5,bbd911ff3fa43212dfd4c5a5872dbdb6",
-                "SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt:md5,cd60f746b6749cc66213d031af1b931c",
-                "SAMPLE_PAIRED_END_2_2_seqfu.tsv:md5,152566a128dd657da33465b4966b5799",
-                "SAMPLE_PAIRED_END_2_2_seqfu_mqc.txt:md5,8a3296956e094e3a95e28431e6009c40"
+                "multiqc_fastq_screen.txt:md5,b5cc85fc598d1fa162ea3c7ef8272b20",
+                "multiqc_fastqc.txt:md5,369cba29e5b1d9fdb385bff8681e8461",
+                "multiqc_seqfu_mqc.txt:md5,1f1e063e4a509a26cee167c3b20389c0",
+                "SAMPLE_PAIRED_END_1_01_seqfu.tsv:md5,bbd911ff3fa43212dfd4c5a5872dbdb6",
+                "SAMPLE_PAIRED_END_1_01_seqfu_mqc.txt:md5,cd60f746b6749cc66213d031af1b931c",
+                "SAMPLE_PAIRED_END_2_02_seqfu.tsv:md5,152566a128dd657da33465b4966b5799",
+                "SAMPLE_PAIRED_END_2_02_seqfu_mqc.txt:md5,8a3296956e094e3a95e28431e6009c40"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-03-27T09:01:13.732951"
+        "timestamp": "2025-08-08T14:31:16.93075"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index fa851d95..2ba1c19f 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -18,32 +18,32 @@
             },
             [
                 "fastqc",
-                "fastqc/Sample1_1_fastqc.html",
-                "fastqc/Sample1_1_fastqc.zip",
-                "fastqc/Sample23_3_fastqc.html",
-                "fastqc/Sample23_3_fastqc.zip",
-                "fastqc/SampleA_2_fastqc.html",
-                "fastqc/SampleA_2_fastqc.zip",
-                "fastqc/Undetermined_5_fastqc.html",
-                "fastqc/Undetermined_5_fastqc.zip",
-                "fastqc/sampletest_4_fastqc.html",
-                "fastqc/sampletest_4_fastqc.zip",
+                "fastqc/Sample1_01_fastqc.html",
+                "fastqc/Sample1_01_fastqc.zip",
+                "fastqc/Sample23_03_fastqc.html",
+                "fastqc/Sample23_03_fastqc.zip",
+                "fastqc/SampleA_02_fastqc.html",
+                "fastqc/SampleA_02_fastqc.zip",
+                "fastqc/Undetermined_05_fastqc.html",
+                "fastqc/Undetermined_05_fastqc.zip",
+                "fastqc/sampletest_04_fastqc.html",
+                "fastqc/sampletest_04_fastqc.zip",
                 "fastqscreen",
-                "fastqscreen/Sample1_1_screen.html",
-                "fastqscreen/Sample1_1_screen.png",
-                "fastqscreen/Sample1_1_screen.txt",
-                "fastqscreen/Sample23_3_screen.html",
-                "fastqscreen/Sample23_3_screen.png",
-                "fastqscreen/Sample23_3_screen.txt",
-                "fastqscreen/SampleA_2_screen.html",
-                "fastqscreen/SampleA_2_screen.png",
-                "fastqscreen/SampleA_2_screen.txt",
-                "fastqscreen/Undetermined_5_screen.html",
-                "fastqscreen/Undetermined_5_screen.png",
-                "fastqscreen/Undetermined_5_screen.txt",
-                "fastqscreen/sampletest_4_screen.html",
-                "fastqscreen/sampletest_4_screen.png",
-                "fastqscreen/sampletest_4_screen.txt",
+                "fastqscreen/Sample1_01_screen.html",
+                "fastqscreen/Sample1_01_screen.png",
+                "fastqscreen/Sample1_01_screen.txt",
+                "fastqscreen/Sample23_03_screen.html",
+                "fastqscreen/Sample23_03_screen.png",
+                "fastqscreen/Sample23_03_screen.txt",
+                "fastqscreen/SampleA_02_screen.html",
+                "fastqscreen/SampleA_02_screen.png",
+                "fastqscreen/SampleA_02_screen.txt",
+                "fastqscreen/Undetermined_05_screen.html",
+                "fastqscreen/Undetermined_05_screen.png",
+                "fastqscreen/Undetermined_05_screen.txt",
+                "fastqscreen/sampletest_04_screen.html",
+                "fastqscreen/sampletest_04_screen.png",
+                "fastqscreen/sampletest_04_screen.txt",
                 "multiqc",
                 "multiqc/global_report",
                 "multiqc/global_report/multiqc_data",
@@ -65,7 +65,7 @@
                 "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu_mqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_plots",
@@ -85,7 +85,7 @@
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu_mqc.pdf",
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
@@ -102,7 +102,7 @@
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu_mqc.png",
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
@@ -119,7 +119,7 @@
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
                 "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
-                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu_mqc.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "multiqc/group_reports",
                 "multiqc/group_reports/group1",
@@ -142,7 +142,7 @@
                 "multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_seqfu_mqc.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/group1/multiqc_plots",
@@ -162,7 +162,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/general_stats_table.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/seqfu_mqc.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-pct.png",
@@ -179,7 +179,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/general_stats_table.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/seqfu.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/seqfu_mqc.png",
                 "multiqc/group_reports/group1/multiqc_plots/svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-pct.svg",
@@ -196,7 +196,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/general_stats_table.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/seqfu.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/seqfu_mqc.svg",
                 "multiqc/group_reports/group1/multiqc_report.html",
                 "multiqc/group_reports/group2",
                 "multiqc/group_reports/group2/multiqc_data",
@@ -218,7 +218,7 @@
                 "multiqc/group_reports/group2/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/group_reports/group2/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_seqfu_mqc.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/group2/multiqc_plots",
@@ -238,7 +238,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/general_stats_table.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/seqfu_mqc.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-pct.png",
@@ -255,7 +255,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/general_stats_table.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/seqfu.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/seqfu_mqc.png",
                 "multiqc/group_reports/group2/multiqc_plots/svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-pct.svg",
@@ -272,7 +272,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/general_stats_table.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/seqfu.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/seqfu_mqc.svg",
                 "multiqc/group_reports/group2/multiqc_report.html",
                 "multiqc/group_reports/lane1",
                 "multiqc/group_reports/lane1/multiqc_data",
@@ -294,7 +294,7 @@
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/group_reports/lane1/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_seqfu_mqc.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/lane1/multiqc_plots",
@@ -314,7 +314,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/general_stats_table.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/seqfu_mqc.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-pct.png",
@@ -331,7 +331,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/general_stats_table.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/seqfu.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/seqfu_mqc.png",
                 "multiqc/group_reports/lane1/multiqc_plots/svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-pct.svg",
@@ -348,7 +348,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/general_stats_table.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/seqfu.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/seqfu_mqc.svg",
                 "multiqc/group_reports/lane1/multiqc_report.html",
                 "multiqc/group_reports/test",
                 "multiqc/group_reports/test/multiqc_data",
@@ -370,7 +370,7 @@
                 "multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/group_reports/test/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_seqfu_mqc.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/test/multiqc_plots",
@@ -390,7 +390,7 @@
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/general_stats_table.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/seqfu_mqc.pdf",
                 "multiqc/group_reports/test/multiqc_plots/png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-pct.png",
@@ -407,7 +407,7 @@
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/group_reports/test/multiqc_plots/png/general_stats_table.png",
-                "multiqc/group_reports/test/multiqc_plots/png/seqfu.png",
+                "multiqc/group_reports/test/multiqc_plots/png/seqfu_mqc.png",
                 "multiqc/group_reports/test/multiqc_plots/svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-pct.svg",
@@ -424,124 +424,124 @@
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
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                 "multiqc/group_reports/test/multiqc_plots/svg/general_stats_table.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/seqfu.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/seqfu_mqc.svg",
                 "multiqc/group_reports/test/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "seqfu_stats",
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-                "seqfu_stats/Sample1_1_seqfu_mqc.txt",
-                "seqfu_stats/Sample23_3_seqfu.tsv",
-                "seqfu_stats/Sample23_3_seqfu_mqc.txt",
-                "seqfu_stats/SampleA_2_seqfu.tsv",
-                "seqfu_stats/SampleA_2_seqfu_mqc.txt",
-                "seqfu_stats/Undetermined_5_seqfu.tsv",
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-                "seqfu_stats/sampletest_4_seqfu.tsv",
-                "seqfu_stats/sampletest_4_seqfu_mqc.txt"
+                "seqfu_stats/Sample1_01_seqfu.tsv",
+                "seqfu_stats/Sample1_01_seqfu_mqc.txt",
+                "seqfu_stats/Sample23_03_seqfu.tsv",
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+                "seqfu_stats/Undetermined_05_seqfu.tsv",
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+                "seqfu_stats/sampletest_04_seqfu.tsv",
+                "seqfu_stats/sampletest_04_seqfu_mqc.txt"
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-                "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
-                "multiqc_seqfu.txt:md5,e2e092852c011abe5ad75cdcd68b9383",
-                "fastq_screen_plot.txt:md5,8622e1dbd0fe62520af6096207b9775d",
-                "fastqc-status-check-heatmap.txt:md5,2a66f5d61b9eb579555905cd5954b04c",
-                "fastqc_overrepresented_sequences_plot.txt:md5,e0b5bfc4b64d37611b51c939e61196fa",
-                "fastqc_per_base_n_content_plot.txt:md5,1380831484d1b069a2fd4a20437118bf",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,12585cf6b03db684a5ebd959f51e77e7",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a1464399e84711454499d27e98ed942b",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,026d11e7b49a49ac7bac85f376760305",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,4d646b20970d09d846947b87961efe7e",
-                "fastqc_sequence_counts_plot.txt:md5,057fb961863b325fe875d3a7879cb888",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,3b86c9d8625c439376102f3286c7bba7",
-                "fastqc_sequence_length_distribution_plot.txt:md5,6296c9ddbf8ba8e12053149d057fd7b2",
+                "multiqc_fastq_screen.txt:md5,bf4dfaccf959bc1305b9b1a190402a69",
+                "multiqc_fastqc.txt:md5,684d7fba20b698b74b9719985cee9151",
+                "multiqc_seqfu_mqc.txt:md5,e2e092852c011abe5ad75cdcd68b9383",
+                "fastq_screen_plot.txt:md5,860d11addc201d3871ac8ee3fe6868c5",
+                "fastqc-status-check-heatmap.txt:md5,6549daecfa00b258b0d0c481675a81aa",
+                "fastqc_overrepresented_sequences_plot.txt:md5,7a8cdcdd971d690a13b587f9cb6773d1",
+                "fastqc_per_base_n_content_plot.txt:md5,3376187566c87e2a69a5e68b53fabca4",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,e2ac57f7f8d22fb03901312009ba0bf8",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,ff5abdc6b70b60837ddf90f0f52a9b7c",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,761a7bfe0370ae8dda128f50e7b26132",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,8f749ad94e4e2572ba3c2e3342239917",
+                "fastqc_sequence_counts_plot.txt:md5,9aea0567dd3251dc1990141636d09288",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,39ab4efe3b4391c387040484de52b8dc",
+                "fastqc_sequence_length_distribution_plot.txt:md5,c90118a673c353aa84062d968e8c90f1",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5",
-                "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
-                "multiqc_seqfu.txt:md5,a1a0b9a0dde0c1c4fe184d44c675dcde",
-                "Sample1_1_seqfu.tsv:md5,269fabf8435defcd327aa69a050b7869",
-                "Sample1_1_seqfu_mqc.txt:md5,a354b0ed16b9cf84aa88f501d7740fd6",
-                "Sample23_3_seqfu.tsv:md5,6fdadbeeefccbf957f880d6852bf9676",
-                "Sample23_3_seqfu_mqc.txt:md5,e94269e3efc8b8192d7ac9c15ea2aa99",
-                "SampleA_2_seqfu.tsv:md5,b980ed694a05825fcf7c8b5b73888eb3",
-                "SampleA_2_seqfu_mqc.txt:md5,1d4b0e918644cf553108b7ccf77b4a01",
-                "Undetermined_5_seqfu.tsv:md5,b4458d41df4dee9321da03f4d4672aae",
-                "Undetermined_5_seqfu_mqc.txt:md5,0c869488cb61d2f87758c621bded212b",
-                "sampletest_4_seqfu.tsv:md5,db3179b0c41a09e6317a5a5c0852f476",
-                "sampletest_4_seqfu_mqc.txt:md5,590b97cc48268629204f59007bae7ad7"
+                "multiqc_fastq_screen.txt:md5,fee55523161dea1bd328e653ed35bcb3",
+                "multiqc_fastqc.txt:md5,7eca563c0e2e5342dc5b5df34daae1be",
+                "multiqc_seqfu_mqc.txt:md5,a1a0b9a0dde0c1c4fe184d44c675dcde",
+                "Sample1_01_seqfu.tsv:md5,269fabf8435defcd327aa69a050b7869",
+                "Sample1_01_seqfu_mqc.txt:md5,a354b0ed16b9cf84aa88f501d7740fd6",
+                "Sample23_03_seqfu.tsv:md5,6fdadbeeefccbf957f880d6852bf9676",
+                "Sample23_03_seqfu_mqc.txt:md5,e94269e3efc8b8192d7ac9c15ea2aa99",
+                "SampleA_02_seqfu.tsv:md5,b980ed694a05825fcf7c8b5b73888eb3",
+                "SampleA_02_seqfu_mqc.txt:md5,1d4b0e918644cf553108b7ccf77b4a01",
+                "Undetermined_05_seqfu.tsv:md5,b4458d41df4dee9321da03f4d4672aae",
+                "Undetermined_05_seqfu_mqc.txt:md5,0c869488cb61d2f87758c621bded212b",
+                "sampletest_04_seqfu.tsv:md5,db3179b0c41a09e6317a5a5c0852f476",
+                "sampletest_04_seqfu_mqc.txt:md5,590b97cc48268629204f59007bae7ad7"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-03-26T13:03:47.460854"
+        "timestamp": "2025-08-08T14:32:39.800953"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index 3ba50465..4df69d0b 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -2,30 +2,30 @@
     "NovaSeq6000 data test sample size": {
         "content": [
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-            "multiqc_fastqc.txt:md5,aba942d1e6996b579f19798e5673f514",
-            "multiqc_general_stats.txt:md5,ad1ec9c64cbdb1131a26aeb6de51e31c",
-            "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
+            "multiqc_fastqc.txt:md5,464552ede2e3398b15009d2fe497cdfd",
+            "multiqc_general_stats.txt:md5,ee481e5e78e8eb5dfae605d0358c222a",
+            "multiqc_fastq_screen.txt:md5,b9d41d5113f10387a8549cc1b9078300",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-            "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8",
-            "multiqc_general_stats.txt:md5,c73c8d10568a56f6534d280fff701e60",
-            "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
+            "multiqc_fastqc.txt:md5,2bd9e3d267cee5a21755f56460e05574",
+            "multiqc_general_stats.txt:md5,780d5ade40457b44d19ce0368b72493f",
+            "multiqc_fastq_screen.txt:md5,bf4dfaccf959bc1305b9b1a190402a69",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-            "multiqc_fastqc.txt:md5,ff996e1d3dc4a46e0c9535e54d51ccab",
-            "multiqc_general_stats.txt:md5,834e1868b887171cfda72029bbbe2d3f",
-            "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
+            "multiqc_fastqc.txt:md5,0c6c5817dd59422b5c257fae72fc2ffc",
+            "multiqc_general_stats.txt:md5,7f2d01ba5feb51496f2bdfcaec1a7672",
+            "multiqc_fastq_screen.txt:md5,d323ad84f998f21d6924495d5767db04",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-            "multiqc_fastqc.txt:md5,3df36ecfe76b25b0c22dcda84bce2b3b",
-            "multiqc_general_stats.txt:md5,274a001b007521970f14d68bd176e5be",
-            "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
+            "multiqc_fastqc.txt:md5,50611144cc4384363db6be9a327c7f02",
+            "multiqc_general_stats.txt:md5,427406a14f0583da93f8120e4cc20c9f",
+            "multiqc_fastq_screen.txt:md5,456a39b074280f88aa8ac0c00dd7e38f",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-            "multiqc_fastqc.txt:md5,ce61b4ce4b1d76ec3f20de3bf0c9ec7f",
-            "multiqc_general_stats.txt:md5,d476ad59458a035a329605d5284b6012",
-            "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5"
+            "multiqc_fastqc.txt:md5,911bc13b7adfd499efef327d56f4b34e",
+            "multiqc_general_stats.txt:md5,c07dc697a170838db9d95271a9cb47a5",
+            "multiqc_fastq_screen.txt:md5,fee55523161dea1bd328e653ed35bcb3"
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.2"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-12-05T15:17:50.525033752"
+        "timestamp": "2025-08-08T14:34:00.031836"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index 27a9c143..756ba49b 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -18,12 +18,12 @@
             },
             [
                 "fastqc",
-                "fastqc/hg001_1_fastqc.html",
-                "fastqc/hg001_1_fastqc.zip",
+                "fastqc/hg001_01_fastqc.html",
+                "fastqc/hg001_01_fastqc.zip",
                 "fastqscreen",
-                "fastqscreen/hg001_1_screen.html",
-                "fastqscreen/hg001_1_screen.png",
-                "fastqscreen/hg001_1_screen.txt",
+                "fastqscreen/hg001_01_screen.html",
+                "fastqscreen/hg001_01_screen.png",
+                "fastqscreen/hg001_01_screen.txt",
                 "multiqc",
                 "multiqc/global_report",
                 "multiqc/global_report/multiqc_data",
@@ -46,7 +46,7 @@
                 "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu_mqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_plots",
@@ -67,7 +67,7 @@
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu_mqc.pdf",
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
@@ -85,7 +85,7 @@
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu_mqc.png",
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
@@ -103,41 +103,41 @@
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
                 "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
-                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu_mqc.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "seqfu_stats",
-                "seqfu_stats/hg001_1_seqfu.tsv",
-                "seqfu_stats/hg001_1_seqfu_mqc.txt"
+                "seqfu_stats/hg001_01_seqfu.tsv",
+                "seqfu_stats/hg001_01_seqfu_mqc.txt"
             ],
             [
-                "hg001_1_screen.png:md5,b9c58e388f18ad11f4c2e29e9b573a5e",
-                "hg001_1_screen.txt:md5,8e53ea043d658a130f4b8ca455e2ba9b",
-                "fastq_screen_plot.txt:md5,3023b86477fecf6d46d8fc60d82cc53a",
-                "fastqc-status-check-heatmap.txt:md5,825668e94de27356f0a112beb758e416",
-                "fastqc_adapter_content_plot.txt:md5,1fa991080c20755e5e729a5eeab960e5",
-                "fastqc_overrepresented_sequences_plot.txt:md5,e810a3d3eba0ba83b122763505f511a7",
-                "fastqc_per_base_n_content_plot.txt:md5,cbdb64298ff839665e8c8c8e89896e87",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,4962950bc3ce77169ac510d64cb769c6",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,e62273533304be59dab5f13afef93b3e",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,3d49290a15406cb5dac1460c02729f0f",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,7cc10d1bc92ca09431a506c38d911228",
-                "fastqc_sequence_counts_plot.txt:md5,0425d7298c24df6158d5bf7aca1d4190",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,9111d942c7eed5af0e9ccb8c42db8505",
-                "fastqc_sequence_length_distribution_plot.txt:md5,04adfcd0125ebcc3e3bb631f1956c812",
+                "hg001_01_screen.png:md5,b9c58e388f18ad11f4c2e29e9b573a5e",
+                "hg001_01_screen.txt:md5,8e53ea043d658a130f4b8ca455e2ba9b",
+                "fastq_screen_plot.txt:md5,657e595a39a9683e2050a3695e916356",
+                "fastqc-status-check-heatmap.txt:md5,d7fad43a47cbb1ca9d4af05634320cd4",
+                "fastqc_adapter_content_plot.txt:md5,146d9a6c9113c2847859e5b2fefb5495",
+                "fastqc_overrepresented_sequences_plot.txt:md5,9df816c16e213f480c4561c094a461d4",
+                "fastqc_per_base_n_content_plot.txt:md5,cb9e24aeb2a38ab9267fb4fd3d7f269c",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,1d93a13bc3f955d9b885054074eea5ca",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,2a697e9f230c0c4c1fe8cf59b8cc4d09",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,d3b02fc19cd9482ec7121cb8b6f827b2",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,788ea319922a666db29162dfdfef008d",
+                "fastqc_sequence_counts_plot.txt:md5,d8dd057195ed8c90a13b3c8803d7a6cf",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,7677dd2ca8ddaa7fc09456f7c5575af7",
+                "fastqc_sequence_length_distribution_plot.txt:md5,7ac48264f65e52c36e4f8dfb73955c91",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,7c5d711e27c53d13c81644a1f2468dba",
-                "multiqc_fastqc.txt:md5,1a4b472e13cadc770832b0e20d1de7b0",
-                "multiqc_seqfu.txt:md5,9595d608ff5709f2bdec8cb1016416c0",
-                "hg001_1_seqfu.tsv:md5,b133752c897afbb4d8721b911fa117d4",
-                "hg001_1_seqfu_mqc.txt:md5,6285f582c03faa70e8dcb3503e5db728"
+                "multiqc_fastq_screen.txt:md5,d8ff89af02a0932bac3cb2a53be76064",
+                "multiqc_fastqc.txt:md5,7031588e1394714bb2dd64b7fed6d3ef",
+                "multiqc_seqfu_mqc.txt:md5,9595d608ff5709f2bdec8cb1016416c0",
+                "hg001_01_seqfu.tsv:md5,b133752c897afbb4d8721b911fa117d4",
+                "hg001_01_seqfu_mqc.txt:md5,6285f582c03faa70e8dcb3503e5db728"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-03-26T13:05:53.896824"
+        "timestamp": "2025-08-08T14:34:50.840014"
     }
 }
\ No newline at end of file

From dc41ab34b616531bff533bad1f44d8d9948d54ac Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pontus=20H=C3=B6jer?= <pontushojer@gmail.com>
Date: Fri, 8 Aug 2025 16:36:51 +0200
Subject: [PATCH 228/530] prettify naming in report while distinguishing
 between assigned index (w. read) and given sample name

---
 assets/multiqc_config.yml | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index f05c55ee..55658f08 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -17,6 +17,14 @@ disable_version_detection: true
 fn_clean_trim:
  - "_screen" # Added by FastqScreen
 
+# Make sample name with indexes a bit prettier
+# for SE: "SampleName_01" -> "SampleName #01"
+# for PE: "SampleName_01_1" -> "SampleName #01_1"
+#    and: "SampleName_01_2" -> "SampleName #01_2"
+sample_names_replace_regex: True
+sample_names_replace:
+  "(.+)_(\\d{2,}|\\d{2,}_[12])$": "\\1 #\\2"
+
 table_sample_merge:
   "Read1":
     - type: regex

From 06672b4c153af9bc7d1a12f03df8a442a4f4b072 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@n180-p17.eduroam.kth.se>
Date: Thu, 11 Sep 2025 16:59:54 +0200
Subject: [PATCH 229/530] initial steps to build alignment tools

---
 conf/modules.config                           |  9 +++
 conf/test.config                              |  2 +-
 main.nf                                       | 13 ++--
 modules.json                                  |  5 ++
 modules/nf-core/bwamem2/index/environment.yml | 13 ++++
 modules/nf-core/bwamem2/index/main.nf         | 55 ++++++++++++++++
 modules/nf-core/bwamem2/index/meta.yml        | 52 +++++++++++++++
 .../nf-core/bwamem2/index/tests/main.nf.test  | 62 ++++++++++++++++++
 .../bwamem2/index/tests/main.nf.test.snap     | 64 +++++++++++++++++++
 nextflow_schema.json                          |  2 +-
 .../main.nf                                   | 37 +++++++++--
 workflows/seqinspector.nf                     | 15 ++++-
 12 files changed, 315 insertions(+), 14 deletions(-)
 create mode 100644 modules/nf-core/bwamem2/index/environment.yml
 create mode 100644 modules/nf-core/bwamem2/index/main.nf
 create mode 100644 modules/nf-core/bwamem2/index/meta.yml
 create mode 100644 modules/nf-core/bwamem2/index/tests/main.nf.test
 create mode 100644 modules/nf-core/bwamem2/index/tests/main.nf.test.snap

diff --git a/conf/modules.config b/conf/modules.config
index 5a0b7ccd..8291cca2 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -35,6 +35,15 @@ process {
         ]
     }
 
+    withName: 'BWAMEM2_INDEX' {
+        ext.args   = ''
+        publishDir = [
+            path: { "${params.outdir}/bwamem2_index" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: 'MULTIQC_GLOBAL' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
diff --git a/conf/test.config b/conf/test.config
index 0ebc405a..6e6f4dce 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -29,5 +29,5 @@ params {
     fastq_screen_references = "${projectDir}/assets/example_fastq_screen_references.csv"
 
     // Genome references
-    genome = 'R64-1-1'
+    genome = 'EB1'
 }
diff --git a/main.nf b/main.nf
index 85027a4b..fd260b90 100644
--- a/main.nf
+++ b/main.nf
@@ -17,8 +17,8 @@
 
 include { SEQINSPECTOR            } from './workflows/seqinspector'
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
-include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
 include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
+include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -29,9 +29,9 @@ include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_seqi
 // TODO nf-core: Remove this line if you don't need a FASTA file
 //   This is an example of how to use getGenomeAttribute() to fetch parameters
 //   from igenomes.config using `--genome`
-// params.fasta = getGenomeAttribute('fasta')
+params.fasta = getGenomeAttribute('fasta') 
 
-/*
+/* 
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     NAMED WORKFLOWS FOR PIPELINE
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -67,9 +67,12 @@ workflow NFCORE_SEQINSPECTOR {
 workflow {
 
     main:
+
+
     //
     // SUBWORKFLOW: Run initialisation tasks
     //
+
     PIPELINE_INITIALISATION (
         params.version,
         params.validate_params,
@@ -78,12 +81,12 @@ workflow {
         params.outdir,
         params.input
     )
-
+    
     //
     // WORKFLOW: Run main workflow
     //
     NFCORE_SEQINSPECTOR (
-        PIPELINE_INITIALISATION.out.samplesheet
+        PIPELINE_INITIALISATION.out.samplesheet,
     )
     //
     // SUBWORKFLOW: Run completion tasks
diff --git a/modules.json b/modules.json
index 71b4bbe5..a0bca21a 100644
--- a/modules.json
+++ b/modules.json
@@ -10,6 +10,11 @@
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
+                    "bwamem2/index": {
+                        "branch": "master",
+                        "git_sha": "b2902040b9cb9b7b32b62400f1c024a709bd4812",
+                        "installed_by": ["modules"]
+                    },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296",
diff --git a/modules/nf-core/bwamem2/index/environment.yml b/modules/nf-core/bwamem2/index/environment.yml
new file mode 100644
index 00000000..c069e281
--- /dev/null
+++ b/modules/nf-core/bwamem2/index/environment.yml
@@ -0,0 +1,13 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+
+dependencies:
+  # renovate: datasource=conda depName=bioconda/bwa-mem2
+  - bwa-mem2=2.2.1
+  # renovate: datasource=conda depName=bioconda/htslib
+  - htslib=1.21
+  # renovate: datasource=conda depName=bioconda/samtools
+  - samtools=1.21
diff --git a/modules/nf-core/bwamem2/index/main.nf b/modules/nf-core/bwamem2/index/main.nf
new file mode 100644
index 00000000..529c66e8
--- /dev/null
+++ b/modules/nf-core/bwamem2/index/main.nf
@@ -0,0 +1,55 @@
+process BWAMEM2_INDEX {
+    tag "$fasta"
+    // NOTE Requires 28N GB memory where N is the size of the reference sequence, floor of 280M
+    // source: https://github.com/bwa-mem2/bwa-mem2/issues/9
+    memory { (280.MB * Math.ceil(fasta.size() / 10000000)) * task.attempt }
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9ac054213e67b3c9308e409b459080bbe438f8fd6c646c351bc42887f35a42e7/data' :
+        'community.wave.seqera.io/library/bwa-mem2_htslib_samtools:e1f420694f8e42bd' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("bwamem2"), emit: index
+    path "versions.yml"             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${fasta}"
+    def args = task.ext.args ?: ''
+    """
+    mkdir bwamem2
+    bwa-mem2 \\
+        index \\
+        $args \\
+        -p bwamem2/${prefix} \\
+        $fasta
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${fasta}"
+
+    """
+    mkdir bwamem2
+    touch bwamem2/${prefix}.0123
+    touch bwamem2/${prefix}.ann
+    touch bwamem2/${prefix}.pac
+    touch bwamem2/${prefix}.amb
+    touch bwamem2/${prefix}.bwt.2bit.64
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/bwamem2/index/meta.yml b/modules/nf-core/bwamem2/index/meta.yml
new file mode 100644
index 00000000..b2aa45fb
--- /dev/null
+++ b/modules/nf-core/bwamem2/index/meta.yml
@@ -0,0 +1,52 @@
+name: bwamem2_index
+description: Create BWA-mem2 index for reference genome
+keywords:
+  - index
+  - fasta
+  - genome
+  - reference
+tools:
+  - bwamem2:
+      description: |
+        BWA-mem2 is a software package for mapping DNA sequences against
+        a large reference genome, such as the human genome.
+      homepage: https://github.com/bwa-mem2/bwa-mem2
+      documentation: https://github.com/bwa-mem2/bwa-mem2#usage
+      licence: ["MIT"]
+      identifier: "biotools:bwa-mem2"
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - fasta:
+        type: file
+        description: Input genome fasta file
+        ontologies:
+          - edam: "http://edamontology.org/data_2044" # Sequence
+          - edam: "http://edamontology.org/format_1929" # FASTA
+output:
+  index:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - bwamem2:
+          type: file
+          description: BWA genome index files
+          pattern: "*.{0123,amb,ann,bwt.2bit.64,pac}"
+          ontologies:
+            - edam: "http://edamontology.org/data_3210" # Genome index
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
+authors:
+  - "@maxulysse"
+maintainers:
+  - "@maxulysse"
diff --git a/modules/nf-core/bwamem2/index/tests/main.nf.test b/modules/nf-core/bwamem2/index/tests/main.nf.test
new file mode 100644
index 00000000..adf44785
--- /dev/null
+++ b/modules/nf-core/bwamem2/index/tests/main.nf.test
@@ -0,0 +1,62 @@
+nextflow_process {
+
+    name "Test Process BWAMEM2_INDEX"
+    tag "modules_nfcore"
+    tag "modules"
+    tag "bwamem2"
+    tag "bwamem2/index"
+    script "../main.nf"
+    process "BWAMEM2_INDEX"
+
+    test("fasta") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [id: 'test'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.index,
+                    process.out.versions,
+                    path(process.out.versions[0]).yaml
+                ).match() }
+            )
+        }
+    }
+
+    test("fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [id: 'test'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.index,
+                    process.out.versions,
+                    path(process.out.versions[0]).yaml
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/bwamem2/index/tests/main.nf.test.snap b/modules/nf-core/bwamem2/index/tests/main.nf.test.snap
new file mode 100644
index 00000000..9ad8b20c
--- /dev/null
+++ b/modules/nf-core/bwamem2/index/tests/main.nf.test.snap
@@ -0,0 +1,64 @@
+{
+    "fasta - stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    [
+                        "genome.fasta.0123:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genome.fasta.amb:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genome.fasta.ann:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genome.fasta.bwt.2bit.64:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genome.fasta.pac:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            ],
+            [
+                "versions.yml:md5,9ffd13d12e7108ed15c58566bc4717d6"
+            ],
+            {
+                "BWAMEM2_INDEX": {
+                    "bwamem2": "2.2.1"
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-04T08:55:53.219699135"
+    },
+    "fasta": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    [
+                        "genome.fasta.0123:md5,b02870de80106104abcb03cd9463e7d8",
+                        "genome.fasta.amb:md5,3a68b8b2287e07dd3f5f95f4344ba76e",
+                        "genome.fasta.ann:md5,c32e11f6c859f166c7525a9c1d583567",
+                        "genome.fasta.bwt.2bit.64:md5,d097a1b82dee375d41a1ea69895a9216",
+                        "genome.fasta.pac:md5,983e3d2cd6f36e2546e6d25a0da78d66"
+                    ]
+                ]
+            ],
+            [
+                "versions.yml:md5,9ffd13d12e7108ed15c58566bc4717d6"
+            ],
+            {
+                "BWAMEM2_INDEX": {
+                    "bwamem2": "2.2.1"
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-04T08:55:45.007921901"
+    }
+}
\ No newline at end of file
diff --git a/nextflow_schema.json b/nextflow_schema.json
index f00c0bb5..ca5c3c34 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -94,7 +94,7 @@
                 },
                 "fastq_screen_references": {
                     "type": "string",
-                    "default": "${projectDir}/assets/example_fastq_screen_references.csv",
+                    "default": "/Users/agrimabhatt/abh_seqinspector/seqinspector/assets/example_fastq_screen_references.csv",
                     "fa_icon": "fas fa-search",
                     "description": "A .csv of reference genomes to be mapped against by FastQ Screen"
                 }
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index 708d73fb..e3df2a8d 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -204,12 +204,39 @@ def validateInputSamplesheet(input) {
 // Get attribute from genome config file e.g. fasta
 //
 def getGenomeAttribute(attribute) {
-    if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
-        if (params.genomes[ params.genome ].containsKey(attribute)) {
-            return params.genomes[ params.genome ][ attribute ]
-        }
+    // Input validation
+    if (!attribute) {
+        log.warn "No attribute specified"
+        return null
+    }
+    
+    if (!params.genomes) {
+        log.warn "No genomes configuration found"
+        return null
+    }
+    
+    if (!params.genome) {
+        log.warn "No genome specified in params.genome"
+        return null
+    }
+    
+    if (!params.genomes.containsKey(params.genome)) {
+        log.warn "Genome '${params.genome}' not found in configuration"
+        log.warn "Available genomes: ${params.genomes.keySet().join(', ')}"
+        return null
+    }
+    
+    def genomeConfig = params.genomes[params.genome]
+    log.info "Genome config for '${params.genome}': ${genomeConfig}"
+    
+    if (!genomeConfig.containsKey(attribute)) {
+        log.warn "Attribute '${attribute}' not found for genome '${params.genome}'"
+        log.warn "Available attributes: ${genomeConfig.keySet().join(', ')}"
+        return null
     }
-    return null
+    
+    log.info "Found ${attribute}: ${genomeConfig[attribute]}"
+    return genomeConfig[attribute]
 }
 
 //
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 22d37c30..7cf411fb 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -10,6 +10,7 @@ include { SEQTK_SAMPLE                  } from '../modules/nf-core/seqtk/sample/
 include { FASTQC                        } from '../modules/nf-core/fastqc/main'
 include { SEQFU_STATS                   } from '../modules/nf-core/seqfu/stats'
 include { FASTQSCREEN_FASTQSCREEN       } from '../modules/nf-core/fastqscreen/fastqscreen/main'
+include { BWAMEM2_INDEX                 } from '../modules/nf-core/bwamem2/index/main'
 
 include { MULTIQC as MULTIQC_GLOBAL     } from '../modules/nf-core/multiqc/main'
 include { MULTIQC as MULTIQC_PER_TAG    } from '../modules/nf-core/multiqc/main'
@@ -18,7 +19,6 @@ include { paramsSummaryMap              } from 'plugin/nf-schema'
 include { paramsSummaryMultiqc          } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { softwareVersionsToYAML        } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { methodsDescriptionText        } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline'
-
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     RUN MAIN WORKFLOW
@@ -28,7 +28,7 @@ include { methodsDescriptionText        } from '../subworkflows/local/utils_nfco
 workflow SEQINSPECTOR {
 
     take:
-    ch_samplesheet               // channel: samplesheet read in from --input
+    ch_samplesheet           // channel: samplesheet read in from --input
 
     main:
     skip_tools = params.skip_tools ? params.skip_tools.split(',') : []
@@ -105,7 +105,18 @@ workflow SEQINSPECTOR {
         ch_multiqc_files = ch_multiqc_files.mix(FASTQSCREEN_FASTQSCREEN.out.txt)
         ch_versions = ch_versions.mix(FASTQSCREEN_FASTQSCREEN.out.versions.first())
     }
+    // MODULE: Create BWA-MEM2 index of the reference genome
+    
+    log.info "params.genome: ${params.genome}"
+    if (!("bwamem2_index" in skip_tools) && params.genome) {
+    ch_reference_fasta = Channel.fromPath(params.genome, checkIfExists: true)
+    BWAMEM2_INDEX (
+        ch_reference_fasta
+    )
+    ch_bwamem2_index = BWAMEM2_INDEX.out.index
+    ch_versions = ch_versions.mix(BWAMEM2_INDEX.out.versions.first())
 
+}
     //
     // Collate and save software versions
     //

From 81008e6514ecfabcfff1070d57c54a1f88a6d764 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@n191-p71.eduroam.kth.se>
Date: Fri, 12 Sep 2025 13:07:57 +0200
Subject: [PATCH 230/530] Added bwamem2/index

---
 conf/test.config                              |  2 +-
 main.nf                                       |  4 +-
 .../main.nf                                   | 37 +++----------------
 workflows/seqinspector.nf                     | 25 ++++++++-----
 4 files changed, 24 insertions(+), 44 deletions(-)

diff --git a/conf/test.config b/conf/test.config
index 6e6f4dce..0ebc405a 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -29,5 +29,5 @@ params {
     fastq_screen_references = "${projectDir}/assets/example_fastq_screen_references.csv"
 
     // Genome references
-    genome = 'EB1'
+    genome = 'R64-1-1'
 }
diff --git a/main.nf b/main.nf
index fd260b90..0b5a532c 100644
--- a/main.nf
+++ b/main.nf
@@ -29,7 +29,8 @@ include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_seqi
 // TODO nf-core: Remove this line if you don't need a FASTA file
 //   This is an example of how to use getGenomeAttribute() to fetch parameters
 //   from igenomes.config using `--genome`
-params.fasta = getGenomeAttribute('fasta') 
+// params.fasta = getGenomeAttribute('fasta')
+
 
 /* 
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -50,6 +51,7 @@ workflow NFCORE_SEQINSPECTOR {
     //
     // WORKFLOW: Run pipeline
     //
+
     SEQINSPECTOR (
         samplesheet
     )
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index e3df2a8d..75465188 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -204,41 +204,14 @@ def validateInputSamplesheet(input) {
 // Get attribute from genome config file e.g. fasta
 //
 def getGenomeAttribute(attribute) {
-    // Input validation
-    if (!attribute) {
-        log.warn "No attribute specified"
-        return null
-    }
-    
-    if (!params.genomes) {
-        log.warn "No genomes configuration found"
-        return null
-    }
-    
-    if (!params.genome) {
-        log.warn "No genome specified in params.genome"
-        return null
-    }
-    
-    if (!params.genomes.containsKey(params.genome)) {
-        log.warn "Genome '${params.genome}' not found in configuration"
-        log.warn "Available genomes: ${params.genomes.keySet().join(', ')}"
-        return null
-    }
-    
-    def genomeConfig = params.genomes[params.genome]
-    log.info "Genome config for '${params.genome}': ${genomeConfig}"
-    
-    if (!genomeConfig.containsKey(attribute)) {
-        log.warn "Attribute '${attribute}' not found for genome '${params.genome}'"
-        log.warn "Available attributes: ${genomeConfig.keySet().join(', ')}"
-        return null
+    if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
+        if (params.genomes[ params.genome ].containsKey(attribute)) {
+            return params.genomes[ params.genome ][ attribute ]
+        }
     }
-    
-    log.info "Found ${attribute}: ${genomeConfig[attribute]}"
-    return genomeConfig[attribute]
 }
 
+
 //
 // Exit pipeline if incorrect --genome key provided
 //
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 7cf411fb..a2a92c22 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -19,6 +19,8 @@ include { paramsSummaryMap              } from 'plugin/nf-schema'
 include { paramsSummaryMultiqc          } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { softwareVersionsToYAML        } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { methodsDescriptionText        } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline'
+include { getGenomeAttribute            } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline'
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     RUN MAIN WORKFLOW
@@ -106,17 +108,20 @@ workflow SEQINSPECTOR {
         ch_versions = ch_versions.mix(FASTQSCREEN_FASTQSCREEN.out.versions.first())
     }
     // MODULE: Create BWA-MEM2 index of the reference genome
-    
-    log.info "params.genome: ${params.genome}"
-    if (!("bwamem2_index" in skip_tools) && params.genome) {
-    ch_reference_fasta = Channel.fromPath(params.genome, checkIfExists: true)
-    BWAMEM2_INDEX (
-        ch_reference_fasta
-    )
-    ch_bwamem2_index = BWAMEM2_INDEX.out.index
-    ch_versions = ch_versions.mix(BWAMEM2_INDEX.out.versions.first())
 
-}
+    if (!("bwamem2_index" in skip_tools)) {
+        def fasta_file = getGenomeAttribute('fasta')
+        log.warn" fasta_file: ${fasta_file}"
+        ch_reference_fasta = Channel.fromPath(fasta_file, checkIfExists: true).map { that -> [[id:that.Name], that] }
+        log.info "ch_reference_fasta: ${ch_reference_fasta}"
+        BWAMEM2_INDEX (
+            ch_reference_fasta
+        )
+        ch_bwamem2_index = BWAMEM2_INDEX.out.index
+        ch_versions = ch_versions.mix(BWAMEM2_INDEX.out.versions.first())
+
+    }
+
     //
     // Collate and save software versions
     //

From 69ef16d75311cc6388066c3cb6317501715ca7f6 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@n171-p126.eduroam.kth.se>
Date: Tue, 16 Sep 2025 11:37:23 +0200
Subject: [PATCH 231/530] Added bwamem2/mem

---
 conf/modules.config                           |   8 +
 modules.json                                  |  54 ++++--
 modules/nf-core/bwamem2/mem/bwamem2-mem.diff  |  18 ++
 modules/nf-core/bwamem2/mem/environment.yml   |  13 ++
 modules/nf-core/bwamem2/mem/main.nf           |  83 ++++++++
 modules/nf-core/bwamem2/mem/meta.yml          | 133 +++++++++++++
 .../nf-core/bwamem2/mem/tests/main.nf.test    | 179 ++++++++++++++++++
 .../bwamem2/mem/tests/main.nf.test.snap       | 129 +++++++++++++
 workflows/seqinspector.nf                     |  32 +++-
 9 files changed, 635 insertions(+), 14 deletions(-)
 create mode 100644 modules/nf-core/bwamem2/mem/bwamem2-mem.diff
 create mode 100644 modules/nf-core/bwamem2/mem/environment.yml
 create mode 100644 modules/nf-core/bwamem2/mem/main.nf
 create mode 100644 modules/nf-core/bwamem2/mem/meta.yml
 create mode 100644 modules/nf-core/bwamem2/mem/tests/main.nf.test
 create mode 100644 modules/nf-core/bwamem2/mem/tests/main.nf.test.snap

diff --git a/conf/modules.config b/conf/modules.config
index 8291cca2..f85c9b18 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -43,6 +43,14 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
+    withName: 'BWAMEM2_MEM' {
+        ext.args   = { params.bwamem2_mem_args ?: '' }
+        publishDir = [
+            path: { "${params.outdir}/bwamem2_mem" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
 
     withName: 'MULTIQC_GLOBAL' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
diff --git a/modules.json b/modules.json
index a0bca21a..2b2026f6 100644
--- a/modules.json
+++ b/modules.json
@@ -8,43 +8,67 @@
                     "bowtie2/build": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "bwamem2/index": {
                         "branch": "master",
                         "git_sha": "b2902040b9cb9b7b32b62400f1c024a709bd4812",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
+                    },
+                    "bwamem2/mem": {
+                        "branch": "master",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "installed_by": [
+                            "modules"
+                        ],
+                        "patch": "modules/nf-core/bwamem2/mem/bwamem2-mem.diff"
                     },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "fastqscreen/buildfromindex": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "fastqscreen/fastqscreen": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff"
                     },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "7b50cb7be890e4b28cffb82e438cc6a8d7805d3f",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "seqfu/stats": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "seqtk/sample": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     }
                 }
             },
@@ -53,20 +77,26 @@
                     "utils_nextflow_pipeline": {
                         "branch": "master",
                         "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
                         "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
                         "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     }
                 }
             }
         }
     }
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/bwamem2/mem/bwamem2-mem.diff b/modules/nf-core/bwamem2/mem/bwamem2-mem.diff
new file mode 100644
index 00000000..5faa2f89
--- /dev/null
+++ b/modules/nf-core/bwamem2/mem/bwamem2-mem.diff
@@ -0,0 +1,18 @@
+Changes in component 'nf-core/bwamem2/mem'
+'modules/nf-core/bwamem2/mem/environment.yml' is unchanged
+'modules/nf-core/bwamem2/mem/meta.yml' is unchanged
+Changes in 'bwamem2/mem/main.nf':
+--- modules/nf-core/bwamem2/mem/main.nf
++++ modules/nf-core/bwamem2/mem/main.nf
+@@ -1,6 +1,6 @@
+ process BWAMEM2_MEM {
+     tag "$meta.id"
+-    label 'process_high'
++    label 'process_low'
+ 
+     conda "${moduleDir}/environment.yml"
+     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+
+'modules/nf-core/bwamem2/mem/tests/main.nf.test.snap' is unchanged
+'modules/nf-core/bwamem2/mem/tests/main.nf.test' is unchanged
+************************************************************
diff --git a/modules/nf-core/bwamem2/mem/environment.yml b/modules/nf-core/bwamem2/mem/environment.yml
new file mode 100644
index 00000000..c069e281
--- /dev/null
+++ b/modules/nf-core/bwamem2/mem/environment.yml
@@ -0,0 +1,13 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+
+dependencies:
+  # renovate: datasource=conda depName=bioconda/bwa-mem2
+  - bwa-mem2=2.2.1
+  # renovate: datasource=conda depName=bioconda/htslib
+  - htslib=1.21
+  # renovate: datasource=conda depName=bioconda/samtools
+  - samtools=1.21
diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf
new file mode 100644
index 00000000..ad510447
--- /dev/null
+++ b/modules/nf-core/bwamem2/mem/main.nf
@@ -0,0 +1,83 @@
+process BWAMEM2_MEM {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9ac054213e67b3c9308e409b459080bbe438f8fd6c646c351bc42887f35a42e7/data' :
+        'community.wave.seqera.io/library/bwa-mem2_htslib_samtools:e1f420694f8e42bd' }"
+
+    input:
+    tuple val(meta), path(reads)
+    tuple val(meta2), path(index)
+    tuple val(meta3), path(fasta)
+    val   sort_bam
+
+    output:
+    tuple val(meta), path("*.sam")  , emit: sam , optional:true
+    tuple val(meta), path("*.bam")  , emit: bam , optional:true
+    tuple val(meta), path("*.cram") , emit: cram, optional:true
+    tuple val(meta), path("*.crai") , emit: crai, optional:true
+    tuple val(meta), path("*.csi")  , emit: csi , optional:true
+    path  "versions.yml"            , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def samtools_command = sort_bam ? 'sort' : 'view'
+
+    def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/
+    def extension_matcher =  (args2 =~ extension_pattern)
+    def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam"
+    def reference = fasta && extension=="cram"  ? "--reference ${fasta}" : ""
+    if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output"
+
+    """
+    INDEX=`find -L ./ -name "*.amb" | sed 's/\\.amb\$//'`
+
+    bwa-mem2 \\
+        mem \\
+        $args \\
+        -t $task.cpus \\
+        \$INDEX \\
+        $reads \\
+        | samtools $samtools_command $args2 -@ $task.cpus ${reference} -o ${prefix}.${extension} -
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+
+    def args2 = task.ext.args2 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/
+    def extension_matcher =  (args2 =~ extension_pattern)
+    def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam"
+    if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output"
+
+    def create_index = ""
+    if (extension == "cram") {
+        create_index = "touch ${prefix}.crai"
+    } else if (extension == "bam") {
+        create_index = "touch ${prefix}.csi"
+    }
+
+    """
+    touch ${prefix}.${extension}
+    ${create_index}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/bwamem2/mem/meta.yml b/modules/nf-core/bwamem2/mem/meta.yml
new file mode 100644
index 00000000..6c7d1728
--- /dev/null
+++ b/modules/nf-core/bwamem2/mem/meta.yml
@@ -0,0 +1,133 @@
+name: bwamem2_mem
+description: Performs fastq alignment to a fasta reference using BWA
+keywords:
+  - mem
+  - bwa
+  - alignment
+  - map
+  - fastq
+  - bam
+  - sam
+tools:
+  - bwa:
+      description: |
+        BWA-mem2 is a software package for mapping DNA sequences against
+        a large reference genome, such as the human genome.
+      homepage: https://github.com/bwa-mem2/bwa-mem2
+      documentation: http://www.htslib.org/doc/samtools.html
+      arxiv: arXiv:1303.3997
+      licence: ["MIT"]
+      identifier: "biotools:bwa-mem2"
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: file
+        description: |
+          List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+          respectively.
+        ontologies:
+          - edam: "http://edamontology.org/data_2044" # Sequence
+          - edam: "http://edamontology.org/format_1930" # FASTQ
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference/index information
+          e.g. [ id:'test' ]
+    - index:
+        type: file
+        description: BWA genome index files
+        pattern: "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}"
+        ontologies:
+          - edam: "http://edamontology.org/data_3210" # Genome index
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'genome' ]
+    - fasta:
+        type: file
+        description: Reference genome in FASTA format
+        pattern: "*.{fa,fasta,fna}"
+        ontologies:
+          - edam: "http://edamontology.org/data_2044" # Sequence
+          - edam: "http://edamontology.org/format_1929" # FASTA
+  - sort_bam:
+      type: boolean
+      description: use samtools sort (true) or samtools view (false)
+      pattern: "true or false"
+output:
+  sam:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.sam":
+          type: file
+          description: Output SAM file containing read alignments
+          pattern: "*.{sam}"
+          ontologies:
+            - edam: "http://edamontology.org/format_2573" # SAM
+  bam:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.bam":
+          type: file
+          description: Output BAM file containing read alignments
+          pattern: "*.{bam}"
+          ontologies:
+            - edam: "http://edamontology.org/format_2572" # BAM
+  cram:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.cram":
+          type: file
+          description: Output CRAM file containing read alignments
+          pattern: "*.{cram}"
+          ontologies:
+            - edam: "http://edamontology.org/format_3462" # CRAM
+  crai:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.crai":
+          type: file
+          description: Index file for CRAM file
+          pattern: "*.{crai}"
+          ontologies: []
+  csi:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.csi":
+          type: file
+          description: Index file for BAM file
+          pattern: "*.{csi}"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
+authors:
+  - "@maxulysse"
+  - "@matthdsm"
+maintainers:
+  - "@maxulysse"
+  - "@matthdsm"
diff --git a/modules/nf-core/bwamem2/mem/tests/main.nf.test b/modules/nf-core/bwamem2/mem/tests/main.nf.test
new file mode 100644
index 00000000..9e0ab14a
--- /dev/null
+++ b/modules/nf-core/bwamem2/mem/tests/main.nf.test
@@ -0,0 +1,179 @@
+nextflow_process {
+
+    name "Test Process BWAMEM2_MEM"
+    script "../main.nf"
+    process "BWAMEM2_MEM"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bwamem2"
+    tag "bwamem2/mem"
+    tag "bwamem2/index"
+
+    setup {
+        run("BWAMEM2_INDEX") {
+            script "../../index/main.nf"
+            process {
+                """
+                input[0] = Channel.of([
+                    [:], // meta map
+                    [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
+                ])
+                """
+            }
+        }
+    }
+
+    test("sarscov2 - fastq, index, fasta, false") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)]
+                ])
+                input[1] = BWAMEM2_INDEX.out.index
+                input[2] = Channel.of([[:], [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]])
+                input[3] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    bam(process.out.bam[0][1]).getHeaderMD5(),
+                    bam(process.out.bam[0][1]).getReadsMD5(),
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - fastq, index, fasta, true") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)]
+                ])
+                input[1] = BWAMEM2_INDEX.out.index
+                input[2] = Channel.of([[:], [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]])
+                input[3] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    bam(process.out.bam[0][1]).getHeaderMD5(),
+                    bam(process.out.bam[0][1]).getReadsMD5(),
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - [fastq1, fastq2], index, fasta, false") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = BWAMEM2_INDEX.out.index
+                input[2] = Channel.of([[:], [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]])
+                input[3] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    bam(process.out.bam[0][1]).getHeaderMD5(),
+                    bam(process.out.bam[0][1]).getReadsMD5(),
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - [fastq1, fastq2], index, fasta, true") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = BWAMEM2_INDEX.out.index
+                input[2] = Channel.of([[:], [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]])
+                input[3] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    bam(process.out.bam[0][1]).getHeaderMD5(),
+                    bam(process.out.bam[0][1]).getReadsMD5(),
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - [fastq1, fastq2], index, fasta, true - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = BWAMEM2_INDEX.out.index
+                input[2] = Channel.of([[:], [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]])
+                input[3] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap b/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap
new file mode 100644
index 00000000..ec90701f
--- /dev/null
+++ b/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap
@@ -0,0 +1,129 @@
+{
+    "sarscov2 - [fastq1, fastq2], index, fasta, false": {
+        "content": [
+            "9505760d66e1d5a5d34ab79a98228c6",
+            "57aeef88ed701a8ebc8e2f0a381b2a6",
+            [
+                "versions.yml:md5,ca1b1dcf82b92fb0751816fca16a477a"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-27T10:57:52.782442426"
+    },
+    "sarscov2 - [fastq1, fastq2], index, fasta, true - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    "versions.yml:md5,ca1b1dcf82b92fb0751816fca16a477a"
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "crai": [
+                    
+                ],
+                "cram": [
+                    
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "sam": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,ca1b1dcf82b92fb0751816fca16a477a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-27T10:58:37.140104324"
+    },
+    "sarscov2 - [fastq1, fastq2], index, fasta, true": {
+        "content": [
+            "e0c38d5772ca5f4d5d9999f4477e933c",
+            "af8628d9df18b2d3d4f6fd47ef2bb872",
+            [
+                "versions.yml:md5,ca1b1dcf82b92fb0751816fca16a477a"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-27T10:58:19.047052261"
+    },
+    "sarscov2 - fastq, index, fasta, false": {
+        "content": [
+            "58d05395bbb819e929885bde415947ae",
+            "798439cbd7fd81cbcc5078022dc5479d",
+            [
+                "versions.yml:md5,ca1b1dcf82b92fb0751816fca16a477a"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-27T10:56:53.456559296"
+    },
+    "sarscov2 - fastq, index, fasta, true": {
+        "content": [
+            "276189f6f003f99a87664e74fad2893d",
+            "94fcf617f5b994584c4e8d4044e16b4f",
+            [
+                "versions.yml:md5,ca1b1dcf82b92fb0751816fca16a477a"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-27T10:57:21.949711746"
+    }
+}
\ No newline at end of file
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index a2a92c22..b342147e 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -11,6 +11,7 @@ include { FASTQC                        } from '../modules/nf-core/fastqc/main'
 include { SEQFU_STATS                   } from '../modules/nf-core/seqfu/stats'
 include { FASTQSCREEN_FASTQSCREEN       } from '../modules/nf-core/fastqscreen/fastqscreen/main'
 include { BWAMEM2_INDEX                 } from '../modules/nf-core/bwamem2/index/main'
+include { BWAMEM2_MEM                   } from '../modules/nf-core/bwamem2/mem/main'                                                                                                                                                                       
 
 include { MULTIQC as MULTIQC_GLOBAL     } from '../modules/nf-core/multiqc/main'
 include { MULTIQC as MULTIQC_PER_TAG    } from '../modules/nf-core/multiqc/main'
@@ -112,16 +113,43 @@ workflow SEQINSPECTOR {
     if (!("bwamem2_index" in skip_tools)) {
         def fasta_file = getGenomeAttribute('fasta')
         log.warn" fasta_file: ${fasta_file}"
-        ch_reference_fasta = Channel.fromPath(fasta_file, checkIfExists: true).map { that -> [[id:that.Name], that] }
+        ch_reference_fasta = Channel.fromPath(fasta_file, checkIfExists: true)
+                               .map { [[id: it.name], it] }
+                               .first()  // ✅ Value channel
         log.info "ch_reference_fasta: ${ch_reference_fasta}"
         BWAMEM2_INDEX (
             ch_reference_fasta
         )
-        ch_bwamem2_index = BWAMEM2_INDEX.out.index
+        ch_bwamem2_index = BWAMEM2_INDEX.out.index.first()
         ch_versions = ch_versions.mix(BWAMEM2_INDEX.out.versions.first())
 
     }
+    // MODULE: Align reads with BWA-MEM2
+    if (!("bwamem2_mem" in skip_tools)) {
+           
+        // // Debug all input channels
+        // ch_sample_sized.count().view { "DEBUG - Samples: $it" }
+        // ch_bwamem2_index.count().view { "DEBUG - Index count: $it" }
+        // ch_bwamem2_index.view { "DEBUG - Index content: $it" }
+        // ch_reference_fasta.count().view { "DEBUG - Fasta count: $it" }
+        // ch_reference_fasta.view { "DEBUG - Fasta content: $it" }
+        
+    //     BWAMEM2_MEM (
+    //     ch_sample_sized.map {meta, subsampled -> [meta, subsampled]},
+    //     ch_bwamem2_index,
+    //     ch_reference_fasta,
+    //     params.sort_bam ?: true  // Example default value, adjust as needed
+    // )
+        BWAMEM2_MEM (
+            ch_sample_sized,        // ✅ Samples: [[meta], [reads]]
+            ch_bwamem2_index,       // ✅ Index: [[meta], [index]]
+            ch_reference_fasta,     // ✅ Fasta: [[meta], [fasta]]
+            params.sort_bam ?: true // ✅ Boolean
+        )
+        ch_bwamem2_mem = BWAMEM2_MEM.out
+        ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions.first())
 
+}
     //
     // Collate and save software versions
     //

From 52c26fc8415611a61d44ded5a0adee50838a70bd Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@n171-p126.eduroam.kth.se>
Date: Tue, 16 Sep 2025 16:15:43 +0200
Subject: [PATCH 232/530] Updated alignment tools

---
 main.nf                                       |  1 -
 modules/nf-core/bwamem2/mem/main.nf           |  2 +-
 .../main.nf                                   |  1 +
 workflows/seqinspector.nf                     | 25 ++++---------------
 4 files changed, 7 insertions(+), 22 deletions(-)

diff --git a/main.nf b/main.nf
index 0b5a532c..7111fbc4 100644
--- a/main.nf
+++ b/main.nf
@@ -31,7 +31,6 @@ include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_seqi
 //   from igenomes.config using `--genome`
 // params.fasta = getGenomeAttribute('fasta')
 
-
 /* 
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     NAMED WORKFLOWS FOR PIPELINE
diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf
index ad510447..eab662a8 100644
--- a/modules/nf-core/bwamem2/mem/main.nf
+++ b/modules/nf-core/bwamem2/mem/main.nf
@@ -1,6 +1,6 @@
 process BWAMEM2_MEM {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_high'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index 75465188..bd117986 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -209,6 +209,7 @@ def getGenomeAttribute(attribute) {
             return params.genomes[ params.genome ][ attribute ]
         }
     }
+    return null
 }
 
 
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index b342147e..50383f85 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -112,11 +112,9 @@ workflow SEQINSPECTOR {
 
     if (!("bwamem2_index" in skip_tools)) {
         def fasta_file = getGenomeAttribute('fasta')
-        log.warn" fasta_file: ${fasta_file}"
         ch_reference_fasta = Channel.fromPath(fasta_file, checkIfExists: true)
                                .map { [[id: it.name], it] }
-                               .first()  // ✅ Value channel
-        log.info "ch_reference_fasta: ${ch_reference_fasta}"
+                               .first()
         BWAMEM2_INDEX (
             ch_reference_fasta
         )
@@ -127,24 +125,11 @@ workflow SEQINSPECTOR {
     // MODULE: Align reads with BWA-MEM2
     if (!("bwamem2_mem" in skip_tools)) {
            
-        // // Debug all input channels
-        // ch_sample_sized.count().view { "DEBUG - Samples: $it" }
-        // ch_bwamem2_index.count().view { "DEBUG - Index count: $it" }
-        // ch_bwamem2_index.view { "DEBUG - Index content: $it" }
-        // ch_reference_fasta.count().view { "DEBUG - Fasta count: $it" }
-        // ch_reference_fasta.view { "DEBUG - Fasta content: $it" }
-        
-    //     BWAMEM2_MEM (
-    //     ch_sample_sized.map {meta, subsampled -> [meta, subsampled]},
-    //     ch_bwamem2_index,
-    //     ch_reference_fasta,
-    //     params.sort_bam ?: true  // Example default value, adjust as needed
-    // )
         BWAMEM2_MEM (
-            ch_sample_sized,        // ✅ Samples: [[meta], [reads]]
-            ch_bwamem2_index,       // ✅ Index: [[meta], [index]]
-            ch_reference_fasta,     // ✅ Fasta: [[meta], [fasta]]
-            params.sort_bam ?: true // ✅ Boolean
+            ch_sample_sized,
+            ch_bwamem2_index,
+            ch_reference_fasta,
+            params.sort_bam ?: true
         )
         ch_bwamem2_mem = BWAMEM2_MEM.out
         ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions.first())

From d7461b6c4278cf606cc76ec755b1b52f8be45903 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@n188-p1.eduroam.kth.se>
Date: Wed, 17 Sep 2025 10:48:07 +0200
Subject: [PATCH 233/530] 	Update snapshots

---
 tests/MiSeq.main.nf.test.snap           | 220 +---------
 tests/MiSeq_PairedEnd.main.nf.test.snap | 232 +---------
 tests/NovaSeq6000.main.nf.test.snap     | 542 +-----------------------
 tests/PromethION.main.nf.test.snap      | 138 +-----
 workflows/seqinspector.nf               |   4 +-
 5 files changed, 44 insertions(+), 1092 deletions(-)

diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index beee2404..7f825c57 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -1,231 +1,53 @@
 {
     "Miseq data test (skip all tools)": {
         "content": [
-            1,
-            {
-                "Workflow": {
-                    "nf-core/seqinspector": "v1.0dev"
-                }
-            },
+            0,
+            null,
             [
-                "multiqc",
-                "multiqc/global_report",
-                "multiqc/global_report/multiqc_data",
-                "multiqc/global_report/multiqc_data/multiqc.log",
-                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
-                "multiqc/global_report/multiqc_data/multiqc_data.json",
-                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
-                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
-                "multiqc/global_report/multiqc_report.html",
-                "pipeline_info",
-                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"
+                "pipeline_info"
             ],
             [
-                "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
+                
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-01-07T13:49:22.707398"
+        "timestamp": "2025-09-17T09:46:18.576771"
     },
     "MiSeq data test (single end reads)": {
         "content": [
-            4,
-            {
-                "FASTQC": {
-                    "fastqc": "0.12.1"
-                },
-                "FASTQSCREEN_FASTQSCREEN": {
-                    "fastqscreen": "0.16.0"
-                },
-                "SEQFU_STATS": {
-                    "seqfu": "1.20.3"
-                },
-                "Workflow": {
-                    "nf-core/seqinspector": "v1.0dev"
-                }
-            },
+            0,
+            null,
             [
-                "fastqc",
-                "fastqc/SAMPLE_SINGLE_END_1_fastqc.html",
-                "fastqc/SAMPLE_SINGLE_END_1_fastqc.zip",
-                "fastqscreen",
-                "fastqscreen/SAMPLE_SINGLE_END_1_screen.html",
-                "fastqscreen/SAMPLE_SINGLE_END_1_screen.png",
-                "fastqscreen/SAMPLE_SINGLE_END_1_screen.txt",
-                "multiqc",
-                "multiqc/global_report",
-                "multiqc/global_report/multiqc_data",
-                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
-                "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
-                "multiqc/global_report/multiqc_data/multiqc.log",
-                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
-                "multiqc/global_report/multiqc_data/multiqc_data.json",
-                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
-                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
-                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
-                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
-                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
-                "multiqc/global_report/multiqc_plots",
-                "multiqc/global_report/multiqc_plots/pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
-                "multiqc/global_report/multiqc_plots/png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu.png",
-                "multiqc/global_report/multiqc_plots/svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
-                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
-                "multiqc/global_report/multiqc_report.html",
-                "pipeline_info",
-                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
-                "seqfu_stats",
-                "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu.tsv",
-                "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu_mqc.txt"
+                "pipeline_info"
             ],
             [
-                "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
-                "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
-                "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
-                "fastqc-status-check-heatmap.txt:md5,8f98652c377741c974e485652a19f37f",
-                "fastqc_overrepresented_sequences_plot.txt:md5,cdc7479933cae03e0043ae794f81c304",
-                "fastqc_per_base_n_content_plot.txt:md5,dd8d6976dc5ea8cf67d9fa2c3be9e24b",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,5f9a98d3068aab17f26731ae0615f41a",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,1de1333bb959189dcf8230706f60dbfc",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,62f140bfa52d462c9c499dfdabc35476",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,5fda43eb9b7c60cf6b4348f734a94b26",
-                "fastqc_sequence_counts_plot.txt:md5,00cd6842465f7aa9ae75434e175946a6",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,c3befe0812d2f1c23d5e75e6fccf0622",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607",
-                "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
-                "multiqc_seqfu.txt:md5,8e6989a2392f599a09a5c3edf8119702",
-                "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,f65c868e562291647d539090698ba5eb",
-                "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
+                
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-03-26T13:00:21.042755"
+        "timestamp": "2025-09-17T09:45:44.557713"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
-            3,
-            {
-                "FASTQSCREEN_FASTQSCREEN": {
-                    "fastqscreen": "0.16.0"
-                },
-                "SEQFU_STATS": {
-                    "seqfu": "1.20.3"
-                },
-                "Workflow": {
-                    "nf-core/seqinspector": "v1.0dev"
-                }
-            },
+            0,
+            null,
             [
-                "fastqscreen",
-                "fastqscreen/SAMPLE_SINGLE_END_1_screen.html",
-                "fastqscreen/SAMPLE_SINGLE_END_1_screen.png",
-                "fastqscreen/SAMPLE_SINGLE_END_1_screen.txt",
-                "multiqc",
-                "multiqc/global_report",
-                "multiqc/global_report/multiqc_data",
-                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
-                "multiqc/global_report/multiqc_data/multiqc.log",
-                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
-                "multiqc/global_report/multiqc_data/multiqc_data.json",
-                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
-                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
-                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
-                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
-                "multiqc/global_report/multiqc_plots",
-                "multiqc/global_report/multiqc_plots/pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
-                "multiqc/global_report/multiqc_plots/png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu.png",
-                "multiqc/global_report/multiqc_plots/svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
-                "multiqc/global_report/multiqc_report.html",
-                "pipeline_info",
-                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
-                "seqfu_stats",
-                "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu.tsv",
-                "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu_mqc.txt"
+                "pipeline_info"
             ],
             [
-                "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
-                "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
-                "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607",
-                "multiqc_seqfu.txt:md5,8e6989a2392f599a09a5c3edf8119702",
-                "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,f65c868e562291647d539090698ba5eb",
-                "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
+                
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-03-26T13:00:53.07934"
+        "timestamp": "2025-09-17T09:46:02.359222"
     }
 }
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index 877fc5e0..456733b0 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -1,237 +1,19 @@
 {
     "MiSeq data test (paired end reads)": {
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-                },
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-                "Workflow": {
-                    "nf-core/seqinspector": "v1.0dev"
-                }
-            },
+            0,
+            null,
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-                "fastqc/SAMPLE_PAIRED_END_1_1_2_fastqc.zip",
-                "fastqc/SAMPLE_PAIRED_END_2_2_1_fastqc.html",
-                "fastqc/SAMPLE_PAIRED_END_2_2_1_fastqc.zip",
-                "fastqc/SAMPLE_PAIRED_END_2_2_2_fastqc.html",
-                "fastqc/SAMPLE_PAIRED_END_2_2_2_fastqc.zip",
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-                "fastqscreen/SAMPLE_PAIRED_END_1_1_1_screen.png",
-                "fastqscreen/SAMPLE_PAIRED_END_1_1_1_screen.txt",
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-                "fastqscreen/SAMPLE_PAIRED_END_2_2_1_screen.png",
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-                "fastqscreen/SAMPLE_PAIRED_END_2_2_2_screen.html",
-                "fastqscreen/SAMPLE_PAIRED_END_2_2_2_screen.png",
-                "fastqscreen/SAMPLE_PAIRED_END_2_2_2_screen.txt",
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-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
-                "multiqc/global_report/multiqc_data/multiqc.log",
-                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
-                "multiqc/global_report/multiqc_data/multiqc_data.json",
-                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
-                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
-                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
-                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
-                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
-                "multiqc/global_report/multiqc_plots",
-                "multiqc/global_report/multiqc_plots/pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
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-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
-                "multiqc/global_report/multiqc_plots/png",
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-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
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-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
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-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
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-                "multiqc/global_report/multiqc_report.html",
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-                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_adapter_content_plot.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_base_n_content_plot.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
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-                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_sequence_counts_plot.txt",
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-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_seqfu.txt",
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+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-03-27T09:01:13.732951"
+        "timestamp": "2025-09-17T09:46:40.244187"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index fa851d95..966a3c41 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -1,547 +1,19 @@
 {
     "NovaSeq6000 data test": {
         "content": [
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-                },
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-                },
-                "Workflow": {
-                    "nf-core/seqinspector": "v1.0dev"
-                }
-            },
+            0,
+            null,
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-                "fastqc/SampleA_2_fastqc.html",
-                "fastqc/SampleA_2_fastqc.zip",
-                "fastqc/Undetermined_5_fastqc.html",
-                "fastqc/Undetermined_5_fastqc.zip",
-                "fastqc/sampletest_4_fastqc.html",
-                "fastqc/sampletest_4_fastqc.zip",
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-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
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-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
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-                "multiqc/group_reports/group1",
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-                "multiqc/group_reports/group1/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
-                "multiqc/group_reports/group1/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
-                "multiqc/group_reports/group1/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
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-                "multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt",
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-                "fastqc_per_base_sequence_quality_plot.txt:md5,12585cf6b03db684a5ebd959f51e77e7",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a1464399e84711454499d27e98ed942b",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,026d11e7b49a49ac7bac85f376760305",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,4d646b20970d09d846947b87961efe7e",
-                "fastqc_sequence_counts_plot.txt:md5,057fb961863b325fe875d3a7879cb888",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,3b86c9d8625c439376102f3286c7bba7",
-                "fastqc_sequence_length_distribution_plot.txt:md5,6296c9ddbf8ba8e12053149d057fd7b2",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5",
-                "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
-                "multiqc_seqfu.txt:md5,a1a0b9a0dde0c1c4fe184d44c675dcde",
-                "Sample1_1_seqfu.tsv:md5,269fabf8435defcd327aa69a050b7869",
-                "Sample1_1_seqfu_mqc.txt:md5,a354b0ed16b9cf84aa88f501d7740fd6",
-                "Sample23_3_seqfu.tsv:md5,6fdadbeeefccbf957f880d6852bf9676",
-                "Sample23_3_seqfu_mqc.txt:md5,e94269e3efc8b8192d7ac9c15ea2aa99",
-                "SampleA_2_seqfu.tsv:md5,b980ed694a05825fcf7c8b5b73888eb3",
-                "SampleA_2_seqfu_mqc.txt:md5,1d4b0e918644cf553108b7ccf77b4a01",
-                "Undetermined_5_seqfu.tsv:md5,b4458d41df4dee9321da03f4d4672aae",
-                "Undetermined_5_seqfu_mqc.txt:md5,0c869488cb61d2f87758c621bded212b",
-                "sampletest_4_seqfu.tsv:md5,db3179b0c41a09e6317a5a5c0852f476",
-                "sampletest_4_seqfu_mqc.txt:md5,590b97cc48268629204f59007bae7ad7"
+                
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-03-26T13:03:47.460854"
+        "timestamp": "2025-09-17T09:47:05.931505"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index 27a9c143..3752877a 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -1,143 +1,19 @@
 {
     "PromethION data test": {
         "content": [
-            4,
-            {
-                "FASTQC": {
-                    "fastqc": "0.12.1"
-                },
-                "FASTQSCREEN_FASTQSCREEN": {
-                    "fastqscreen": "0.16.0"
-                },
-                "SEQFU_STATS": {
-                    "seqfu": "1.20.3"
-                },
-                "Workflow": {
-                    "nf-core/seqinspector": "v1.0dev"
-                }
-            },
+            0,
+            null,
             [
-                "fastqc",
-                "fastqc/hg001_1_fastqc.html",
-                "fastqc/hg001_1_fastqc.zip",
-                "fastqscreen",
-                "fastqscreen/hg001_1_screen.html",
-                "fastqscreen/hg001_1_screen.png",
-                "fastqscreen/hg001_1_screen.txt",
-                "multiqc",
-                "multiqc/global_report",
-                "multiqc/global_report/multiqc_data",
-                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
-                "multiqc/global_report/multiqc_data/fastqc_adapter_content_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
-                "multiqc/global_report/multiqc_data/multiqc.log",
-                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
-                "multiqc/global_report/multiqc_data/multiqc_data.json",
-                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
-                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
-                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
-                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
-                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
-                "multiqc/global_report/multiqc_plots",
-                "multiqc/global_report/multiqc_plots/pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
-                "multiqc/global_report/multiqc_plots/png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_adapter_content_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu.png",
-                "multiqc/global_report/multiqc_plots/svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
-                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
-                "multiqc/global_report/multiqc_report.html",
-                "pipeline_info",
-                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
-                "seqfu_stats",
-                "seqfu_stats/hg001_1_seqfu.tsv",
-                "seqfu_stats/hg001_1_seqfu_mqc.txt"
+                "pipeline_info"
             ],
             [
-                "hg001_1_screen.png:md5,b9c58e388f18ad11f4c2e29e9b573a5e",
-                "hg001_1_screen.txt:md5,8e53ea043d658a130f4b8ca455e2ba9b",
-                "fastq_screen_plot.txt:md5,3023b86477fecf6d46d8fc60d82cc53a",
-                "fastqc-status-check-heatmap.txt:md5,825668e94de27356f0a112beb758e416",
-                "fastqc_adapter_content_plot.txt:md5,1fa991080c20755e5e729a5eeab960e5",
-                "fastqc_overrepresented_sequences_plot.txt:md5,e810a3d3eba0ba83b122763505f511a7",
-                "fastqc_per_base_n_content_plot.txt:md5,cbdb64298ff839665e8c8c8e89896e87",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,4962950bc3ce77169ac510d64cb769c6",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,e62273533304be59dab5f13afef93b3e",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,3d49290a15406cb5dac1460c02729f0f",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,7cc10d1bc92ca09431a506c38d911228",
-                "fastqc_sequence_counts_plot.txt:md5,0425d7298c24df6158d5bf7aca1d4190",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,9111d942c7eed5af0e9ccb8c42db8505",
-                "fastqc_sequence_length_distribution_plot.txt:md5,04adfcd0125ebcc3e3bb631f1956c812",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,7c5d711e27c53d13c81644a1f2468dba",
-                "multiqc_fastqc.txt:md5,1a4b472e13cadc770832b0e20d1de7b0",
-                "multiqc_seqfu.txt:md5,9595d608ff5709f2bdec8cb1016416c0",
-                "hg001_1_seqfu.tsv:md5,b133752c897afbb4d8721b911fa117d4",
-                "hg001_1_seqfu_mqc.txt:md5,6285f582c03faa70e8dcb3503e5db728"
+                
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-03-26T13:05:53.896824"
+        "timestamp": "2025-09-17T09:47:47.762241"
     }
 }
\ No newline at end of file
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 50383f85..c979c37e 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -113,8 +113,8 @@ workflow SEQINSPECTOR {
     if (!("bwamem2_index" in skip_tools)) {
         def fasta_file = getGenomeAttribute('fasta')
         ch_reference_fasta = Channel.fromPath(fasta_file, checkIfExists: true)
-                               .map { [[id: it.name], it] }
-                               .first()
+                                    .map { [[id: it.name], it] }
+                                    .first()
         BWAMEM2_INDEX (
             ch_reference_fasta
         )

From 911d5b780a66ebad777415f5e4ba4d52e8743ee4 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@n188-p1.eduroam.kth.se>
Date: Wed, 17 Sep 2025 10:54:13 +0200
Subject: [PATCH 234/530] Added prettier

---
 modules.json | 50 +++++++++++++-------------------------------------
 1 file changed, 13 insertions(+), 37 deletions(-)

diff --git a/modules.json b/modules.json
index 2b2026f6..e3b68325 100644
--- a/modules.json
+++ b/modules.json
@@ -8,67 +8,49 @@
                     "bowtie2/build": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "bwamem2/index": {
                         "branch": "master",
                         "git_sha": "b2902040b9cb9b7b32b62400f1c024a709bd4812",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "bwamem2/mem": {
                         "branch": "master",
                         "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
-                        "installed_by": [
-                            "modules"
-                        ],
+                        "installed_by": ["modules"],
                         "patch": "modules/nf-core/bwamem2/mem/bwamem2-mem.diff"
                     },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "fastqscreen/buildfromindex": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "fastqscreen/fastqscreen": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": [
-                            "modules"
-                        ],
+                        "installed_by": ["modules"],
                         "patch": "modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff"
                     },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "7b50cb7be890e4b28cffb82e438cc6a8d7805d3f",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "seqfu/stats": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "seqtk/sample": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     }
                 }
             },
@@ -77,26 +59,20 @@
                     "utils_nextflow_pipeline": {
                         "branch": "master",
                         "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
-                        "installed_by": [
-                            "subworkflows"
-                        ]
+                        "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
                         "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a",
-                        "installed_by": [
-                            "subworkflows"
-                        ]
+                        "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
                         "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
-                        "installed_by": [
-                            "subworkflows"
-                        ]
+                        "installed_by": ["subworkflows"]
                     }
                 }
             }
         }
     }
-}
\ No newline at end of file
+}

From 715fbb37bebb18e3850e50efa48373624a4c3aab Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@n188-p1.eduroam.kth.se>
Date: Wed, 17 Sep 2025 11:04:23 +0200
Subject: [PATCH 235/530] removed spaces

---
 main.nf                   | 4 ++--
 workflows/seqinspector.nf | 3 +--
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/main.nf b/main.nf
index 7111fbc4..2b25c3fc 100644
--- a/main.nf
+++ b/main.nf
@@ -31,7 +31,7 @@ include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_seqi
 //   from igenomes.config using `--genome`
 // params.fasta = getGenomeAttribute('fasta')
 
-/* 
+/*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     NAMED WORKFLOWS FOR PIPELINE
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -82,7 +82,7 @@ workflow {
         params.outdir,
         params.input
     )
-    
+
     //
     // WORKFLOW: Run main workflow
     //
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index c979c37e..6efca6d4 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -11,7 +11,7 @@ include { FASTQC                        } from '../modules/nf-core/fastqc/main'
 include { SEQFU_STATS                   } from '../modules/nf-core/seqfu/stats'
 include { FASTQSCREEN_FASTQSCREEN       } from '../modules/nf-core/fastqscreen/fastqscreen/main'
 include { BWAMEM2_INDEX                 } from '../modules/nf-core/bwamem2/index/main'
-include { BWAMEM2_MEM                   } from '../modules/nf-core/bwamem2/mem/main'                                                                                                                                                                       
+include { BWAMEM2_MEM                   } from '../modules/nf-core/bwamem2/mem/main'
 
 include { MULTIQC as MULTIQC_GLOBAL     } from '../modules/nf-core/multiqc/main'
 include { MULTIQC as MULTIQC_PER_TAG    } from '../modules/nf-core/multiqc/main'
@@ -124,7 +124,6 @@ workflow SEQINSPECTOR {
     }
     // MODULE: Align reads with BWA-MEM2
     if (!("bwamem2_mem" in skip_tools)) {
-           
         BWAMEM2_MEM (
             ch_sample_sized,
             ch_bwamem2_index,

From fa6676773b7918e83f3d3bd0c3dbd539c7082bbc Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@n188-p1.eduroam.kth.se>
Date: Wed, 17 Sep 2025 13:29:17 +0200
Subject: [PATCH 236/530] removed first() warnings

---
 conf/modules.config                 | 2 +-
 modules/nf-core/bwamem2/mem/main.nf | 2 +-
 nextflow.config                     | 1 +
 workflows/seqinspector.nf           | 7 ++++---
 4 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index f85c9b18..22cd4d8a 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -44,7 +44,7 @@ process {
         ]
     }
     withName: 'BWAMEM2_MEM' {
-        ext.args   = { params.bwamem2_mem_args ?: '' }
+        ext.args   =  ''
         publishDir = [
             path: { "${params.outdir}/bwamem2_mem" },
             mode: params.publish_dir_mode,
diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf
index eab662a8..ad510447 100644
--- a/modules/nf-core/bwamem2/mem/main.nf
+++ b/modules/nf-core/bwamem2/mem/main.nf
@@ -1,6 +1,6 @@
 process BWAMEM2_MEM {
     tag "$meta.id"
-    label 'process_high'
+    label 'process_low'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/nextflow.config b/nextflow.config
index f9db2601..10772b07 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -20,6 +20,7 @@ params {
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
     igenomes_ignore            = false
 
+
     // Fastqscreen options
     fastq_screen_references    = "${projectDir}/assets/example_fastq_screen_references.csv"
 
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 6efca6d4..576e2cfa 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -115,11 +115,12 @@ workflow SEQINSPECTOR {
         ch_reference_fasta = Channel.fromPath(fasta_file, checkIfExists: true)
                                     .map { [[id: it.name], it] }
                                     .first()
+
         BWAMEM2_INDEX (
             ch_reference_fasta
         )
-        ch_bwamem2_index = BWAMEM2_INDEX.out.index.first()
-        ch_versions = ch_versions.mix(BWAMEM2_INDEX.out.versions.first())
+        ch_bwamem2_index = BWAMEM2_INDEX.out.index
+        ch_versions = ch_versions.mix(BWAMEM2_INDEX.out.versions)
 
     }
     // MODULE: Align reads with BWA-MEM2
@@ -131,7 +132,7 @@ workflow SEQINSPECTOR {
             params.sort_bam ?: true
         )
         ch_bwamem2_mem = BWAMEM2_MEM.out
-        ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions.first())
+        ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions)
 
 }
     //

From 1f11e757c94d48774920ec4444e70e3a08ea4ea7 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@n188-p1.eduroam.kth.se>
Date: Wed, 17 Sep 2025 13:50:04 +0200
Subject: [PATCH 237/530] added sort_bam parameter

---
 modules/nf-core/bwamem2/mem/main.nf | 2 +-
 nextflow.config                     | 2 +-
 nextflow_schema.json                | 6 ++++++
 3 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf
index ad510447..eab662a8 100644
--- a/modules/nf-core/bwamem2/mem/main.nf
+++ b/modules/nf-core/bwamem2/mem/main.nf
@@ -1,6 +1,6 @@
 process BWAMEM2_MEM {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_high'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/nextflow.config b/nextflow.config
index 10772b07..cecca681 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -19,7 +19,7 @@ params {
     fasta                      = null
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
     igenomes_ignore            = false
-
+    sort_bam                   = true
 
     // Fastqscreen options
     fastq_screen_references    = "${projectDir}/assets/example_fastq_screen_references.csv"
diff --git a/nextflow_schema.json b/nextflow_schema.json
index ca5c3c34..095fe25c 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -161,6 +161,12 @@
                     "fa_icon": "fas fa-question-circle",
                     "hidden": true
                 },
+                "sort_bam": {
+                    "type": "boolean",
+                    "default": true,
+                    "description": "Sort BAM files after alignment",
+                    "help_text": "If true, BAM files produced by alignment will be sorted by genomic coordinates."
+               },
                 "publish_dir_mode": {
                     "type": "string",
                     "default": "copy",

From 9fa7cf5998730f42d315a0a8c26fb4b01753f6a6 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@n188-p1.eduroam.kth.se>
Date: Wed, 17 Sep 2025 14:24:23 +0200
Subject: [PATCH 238/530] style: apply prettier formatting to
 nextflow_schema.json

---
 nextflow_schema.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 095fe25c..3525395f 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -166,7 +166,7 @@
                     "default": true,
                     "description": "Sort BAM files after alignment",
                     "help_text": "If true, BAM files produced by alignment will be sorted by genomic coordinates."
-               },
+                },
                 "publish_dir_mode": {
                     "type": "string",
                     "default": "copy",

From aaa0be13c039c81e2b911b6d7e864847c7521fc8 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Wed, 17 Sep 2025 15:27:31 +0200
Subject: [PATCH 239/530] add module test path and sort the parameters in the
 tests

---
 nextflow.config       | 1 +
 nextflow_schema.json  | 7 ++++++-
 tests/nextflow.config | 5 ++---
 3 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index cecca681..dedd6041 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -44,6 +44,7 @@ params {
     show_hidden                  = false
     version                      = false
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
+    modules_testdata_base_path   = 's3://ngi-igenomes/testdata/nf-core/modules/'
     trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')// Config options
     config_profile_name        = null
     config_profile_description = null
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 095fe25c..4f835828 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -166,7 +166,7 @@
                     "default": true,
                     "description": "Sort BAM files after alignment",
                     "help_text": "If true, BAM files produced by alignment will be sorted by genomic coordinates."
-               },
+                },
                 "publish_dir_mode": {
                     "type": "string",
                     "default": "copy",
@@ -211,6 +211,11 @@
                     "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
                     "hidden": true
                 },
+                "modules_testdata_base_path": {
+                    "type": "string",
+                    "description": "Base path / URL for data used in the modules",
+                    "hidden": true
+                },
                 "multiqc_config": {
                     "type": "string",
                     "format": "file-path",
diff --git a/tests/nextflow.config b/tests/nextflow.config
index 1e56f44d..5ff1eef6 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -8,8 +8,7 @@ params {
     config_profile_name        = 'nf-test profile'
     config_profile_description = 'Configuration profile to use for nf-test.'
 
-    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
-    modules_testdata_base_path   = 's3://ngi-igenomes/testdata/nf-core/modules/'
+    pipelines_testdata_base_path   = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
+    modules_testdata_base_path     = 's3://ngi-igenomes/testdata/nf-core/modules/'
 
-    validationSchemaIgnoreParams = 'genomes,igenomes_base,pipelines_testdata_base_path'
 }

From 0966733b853f932ba1b105445e6a049ae6c58b0c Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Wed, 17 Sep 2025 16:05:04 +0200
Subject: [PATCH 240/530] replace first with collect and add _ to suppress LS
 warning

---
 workflows/seqinspector.nf | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 576e2cfa..fb568344 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -113,8 +113,7 @@ workflow SEQINSPECTOR {
     if (!("bwamem2_index" in skip_tools)) {
         def fasta_file = getGenomeAttribute('fasta')
         ch_reference_fasta = Channel.fromPath(fasta_file, checkIfExists: true)
-                                    .map { [[id: it.name], it] }
-                                    .first()
+                                    .map { [[id: it.name], it] }.collect()
 
         BWAMEM2_INDEX (
             ch_reference_fasta
@@ -190,7 +189,7 @@ workflow SEQINSPECTOR {
     )
 
     ch_tags = ch_multiqc_files
-        .map { meta, sample -> meta.tags }
+        .map { meta, _sample -> meta.tags }
         .flatten()
         .unique()
 
@@ -200,13 +199,13 @@ workflow SEQINSPECTOR {
     // Group samples by tag
     tagged_mqc_files = ch_tags
         .combine(ch_multiqc_files)
-        .filter { sample_tag, meta, sample -> sample_tag in meta.tags }
-        .map { sample_tag, meta, sample -> [sample_tag, sample] }
+        .filter { sample_tag, meta, _sample -> sample_tag in meta.tags }
+        .map { sample_tag, _meta, sample -> [sample_tag, sample] }
         .mix(multiqc_extra_files_per_tag)
         .groupTuple()
         .tap { mqc_by_tag }
         .collectFile {
-            sample_tag, samples ->
+            sample_tag, _samples ->
             def prefix_tag = "[TAG:${sample_tag}]"
             [
                 "${prefix_tag}_multiqc_extra_config.yml",
@@ -219,7 +218,7 @@ workflow SEQINSPECTOR {
         }
         .map { file -> [ (file =~ /\[TAG:(.+)\]/)[0][1], file ] }
         .join(mqc_by_tag)
-        .multiMap { sample_tag, config, samples ->
+        .multiMap { _sample_tag, config, samples ->
             samples_per_tag: samples.flatten()
             config: config
         }

From 4a93f9f88933267c2f9d88424cfde4bbda37aec7 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@Mac.home>
Date: Thu, 18 Sep 2025 11:54:06 +0200
Subject: [PATCH 241/530] Tests snapshots updated

---
 modules/nf-core/bwamem2/mem/main.nf     |   2 +-
 nextflow_schema.json                    |   2 +-
 tests/MiSeq.main.nf.test.snap           | 226 ++++++++++++++--
 tests/MiSeq_PairedEnd.main.nf.test.snap | 170 +++++++++++-
 tests/NovaSeq6000.main.nf.test.snap     | 330 +++++++++++++++++++++++-
 tests/PromethION.main.nf.test.snap      |  54 +++-
 tests/nextflow.config                   |   1 +
 7 files changed, 747 insertions(+), 38 deletions(-)

diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf
index eab662a8..ad510447 100644
--- a/modules/nf-core/bwamem2/mem/main.nf
+++ b/modules/nf-core/bwamem2/mem/main.nf
@@ -1,6 +1,6 @@
 process BWAMEM2_MEM {
     tag "$meta.id"
-    label 'process_high'
+    label 'process_low'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 4f835828..927a08e8 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -94,7 +94,7 @@
                 },
                 "fastq_screen_references": {
                     "type": "string",
-                    "default": "/Users/agrimabhatt/abh_seqinspector/seqinspector/assets/example_fastq_screen_references.csv",
+                    "default": "${projectDir}/assets/example_fastq_screen_references.csv",
                     "fa_icon": "fas fa-search",
                     "description": "A .csv of reference genomes to be mapped against by FastQ Screen"
                 }
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 7f825c57..3886fd53 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -1,53 +1,243 @@
 {
     "Miseq data test (skip all tools)": {
         "content": [
-            0,
-            null,
+            3,
+            {
+                "BWAMEM2_INDEX": {
+                    "bwamem2": "2.2.1"
+                },
+                "BWAMEM2_MEM": {
+                    "bwamem2": "2.2.1",
+                    "samtools": 1.21
+                },
+                "Workflow": {
+                    "nf-core/seqinspector": "v1.0dev"
+                }
+            },
             [
-                "pipeline_info"
+                "bwamem2_index",
+                "bwamem2_index/bwamem2",
+                "bwamem2_index/bwamem2/genome.fa.0123",
+                "bwamem2_index/bwamem2/genome.fa.amb",
+                "bwamem2_index/bwamem2/genome.fa.ann",
+                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
+                "bwamem2_index/bwamem2/genome.fa.pac",
+                "bwamem2_mem",
+                "bwamem2_mem/SAMPLE_SINGLE_END_1.bam",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"
             ],
             [
-                
+                "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
+                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
+                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
+                "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
+                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
+                "SAMPLE_SINGLE_END_1.bam:md5,ed3f6acd94560448218a288623c810e6",
+                "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-09-17T09:46:18.576771"
+        "timestamp": "2025-09-18T11:05:17.619991"
     },
     "MiSeq data test (single end reads)": {
         "content": [
-            0,
-            null,
+            6,
+            {
+                "BWAMEM2_INDEX": {
+                    "bwamem2": "2.2.1"
+                },
+                "BWAMEM2_MEM": {
+                    "bwamem2": "2.2.1",
+                    "samtools": 1.21
+                },
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "FASTQSCREEN_FASTQSCREEN": {
+                    "fastqscreen": "0.16.0"
+                },
+                "SEQFU_STATS": {
+                    "seqfu": "1.20.3"
+                },
+                "Workflow": {
+                    "nf-core/seqinspector": "v1.0dev"
+                }
+            },
             [
-                "pipeline_info"
+                "bwamem2_index",
+                "bwamem2_index/bwamem2",
+                "bwamem2_index/bwamem2/genome.fa.0123",
+                "bwamem2_index/bwamem2/genome.fa.amb",
+                "bwamem2_index/bwamem2/genome.fa.ann",
+                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
+                "bwamem2_index/bwamem2/genome.fa.pac",
+                "bwamem2_mem",
+                "bwamem2_mem/SAMPLE_SINGLE_END_1.bam",
+                "fastqc",
+                "fastqc/SAMPLE_SINGLE_END_1_fastqc.html",
+                "fastqc/SAMPLE_SINGLE_END_1_fastqc.zip",
+                "fastqscreen",
+                "fastqscreen/SAMPLE_SINGLE_END_1_screen.html",
+                "fastqscreen/SAMPLE_SINGLE_END_1_screen.png",
+                "fastqscreen/SAMPLE_SINGLE_END_1_screen.txt",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_plots",
+                "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "seqfu_stats",
+                "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu.tsv",
+                "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu_mqc.txt"
             ],
             [
-                
+                "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
+                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
+                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
+                "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
+                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
+                "SAMPLE_SINGLE_END_1.bam:md5,ed3f6acd94560448218a288623c810e6",
+                "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
+                "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
+                "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
+                "fastqc-status-check-heatmap.txt:md5,8f98652c377741c974e485652a19f37f",
+                "fastqc_overrepresented_sequences_plot.txt:md5,cdc7479933cae03e0043ae794f81c304",
+                "fastqc_per_base_n_content_plot.txt:md5,dd8d6976dc5ea8cf67d9fa2c3be9e24b",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,5f9a98d3068aab17f26731ae0615f41a",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,1de1333bb959189dcf8230706f60dbfc",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,62f140bfa52d462c9c499dfdabc35476",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,5fda43eb9b7c60cf6b4348f734a94b26",
+                "fastqc_sequence_counts_plot.txt:md5,00cd6842465f7aa9ae75434e175946a6",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,c3befe0812d2f1c23d5e75e6fccf0622",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607",
+                "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
+                "multiqc_seqfu.txt:md5,8e6989a2392f599a09a5c3edf8119702",
+                "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,f65c868e562291647d539090698ba5eb",
+                "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-09-17T09:45:44.557713"
+        "timestamp": "2025-09-18T11:02:54.782814"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
-            0,
-            null,
+            5,
+            {
+                "BWAMEM2_INDEX": {
+                    "bwamem2": "2.2.1"
+                },
+                "BWAMEM2_MEM": {
+                    "bwamem2": "2.2.1",
+                    "samtools": 1.21
+                },
+                "FASTQSCREEN_FASTQSCREEN": {
+                    "fastqscreen": "0.16.0"
+                },
+                "SEQFU_STATS": {
+                    "seqfu": "1.20.3"
+                },
+                "Workflow": {
+                    "nf-core/seqinspector": "v1.0dev"
+                }
+            },
             [
-                "pipeline_info"
+                "bwamem2_index",
+                "bwamem2_index/bwamem2",
+                "bwamem2_index/bwamem2/genome.fa.0123",
+                "bwamem2_index/bwamem2/genome.fa.amb",
+                "bwamem2_index/bwamem2/genome.fa.ann",
+                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
+                "bwamem2_index/bwamem2/genome.fa.pac",
+                "bwamem2_mem",
+                "bwamem2_mem/SAMPLE_SINGLE_END_1.bam",
+                "fastqscreen",
+                "fastqscreen/SAMPLE_SINGLE_END_1_screen.html",
+                "fastqscreen/SAMPLE_SINGLE_END_1_screen.png",
+                "fastqscreen/SAMPLE_SINGLE_END_1_screen.txt",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_plots",
+                "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "seqfu_stats",
+                "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu.tsv",
+                "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu_mqc.txt"
             ],
             [
-                
+                "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
+                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
+                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
+                "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
+                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
+                "SAMPLE_SINGLE_END_1.bam:md5,ed3f6acd94560448218a288623c810e6",
+                "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
+                "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
+                "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607",
+                "multiqc_seqfu.txt:md5,8e6989a2392f599a09a5c3edf8119702",
+                "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,f65c868e562291647d539090698ba5eb",
+                "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-09-17T09:46:02.359222"
+        "timestamp": "2025-09-18T11:04:10.524764"
     }
 }
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index 456733b0..213695a1 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -1,19 +1,177 @@
 {
     "MiSeq data test (paired end reads)": {
         "content": [
-            0,
-            null,
+            11,
+            {
+                "BWAMEM2_INDEX": {
+                    "bwamem2": "2.2.1"
+                },
+                "BWAMEM2_MEM": {
+                    "bwamem2": "2.2.1",
+                    "samtools": 1.21
+                },
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "FASTQSCREEN_FASTQSCREEN": {
+                    "fastqscreen": "0.16.0"
+                },
+                "SEQFU_STATS": {
+                    "seqfu": "1.20.3"
+                },
+                "Workflow": {
+                    "nf-core/seqinspector": "v1.0dev"
+                }
+            },
             [
-                "pipeline_info"
+                "bwamem2_index",
+                "bwamem2_index/bwamem2",
+                "bwamem2_index/bwamem2/genome.fa.0123",
+                "bwamem2_index/bwamem2/genome.fa.amb",
+                "bwamem2_index/bwamem2/genome.fa.ann",
+                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
+                "bwamem2_index/bwamem2/genome.fa.pac",
+                "bwamem2_mem",
+                "bwamem2_mem/SAMPLE_PAIRED_END_1_1.bam",
+                "bwamem2_mem/SAMPLE_PAIRED_END_2_2.bam",
+                "fastqc",
+                "fastqc/SAMPLE_PAIRED_END_1_1_1_fastqc.html",
+                "fastqc/SAMPLE_PAIRED_END_1_1_1_fastqc.zip",
+                "fastqc/SAMPLE_PAIRED_END_1_1_2_fastqc.html",
+                "fastqc/SAMPLE_PAIRED_END_1_1_2_fastqc.zip",
+                "fastqc/SAMPLE_PAIRED_END_2_2_1_fastqc.html",
+                "fastqc/SAMPLE_PAIRED_END_2_2_1_fastqc.zip",
+                "fastqc/SAMPLE_PAIRED_END_2_2_2_fastqc.html",
+                "fastqc/SAMPLE_PAIRED_END_2_2_2_fastqc.zip",
+                "fastqscreen",
+                "fastqscreen/SAMPLE_PAIRED_END_1_1_1_screen.html",
+                "fastqscreen/SAMPLE_PAIRED_END_1_1_1_screen.png",
+                "fastqscreen/SAMPLE_PAIRED_END_1_1_1_screen.txt",
+                "fastqscreen/SAMPLE_PAIRED_END_1_1_2_screen.html",
+                "fastqscreen/SAMPLE_PAIRED_END_1_1_2_screen.png",
+                "fastqscreen/SAMPLE_PAIRED_END_1_1_2_screen.txt",
+                "fastqscreen/SAMPLE_PAIRED_END_2_2_1_screen.html",
+                "fastqscreen/SAMPLE_PAIRED_END_2_2_1_screen.png",
+                "fastqscreen/SAMPLE_PAIRED_END_2_2_1_screen.txt",
+                "fastqscreen/SAMPLE_PAIRED_END_2_2_2_screen.html",
+                "fastqscreen/SAMPLE_PAIRED_END_2_2_2_screen.png",
+                "fastqscreen/SAMPLE_PAIRED_END_2_2_2_screen.txt",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/global_report/multiqc_data/fastqc_adapter_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_plots",
+                "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_report.html",
+                "multiqc/group_reports",
+                "multiqc/group_reports/Bpacificus",
+                "multiqc/group_reports/Bpacificus/multiqc_data",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_adapter_content_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc.log",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_citations.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_data.json",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_plots",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg",
+                "multiqc/group_reports/Bpacificus/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "seqfu_stats",
+                "seqfu_stats/SAMPLE_PAIRED_END_1_1_seqfu.tsv",
+                "seqfu_stats/SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt",
+                "seqfu_stats/SAMPLE_PAIRED_END_2_2_seqfu.tsv",
+                "seqfu_stats/SAMPLE_PAIRED_END_2_2_seqfu_mqc.txt"
             ],
             [
-                
+                "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
+                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
+                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
+                "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
+                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
+                "SAMPLE_PAIRED_END_1_1.bam:md5,00431260e6fb11e87b1c8e276194ab5b",
+                "SAMPLE_PAIRED_END_2_2.bam:md5,9bb10554f5f7ac3187dd30e44f59bbd0",
+                "SAMPLE_PAIRED_END_1_1_1_screen.png:md5,f52ddd0e65f23f68dd8d58d5453417db",
+                "SAMPLE_PAIRED_END_1_1_1_screen.txt:md5,921b08eeb461a2aa1bd42bba53900f70",
+                "SAMPLE_PAIRED_END_1_1_2_screen.png:md5,908f4fceea8aa546106efdaa7ca78f7d",
+                "SAMPLE_PAIRED_END_1_1_2_screen.txt:md5,e9ea5789e356f666de27ba658704e80d",
+                "SAMPLE_PAIRED_END_2_2_1_screen.png:md5,48d546767ed2a34a1eda59d97dd00c18",
+                "SAMPLE_PAIRED_END_2_2_1_screen.txt:md5,a5b047f495d01bf9dcb0ae516d3c7fc3",
+                "SAMPLE_PAIRED_END_2_2_2_screen.png:md5,e3684b17339d16e6fb64ace7593cc388",
+                "SAMPLE_PAIRED_END_2_2_2_screen.txt:md5,fc95e5058e764596d5da182cbc0614cf",
+                "fastq_screen_plot.txt:md5,642264b93871c724aaa5d38b91c752dd",
+                "fastqc-status-check-heatmap.txt:md5,8e29ad6b23e03267c33bd9ed3385a44b",
+                "fastqc_adapter_content_plot.txt:md5,46fbd727a4996a3f0310d0423c628445",
+                "fastqc_per_base_n_content_plot.txt:md5,4eca1ef40d4d3d318b82e68e9fa3c589",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,218757a51c3de79a39a704c979df03da",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a4035ac9f0a0c07574130758b06630d7",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,637b937e023c84115ec06b529cc8ec1b",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,47d60153a430e2b8da51655704c2b31b",
+                "fastqc_sequence_counts_plot.txt:md5,10737092a3473fba81fbe49555512b2b",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,6412f57686de02e1f1c3751a7ca2be8b",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,5ef00028497d3271c9f0ea9a961db1e5",
+                "multiqc_fastqc.txt:md5,bc499ad273fd1c887056c31b82544984",
+                "multiqc_seqfu.txt:md5,1f1e063e4a509a26cee167c3b20389c0",
+                "fastq_screen_plot.txt:md5,642264b93871c724aaa5d38b91c752dd",
+                "fastqc-status-check-heatmap.txt:md5,8e29ad6b23e03267c33bd9ed3385a44b",
+                "fastqc_adapter_content_plot.txt:md5,46fbd727a4996a3f0310d0423c628445",
+                "fastqc_per_base_n_content_plot.txt:md5,4eca1ef40d4d3d318b82e68e9fa3c589",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,218757a51c3de79a39a704c979df03da",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a4035ac9f0a0c07574130758b06630d7",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,637b937e023c84115ec06b529cc8ec1b",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,47d60153a430e2b8da51655704c2b31b",
+                "fastqc_sequence_counts_plot.txt:md5,10737092a3473fba81fbe49555512b2b",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,6412f57686de02e1f1c3751a7ca2be8b",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,5ef00028497d3271c9f0ea9a961db1e5",
+                "multiqc_fastqc.txt:md5,bc499ad273fd1c887056c31b82544984",
+                "multiqc_seqfu.txt:md5,1f1e063e4a509a26cee167c3b20389c0",
+                "SAMPLE_PAIRED_END_1_1_seqfu.tsv:md5,bbd911ff3fa43212dfd4c5a5872dbdb6",
+                "SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt:md5,cd60f746b6749cc66213d031af1b931c",
+                "SAMPLE_PAIRED_END_2_2_seqfu.tsv:md5,152566a128dd657da33465b4966b5799",
+                "SAMPLE_PAIRED_END_2_2_seqfu_mqc.txt:md5,8a3296956e094e3a95e28431e6009c40"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-09-17T09:46:40.244187"
+        "timestamp": "2025-09-18T11:08:35.522492"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index 966a3c41..2952abc2 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -1,19 +1,337 @@
 {
     "NovaSeq6000 data test": {
         "content": [
-            0,
-            null,
+            26,
+            {
+                "BWAMEM2_INDEX": {
+                    "bwamem2": "2.2.1"
+                },
+                "BWAMEM2_MEM": {
+                    "bwamem2": "2.2.1",
+                    "samtools": 1.21
+                },
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "FASTQSCREEN_FASTQSCREEN": {
+                    "fastqscreen": "0.16.0"
+                },
+                "SEQFU_STATS": {
+                    "seqfu": "1.20.3"
+                },
+                "Workflow": {
+                    "nf-core/seqinspector": "v1.0dev"
+                }
+            },
             [
-                "pipeline_info"
+                "bwamem2_index",
+                "bwamem2_index/bwamem2",
+                "bwamem2_index/bwamem2/genome.fa.0123",
+                "bwamem2_index/bwamem2/genome.fa.amb",
+                "bwamem2_index/bwamem2/genome.fa.ann",
+                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
+                "bwamem2_index/bwamem2/genome.fa.pac",
+                "bwamem2_mem",
+                "bwamem2_mem/Sample1_1.bam",
+                "bwamem2_mem/Sample23_3.bam",
+                "bwamem2_mem/SampleA_2.bam",
+                "bwamem2_mem/Undetermined_5.bam",
+                "bwamem2_mem/sampletest_4.bam",
+                "fastqc",
+                "fastqc/Sample1_1_fastqc.html",
+                "fastqc/Sample1_1_fastqc.zip",
+                "fastqc/Sample23_3_fastqc.html",
+                "fastqc/Sample23_3_fastqc.zip",
+                "fastqc/SampleA_2_fastqc.html",
+                "fastqc/SampleA_2_fastqc.zip",
+                "fastqc/Undetermined_5_fastqc.html",
+                "fastqc/Undetermined_5_fastqc.zip",
+                "fastqc/sampletest_4_fastqc.html",
+                "fastqc/sampletest_4_fastqc.zip",
+                "fastqscreen",
+                "fastqscreen/Sample1_1_screen.html",
+                "fastqscreen/Sample1_1_screen.png",
+                "fastqscreen/Sample1_1_screen.txt",
+                "fastqscreen/Sample23_3_screen.html",
+                "fastqscreen/Sample23_3_screen.png",
+                "fastqscreen/Sample23_3_screen.txt",
+                "fastqscreen/SampleA_2_screen.html",
+                "fastqscreen/SampleA_2_screen.png",
+                "fastqscreen/SampleA_2_screen.txt",
+                "fastqscreen/Undetermined_5_screen.html",
+                "fastqscreen/Undetermined_5_screen.png",
+                "fastqscreen/Undetermined_5_screen.txt",
+                "fastqscreen/sampletest_4_screen.html",
+                "fastqscreen/sampletest_4_screen.png",
+                "fastqscreen/sampletest_4_screen.txt",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_plots",
+                "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_report.html",
+                "multiqc/group_reports",
+                "multiqc/group_reports/group1",
+                "multiqc/group_reports/group1/multiqc_data",
+                "multiqc/group_reports/group1/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc.log",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_citations.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_data.json",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_sources.txt",
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+                "multiqc/group_reports/group1/multiqc_plots/pdf",
+                "multiqc/group_reports/group1/multiqc_plots/png",
+                "multiqc/group_reports/group1/multiqc_plots/svg",
+                "multiqc/group_reports/group1/multiqc_report.html",
+                "multiqc/group_reports/group2",
+                "multiqc/group_reports/group2/multiqc_data",
+                "multiqc/group_reports/group2/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/group_reports/group2/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/group_reports/group2/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/group_reports/group2/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/group_reports/group2/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/group_reports/group2/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/group_reports/group2/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/group_reports/group2/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/group_reports/group2/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/group_reports/group2/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/group_reports/group2/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/group_reports/group2/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc.log",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_citations.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_data.json",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/group2/multiqc_plots",
+                "multiqc/group_reports/group2/multiqc_plots/pdf",
+                "multiqc/group_reports/group2/multiqc_plots/png",
+                "multiqc/group_reports/group2/multiqc_plots/svg",
+                "multiqc/group_reports/group2/multiqc_report.html",
+                "multiqc/group_reports/lane1",
+                "multiqc/group_reports/lane1/multiqc_data",
+                "multiqc/group_reports/lane1/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/group_reports/lane1/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/group_reports/lane1/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/group_reports/lane1/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/group_reports/lane1/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/group_reports/lane1/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/group_reports/lane1/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/group_reports/lane1/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/group_reports/lane1/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/group_reports/lane1/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/group_reports/lane1/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/group_reports/lane1/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc.log",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_citations.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_data.json",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/lane1/multiqc_plots",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/png",
+                "multiqc/group_reports/lane1/multiqc_plots/svg",
+                "multiqc/group_reports/lane1/multiqc_report.html",
+                "multiqc/group_reports/test",
+                "multiqc/group_reports/test/multiqc_data",
+                "multiqc/group_reports/test/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc.log",
+                "multiqc/group_reports/test/multiqc_data/multiqc_citations.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_data.json",
+                "multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/test/multiqc_plots",
+                "multiqc/group_reports/test/multiqc_plots/pdf",
+                "multiqc/group_reports/test/multiqc_plots/png",
+                "multiqc/group_reports/test/multiqc_plots/svg",
+                "multiqc/group_reports/test/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "seqfu_stats",
+                "seqfu_stats/Sample1_1_seqfu.tsv",
+                "seqfu_stats/Sample1_1_seqfu_mqc.txt",
+                "seqfu_stats/Sample23_3_seqfu.tsv",
+                "seqfu_stats/Sample23_3_seqfu_mqc.txt",
+                "seqfu_stats/SampleA_2_seqfu.tsv",
+                "seqfu_stats/SampleA_2_seqfu_mqc.txt",
+                "seqfu_stats/Undetermined_5_seqfu.tsv",
+                "seqfu_stats/Undetermined_5_seqfu_mqc.txt",
+                "seqfu_stats/sampletest_4_seqfu.tsv",
+                "seqfu_stats/sampletest_4_seqfu_mqc.txt"
             ],
             [
-                
+                "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
+                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
+                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
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+                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
+                "Sample1_1.bam:md5,39c3c91eedd90307315acec7aa0b9a35",
+                "Sample23_3.bam:md5,3d536a6680470138eb361eed198a8efd",
+                "SampleA_2.bam:md5,ad691a2590eed5bbc56a56dd24493e4e",
+                "Undetermined_5.bam:md5,06077f7de3641b4b86e08f6a9cdb5a97",
+                "sampletest_4.bam:md5,7dcb21eb9fec77b862af33e692678dbd",
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+                "Sample1_1_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "Sample23_3_screen.png:md5,6bb2caf67b9b2ed25d3d5f32c343e9ab",
+                "Sample23_3_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "SampleA_2_screen.png:md5,b2c3e95e034f5c038754bf108537de0e",
+                "SampleA_2_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "Undetermined_5_screen.png:md5,fc5d53f8876dfae3d1a781fa512ea1db",
+                "Undetermined_5_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "sampletest_4_screen.png:md5,1fb60070e8f4b70de0c1b3786b54f27e",
+                "sampletest_4_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "fastq_screen_plot.txt:md5,562b783630f698c3220c951b73b87027",
+                "fastqc-status-check-heatmap.txt:md5,6cd55dc80642c78b5e0d71821b83fe2e",
+                "fastqc_overrepresented_sequences_plot.txt:md5,37fd53c396d047467fbd38c5c4a0c4ba",
+                "fastqc_per_base_n_content_plot.txt:md5,75aee7627205c6513389d7a52e7a383b",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,2a60a8518caad855e842cf70a8037dad",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,1325b4b3971f7d4d544d9e252abf47b9",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,ef663c12746dfb88f7297b891756fadd",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,5a224c4e837ba42c16b724289bb1bf32",
+                "fastqc_sequence_counts_plot.txt:md5,20364b3b979bc99ae375a2dffcaf1cc1",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,7f33f3d0e2eb3405eb6456acbd18dfd4",
+                "fastqc_sequence_length_distribution_plot.txt:md5,9472fb38f57150d55fb9e4995aaeeb90",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
+                "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d",
+                "multiqc_seqfu.txt:md5,5b54a49079169985795537d83d58bdd9",
+                "fastq_screen_plot.txt:md5,c25d34568f10f131156294d31fbfa994",
+                "fastqc-status-check-heatmap.txt:md5,67afbf7ec626c4fc7a28b4922352bc84",
+                "fastqc_overrepresented_sequences_plot.txt:md5,0356d007eaf807f7b63714b438b11289",
+                "fastqc_per_base_n_content_plot.txt:md5,4c5bfb1594b391f3e36a9e1223b43a94",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,6251cde1646484446499252bd15c58a2",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,f645e38916efafd07d4c2c3d5c7cd051",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,a9d3152a43988e39fae4a75faa3a5aa4",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,aef487a8b267a14a92be64b0b01d9b5c",
+                "fastqc_sequence_counts_plot.txt:md5,5021496dd00366d08064804bbb5192e3",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,e37e8e4584f0157a5fa0d53b4834e836",
+                "fastqc_sequence_length_distribution_plot.txt:md5,393cc090200a5151561efb1ed5280b89",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
+                "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
+                "multiqc_seqfu.txt:md5,5579172a6f8ac09a5ffcb3ce6a99590e",
+                "fastq_screen_plot.txt:md5,44fca6453b0a3d0590271bd7a31cc740",
+                "fastqc-status-check-heatmap.txt:md5,b6872d9dbaa3cce396d48dc137076e53",
+                "fastqc_overrepresented_sequences_plot.txt:md5,eac8d0fd31c614d8d0f56bd54ee8c78c",
+                "fastqc_per_base_n_content_plot.txt:md5,b7b249afe807ca2321e6dd839961795c",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,3bca5f0121d27b0777a40a4ab44e2abc",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,ee29af5517a8c6f872adbaccea4ff2f8",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,3eaf12f9267c10e4e457a2bb9bdc70ea",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,1818e0b917e45a583740f2cbb0638f8d",
+                "fastqc_sequence_counts_plot.txt:md5,0c4863a5475a2444cd00b053eb8941b1",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,a7a050f827a4f821117efd8d25668c51",
+                "fastqc_sequence_length_distribution_plot.txt:md5,9c0761008be04d8ccf4c0e16acc6348c",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
+                "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
+                "multiqc_seqfu.txt:md5,b5434520fa5be5c98be5ed164a464d23",
+                "fastq_screen_plot.txt:md5,5f748d33a7a396547fe8c260b728aa06",
+                "fastqc-status-check-heatmap.txt:md5,08228a8f3d6f11b174b98626bb22bda1",
+                "fastqc_overrepresented_sequences_plot.txt:md5,3434dfb79f150e2e584e85866983ba01",
+                "fastqc_per_base_n_content_plot.txt:md5,e371981072ec99d11c6adb5a4034808c",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,bf83d019eaaeb1ca659ff28cfb2bdfea",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,3f40b8ee69d3eaefe657cc5ed622cc8b",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,86b61d09437a96448e1325e6be834048",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,9f7307469b112bd054f8ee0cc2cf4d65",
+                "fastqc_sequence_counts_plot.txt:md5,f0c693cc281a6e61ba219bab04f59a47",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,8c2aa91358fd4a2e946cbcc1f312f9b6",
+                "fastqc_sequence_length_distribution_plot.txt:md5,875ebcd6726bb9d36ffa64265e5071d0",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
+                "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
+                "multiqc_seqfu.txt:md5,e2e092852c011abe5ad75cdcd68b9383",
+                "fastq_screen_plot.txt:md5,8622e1dbd0fe62520af6096207b9775d",
+                "fastqc-status-check-heatmap.txt:md5,2a66f5d61b9eb579555905cd5954b04c",
+                "fastqc_overrepresented_sequences_plot.txt:md5,e0b5bfc4b64d37611b51c939e61196fa",
+                "fastqc_per_base_n_content_plot.txt:md5,1380831484d1b069a2fd4a20437118bf",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,12585cf6b03db684a5ebd959f51e77e7",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a1464399e84711454499d27e98ed942b",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,026d11e7b49a49ac7bac85f376760305",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,4d646b20970d09d846947b87961efe7e",
+                "fastqc_sequence_counts_plot.txt:md5,057fb961863b325fe875d3a7879cb888",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,3b86c9d8625c439376102f3286c7bba7",
+                "fastqc_sequence_length_distribution_plot.txt:md5,6296c9ddbf8ba8e12053149d057fd7b2",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5",
+                "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
+                "multiqc_seqfu.txt:md5,a1a0b9a0dde0c1c4fe184d44c675dcde",
+                "Sample1_1_seqfu.tsv:md5,269fabf8435defcd327aa69a050b7869",
+                "Sample1_1_seqfu_mqc.txt:md5,a354b0ed16b9cf84aa88f501d7740fd6",
+                "Sample23_3_seqfu.tsv:md5,6fdadbeeefccbf957f880d6852bf9676",
+                "Sample23_3_seqfu_mqc.txt:md5,e94269e3efc8b8192d7ac9c15ea2aa99",
+                "SampleA_2_seqfu.tsv:md5,b980ed694a05825fcf7c8b5b73888eb3",
+                "SampleA_2_seqfu_mqc.txt:md5,1d4b0e918644cf553108b7ccf77b4a01",
+                "Undetermined_5_seqfu.tsv:md5,b4458d41df4dee9321da03f4d4672aae",
+                "Undetermined_5_seqfu_mqc.txt:md5,0c869488cb61d2f87758c621bded212b",
+                "sampletest_4_seqfu.tsv:md5,db3179b0c41a09e6317a5a5c0852f476",
+                "sampletest_4_seqfu_mqc.txt:md5,590b97cc48268629204f59007bae7ad7"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-09-17T09:47:05.931505"
+        "timestamp": "2025-09-18T11:15:39.145326"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index 3752877a..f5e345ae 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -1,19 +1,61 @@
 {
     "PromethION data test": {
         "content": [
-            0,
-            null,
+            4,
+            {
+                "BWAMEM2_INDEX": {
+                    "bwamem2": "2.2.1"
+                },
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "FASTQSCREEN_FASTQSCREEN": {
+                    "fastqscreen": "0.16.0"
+                },
+                "SEQFU_STATS": {
+                    "seqfu": "1.20.3"
+                },
+                "Workflow": {
+                    "nf-core/seqinspector": "v1.0dev"
+                }
+            },
             [
-                "pipeline_info"
+                "bwamem2_index",
+                "bwamem2_index/bwamem2",
+                "bwamem2_index/bwamem2/genome.fa.0123",
+                "bwamem2_index/bwamem2/genome.fa.amb",
+                "bwamem2_index/bwamem2/genome.fa.ann",
+                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
+                "bwamem2_index/bwamem2/genome.fa.pac",
+                "fastqc",
+                "fastqc/hg001_1_fastqc.html",
+                "fastqc/hg001_1_fastqc.zip",
+                "fastqscreen",
+                "fastqscreen/hg001_1_screen.html",
+                "fastqscreen/hg001_1_screen.png",
+                "fastqscreen/hg001_1_screen.txt",
+                "pipeline_info",
+                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "seqfu_stats",
+                "seqfu_stats/hg001_1_seqfu.tsv",
+                "seqfu_stats/hg001_1_seqfu_mqc.txt"
             ],
             [
-                
+                "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
+                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
+                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
+                "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
+                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
+                "hg001_1_screen.png:md5,b9c58e388f18ad11f4c2e29e9b573a5e",
+                "hg001_1_screen.txt:md5,8e53ea043d658a130f4b8ca455e2ba9b",
+                "hg001_1_seqfu.tsv:md5,b133752c897afbb4d8721b911fa117d4",
+                "hg001_1_seqfu_mqc.txt:md5,6285f582c03faa70e8dcb3503e5db728"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-09-17T09:47:47.762241"
+        "timestamp": "2025-09-18T11:49:53.715982"
     }
 }
\ No newline at end of file
diff --git a/tests/nextflow.config b/tests/nextflow.config
index 5ff1eef6..d5d44a72 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -12,3 +12,4 @@ params {
     modules_testdata_base_path     = 's3://ngi-igenomes/testdata/nf-core/modules/'
 
 }
+

From 9fc1a955e08bd8c4c299ea0d48eb4a69edf37e79 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@n162-p178.eduroam.kth.se>
Date: Fri, 19 Sep 2025 13:05:05 +0200
Subject: [PATCH 242/530] added  GRCh38

---
 modules/nf-core/bwamem2/mem/main.nf  |  2 +-
 nextflow_schema.json                 |  2 +-
 tests/MiSeq.main.nf.test.snap        | 68 +---------------------------
 tests/PromethION.main.nf.test.config |  1 +
 tests/PromethION.main.nf.test.snap   |  5 +-
 5 files changed, 6 insertions(+), 72 deletions(-)

diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf
index ad510447..eab662a8 100644
--- a/modules/nf-core/bwamem2/mem/main.nf
+++ b/modules/nf-core/bwamem2/mem/main.nf
@@ -1,6 +1,6 @@
 process BWAMEM2_MEM {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_high'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 927a08e8..267afaa9 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -51,7 +51,7 @@
                 "skip_tools": {
                     "type": "string",
                     "description": "Comma-separated string of tools to skip",
-                    "pattern": "^((fastqc|fastqscreen|seqfu_stats|seqtk_sample)?,?)*(?<!,)$"
+                    "pattern": "^((fastqc|fastqscreen|seqfu_stats|seqtk_sample|bwamem2_index|bwamem2_mem)?,?)*(?<!,)$"
                 }
             }
         },
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 3886fd53..2a042439 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -54,15 +54,8 @@
     },
     "MiSeq data test (single end reads)": {
         "content": [
-            6,
+            3,
             {
-                "BWAMEM2_INDEX": {
-                    "bwamem2": "2.2.1"
-                },
-                "BWAMEM2_MEM": {
-                    "bwamem2": "2.2.1",
-                    "samtools": 1.21
-                },
                 "FASTQC": {
                     "fastqc": "0.12.1"
                 },
@@ -77,15 +70,6 @@
                 }
             },
             [
-                "bwamem2_index",
-                "bwamem2_index/bwamem2",
-                "bwamem2_index/bwamem2/genome.fa.0123",
-                "bwamem2_index/bwamem2/genome.fa.amb",
-                "bwamem2_index/bwamem2/genome.fa.ann",
-                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
-                "bwamem2_index/bwamem2/genome.fa.pac",
-                "bwamem2_mem",
-                "bwamem2_mem/SAMPLE_SINGLE_END_1.bam",
                 "fastqc",
                 "fastqc/SAMPLE_SINGLE_END_1_fastqc.html",
                 "fastqc/SAMPLE_SINGLE_END_1_fastqc.zip",
@@ -93,34 +77,6 @@
                 "fastqscreen/SAMPLE_SINGLE_END_1_screen.html",
                 "fastqscreen/SAMPLE_SINGLE_END_1_screen.png",
                 "fastqscreen/SAMPLE_SINGLE_END_1_screen.txt",
-                "multiqc",
-                "multiqc/global_report",
-                "multiqc/global_report/multiqc_data",
-                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
-                "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
-                "multiqc/global_report/multiqc_data/multiqc.log",
-                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
-                "multiqc/global_report/multiqc_data/multiqc_data.json",
-                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
-                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
-                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
-                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
-                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
-                "multiqc/global_report/multiqc_plots",
-                "multiqc/global_report/multiqc_plots/pdf",
-                "multiqc/global_report/multiqc_plots/png",
-                "multiqc/global_report/multiqc_plots/svg",
-                "multiqc/global_report/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "seqfu_stats",
@@ -128,28 +84,8 @@
                 "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu_mqc.txt"
             ],
             [
-                "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
-                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
-                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
-                "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
-                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "SAMPLE_SINGLE_END_1.bam:md5,ed3f6acd94560448218a288623c810e6",
                 "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
                 "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
-                "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
-                "fastqc-status-check-heatmap.txt:md5,8f98652c377741c974e485652a19f37f",
-                "fastqc_overrepresented_sequences_plot.txt:md5,cdc7479933cae03e0043ae794f81c304",
-                "fastqc_per_base_n_content_plot.txt:md5,dd8d6976dc5ea8cf67d9fa2c3be9e24b",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,5f9a98d3068aab17f26731ae0615f41a",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,1de1333bb959189dcf8230706f60dbfc",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,62f140bfa52d462c9c499dfdabc35476",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,5fda43eb9b7c60cf6b4348f734a94b26",
-                "fastqc_sequence_counts_plot.txt:md5,00cd6842465f7aa9ae75434e175946a6",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,c3befe0812d2f1c23d5e75e6fccf0622",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607",
-                "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
-                "multiqc_seqfu.txt:md5,8e6989a2392f599a09a5c3edf8119702",
                 "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,f65c868e562291647d539090698ba5eb",
                 "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
             ]
@@ -158,7 +94,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.7"
         },
-        "timestamp": "2025-09-18T11:02:54.782814"
+        "timestamp": "2025-09-18T16:56:47.640388"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
diff --git a/tests/PromethION.main.nf.test.config b/tests/PromethION.main.nf.test.config
index e1498a49..429de63f 100644
--- a/tests/PromethION.main.nf.test.config
+++ b/tests/PromethION.main.nf.test.config
@@ -4,4 +4,5 @@ includeConfig 'nextflow.config'
 // Load the correct samplesheet for that test
 params {
     input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/PromethION/samplesheet.csv'
+    genome = 'GRCh38'
 }
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index f5e345ae..541fbde2 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -9,9 +9,6 @@
                 "FASTQC": {
                     "fastqc": "0.12.1"
                 },
-                "FASTQSCREEN_FASTQSCREEN": {
-                    "fastqscreen": "0.16.0"
-                },
                 "SEQFU_STATS": {
                     "seqfu": "1.20.3"
                 },
@@ -56,6 +53,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.7"
         },
-        "timestamp": "2025-09-18T11:49:53.715982"
+        "timestamp": "2025-09-19T10:26:18.425518"
     }
 }
\ No newline at end of file

From 6e3009f61dd1c4bd085721a4a2b2d2759f9866aa Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@n162-p178.eduroam.kth.se>
Date: Fri, 19 Sep 2025 15:13:30 +0200
Subject: [PATCH 243/530] added EB1

---
 modules/nf-core/bwamem2/mem/main.nf  |  2 +-
 tests/MiSeq.main.nf.test.snap        | 68 +++++++++++++++++++++++++++-
 tests/PromethION.main.nf.test.config |  2 +-
 tests/PromethION.main.nf.test.snap   | 22 ++-------
 4 files changed, 73 insertions(+), 21 deletions(-)

diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf
index eab662a8..ad510447 100644
--- a/modules/nf-core/bwamem2/mem/main.nf
+++ b/modules/nf-core/bwamem2/mem/main.nf
@@ -1,6 +1,6 @@
 process BWAMEM2_MEM {
     tag "$meta.id"
-    label 'process_high'
+    label 'process_low'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 2a042439..eb8b541f 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -54,8 +54,15 @@
     },
     "MiSeq data test (single end reads)": {
         "content": [
-            3,
+            6,
             {
+                "BWAMEM2_INDEX": {
+                    "bwamem2": "2.2.1"
+                },
+                "BWAMEM2_MEM": {
+                    "bwamem2": "2.2.1",
+                    "samtools": 1.21
+                },
                 "FASTQC": {
                     "fastqc": "0.12.1"
                 },
@@ -70,6 +77,15 @@
                 }
             },
             [
+                "bwamem2_index",
+                "bwamem2_index/bwamem2",
+                "bwamem2_index/bwamem2/genome.fa.0123",
+                "bwamem2_index/bwamem2/genome.fa.amb",
+                "bwamem2_index/bwamem2/genome.fa.ann",
+                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
+                "bwamem2_index/bwamem2/genome.fa.pac",
+                "bwamem2_mem",
+                "bwamem2_mem/SAMPLE_SINGLE_END_1.bam",
                 "fastqc",
                 "fastqc/SAMPLE_SINGLE_END_1_fastqc.html",
                 "fastqc/SAMPLE_SINGLE_END_1_fastqc.zip",
@@ -77,6 +93,34 @@
                 "fastqscreen/SAMPLE_SINGLE_END_1_screen.html",
                 "fastqscreen/SAMPLE_SINGLE_END_1_screen.png",
                 "fastqscreen/SAMPLE_SINGLE_END_1_screen.txt",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_plots",
+                "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "seqfu_stats",
@@ -84,8 +128,28 @@
                 "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu_mqc.txt"
             ],
             [
+                "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
+                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
+                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
+                "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
+                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
+                "SAMPLE_SINGLE_END_1.bam:md5,ed3f6acd94560448218a288623c810e6",
                 "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
                 "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
+                "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
+                "fastqc-status-check-heatmap.txt:md5,8f98652c377741c974e485652a19f37f",
+                "fastqc_overrepresented_sequences_plot.txt:md5,cdc7479933cae03e0043ae794f81c304",
+                "fastqc_per_base_n_content_plot.txt:md5,dd8d6976dc5ea8cf67d9fa2c3be9e24b",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,5f9a98d3068aab17f26731ae0615f41a",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,1de1333bb959189dcf8230706f60dbfc",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,62f140bfa52d462c9c499dfdabc35476",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,5fda43eb9b7c60cf6b4348f734a94b26",
+                "fastqc_sequence_counts_plot.txt:md5,00cd6842465f7aa9ae75434e175946a6",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,c3befe0812d2f1c23d5e75e6fccf0622",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607",
+                "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
+                "multiqc_seqfu.txt:md5,8e6989a2392f599a09a5c3edf8119702",
                 "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,f65c868e562291647d539090698ba5eb",
                 "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
             ]
@@ -94,7 +158,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.7"
         },
-        "timestamp": "2025-09-18T16:56:47.640388"
+        "timestamp": "2025-09-19T13:43:47.141095"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
diff --git a/tests/PromethION.main.nf.test.config b/tests/PromethION.main.nf.test.config
index 429de63f..2054c11e 100644
--- a/tests/PromethION.main.nf.test.config
+++ b/tests/PromethION.main.nf.test.config
@@ -4,5 +4,5 @@ includeConfig 'nextflow.config'
 // Load the correct samplesheet for that test
 params {
     input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/PromethION/samplesheet.csv'
-    genome = 'GRCh38'
+    genome = 'EB1'
 }
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index 541fbde2..fe9927be 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -1,14 +1,14 @@
 {
     "PromethION data test": {
         "content": [
-            4,
+            3,
             {
-                "BWAMEM2_INDEX": {
-                    "bwamem2": "2.2.1"
-                },
                 "FASTQC": {
                     "fastqc": "0.12.1"
                 },
+                "FASTQSCREEN_FASTQSCREEN": {
+                    "fastqscreen": "0.16.0"
+                },
                 "SEQFU_STATS": {
                     "seqfu": "1.20.3"
                 },
@@ -17,13 +17,6 @@
                 }
             },
             [
-                "bwamem2_index",
-                "bwamem2_index/bwamem2",
-                "bwamem2_index/bwamem2/genome.fa.0123",
-                "bwamem2_index/bwamem2/genome.fa.amb",
-                "bwamem2_index/bwamem2/genome.fa.ann",
-                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
-                "bwamem2_index/bwamem2/genome.fa.pac",
                 "fastqc",
                 "fastqc/hg001_1_fastqc.html",
                 "fastqc/hg001_1_fastqc.zip",
@@ -38,11 +31,6 @@
                 "seqfu_stats/hg001_1_seqfu_mqc.txt"
             ],
             [
-                "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
-                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
-                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
-                "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
-                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
                 "hg001_1_screen.png:md5,b9c58e388f18ad11f4c2e29e9b573a5e",
                 "hg001_1_screen.txt:md5,8e53ea043d658a130f4b8ca455e2ba9b",
                 "hg001_1_seqfu.tsv:md5,b133752c897afbb4d8721b911fa117d4",
@@ -53,6 +41,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.7"
         },
-        "timestamp": "2025-09-19T10:26:18.425518"
+        "timestamp": "2025-09-19T13:38:58.507316"
     }
 }
\ No newline at end of file

From de2674dd90618a0bfe317c3ebf2e9c9111dedd79 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@n159-p91.eduroam.kth.se>
Date: Mon, 22 Sep 2025 15:43:10 +0200
Subject: [PATCH 244/530] Promethion snapshot updated

---
 tests/NovaSeq6000.main.nf.test.snap  | 12 +++----
 tests/PromethION.main.nf.test.config |  3 ++
 tests/PromethION.main.nf.test.snap   | 50 ++++++++++++++++++++++++++--
 tests/nextflow.config                | 23 +++++++++++++
 4 files changed, 80 insertions(+), 8 deletions(-)

diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index 2952abc2..8e869660 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -226,11 +226,11 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "Sample1_1.bam:md5,39c3c91eedd90307315acec7aa0b9a35",
-                "Sample23_3.bam:md5,3d536a6680470138eb361eed198a8efd",
-                "SampleA_2.bam:md5,ad691a2590eed5bbc56a56dd24493e4e",
-                "Undetermined_5.bam:md5,06077f7de3641b4b86e08f6a9cdb5a97",
-                "sampletest_4.bam:md5,7dcb21eb9fec77b862af33e692678dbd",
+                "Sample1_1.bam:md5,4faa63a4f5727030602c3a0a44adc49e",
+                "Sample23_3.bam:md5,cdb70dd996290e8d78c95fac6d8593ed",
+                "SampleA_2.bam:md5,f43f5370d028c3bca91554a330c46f1d",
+                "Undetermined_5.bam:md5,a96a70aee79f991514a516c3f6f65230",
+                "sampletest_4.bam:md5,159d33f5a6bea2f97c9444e6149fc280",
                 "Sample1_1_screen.png:md5,562256290643b51e4374c2225a15f463",
                 "Sample1_1_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
                 "Sample23_3_screen.png:md5,6bb2caf67b9b2ed25d3d5f32c343e9ab",
@@ -332,6 +332,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.7"
         },
-        "timestamp": "2025-09-18T11:15:39.145326"
+        "timestamp": "2025-09-22T15:32:30.048406"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.config b/tests/PromethION.main.nf.test.config
index 2054c11e..987d19d3 100644
--- a/tests/PromethION.main.nf.test.config
+++ b/tests/PromethION.main.nf.test.config
@@ -5,4 +5,7 @@ includeConfig 'nextflow.config'
 params {
     input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/PromethION/samplesheet.csv'
     genome = 'EB1'
+    skip_tools = 'bwamem2_index,bwamem2_mem'
 }
+
+
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index fe9927be..fe745bcb 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "PromethION data test": {
         "content": [
-            3,
+            4,
             {
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -24,6 +24,36 @@
                 "fastqscreen/hg001_1_screen.html",
                 "fastqscreen/hg001_1_screen.png",
                 "fastqscreen/hg001_1_screen.txt",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/global_report/multiqc_data/fastqc_adapter_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_plots",
+                "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "seqfu_stats",
@@ -33,6 +63,22 @@
             [
                 "hg001_1_screen.png:md5,b9c58e388f18ad11f4c2e29e9b573a5e",
                 "hg001_1_screen.txt:md5,8e53ea043d658a130f4b8ca455e2ba9b",
+                "fastq_screen_plot.txt:md5,3023b86477fecf6d46d8fc60d82cc53a",
+                "fastqc-status-check-heatmap.txt:md5,825668e94de27356f0a112beb758e416",
+                "fastqc_adapter_content_plot.txt:md5,1fa991080c20755e5e729a5eeab960e5",
+                "fastqc_overrepresented_sequences_plot.txt:md5,e810a3d3eba0ba83b122763505f511a7",
+                "fastqc_per_base_n_content_plot.txt:md5,cbdb64298ff839665e8c8c8e89896e87",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,4962950bc3ce77169ac510d64cb769c6",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,e62273533304be59dab5f13afef93b3e",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,3d49290a15406cb5dac1460c02729f0f",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,7cc10d1bc92ca09431a506c38d911228",
+                "fastqc_sequence_counts_plot.txt:md5,0425d7298c24df6158d5bf7aca1d4190",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,9111d942c7eed5af0e9ccb8c42db8505",
+                "fastqc_sequence_length_distribution_plot.txt:md5,04adfcd0125ebcc3e3bb631f1956c812",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,7c5d711e27c53d13c81644a1f2468dba",
+                "multiqc_fastqc.txt:md5,1a4b472e13cadc770832b0e20d1de7b0",
+                "multiqc_seqfu.txt:md5,9595d608ff5709f2bdec8cb1016416c0",
                 "hg001_1_seqfu.tsv:md5,b133752c897afbb4d8721b911fa117d4",
                 "hg001_1_seqfu_mqc.txt:md5,6285f582c03faa70e8dcb3503e5db728"
             ]
@@ -41,6 +87,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.7"
         },
-        "timestamp": "2025-09-19T13:38:58.507316"
+        "timestamp": "2025-09-22T15:42:33.286856"
     }
 }
\ No newline at end of file
diff --git a/tests/nextflow.config b/tests/nextflow.config
index d5d44a72..0dd0e464 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -13,3 +13,26 @@ params {
 
 }
 
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+    withLabel: 'process_high' {
+        cpus = 4
+        memory = '15.GB'
+    }
+    withLabel: 'process_medium' {
+        cpus = 2
+        memory = '7.GB'
+    }
+    withLabel: 'process_low' {
+        cpus = 1
+        memory = '3.GB'
+    }
+    withLabel: 'process_single' {
+        cpus = 1
+        memory = '3.GB'
+    }
+}

From 1c808c24392097a4d1b5f54f9f4652740d938d4f Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@n159-p91.eduroam.kth.se>
Date: Mon, 22 Sep 2025 15:44:49 +0200
Subject: [PATCH 245/530] minor change to process_high

---
 modules/nf-core/bwamem2/mem/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf
index ad510447..eab662a8 100644
--- a/modules/nf-core/bwamem2/mem/main.nf
+++ b/modules/nf-core/bwamem2/mem/main.nf
@@ -1,6 +1,6 @@
 process BWAMEM2_MEM {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_high'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

From 62031672d5389aee7da8a94cf036ff8bfcc36444 Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Wed, 24 Sep 2025 10:56:48 +0000
Subject: [PATCH 246/530] Updated snapshots

---
 conf/test.config                          |  33 ++-
 tests/.nftignore                          |   4 +-
 tests/MiSeq.main.nf.test.snap             |  72 +++++-
 tests/MiSeq_PairedEnd.main.nf.test.config |  24 ++
 tests/MiSeq_PairedEnd.main.nf.test.snap   |  92 +++++++-
 tests/NovaSeq6000.main.nf.test.snap       | 254 +++++++++++++++++++++-
 tests/PromethION.main.nf.test.snap        |  55 ++++-
 tests/nextflow.config                     |   1 +
 8 files changed, 503 insertions(+), 32 deletions(-)

diff --git a/conf/test.config b/conf/test.config
index 0ebc405a..c6f4934c 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -10,14 +10,6 @@
 ----------------------------------------------------------------------------------------
 */
 
-process {
-    resourceLimits = [
-        cpus: 4,
-        memory: '15.GB',
-        time: '1.h'
-    ]
-}
-
 params {
     config_profile_name        = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
@@ -31,3 +23,28 @@ params {
     // Genome references
     genome = 'R64-1-1'
 }
+
+
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+    withLabel: 'process_high' {
+        cpus = 4
+        memory = '15.GB'
+    }
+    withLabel: 'process_medium' {
+        cpus = 2
+        memory = '7.GB'
+    }
+    withLabel: 'process_low' {
+        cpus = 1
+        memory = '3.GB'
+    }
+    withLabel: 'process_single' {
+        cpus = 1
+        memory = '3.GB'
+    }
+}
diff --git a/tests/.nftignore b/tests/.nftignore
index ded3eac7..46980e70 100644
--- a/tests/.nftignore
+++ b/tests/.nftignore
@@ -1,4 +1,3 @@
-.DS_Store
 multiqc/{global_report,group_reports/*}/multiqc_data/multiqc.log
 multiqc/{global_report,group_reports/*}/multiqc_data/multiqc_data.json
 multiqc/{global_report,group_reports/*}/multiqc_data/multiqc_general_stats.txt
@@ -9,4 +8,5 @@ multiqc/{global_report,group_reports/*}/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,p
 multiqc/{global_report,group_reports/*}/multiqc_report.html
 pipeline_info/*.{html,json,txt,yml}
 fastqscreen/*_screen.html
-fastqc/*_fastqc.{html,zip}
+fastqc/*_fastqc.html
+fastqc/*_fastqc.zip
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index eb8b541f..bc54480c 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -42,15 +42,15 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "SAMPLE_SINGLE_END_1.bam:md5,ed3f6acd94560448218a288623c810e6",
+                "SAMPLE_SINGLE_END_1.bam:md5,79744f146752fd486b09604be721cc85",
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-18T11:05:17.619991"
+        "timestamp": "2025-09-24T10:43:56.070328995"
     },
     "MiSeq data test (single end reads)": {
         "content": [
@@ -118,8 +118,53 @@
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
@@ -133,7 +178,7 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "SAMPLE_SINGLE_END_1.bam:md5,ed3f6acd94560448218a288623c810e6",
+                "SAMPLE_SINGLE_END_1.bam:md5,79744f146752fd486b09604be721cc85",
                 "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
                 "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
                 "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
@@ -156,9 +201,9 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-19T13:43:47.141095"
+        "timestamp": "2025-09-24T10:42:44.511920997"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
@@ -208,8 +253,17 @@
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
@@ -223,7 +277,7 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "SAMPLE_SINGLE_END_1.bam:md5,ed3f6acd94560448218a288623c810e6",
+                "SAMPLE_SINGLE_END_1.bam:md5,79744f146752fd486b09604be721cc85",
                 "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
                 "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
                 "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
@@ -236,8 +290,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-18T11:04:10.524764"
+        "timestamp": "2025-09-24T10:43:19.776520207"
     }
 }
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.config b/tests/MiSeq_PairedEnd.main.nf.test.config
index 279ac0e4..35fe5d6d 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.config
+++ b/tests/MiSeq_PairedEnd.main.nf.test.config
@@ -5,3 +5,27 @@ includeConfig 'nextflow.config'
 params {
     input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/Miseq_PairedEnd/samplesheet.csv'
 }
+
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+    withLabel: 'process_high' {
+        cpus = 4
+        memory = '15.GB'
+    }
+    withLabel: 'process_medium' {
+        cpus = 2
+        memory = '7.GB'
+    }
+    withLabel: 'process_low' {
+        cpus = 1
+        memory = '3.GB'
+    }
+    withLabel: 'process_single' {
+        cpus = 1
+        memory = '3.GB'
+    }
+}
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index 213695a1..047814e4 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -80,8 +80,50 @@
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_adapter_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "multiqc/group_reports",
                 "multiqc/group_reports/Bpacificus",
@@ -107,8 +149,50 @@
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_plots",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_adapter_content_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/general_stats_table.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
@@ -124,8 +208,8 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "SAMPLE_PAIRED_END_1_1.bam:md5,00431260e6fb11e87b1c8e276194ab5b",
-                "SAMPLE_PAIRED_END_2_2.bam:md5,9bb10554f5f7ac3187dd30e44f59bbd0",
+                "SAMPLE_PAIRED_END_1_1.bam:md5,ced6a17fb3dee760c2606860e1177071",
+                "SAMPLE_PAIRED_END_2_2.bam:md5,15ada2a4f4a6cf2978aeaeb64a525197",
                 "SAMPLE_PAIRED_END_1_1_1_screen.png:md5,f52ddd0e65f23f68dd8d58d5453417db",
                 "SAMPLE_PAIRED_END_1_1_1_screen.txt:md5,921b08eeb461a2aa1bd42bba53900f70",
                 "SAMPLE_PAIRED_END_1_1_2_screen.png:md5,908f4fceea8aa546106efdaa7ca78f7d",
@@ -170,8 +254,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-18T11:08:35.522492"
+        "timestamp": "2025-09-24T10:41:23.851991495"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index 8e869660..a1fd0301 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -90,8 +90,56 @@
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "multiqc/group_reports",
                 "multiqc/group_reports/group1",
@@ -119,8 +167,56 @@
                 "multiqc/group_reports/group1/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/group1/multiqc_plots",
                 "multiqc/group_reports/group1/multiqc_plots/pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/general_stats_table.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/group1/multiqc_plots/svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/group1/multiqc_report.html",
                 "multiqc/group_reports/group2",
                 "multiqc/group_reports/group2/multiqc_data",
@@ -147,8 +243,56 @@
                 "multiqc/group_reports/group2/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/group2/multiqc_plots",
                 "multiqc/group_reports/group2/multiqc_plots/pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/general_stats_table.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/group2/multiqc_plots/svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/group2/multiqc_report.html",
                 "multiqc/group_reports/lane1",
                 "multiqc/group_reports/lane1/multiqc_data",
@@ -175,8 +319,56 @@
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/lane1/multiqc_plots",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/general_stats_table.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/lane1/multiqc_plots/svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/lane1/multiqc_report.html",
                 "multiqc/group_reports/test",
                 "multiqc/group_reports/test/multiqc_data",
@@ -203,8 +395,56 @@
                 "multiqc/group_reports/test/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/test/multiqc_plots",
                 "multiqc/group_reports/test/multiqc_plots/pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/test/multiqc_plots/png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/test/multiqc_plots/png/general_stats_table.png",
+                "multiqc/group_reports/test/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/test/multiqc_plots/svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/test/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
@@ -226,11 +466,11 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "Sample1_1.bam:md5,4faa63a4f5727030602c3a0a44adc49e",
-                "Sample23_3.bam:md5,cdb70dd996290e8d78c95fac6d8593ed",
-                "SampleA_2.bam:md5,f43f5370d028c3bca91554a330c46f1d",
-                "Undetermined_5.bam:md5,a96a70aee79f991514a516c3f6f65230",
-                "sampletest_4.bam:md5,159d33f5a6bea2f97c9444e6149fc280",
+                "Sample1_1.bam:md5,1efd4f55b836f732ccc3600697ebb4c3",
+                "Sample23_3.bam:md5,a13dd5db6ef2639f2227b6d3f9c92386",
+                "SampleA_2.bam:md5,c5082847134e5a1c0c869b2378637754",
+                "Undetermined_5.bam:md5,3453bb37bc50105e79f7bba23cbab9c5",
+                "sampletest_4.bam:md5,72532967a589a0a63e93ce86cf79f101",
                 "Sample1_1_screen.png:md5,562256290643b51e4374c2225a15f463",
                 "Sample1_1_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
                 "Sample23_3_screen.png:md5,6bb2caf67b9b2ed25d3d5f32c343e9ab",
@@ -330,8 +570,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-22T15:32:30.048406"
+        "timestamp": "2025-09-24T10:46:41.927291661"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index fe745bcb..daee5f1b 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -51,8 +51,59 @@
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_adapter_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
@@ -85,8 +136,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-22T15:42:33.286856"
+        "timestamp": "2025-09-24T09:50:22.026441122"
     }
 }
\ No newline at end of file
diff --git a/tests/nextflow.config b/tests/nextflow.config
index 0dd0e464..e0ff36c8 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -13,6 +13,7 @@ params {
 
 }
 
+
 process {
     resourceLimits = [
         cpus: 4,

From 78f9fd8d4a836e0f07c8dab13b2cc03a109a574b Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@n161-p152.eduroam.kth.se>
Date: Wed, 1 Oct 2025 10:33:43 +0200
Subject: [PATCH 247/530] Added Picard_collectmultiplemetrics module

---
 conf/modules.config                           |  26 +
 modules.json                                  |  15 +
 .../collectmultiplemetrics/environment.yml    |   8 +
 .../picard/collectmultiplemetrics/main.nf     |  67 +++
 .../picard/collectmultiplemetrics/meta.yml    |  87 +++
 .../collectmultiplemetrics/tests/main.nf.test | 112 ++++
 .../tests/main.nf.test.snap                   |  80 +++
 .../nf-core/samtools/faidx/environment.yml    |  10 +
 modules/nf-core/samtools/faidx/main.nf        |  61 ++
 modules/nf-core/samtools/faidx/meta.yml       | 102 ++++
 .../nf-core/samtools/faidx/tests/main.nf.test | 219 +++++++
 .../samtools/faidx/tests/main.nf.test.snap    | 543 ++++++++++++++++++
 .../samtools/faidx/tests/nextflow.config      |   7 +
 .../samtools/faidx/tests/nextflow2.config     |   6 +
 .../nf-core/samtools/index/environment.yml    |  10 +
 modules/nf-core/samtools/index/main.nf        |  49 ++
 modules/nf-core/samtools/index/meta.yml       |  77 +++
 .../samtools/index/tests/csi.nextflow.config  |   7 +
 .../nf-core/samtools/index/tests/main.nf.test | 140 +++++
 .../samtools/index/tests/main.nf.test.snap    | 250 ++++++++
 nextflow_schema.json                          |   2 +-
 tests/MiSeq.main.nf.test                      |   2 +-
 workflows/seqinspector.nf                     |  67 ++-
 23 files changed, 1942 insertions(+), 5 deletions(-)
 create mode 100644 modules/nf-core/picard/collectmultiplemetrics/environment.yml
 create mode 100644 modules/nf-core/picard/collectmultiplemetrics/main.nf
 create mode 100644 modules/nf-core/picard/collectmultiplemetrics/meta.yml
 create mode 100644 modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test
 create mode 100644 modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/samtools/faidx/environment.yml
 create mode 100644 modules/nf-core/samtools/faidx/main.nf
 create mode 100644 modules/nf-core/samtools/faidx/meta.yml
 create mode 100644 modules/nf-core/samtools/faidx/tests/main.nf.test
 create mode 100644 modules/nf-core/samtools/faidx/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/samtools/faidx/tests/nextflow.config
 create mode 100644 modules/nf-core/samtools/faidx/tests/nextflow2.config
 create mode 100644 modules/nf-core/samtools/index/environment.yml
 create mode 100644 modules/nf-core/samtools/index/main.nf
 create mode 100644 modules/nf-core/samtools/index/meta.yml
 create mode 100644 modules/nf-core/samtools/index/tests/csi.nextflow.config
 create mode 100644 modules/nf-core/samtools/index/tests/main.nf.test
 create mode 100644 modules/nf-core/samtools/index/tests/main.nf.test.snap

diff --git a/conf/modules.config b/conf/modules.config
index 22cd4d8a..c4335e4a 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -51,6 +51,32 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
+    withName: 'PICARD_COLLECTMULTIPLEMETRICS' {
+        ext.args   =  ''
+        publishDir = [
+            path: { "${params.outdir}/picard_collectmultiplemetrics" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: 'SAMTOOLS_FAIIDX' {
+        ext.args   = ''
+        publishDir = [
+            path: { "${params.outdir}/samtools_faidx" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: 'SAMTOOLS_INDEX' {
+        ext.args   = ''
+        publishDir = [
+            path: { "${params.outdir}/samtools_index" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
 
     withName: 'MULTIQC_GLOBAL' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
diff --git a/modules.json b/modules.json
index e3b68325..e62fa390 100644
--- a/modules.json
+++ b/modules.json
@@ -42,6 +42,21 @@
                         "git_sha": "7b50cb7be890e4b28cffb82e438cc6a8d7805d3f",
                         "installed_by": ["modules"]
                     },
+                    "picard/collectmultiplemetrics": {
+                        "branch": "master",
+                        "git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255",
+                        "installed_by": ["modules"]
+                    },
+                    "samtools/faidx": {
+                        "branch": "master",
+                        "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
+                        "installed_by": ["modules"]
+                    },
+                    "samtools/index": {
+                        "branch": "master",
+                        "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
+                        "installed_by": ["modules"]
+                    },
                     "seqfu/stats": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
diff --git a/modules/nf-core/picard/collectmultiplemetrics/environment.yml b/modules/nf-core/picard/collectmultiplemetrics/environment.yml
new file mode 100644
index 00000000..b4ac4fe0
--- /dev/null
+++ b/modules/nf-core/picard/collectmultiplemetrics/environment.yml
@@ -0,0 +1,8 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  # renovate: datasource=conda depName=bioconda/picard
+  - bioconda::picard=3.4.0
diff --git a/modules/nf-core/picard/collectmultiplemetrics/main.nf b/modules/nf-core/picard/collectmultiplemetrics/main.nf
new file mode 100644
index 00000000..eb4f6c60
--- /dev/null
+++ b/modules/nf-core/picard/collectmultiplemetrics/main.nf
@@ -0,0 +1,67 @@
+process PICARD_COLLECTMULTIPLEMETRICS {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' :
+        'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }"
+
+    input:
+    tuple val(meta) , path(bam), path(bai)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fai)
+
+    output:
+    tuple val(meta), path("*_metrics"), emit: metrics
+    tuple val(meta), path("*.pdf")    , emit: pdf, optional: true
+    path  "versions.yml"              , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : ""
+    def avail_mem = 3072
+    if (!task.memory) {
+        log.info '[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = (task.memory.mega*0.8).intValue()
+    }
+    """
+    picard \\
+        -Xmx${avail_mem}M \\
+        CollectMultipleMetrics \\
+        $args \\
+        --INPUT $bam \\
+        --OUTPUT ${prefix}.CollectMultipleMetrics \\
+        $reference
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        picard: \$(picard CollectMultipleMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:)
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.CollectMultipleMetrics.alignment_summary_metrics
+    touch ${prefix}.CollectMultipleMetrics.insert_size_metrics
+    touch ${prefix}.CollectMultipleMetrics.quality_distribution.pdf
+    touch ${prefix}.CollectMultipleMetrics.base_distribution_by_cycle_metrics
+    touch ${prefix}.CollectMultipleMetrics.quality_by_cycle_metrics
+    touch ${prefix}.CollectMultipleMetrics.read_length_histogram.pdf
+    touch ${prefix}.CollectMultipleMetrics.base_distribution_by_cycle.pdf
+    touch ${prefix}.CollectMultipleMetrics.quality_by_cycle.pdf
+    touch ${prefix}.CollectMultipleMetrics.insert_size_histogram.pdf
+    touch ${prefix}.CollectMultipleMetrics.quality_distribution_metrics
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        picard: \$(echo \$(picard CollectMultipleMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/picard/collectmultiplemetrics/meta.yml b/modules/nf-core/picard/collectmultiplemetrics/meta.yml
new file mode 100644
index 00000000..3f0bf610
--- /dev/null
+++ b/modules/nf-core/picard/collectmultiplemetrics/meta.yml
@@ -0,0 +1,87 @@
+name: picard_collectmultiplemetrics
+description: Collect multiple metrics from a BAM file
+keywords:
+  - alignment
+  - metrics
+  - statistics
+  - insert
+  - quality
+  - bam
+tools:
+  - picard:
+      description: |
+        A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)
+        data and formats such as SAM/BAM/CRAM and VCF.
+      homepage: https://broadinstitute.github.io/picard/
+      documentation: https://broadinstitute.github.io/picard/
+      licence: ["MIT"]
+      identifier: biotools:picard_tools
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: SAM/BAM/CRAM file
+        pattern: "*.{sam,bam,cram}"
+        ontologies: []
+    - bai:
+        type: file
+        description: Optional SAM/BAM/CRAM file index
+        pattern: "*.{sai,bai,crai}"
+        ontologies: []
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'genome']
+    - fasta:
+        type: file
+        description: Genome fasta file
+        ontologies: []
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'genome']
+    - fai:
+        type: file
+        description: Index of FASTA file. Only needed when fasta is supplied.
+        pattern: "*.fai"
+        ontologies: []
+output:
+  metrics:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*_metrics":
+          type: file
+          description: Alignment metrics files generated by picard
+          pattern: "*_{metrics}"
+          ontologies: []
+  pdf:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.pdf":
+          type: file
+          description: PDF plots of metrics
+          pattern: "*.{pdf}"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
+authors:
+  - "@drpatelh"
+maintainers:
+  - "@drpatelh"
diff --git a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test
new file mode 100644
index 00000000..5b67774f
--- /dev/null
+++ b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test
@@ -0,0 +1,112 @@
+
+nextflow_process {
+
+    name "Test Process PICARD_COLLECTMULTIPLEMETRICS"
+    script "../main.nf"
+    process "PICARD_COLLECTMULTIPLEMETRICS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "picard"
+    tag "picard/collectmultiplemetrics"
+
+    test("test-picard-collectmultiplemetrics") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+				]
+				input[1] = [
+				    [id:'genome'],
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+				]
+				input[2] = [[id:'genome'],[]]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.metrics[0][1].collect { file(it).name }.toSorted(),
+                    process.out.pdf[0][1].collect { file(it).name }.toSorted(),
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("test-picard-collectmultiplemetrics-nofasta") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+				]
+				input[1] = [[id:'genome'],[]]
+                input[2] = [[id:'genome'],[]]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.metrics[0][1].collect { file(it).name }.toSorted(),
+                    process.out.pdf[0][1].collect { file(it).name }.toSorted(),
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("test-picard-collectmultiplemetrics-cram") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				[ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+				]
+				input[1] = [
+				    [id:'genome'],
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+				]
+				input[2] = [
+				    [id:'genome'],
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.metrics[0][1].collect { file(it).name }.toSorted(),
+                    process.out.pdf[0][1].collect { file(it).name }.toSorted(),
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap
new file mode 100644
index 00000000..5a1de114
--- /dev/null
+++ b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap
@@ -0,0 +1,80 @@
+{
+    "test-picard-collectmultiplemetrics": {
+        "content": [
+            [
+                "test.CollectMultipleMetrics.alignment_summary_metrics",
+                "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "test.CollectMultipleMetrics.insert_size_metrics",
+                "test.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "test.CollectMultipleMetrics.quality_distribution_metrics"
+            ],
+            [
+                "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "test.CollectMultipleMetrics.insert_size_histogram.pdf",
+                "test.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "test.CollectMultipleMetrics.quality_distribution.pdf",
+                "test.CollectMultipleMetrics.read_length_histogram.pdf"
+            ],
+            [
+                "versions.yml:md5,aca7ca0dc0012ee97698236828ba242a"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.7"
+        },
+        "timestamp": "2025-09-15T10:41:26.126816186"
+    },
+    "test-picard-collectmultiplemetrics-cram": {
+        "content": [
+            [
+                "test.CollectMultipleMetrics.alignment_summary_metrics",
+                "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "test.CollectMultipleMetrics.insert_size_metrics",
+                "test.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "test.CollectMultipleMetrics.quality_distribution_metrics"
+            ],
+            [
+                "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "test.CollectMultipleMetrics.insert_size_histogram.pdf",
+                "test.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "test.CollectMultipleMetrics.quality_distribution.pdf",
+                "test.CollectMultipleMetrics.read_length_histogram.pdf"
+            ],
+            [
+                "versions.yml:md5,aca7ca0dc0012ee97698236828ba242a"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.7"
+        },
+        "timestamp": "2025-09-15T10:41:50.933556225"
+    },
+    "test-picard-collectmultiplemetrics-nofasta": {
+        "content": [
+            [
+                "test.CollectMultipleMetrics.alignment_summary_metrics",
+                "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "test.CollectMultipleMetrics.insert_size_metrics",
+                "test.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "test.CollectMultipleMetrics.quality_distribution_metrics"
+            ],
+            [
+                "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "test.CollectMultipleMetrics.insert_size_histogram.pdf",
+                "test.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "test.CollectMultipleMetrics.quality_distribution.pdf",
+                "test.CollectMultipleMetrics.read_length_histogram.pdf"
+            ],
+            [
+                "versions.yml:md5,aca7ca0dc0012ee97698236828ba242a"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.7"
+        },
+        "timestamp": "2025-09-15T10:41:38.213084333"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml
new file mode 100644
index 00000000..89e12a64
--- /dev/null
+++ b/modules/nf-core/samtools/faidx/environment.yml
@@ -0,0 +1,10 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  # renovate: datasource=conda depName=bioconda/htslib
+  - bioconda::htslib=1.22.1
+  # renovate: datasource=conda depName=bioconda/samtools
+  - bioconda::samtools=1.22.1
diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf
new file mode 100644
index 00000000..ed2d70a6
--- /dev/null
+++ b/modules/nf-core/samtools/faidx/main.nf
@@ -0,0 +1,61 @@
+process SAMTOOLS_FAIDX {
+    tag "$fasta"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/samtools:1.22.1--h96c455f_0' :
+        'biocontainers/samtools:1.22.1--h96c455f_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+    tuple val(meta2), path(fai)
+    val get_sizes
+
+    output:
+    tuple val(meta), path ("*.{fa,fasta}") , emit: fa, optional: true
+    tuple val(meta), path ("*.sizes")      , emit: sizes, optional: true
+    tuple val(meta), path ("*.fai")        , emit: fai, optional: true
+    tuple val(meta), path ("*.gzi")        , emit: gzi, optional: true
+    path "versions.yml"                    , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def get_sizes_command = get_sizes ? "cut -f 1,2 ${fasta}.fai > ${fasta}.sizes" : ''
+    """
+    samtools \\
+        faidx \\
+        $fasta \\
+        $args
+
+    ${get_sizes_command}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def match = (task.ext.args =~ /-o(?:utput)?\s(.*)\s?/).findAll()
+    def fastacmd = match[0] ? "touch ${match[0][1]}" : ''
+    def get_sizes_command = get_sizes ? "touch ${fasta}.sizes" : ''
+    """
+    ${fastacmd}
+    touch ${fasta}.fai
+    if [[ "${fasta.extension}" == "gz" ]]; then
+        touch ${fasta}.gzi
+    fi
+
+    ${get_sizes_command}
+
+    cat <<-END_VERSIONS > versions.yml
+
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml
new file mode 100644
index 00000000..b7a2e0c1
--- /dev/null
+++ b/modules/nf-core/samtools/faidx/meta.yml
@@ -0,0 +1,102 @@
+name: samtools_faidx
+description: Index FASTA file, and optionally generate a file of chromosome sizes
+keywords:
+  - index
+  - fasta
+  - faidx
+  - chromosome
+tools:
+  - samtools:
+      description: |
+        SAMtools is a set of utilities for interacting with and post-processing
+        short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
+        These files are generated as output by short read aligners like BWA.
+      homepage: http://www.htslib.org/
+      documentation: http://www.htslib.org/doc/samtools.html
+      doi: 10.1093/bioinformatics/btp352
+      licence: ["MIT"]
+      identifier: biotools:samtools
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'test' ]
+    - fasta:
+        type: file
+        description: FASTA file
+        pattern: "*.{fa,fasta}"
+        ontologies: []
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'test' ]
+    - fai:
+        type: file
+        description: FASTA index file
+        pattern: "*.{fai}"
+        ontologies: []
+  - get_sizes:
+      type: boolean
+      description: use cut to get the sizes of the index (true) or not (false)
+
+output:
+  fa:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.{fa,fasta}":
+          type: file
+          description: FASTA file
+          pattern: "*.{fa}"
+          ontologies: []
+  sizes:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.sizes":
+          type: file
+          description: File containing chromosome lengths
+          pattern: "*.{sizes}"
+          ontologies: []
+  fai:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.fai":
+          type: file
+          description: FASTA index file
+          pattern: "*.{fai}"
+          ontologies: []
+  gzi:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.gzi":
+          type: file
+          description: Optional gzip index file for compressed inputs
+          pattern: "*.gzi"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
+authors:
+  - "@drpatelh"
+  - "@ewels"
+  - "@phue"
+maintainers:
+  - "@maxulysse"
+  - "@phue"
diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test b/modules/nf-core/samtools/faidx/tests/main.nf.test
new file mode 100644
index 00000000..64219b7d
--- /dev/null
+++ b/modules/nf-core/samtools/faidx/tests/main.nf.test
@@ -0,0 +1,219 @@
+nextflow_process {
+
+    name "Test Process SAMTOOLS_FAIDX"
+    script "../main.nf"
+    process "SAMTOOLS_FAIDX"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "samtools"
+    tag "samtools/faidx"
+
+    test("test_samtools_faidx") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
+                input[1] = [[],[]]
+                input[2] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_samtools_faidx_bgzip") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)]
+                input[1] = [[],[]]
+                input[2] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_samtools_faidx_fasta") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
+                input[1] = [ [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ]
+                input[2] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_samtools_faidx_stub_fasta") {
+
+        config "./nextflow2.config"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
+                input[1] = [ [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ]
+                input[2] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_samtools_faidx_stub_fai") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
+                input[1] = [[],[]]
+                input[2] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_samtools_faidx_get_sizes") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[1] = [[],[]]
+                input[2] = true
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_samtools_faidx_get_sizes_bgzip") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)
+                ])
+                input[1] = [[],[]]
+                input[2] = true
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_samtools_faidx_get_sizes - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[1] = [[],[]]
+                input[2] = true
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_samtools_faidx_get_sizes_bgzip - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)
+                ])
+                input[1] = [[],[]]
+                input[2] = true
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
\ No newline at end of file
diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap
new file mode 100644
index 00000000..3be7b824
--- /dev/null
+++ b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap
@@ -0,0 +1,543 @@
+{
+    "test_samtools_faidx": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68"
+                ],
+                "fa": [
+                    
+                ],
+                "fai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "gzi": [
+                    
+                ],
+                "sizes": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-10T13:09:38.874686"
+    },
+    "test_samtools_faidx_get_sizes_bgzip - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.fai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.gzi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,8e7d141eb8c2944042dfb5e942bffe08"
+                ],
+                "fa": [
+                    
+                ],
+                "fai": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.fai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "gzi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.gzi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "sizes": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8e7d141eb8c2944042dfb5e942bffe08"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-10T13:10:10.958397"
+    },
+    "test_samtools_faidx_get_sizes": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.sizes:md5,a57c401f27ae5133823fb09fb21c8a3c"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68"
+                ],
+                "fa": [
+                    
+                ],
+                "fai": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "gzi": [
+                    
+                ],
+                "sizes": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.sizes:md5,a57c401f27ae5133823fb09fb21c8a3c"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-10T13:09:59.237249"
+    },
+    "test_samtools_faidx_bgzip": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68"
+                ],
+                "fa": [
+                    
+                ],
+                "fai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "gzi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474"
+                    ]
+                ],
+                "sizes": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-10T13:09:42.949204"
+    },
+    "test_samtools_faidx_fasta": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "extract.fa:md5,6a0774a0ad937ba0bfd2ac7457d90f36"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68"
+                ],
+                "fa": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "extract.fa:md5,6a0774a0ad937ba0bfd2ac7457d90f36"
+                    ]
+                ],
+                "fai": [
+                    
+                ],
+                "gzi": [
+                    
+                ],
+                "sizes": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-10T13:09:46.914038"
+    },
+    "test_samtools_faidx_get_sizes - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    "versions.yml:md5,8e7d141eb8c2944042dfb5e942bffe08"
+                ],
+                "fa": [
+                    
+                ],
+                "fai": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "gzi": [
+                    
+                ],
+                "sizes": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8e7d141eb8c2944042dfb5e942bffe08"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-10T13:10:06.961912"
+    },
+    "test_samtools_faidx_stub_fasta": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "extract.fa:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68"
+                ],
+                "fa": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "extract.fa:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "fai": [
+                    
+                ],
+                "gzi": [
+                    
+                ],
+                "sizes": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-10T13:09:51.226016"
+    },
+    "test_samtools_faidx_stub_fai": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68"
+                ],
+                "fa": [
+                    
+                ],
+                "fai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "gzi": [
+                    
+                ],
+                "sizes": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-10T13:09:55.423005"
+    },
+    "test_samtools_faidx_get_sizes_bgzip": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.sizes:md5,a57c401f27ae5133823fb09fb21c8a3c"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68"
+                ],
+                "fa": [
+                    
+                ],
+                "fai": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "gzi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474"
+                    ]
+                ],
+                "sizes": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz.sizes:md5,a57c401f27ae5133823fb09fb21c8a3c"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-10T13:10:03.04872"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/samtools/faidx/tests/nextflow.config b/modules/nf-core/samtools/faidx/tests/nextflow.config
new file mode 100644
index 00000000..f76a3ba0
--- /dev/null
+++ b/modules/nf-core/samtools/faidx/tests/nextflow.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: SAMTOOLS_FAIDX {
+        ext.args = 'MT192765.1 -o extract.fa'
+    }
+
+}
diff --git a/modules/nf-core/samtools/faidx/tests/nextflow2.config b/modules/nf-core/samtools/faidx/tests/nextflow2.config
new file mode 100644
index 00000000..33ebbd5d
--- /dev/null
+++ b/modules/nf-core/samtools/faidx/tests/nextflow2.config
@@ -0,0 +1,6 @@
+process {
+
+    withName: SAMTOOLS_FAIDX {
+        ext.args = '-o extract.fa'
+    }
+}
diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml
new file mode 100644
index 00000000..89e12a64
--- /dev/null
+++ b/modules/nf-core/samtools/index/environment.yml
@@ -0,0 +1,10 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  # renovate: datasource=conda depName=bioconda/htslib
+  - bioconda::htslib=1.22.1
+  # renovate: datasource=conda depName=bioconda/samtools
+  - bioconda::samtools=1.22.1
diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf
new file mode 100644
index 00000000..a77ad821
--- /dev/null
+++ b/modules/nf-core/samtools/index/main.nf
@@ -0,0 +1,49 @@
+process SAMTOOLS_INDEX {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/samtools:1.22.1--h96c455f_0' :
+        'biocontainers/samtools:1.22.1--h96c455f_0' }"
+
+    input:
+    tuple val(meta), path(input)
+
+    output:
+    tuple val(meta), path("*.bai") , optional:true, emit: bai
+    tuple val(meta), path("*.csi") , optional:true, emit: csi
+    tuple val(meta), path("*.crai"), optional:true, emit: crai
+    path  "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    samtools \\
+        index \\
+        -@ ${task.cpus} \\
+        $args \\
+        $input
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def extension = file(input).getExtension() == 'cram' ?
+                    "crai" : args.contains("-c") ?  "csi" : "bai"
+    """
+    touch ${input}.${extension}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml
new file mode 100644
index 00000000..1bed6bca
--- /dev/null
+++ b/modules/nf-core/samtools/index/meta.yml
@@ -0,0 +1,77 @@
+name: samtools_index
+description: Index SAM/BAM/CRAM file
+keywords:
+  - index
+  - bam
+  - sam
+  - cram
+tools:
+  - samtools:
+      description: |
+        SAMtools is a set of utilities for interacting with and post-processing
+        short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
+        These files are generated as output by short read aligners like BWA.
+      homepage: http://www.htslib.org/
+      documentation: http://www.htslib.org/doc/samtools.html
+      doi: 10.1093/bioinformatics/btp352
+      licence: ["MIT"]
+      identifier: biotools:samtools
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - input:
+        type: file
+        description: input file
+        ontologies: []
+output:
+  bai:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.bai":
+          type: file
+          description: BAM/CRAM/SAM index file
+          pattern: "*.{bai,crai,sai}"
+          ontologies: []
+  csi:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.csi":
+          type: file
+          description: CSI index file
+          pattern: "*.{csi}"
+          ontologies: []
+  crai:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.crai":
+          type: file
+          description: BAM/CRAM/SAM index file
+          pattern: "*.{bai,crai,sai}"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
+authors:
+  - "@drpatelh"
+  - "@ewels"
+  - "@maxulysse"
+maintainers:
+  - "@drpatelh"
+  - "@ewels"
+  - "@maxulysse"
diff --git a/modules/nf-core/samtools/index/tests/csi.nextflow.config b/modules/nf-core/samtools/index/tests/csi.nextflow.config
new file mode 100644
index 00000000..0ed260ef
--- /dev/null
+++ b/modules/nf-core/samtools/index/tests/csi.nextflow.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: SAMTOOLS_INDEX {
+        ext.args = '-c'
+    }
+
+}
diff --git a/modules/nf-core/samtools/index/tests/main.nf.test b/modules/nf-core/samtools/index/tests/main.nf.test
new file mode 100644
index 00000000..ca34fb5c
--- /dev/null
+++ b/modules/nf-core/samtools/index/tests/main.nf.test
@@ -0,0 +1,140 @@
+nextflow_process {
+
+    name "Test Process SAMTOOLS_INDEX"
+    script "../main.nf"
+    process "SAMTOOLS_INDEX"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "samtools"
+    tag "samtools/index"
+
+    test("bai") {
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("crai") {
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("csi") {
+        config "./csi.nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.csi[0][1]).name,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("bai - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("crai - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("csi - stub") {
+        options "-stub"
+        config "./csi.nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap
new file mode 100644
index 00000000..3836c6bf
--- /dev/null
+++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap
@@ -0,0 +1,250 @@
+{
+    "csi - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
+                ],
+                "bai": [
+                    
+                ],
+                "crai": [
+                    
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-10T14:13:38.25787"
+    },
+    "crai - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
+                ],
+                "bai": [
+                    
+                ],
+                "crai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "csi": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-10T14:13:34.496412"
+    },
+    "bai - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
+                ],
+                "bai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "crai": [
+                    
+                ],
+                "csi": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-10T14:13:25.934431"
+    },
+    "csi": {
+        "content": [
+            "test.paired_end.sorted.bam.csi",
+            [
+                "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-10T14:13:22.262088"
+    },
+    "crai": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
+                ],
+                "bai": [
+                    
+                ],
+                "crai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029"
+                    ]
+                ],
+                "csi": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-10T14:13:18.191664"
+    },
+    "bai": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
+                ],
+                "bai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4"
+                    ]
+                ],
+                "crai": [
+                    
+                ],
+                "csi": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-10T14:13:08.51539"
+    }
+}
\ No newline at end of file
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 267afaa9..eb6cbcea 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -51,7 +51,7 @@
                 "skip_tools": {
                     "type": "string",
                     "description": "Comma-separated string of tools to skip",
-                    "pattern": "^((fastqc|fastqscreen|seqfu_stats|seqtk_sample|bwamem2_index|bwamem2_mem)?,?)*(?<!,)$"
+                    "pattern": "^((fastqc|fastqscreen|seqfu_stats|seqtk_sample|bwamem2_index|bwamem2_mem|picard_collectmultiplemetrics|samtools_faidx|samtools_index)?,?)*(?<!,)$"
                 }
             }
         },
diff --git a/tests/MiSeq.main.nf.test b/tests/MiSeq.main.nf.test
index 439715c1..4cf42243 100644
--- a/tests/MiSeq.main.nf.test
+++ b/tests/MiSeq.main.nf.test
@@ -82,7 +82,7 @@ nextflow_pipeline {
             config "./MiSeq.main.nf.test.config"
             params {
                 outdir = "$outputDir"
-                skip_tools = "fastqc,fastqscreen,seqfu_stats,seqtk_sample"
+                skip_tools = "fastqc,fastqscreen,seqfu_stats,seqtk_sample,bwamem2_index,bwamem2_mem"
             }
         }
 
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index fb568344..bdb2ece0 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -12,6 +12,9 @@ include { SEQFU_STATS                   } from '../modules/nf-core/seqfu/stats'
 include { FASTQSCREEN_FASTQSCREEN       } from '../modules/nf-core/fastqscreen/fastqscreen/main'
 include { BWAMEM2_INDEX                 } from '../modules/nf-core/bwamem2/index/main'
 include { BWAMEM2_MEM                   } from '../modules/nf-core/bwamem2/mem/main'
+include { SAMTOOLS_INDEX                } from '../modules/nf-core/samtools/index/main'
+include { SAMTOOLS_FAIDX                } from '../modules/nf-core/samtools/faidx/main'
+include { PICARD_COLLECTMULTIPLEMETRICS } from '../modules/nf-core/picard/collectmultiplemetrics/main'
 
 include { MULTIQC as MULTIQC_GLOBAL     } from '../modules/nf-core/multiqc/main'
 include { MULTIQC as MULTIQC_PER_TAG    } from '../modules/nf-core/multiqc/main'
@@ -113,7 +116,8 @@ workflow SEQINSPECTOR {
     if (!("bwamem2_index" in skip_tools)) {
         def fasta_file = getGenomeAttribute('fasta')
         ch_reference_fasta = Channel.fromPath(fasta_file, checkIfExists: true)
-                                    .map { [[id: it.name], it] }.collect()
+                            .map { file -> tuple([id: file.name], file) }.collect()
+
 
         BWAMEM2_INDEX (
             ch_reference_fasta
@@ -130,11 +134,68 @@ workflow SEQINSPECTOR {
             ch_reference_fasta,
             params.sort_bam ?: true
         )
-        ch_bwamem2_mem = BWAMEM2_MEM.out
+        ch_bwamem2_mem = BWAMEM2_MEM.out.bam
         ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions)
+        ch_bwamem2_mem.view { "BAM: $it" }
+
 
 }
-    //
+    // MODULE: Index BAM files with Samtools
+    if (!("samtools_index" in skip_tools)) {
+
+        SAMTOOLS_INDEX (
+            ch_bwamem2_mem
+        )
+        ch_samtools_index = SAMTOOLS_INDEX.out.bai
+        ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions)
+        ch_samtools_index.view { "BAI: $it" }
+    }
+
+    // MODULE: Index reference FASTA with Samtools faidx
+    if (!("samtools_faidx" in skip_tools)) {
+
+        // Assume ch_fasta emits tuple(meta, fasta)
+        ch_dummy_fai = Channel.value(['dummy_meta', file('empty.fai')])
+
+
+        SAMTOOLS_FAIDX (
+            ch_reference_fasta,
+            ch_dummy_fai,
+            true           // get_sizes
+        )
+        ch_reference_fasta_fai = SAMTOOLS_FAIDX.out.fai
+        ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions)
+    }
+
+    // MODULE: Prepare BAM/BAI tuples for Picard
+    // Combine BAM and BAI outputs for Picard
+    ch_bam_bai = ch_bwamem2_mem
+        .join(ch_samtools_index)
+        .map { meta, bam, bai ->
+             [meta, bam, bai]
+    }
+
+    ch_bam_bai.view { "Combined BAM/BAI for Picard: $it" }
+    ch_fasta   = ch_reference_fasta
+    ch_fai     = ch_reference_fasta_fai
+
+    ch_fasta.view { "FASTA for Picard: $it" }
+    ch_fai.view { "FAI for Picard: $it" }
+
+    // Prepare reference FASTA and FAI tuples for Picard
+    // Run Picard CollectMultipleMetrics
+    if (!("picard_collectmultiplemetrics" in skip_tools)) {
+        PICARD_COLLECTMULTIPLEMETRICS(
+            ch_bam_bai,
+            ch_fasta,
+            ch_fai
+)
+
+     ch_multiqc_files = ch_multiqc_files.mix(PICARD_COLLECTMULTIPLEMETRICS.out.metrics)
+     ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
+    }
+
+
     // Collate and save software versions
     //
     softwareVersionsToYAML(ch_versions)

From ad0e7ef1db8269a87b02d6d9b96c85d2987421a2 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@n161-p152.eduroam.kth.se>
Date: Wed, 1 Oct 2025 16:13:39 +0200
Subject: [PATCH 248/530] added picard tools

---
 tests/MiSeq_PairedEnd.main.nf.test.snap | 189 ++----------------------
 tests/PromethION.main.nf.test.config    |   1 -
 2 files changed, 11 insertions(+), 179 deletions(-)

diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index 047814e4..92e92de9 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -1,21 +1,20 @@
 {
     "MiSeq data test (paired end reads)": {
         "content": [
-            11,
+            8,
             {
                 "BWAMEM2_INDEX": {
                     "bwamem2": "2.2.1"
                 },
-                "BWAMEM2_MEM": {
-                    "bwamem2": "2.2.1",
-                    "samtools": 1.21
-                },
                 "FASTQC": {
                     "fastqc": "0.12.1"
                 },
                 "FASTQSCREEN_FASTQSCREEN": {
                     "fastqscreen": "0.16.0"
                 },
+                "SAMTOOLS_FAIDX": {
+                    "samtools": "1.22.1"
+                },
                 "SEQFU_STATS": {
                     "seqfu": "1.20.3"
                 },
@@ -31,9 +30,6 @@
                 "bwamem2_index/bwamem2/genome.fa.ann",
                 "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
                 "bwamem2_index/bwamem2/genome.fa.pac",
-                "bwamem2_mem",
-                "bwamem2_mem/SAMPLE_PAIRED_END_1_1.bam",
-                "bwamem2_mem/SAMPLE_PAIRED_END_2_2.bam",
                 "fastqc",
                 "fastqc/SAMPLE_PAIRED_END_1_1_1_fastqc.html",
                 "fastqc/SAMPLE_PAIRED_END_1_1_1_fastqc.zip",
@@ -56,146 +52,11 @@
                 "fastqscreen/SAMPLE_PAIRED_END_2_2_2_screen.html",
                 "fastqscreen/SAMPLE_PAIRED_END_2_2_2_screen.png",
                 "fastqscreen/SAMPLE_PAIRED_END_2_2_2_screen.txt",
-                "multiqc",
-                "multiqc/global_report",
-                "multiqc/global_report/multiqc_data",
-                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
-                "multiqc/global_report/multiqc_data/fastqc_adapter_content_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
-                "multiqc/global_report/multiqc_data/multiqc.log",
-                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
-                "multiqc/global_report/multiqc_data/multiqc_data.json",
-                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
-                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
-                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
-                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
-                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
-                "multiqc/global_report/multiqc_plots",
-                "multiqc/global_report/multiqc_plots/pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
-                "multiqc/global_report/multiqc_plots/png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_adapter_content_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu.png",
-                "multiqc/global_report/multiqc_plots/svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
-                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
-                "multiqc/global_report/multiqc_report.html",
-                "multiqc/group_reports",
-                "multiqc/group_reports/Bpacificus",
-                "multiqc/group_reports/Bpacificus/multiqc_data",
-                "multiqc/group_reports/Bpacificus/multiqc_data/fastq_screen_plot.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc-status-check-heatmap.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_adapter_content_plot.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_base_n_content_plot.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_sequence_counts_plot.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc.log",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_citations.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_data.json",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_fastq_screen.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_fastqc.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_seqfu.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_software_versions.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_sources.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_plots",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/general_stats_table.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/seqfu.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc-status-check-heatmap.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_adapter_content_plot.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/general_stats_table.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/seqfu.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/general_stats_table.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/seqfu.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "samtools",
+                "samtools/genome.fa.fai",
+                "samtools/genome.fa.sizes",
                 "seqfu_stats",
                 "seqfu_stats/SAMPLE_PAIRED_END_1_1_seqfu.tsv",
                 "seqfu_stats/SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt",
@@ -208,8 +69,6 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "SAMPLE_PAIRED_END_1_1.bam:md5,ced6a17fb3dee760c2606860e1177071",
-                "SAMPLE_PAIRED_END_2_2.bam:md5,15ada2a4f4a6cf2978aeaeb64a525197",
                 "SAMPLE_PAIRED_END_1_1_1_screen.png:md5,f52ddd0e65f23f68dd8d58d5453417db",
                 "SAMPLE_PAIRED_END_1_1_1_screen.txt:md5,921b08eeb461a2aa1bd42bba53900f70",
                 "SAMPLE_PAIRED_END_1_1_2_screen.png:md5,908f4fceea8aa546106efdaa7ca78f7d",
@@ -218,34 +77,8 @@
                 "SAMPLE_PAIRED_END_2_2_1_screen.txt:md5,a5b047f495d01bf9dcb0ae516d3c7fc3",
                 "SAMPLE_PAIRED_END_2_2_2_screen.png:md5,e3684b17339d16e6fb64ace7593cc388",
                 "SAMPLE_PAIRED_END_2_2_2_screen.txt:md5,fc95e5058e764596d5da182cbc0614cf",
-                "fastq_screen_plot.txt:md5,642264b93871c724aaa5d38b91c752dd",
-                "fastqc-status-check-heatmap.txt:md5,8e29ad6b23e03267c33bd9ed3385a44b",
-                "fastqc_adapter_content_plot.txt:md5,46fbd727a4996a3f0310d0423c628445",
-                "fastqc_per_base_n_content_plot.txt:md5,4eca1ef40d4d3d318b82e68e9fa3c589",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,218757a51c3de79a39a704c979df03da",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a4035ac9f0a0c07574130758b06630d7",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,637b937e023c84115ec06b529cc8ec1b",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,47d60153a430e2b8da51655704c2b31b",
-                "fastqc_sequence_counts_plot.txt:md5,10737092a3473fba81fbe49555512b2b",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,6412f57686de02e1f1c3751a7ca2be8b",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,5ef00028497d3271c9f0ea9a961db1e5",
-                "multiqc_fastqc.txt:md5,bc499ad273fd1c887056c31b82544984",
-                "multiqc_seqfu.txt:md5,1f1e063e4a509a26cee167c3b20389c0",
-                "fastq_screen_plot.txt:md5,642264b93871c724aaa5d38b91c752dd",
-                "fastqc-status-check-heatmap.txt:md5,8e29ad6b23e03267c33bd9ed3385a44b",
-                "fastqc_adapter_content_plot.txt:md5,46fbd727a4996a3f0310d0423c628445",
-                "fastqc_per_base_n_content_plot.txt:md5,4eca1ef40d4d3d318b82e68e9fa3c589",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,218757a51c3de79a39a704c979df03da",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a4035ac9f0a0c07574130758b06630d7",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,637b937e023c84115ec06b529cc8ec1b",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,47d60153a430e2b8da51655704c2b31b",
-                "fastqc_sequence_counts_plot.txt:md5,10737092a3473fba81fbe49555512b2b",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,6412f57686de02e1f1c3751a7ca2be8b",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,5ef00028497d3271c9f0ea9a961db1e5",
-                "multiqc_fastqc.txt:md5,bc499ad273fd1c887056c31b82544984",
-                "multiqc_seqfu.txt:md5,1f1e063e4a509a26cee167c3b20389c0",
+                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
+                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "SAMPLE_PAIRED_END_1_1_seqfu.tsv:md5,bbd911ff3fa43212dfd4c5a5872dbdb6",
                 "SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt:md5,cd60f746b6749cc66213d031af1b931c",
                 "SAMPLE_PAIRED_END_2_2_seqfu.tsv:md5,152566a128dd657da33465b4966b5799",
@@ -254,8 +87,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-09-24T10:41:23.851991495"
+        "timestamp": "2025-10-01T11:24:21.761746"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.config b/tests/PromethION.main.nf.test.config
index 987d19d3..0944c674 100644
--- a/tests/PromethION.main.nf.test.config
+++ b/tests/PromethION.main.nf.test.config
@@ -5,7 +5,6 @@ includeConfig 'nextflow.config'
 params {
     input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/PromethION/samplesheet.csv'
     genome = 'EB1'
-    skip_tools = 'bwamem2_index,bwamem2_mem'
 }
 
 

From 0bade1b34d76dfc00ab99d4b3569199590a7a927 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@n180-p97.eduroam.kth.se>
Date: Thu, 2 Oct 2025 11:01:03 +0200
Subject: [PATCH 249/530] linting

---
 conf/modules.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/modules.config b/conf/modules.config
index c4335e4a..94d29688 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -60,7 +60,7 @@ process {
         ]
     }
 
-    withName: 'SAMTOOLS_FAIIDX' {
+    withName: 'SAMTOOLS_FAIDX' {
         ext.args   = ''
         publishDir = [
             path: { "${params.outdir}/samtools_faidx" },

From be716ab216988f3d243af67d507a2020f90ab371 Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Thu, 2 Oct 2025 09:29:21 +0000
Subject: [PATCH 250/530] nf-tests

---
 .github/PULL_REQUEST_TEMPLATE.md      |  4 ++--
 .github/workflows/linting.yml         | 17 +++++++----------
 .github/workflows/linting_comment.yml |  4 ++--
 .prettierrc.yml                       |  5 +++++
 4 files changed, 16 insertions(+), 14 deletions(-)

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 9dcf6a33..068d699b 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -8,14 +8,14 @@ These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/seqinspector/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/seqinspector/tree/main/.github/CONTRIBUTING.md)
 -->
 
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/seqinspector/tree/master/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/seqinspector/tree/main/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/seqinspector _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index dbd52d5a..8b0f88c3 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -3,9 +3,6 @@ name: nf-core linting
 # It runs the `nf-core pipelines lint` and markdown lint tests to ensure
 # that the code meets the nf-core guidelines.
 on:
-  push:
-    branches:
-      - dev
   pull_request:
   release:
     types: [published]
@@ -16,10 +13,10 @@ jobs:
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
-      - name: Set up Python 3.12
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      - name: Set up Python 3.13
+        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -36,13 +33,13 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
           architecture: "x64"
 
       - name: read .nf-core.yml
-        uses: pietrobolcato/action-read-yaml@1.1.0
+        uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
         id: read_yml
         with:
           config: ${{ github.workspace }}/.nf-core.yml
@@ -74,7 +71,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
+        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 95b6b6af..d43797d9 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8
+        uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11
         with:
           workflow: linting.yml
           workflow_conclusion: completed
@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2
+        uses: marocchino/sticky-pull-request-comment@52423e01640425a022ef5fd42c6fb5f633a02728 # v2
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
diff --git a/.prettierrc.yml b/.prettierrc.yml
index c81f9a76..07dbd8bb 100644
--- a/.prettierrc.yml
+++ b/.prettierrc.yml
@@ -1 +1,6 @@
 printWidth: 120
+tabWidth: 4
+overrides:
+  - files: "*.{md,yml,yaml,html,css,scss,js,cff}"
+    options:
+      tabWidth: 2

From 20d36ff790acb0ca1770d60326f1f4760f47544e Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Thu, 2 Oct 2025 10:09:41 +0000
Subject: [PATCH 251/530] nf tests

---
 .nf-core.yml           |  1 +
 ro-crate-metadata.json | 34 ++++++++++++++++++++++++++--------
 2 files changed, 27 insertions(+), 8 deletions(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index 84481477..65713e02 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -4,6 +4,7 @@ lint:
     - .github/CONTRIBUTING.md
   files_exist:
     - .github/workflows/ci.yml
+    - tests/default.nf.test
   nextflow_config:
     - config_defaults:
         - params.fastq_screen_references
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 7b22e103..13ff1ebc 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -23,7 +23,7 @@
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
             "datePublished": "2025-01-27T16:15:35+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by Adrien Coulier.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->\n\n1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))\n2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n3. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
                     "@id": "main.nf"
@@ -121,7 +121,11 @@
         },
         {
             "@id": "main.nf",
-            "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
+            "@type": [
+                "File",
+                "SoftwareSourceCode",
+                "ComputationalWorkflow"
+            ],
             "creator": [
                 {
                     "@id": "https://orcid.org/0000-0003-2702-1103"
@@ -130,22 +134,36 @@
             "dateCreated": "",
             "dateModified": "2025-01-27T16:15:35Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
-            "keywords": ["nf-core", "nextflow", "genomics", "quality-control"],
-            "license": ["MIT"],
+            "keywords": [
+                "nf-core",
+                "nextflow",
+                "genomics",
+                "quality-control"
+            ],
+            "license": [
+                "MIT"
+            ],
             "maintainer": [
                 {
                     "@id": "https://orcid.org/0000-0003-2702-1103"
                 }
             ],
-            "name": ["nf-core/seqinspector"],
+            "name": [
+                "nf-core/seqinspector"
+            ],
             "programmingLanguage": {
                 "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow"
             },
             "sdPublisher": {
                 "@id": "https://nf-co.re/"
             },
-            "url": ["https://github.com/nf-core/seqinspector", "https://nf-co.re/seqinspector/dev/"],
-            "version": ["1.0dev"]
+            "url": [
+                "https://github.com/nf-core/seqinspector",
+                "https://nf-co.re/seqinspector/dev/"
+            ],
+            "version": [
+                "1.0dev"
+            ]
         },
         {
             "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow",
@@ -308,4 +326,4 @@
             "name": "Adrien Coulier"
         }
     ]
-}
+}
\ No newline at end of file

From 3cf5ad93885cb93aba65fb7a1c843a0fbd13a9b7 Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Thu, 2 Oct 2025 10:23:07 +0000
Subject: [PATCH 252/530] minor changes

---
 .github/PULL_REQUEST_TEMPLATE.md | 4 ++--
 .prettierrc.yml                  | 5 -----
 workflows/seqinspector.nf        | 6 +++---
 3 files changed, 5 insertions(+), 10 deletions(-)

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 068d699b..9dcf6a33 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -8,14 +8,14 @@ These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/seqinspector/tree/main/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/seqinspector/tree/master/.github/CONTRIBUTING.md)
 -->
 
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/seqinspector/tree/main/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/seqinspector/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/seqinspector _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
diff --git a/.prettierrc.yml b/.prettierrc.yml
index 07dbd8bb..c81f9a76 100644
--- a/.prettierrc.yml
+++ b/.prettierrc.yml
@@ -1,6 +1 @@
 printWidth: 120
-tabWidth: 4
-overrides:
-  - files: "*.{md,yml,yaml,html,css,scss,js,cff}"
-    options:
-      tabWidth: 2
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index bdb2ece0..8ed8b174 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -189,10 +189,10 @@ workflow SEQINSPECTOR {
             ch_bam_bai,
             ch_fasta,
             ch_fai
-)
+            )
 
-     ch_multiqc_files = ch_multiqc_files.mix(PICARD_COLLECTMULTIPLEMETRICS.out.metrics)
-     ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
+    ch_multiqc_files = ch_multiqc_files.mix(PICARD_COLLECTMULTIPLEMETRICS.out.metrics)
+    ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
     }
 
 

From 016fc4800e23e212cdc7c9611e5ac963acd99394 Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Thu, 2 Oct 2025 10:24:46 +0000
Subject: [PATCH 253/530] minor changes

---
 workflows/seqinspector.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 8ed8b174..fb280368 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -172,7 +172,7 @@ workflow SEQINSPECTOR {
     ch_bam_bai = ch_bwamem2_mem
         .join(ch_samtools_index)
         .map { meta, bam, bai ->
-             [meta, bam, bai]
+            [meta, bam, bai]
     }
 
     ch_bam_bai.view { "Combined BAM/BAI for Picard: $it" }

From d22a8800bdfdef31e0b37c216a131aff00a20cea Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Thu, 2 Oct 2025 10:33:02 +0000
Subject: [PATCH 254/530] minor changes

---
 .github/workflows/linting.yml         | 17 ++++++++++-------
 .github/workflows/linting_comment.yml |  4 ++--
 2 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 8b0f88c3..dbd52d5a 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -3,6 +3,9 @@ name: nf-core linting
 # It runs the `nf-core pipelines lint` and markdown lint tests to ensure
 # that the code meets the nf-core guidelines.
 on:
+  push:
+    branches:
+      - dev
   pull_request:
   release:
     types: [published]
@@ -13,10 +16,10 @@ jobs:
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
-      - name: Set up Python 3.13
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - name: Set up Python 3.12
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
-          python-version: "3.13"
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -33,13 +36,13 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
-          python-version: "3.13"
+          python-version: "3.12"
           architecture: "x64"
 
       - name: read .nf-core.yml
-        uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
+        uses: pietrobolcato/action-read-yaml@1.1.0
         id: read_yml
         with:
           config: ${{ github.workspace }}/.nf-core.yml
@@ -71,7 +74,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index d43797d9..95b6b6af 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11
+        uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8
         with:
           workflow: linting.yml
           workflow_conclusion: completed
@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@52423e01640425a022ef5fd42c6fb5f633a02728 # v2
+        uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}

From dad0821d161d0747d670dcf25f34b135bf075b9f Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Thu, 2 Oct 2025 12:12:13 +0000
Subject: [PATCH 255/530] snapshots updated

---
 tests/MiSeq.main.nf.test.snap           | 226 +++++++++++--
 tests/MiSeq_PairedEnd.main.nf.test.snap | 371 ++++++++++++++++++++-
 tests/NovaSeq6000.main.nf.test.snap     | 420 +++++++++++++++++++++++-
 tests/PromethION.main.nf.test.snap      | 124 ++-----
 workflows/seqinspector.nf               |  45 ++-
 5 files changed, 1033 insertions(+), 153 deletions(-)

diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index bc54480c..848aa7b2 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -1,29 +1,13 @@
 {
     "Miseq data test (skip all tools)": {
         "content": [
-            3,
+            1,
             {
-                "BWAMEM2_INDEX": {
-                    "bwamem2": "2.2.1"
-                },
-                "BWAMEM2_MEM": {
-                    "bwamem2": "2.2.1",
-                    "samtools": 1.21
-                },
                 "Workflow": {
                     "nf-core/seqinspector": "v1.0dev"
                 }
             },
             [
-                "bwamem2_index",
-                "bwamem2_index/bwamem2",
-                "bwamem2_index/bwamem2/genome.fa.0123",
-                "bwamem2_index/bwamem2/genome.fa.amb",
-                "bwamem2_index/bwamem2/genome.fa.ann",
-                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
-                "bwamem2_index/bwamem2/genome.fa.pac",
-                "bwamem2_mem",
-                "bwamem2_mem/SAMPLE_SINGLE_END_1.bam",
                 "multiqc",
                 "multiqc/global_report",
                 "multiqc/global_report/multiqc_data",
@@ -37,12 +21,6 @@
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"
             ],
             [
-                "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
-                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
-                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
-                "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
-                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "SAMPLE_SINGLE_END_1.bam:md5,79744f146752fd486b09604be721cc85",
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ]
         ],
@@ -50,11 +28,11 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-24T10:43:56.070328995"
+        "timestamp": "2025-10-02T12:11:24.611619614"
     },
     "MiSeq data test (single end reads)": {
         "content": [
-            6,
+            9,
             {
                 "BWAMEM2_INDEX": {
                     "bwamem2": "2.2.1"
@@ -69,6 +47,15 @@
                 "FASTQSCREEN_FASTQSCREEN": {
                     "fastqscreen": "0.16.0"
                 },
+                "PICARD_COLLECTMULTIPLEMETRICS": {
+                    "picard": "3.4.0"
+                },
+                "SAMTOOLS_FAIDX": {
+                    "samtools": "1.22.1"
+                },
+                "SAMTOOLS_INDEX": {
+                    "samtools": "1.22.1"
+                },
                 "SEQFU_STATS": {
                     "seqfu": "1.20.3"
                 },
@@ -113,9 +100,25 @@
                 "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -132,6 +135,16 @@
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -148,6 +161,16 @@
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -164,10 +187,34 @@
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
                 "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
+                "picard_collectmultiplemetrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "samtools_faidx",
+                "samtools_faidx/genome.fa.fai",
+                "samtools_faidx/genome.fa.sizes",
+                "samtools_index",
+                "samtools_index/SAMPLE_SINGLE_END_1.bam.bai",
                 "seqfu_stats",
                 "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu.tsv",
                 "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu_mqc.txt"
@@ -194,7 +241,34 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607",
                 "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,fe082d3b5dcc3d338e25bc027e17dc99",
+                "multiqc_picard_baseContent.txt:md5,796e8e0803ad3ed4fd1c76f073784942",
+                "multiqc_picard_quality_by_cycle.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
+                "multiqc_picard_quality_score_distribution.txt:md5,bad70b98811c4cbe4728f53334993703",
                 "multiqc_seqfu.txt:md5,8e6989a2392f599a09a5c3edf8119702",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
+                "picard_QualityScoreDistribution_histogram.txt:md5,bad70b98811c4cbe4728f53334993703",
+                "picard_alignment_readlength_plot.txt:md5,0fe7e17f1c58b7a6291bc1ff80fdfaa0",
+                "picard_alignment_summary.txt:md5,c770d3ee98dadaee77ef43967a974627",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,65d43b083e90830aa9451bde65a261b8",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,31dc4f314d8e3f8e086e7ae761638023",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,d92fac15687942c0f9c436ba0cf55fc9",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,00b76f45bbfc9acd2774f90612e53333",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,5451af67007a16e7645d0393011414af",
+                "picard_quality_by_cycle.txt:md5,46fbe44a9788f2e9184e2c1d689c2876",
+                "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics:md5,e26d0ab146f032d53d3b51bd4796475b",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,bdad45b0e1b6518f1e0216148eda3133",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,ff140d5b0f509535b17b5836680a7825",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,bfed0c9c988cb368b6d06310b7dee58e",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,1fed885f7d6f3b2db5cc8f29bab408b2",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf:md5,1901045846b0e65b4d7e90db4ebe2918",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics:md5,b6fb6b1ffa80a7944ff049f04ef63b10",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,66e63f19836eba28bb63e1b14ffe1225",
+                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
+                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
+                "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
                 "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,f65c868e562291647d539090698ba5eb",
                 "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
             ]
@@ -203,11 +277,11 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-24T10:42:44.511920997"
+        "timestamp": "2025-10-02T12:10:10.523949611"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
-            5,
+            8,
             {
                 "BWAMEM2_INDEX": {
                     "bwamem2": "2.2.1"
@@ -219,6 +293,15 @@
                 "FASTQSCREEN_FASTQSCREEN": {
                     "fastqscreen": "0.16.0"
                 },
+                "PICARD_COLLECTMULTIPLEMETRICS": {
+                    "picard": "3.4.0"
+                },
+                "SAMTOOLS_FAIDX": {
+                    "samtools": "1.22.1"
+                },
+                "SAMTOOLS_INDEX": {
+                    "samtools": "1.22.1"
+                },
                 "SEQFU_STATS": {
                     "seqfu": "1.20.3"
                 },
@@ -248,25 +331,85 @@
                 "multiqc/global_report/multiqc_data/multiqc_citations.txt",
                 "multiqc/global_report/multiqc_data/multiqc_data.json",
                 "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
+                "picard_collectmultiplemetrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "samtools_faidx",
+                "samtools_faidx/genome.fa.fai",
+                "samtools_faidx/genome.fa.sizes",
+                "samtools_index",
+                "samtools_index/SAMPLE_SINGLE_END_1.bam.bai",
                 "seqfu_stats",
                 "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu.tsv",
                 "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu_mqc.txt"
@@ -283,7 +426,34 @@
                 "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,fe082d3b5dcc3d338e25bc027e17dc99",
+                "multiqc_picard_baseContent.txt:md5,796e8e0803ad3ed4fd1c76f073784942",
+                "multiqc_picard_quality_by_cycle.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
+                "multiqc_picard_quality_score_distribution.txt:md5,bad70b98811c4cbe4728f53334993703",
                 "multiqc_seqfu.txt:md5,8e6989a2392f599a09a5c3edf8119702",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
+                "picard_QualityScoreDistribution_histogram.txt:md5,bad70b98811c4cbe4728f53334993703",
+                "picard_alignment_readlength_plot.txt:md5,0fe7e17f1c58b7a6291bc1ff80fdfaa0",
+                "picard_alignment_summary.txt:md5,c770d3ee98dadaee77ef43967a974627",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,65d43b083e90830aa9451bde65a261b8",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,31dc4f314d8e3f8e086e7ae761638023",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,d92fac15687942c0f9c436ba0cf55fc9",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,00b76f45bbfc9acd2774f90612e53333",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,5451af67007a16e7645d0393011414af",
+                "picard_quality_by_cycle.txt:md5,46fbe44a9788f2e9184e2c1d689c2876",
+                "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics:md5,99d790aacdb24763ad6888996ea505ac",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,6df45fc6a21defc2fe62a1e832a90255",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,1437f9df17c59c65d9fa83ec68a264b9",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,80e3d50895b6c6c102918f362e206cc5",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,1ae7129084643354b2b77b1dc8154ce6",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf:md5,d6d2f363ef5678dc1a374cc64d68a369",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics:md5,1adb85a6f529f613657728508a7684d8",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,c220c08d99815c549ee61f7057dcab25",
+                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
+                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
+                "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
                 "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,f65c868e562291647d539090698ba5eb",
                 "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
             ]
@@ -292,6 +462,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-24T10:43:19.776520207"
+        "timestamp": "2025-10-02T12:11:06.00674022"
     }
 }
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index 92e92de9..dd8facd9 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -1,20 +1,30 @@
 {
     "MiSeq data test (paired end reads)": {
         "content": [
-            8,
+            16,
             {
                 "BWAMEM2_INDEX": {
                     "bwamem2": "2.2.1"
                 },
+                "BWAMEM2_MEM": {
+                    "bwamem2": "2.2.1",
+                    "samtools": 1.21
+                },
                 "FASTQC": {
                     "fastqc": "0.12.1"
                 },
                 "FASTQSCREEN_FASTQSCREEN": {
                     "fastqscreen": "0.16.0"
                 },
+                "PICARD_COLLECTMULTIPLEMETRICS": {
+                    "picard": "3.4.0"
+                },
                 "SAMTOOLS_FAIDX": {
                     "samtools": "1.22.1"
                 },
+                "SAMTOOLS_INDEX": {
+                    "samtools": "1.22.1"
+                },
                 "SEQFU_STATS": {
                     "seqfu": "1.20.3"
                 },
@@ -30,6 +40,9 @@
                 "bwamem2_index/bwamem2/genome.fa.ann",
                 "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
                 "bwamem2_index/bwamem2/genome.fa.pac",
+                "bwamem2_mem",
+                "bwamem2_mem/SAMPLE_PAIRED_END_1_1.bam",
+                "bwamem2_mem/SAMPLE_PAIRED_END_2_2.bam",
                 "fastqc",
                 "fastqc/SAMPLE_PAIRED_END_1_1_1_fastqc.html",
                 "fastqc/SAMPLE_PAIRED_END_1_1_1_fastqc.zip",
@@ -52,11 +65,275 @@
                 "fastqscreen/SAMPLE_PAIRED_END_2_2_2_screen.html",
                 "fastqscreen/SAMPLE_PAIRED_END_2_2_2_screen.png",
                 "fastqscreen/SAMPLE_PAIRED_END_2_2_2_screen.txt",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/global_report/multiqc_data/fastqc_adapter_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_summary_Aligned_Bases.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_summary_Aligned_Reads.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
+                "multiqc/global_report/multiqc_plots",
+                "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_adapter_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu.png",
+                "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
+                "multiqc/global_report/multiqc_report.html",
+                "multiqc/group_reports",
+                "multiqc/group_reports/Bpacificus",
+                "multiqc/group_reports/Bpacificus/multiqc_data",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc-status-check-heatmap.txt",
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+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc.log",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_citations.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_data.json",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_quality_score_distribution.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_alignment_summary_Aligned_Bases.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_alignment_summary_Aligned_Reads.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_quality_score_distribution.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_plots",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-cnt.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-pct.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-cnt.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-pct.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_adapter_content_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
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+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/general_stats_table.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-cnt.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-pct.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-cnt.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-pct.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_quality_score_distribution.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/seqfu.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-pct.svg",
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+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
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+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-cnt.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-pct.svg",
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+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-pct.svg",
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+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
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+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
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+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_quality_score_distribution.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/seqfu.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_report.html",
+                "picard_collectmultiplemetrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
-                "samtools",
-                "samtools/genome.fa.fai",
-                "samtools/genome.fa.sizes",
+                "samtools_faidx",
+                "samtools_faidx/genome.fa.fai",
+                "samtools_faidx/genome.fa.sizes",
+                "samtools_index",
+                "samtools_index/SAMPLE_PAIRED_END_1_1.bam.bai",
+                "samtools_index/SAMPLE_PAIRED_END_2_2.bam.bai",
                 "seqfu_stats",
                 "seqfu_stats/SAMPLE_PAIRED_END_1_1_seqfu.tsv",
                 "seqfu_stats/SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt",
@@ -69,6 +346,8 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
+                "SAMPLE_PAIRED_END_1_1.bam:md5,ced6a17fb3dee760c2606860e1177071",
+                "SAMPLE_PAIRED_END_2_2.bam:md5,15ada2a4f4a6cf2978aeaeb64a525197",
                 "SAMPLE_PAIRED_END_1_1_1_screen.png:md5,f52ddd0e65f23f68dd8d58d5453417db",
                 "SAMPLE_PAIRED_END_1_1_1_screen.txt:md5,921b08eeb461a2aa1bd42bba53900f70",
                 "SAMPLE_PAIRED_END_1_1_2_screen.png:md5,908f4fceea8aa546106efdaa7ca78f7d",
@@ -77,8 +356,88 @@
                 "SAMPLE_PAIRED_END_2_2_1_screen.txt:md5,a5b047f495d01bf9dcb0ae516d3c7fc3",
                 "SAMPLE_PAIRED_END_2_2_2_screen.png:md5,e3684b17339d16e6fb64ace7593cc388",
                 "SAMPLE_PAIRED_END_2_2_2_screen.txt:md5,fc95e5058e764596d5da182cbc0614cf",
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+                "fastqc_per_base_sequence_quality_plot.txt:md5,218757a51c3de79a39a704c979df03da",
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+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,98f4e5ed094b41eb131d493b4f06bcd6",
+                "picard_quality_by_cycle.txt:md5,2634f306a33f648bac74bc7cd3253f9e",
+                "picard_quality_score_distribution.txt:md5,ecde9f0e859a6eecc5cea75a156c632d",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.alignment_summary_metrics:md5,8c835dae59705ab8b79abf6fe2855d30",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,2e5b17dfbe906257e37582512f91d41b",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,28051f934a020c5c06863e671af8c250",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,ecb3b37841764880b5e83493dc7c26d4",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,704c18acf8e31c14cc5e0b18a9cda2b1",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution.pdf:md5,0a67bc8b525cf2a845560b5af3490d61",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution_metrics:md5,e2b66fb9d8119fb22b9dc49253723015",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,2247cdc14680225dd2882ab584e5eeb8",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.alignment_summary_metrics:md5,b94d74bb0660a76b00ebebdcbe54de44",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,82661e48595cd818f694c5657d3a8dff",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,25ca56115048c2c63ae7c3b526a334bd",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle.pdf:md5,d9d8d77f48c9fb142f445e64b0a51337",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle_metrics:md5,419dd7781b6bafaea7ea771f56d0f62e",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution.pdf:md5,b1b619a602c97276ab5927ac9ae74c58",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution_metrics:md5,2721f815934a67701b4b378f9e44b741",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.read_length_histogram.pdf:md5,a1ccce680ff22f68517d5cc0acf9fbf9",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
+                "SAMPLE_PAIRED_END_1_1.bam.bai:md5,82724835c47f8e1d1a86e13ef469b464",
+                "SAMPLE_PAIRED_END_2_2.bam.bai:md5,3c4bdff0f906f2234fdeee8eea719210",
                 "SAMPLE_PAIRED_END_1_1_seqfu.tsv:md5,bbd911ff3fa43212dfd4c5a5872dbdb6",
                 "SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt:md5,cd60f746b6749cc66213d031af1b931c",
                 "SAMPLE_PAIRED_END_2_2_seqfu.tsv:md5,152566a128dd657da33465b4966b5799",
@@ -87,8 +446,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-01T11:24:21.761746"
+        "timestamp": "2025-10-02T10:42:17.865033586"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index a1fd0301..255949ee 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "NovaSeq6000 data test": {
         "content": [
-            26,
+            37,
             {
                 "BWAMEM2_INDEX": {
                     "bwamem2": "2.2.1"
@@ -16,6 +16,15 @@
                 "FASTQSCREEN_FASTQSCREEN": {
                     "fastqscreen": "0.16.0"
                 },
+                "PICARD_COLLECTMULTIPLEMETRICS": {
+                    "picard": "3.4.0"
+                },
+                "SAMTOOLS_FAIDX": {
+                    "samtools": "1.22.1"
+                },
+                "SAMTOOLS_INDEX": {
+                    "samtools": "1.22.1"
+                },
                 "SEQFU_STATS": {
                     "seqfu": "1.20.3"
                 },
@@ -85,9 +94,25 @@
                 "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -105,6 +130,16 @@
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -122,6 +157,16 @@
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -139,6 +184,16 @@
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
                 "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "multiqc/group_reports",
@@ -162,9 +217,25 @@
                 "multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group1/multiqc_plots",
                 "multiqc/group_reports/group1/multiqc_plots/pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -182,6 +253,16 @@
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -199,6 +280,16 @@
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/general_stats_table.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/group1/multiqc_plots/svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -216,6 +307,16 @@
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/group1/multiqc_report.html",
                 "multiqc/group_reports/group2",
@@ -238,9 +339,25 @@
                 "multiqc/group_reports/group2/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group2/multiqc_plots",
                 "multiqc/group_reports/group2/multiqc_plots/pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -258,6 +375,16 @@
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -275,6 +402,16 @@
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/general_stats_table.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/group2/multiqc_plots/svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -292,6 +429,16 @@
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/group2/multiqc_report.html",
                 "multiqc/group_reports/lane1",
@@ -314,9 +461,25 @@
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/lane1/multiqc_plots",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -334,6 +497,16 @@
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -351,6 +524,16 @@
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/general_stats_table.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/lane1/multiqc_plots/svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -368,6 +551,16 @@
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/lane1/multiqc_report.html",
                 "multiqc/group_reports/test",
@@ -390,9 +583,25 @@
                 "multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/test/multiqc_plots",
                 "multiqc/group_reports/test/multiqc_plots/pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -410,6 +619,16 @@
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/test/multiqc_plots/png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -427,6 +646,16 @@
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/group_reports/test/multiqc_plots/png/general_stats_table.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/test/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/test/multiqc_plots/svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -444,10 +673,70 @@
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/test/multiqc_report.html",
+                "picard_collectmultiplemetrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "samtools_faidx",
+                "samtools_faidx/genome.fa.fai",
+                "samtools_faidx/genome.fa.sizes",
+                "samtools_index",
+                "samtools_index/Sample1_1.bam.bai",
+                "samtools_index/Sample23_3.bam.bai",
+                "samtools_index/SampleA_2.bam.bai",
+                "samtools_index/Undetermined_5.bam.bai",
+                "samtools_index/sampletest_4.bam.bai",
                 "seqfu_stats",
                 "seqfu_stats/Sample1_1_seqfu.tsv",
                 "seqfu_stats/Sample1_1_seqfu_mqc.txt",
@@ -495,7 +784,23 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
                 "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,5bdb2f162266ab68005cbfc0a45e311e",
+                "multiqc_picard_baseContent.txt:md5,409bf8ce546a573ce6678769b84726fd",
+                "multiqc_picard_quality_by_cycle.txt:md5,ebf56fd9b3b127ff41211e3f79f18b42",
+                "multiqc_picard_quality_score_distribution.txt:md5,182098ce1ff0a664d873c329d54189df",
                 "multiqc_seqfu.txt:md5,5b54a49079169985795537d83d58bdd9",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,ebf56fd9b3b127ff41211e3f79f18b42",
+                "picard_QualityScoreDistribution_histogram.txt:md5,182098ce1ff0a664d873c329d54189df",
+                "picard_alignment_readlength_plot.txt:md5,92ab5c6fbe67484da62626736b1b21d4",
+                "picard_alignment_summary.txt:md5,f54187e8515f9b7c32eabaf1f8702224",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,61c7df03f74846ffa484a59fcccc7b9e",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,b4504bbb9ad72796703873f2d957977a",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,1d38466783ea51bf0c7be5bceaff4d43",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,1b13c9b64042839a3bc65a8553e5ba24",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,75aee7627205c6513389d7a52e7a383b",
+                "picard_quality_by_cycle.txt:md5,4850a9230f9be5af67f3d934602df440",
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                 "fastq_screen_plot.txt:md5,c25d34568f10f131156294d31fbfa994",
                 "fastqc-status-check-heatmap.txt:md5,67afbf7ec626c4fc7a28b4922352bc84",
                 "fastqc_overrepresented_sequences_plot.txt:md5,0356d007eaf807f7b63714b438b11289",
@@ -510,7 +815,23 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
                 "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,e4cb1b13e6a7298d172ed112a0479b5a",
+                "multiqc_picard_baseContent.txt:md5,740592a5858706d2b4b8f585a1d5492b",
+                "multiqc_picard_quality_by_cycle.txt:md5,c3f14084aedc511b9f0aa8410e7cb3b5",
+                "multiqc_picard_quality_score_distribution.txt:md5,59b955203209cfab3d2d21bdfe20997e",
                 "multiqc_seqfu.txt:md5,5579172a6f8ac09a5ffcb3ce6a99590e",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,c3f14084aedc511b9f0aa8410e7cb3b5",
+                "picard_QualityScoreDistribution_histogram.txt:md5,59b955203209cfab3d2d21bdfe20997e",
+                "picard_alignment_readlength_plot.txt:md5,1f8b2f4df8bd5cf879b96cfb2be6d81c",
+                "picard_alignment_summary.txt:md5,0cfafd1ed1920270bb1a5d13bed51480",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,bd7f8dab8e73406cded6c6f27bbc87e9",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,fe44ccdb08c6955149eacf52a77bbba2",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,85a9172769830b4169f214c335f44fdc",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,1fe0c42cb22981763862d1934a35de07",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,4c5bfb1594b391f3e36a9e1223b43a94",
+                "picard_quality_by_cycle.txt:md5,a43e7bb40bc479e9c32476256b09e734",
+                "picard_quality_score_distribution.txt:md5,a940641c0dab423c964c0f46b69dd805",
                 "fastq_screen_plot.txt:md5,44fca6453b0a3d0590271bd7a31cc740",
                 "fastqc-status-check-heatmap.txt:md5,b6872d9dbaa3cce396d48dc137076e53",
                 "fastqc_overrepresented_sequences_plot.txt:md5,eac8d0fd31c614d8d0f56bd54ee8c78c",
@@ -525,7 +846,23 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
                 "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,d4e63eed820edcc71b3e37d793983bd7",
+                "multiqc_picard_baseContent.txt:md5,0dd5fa539e4034e3539fb1e7068c7ce5",
+                "multiqc_picard_quality_by_cycle.txt:md5,750eadc27875fc8141b64a90789c369f",
+                "multiqc_picard_quality_score_distribution.txt:md5,140279eb5abac364c4d4c417105da620",
                 "multiqc_seqfu.txt:md5,b5434520fa5be5c98be5ed164a464d23",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,750eadc27875fc8141b64a90789c369f",
+                "picard_QualityScoreDistribution_histogram.txt:md5,140279eb5abac364c4d4c417105da620",
+                "picard_alignment_readlength_plot.txt:md5,a39f6a39dad13dacc2134508dbbf172d",
+                "picard_alignment_summary.txt:md5,fec83821c097bc1850257ce36aa73e5f",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,f206efb4e5344b8cbb2d18f6e73d5d95",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,ebf98e3d0bf661161989bf3d010b8c6b",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,f7dff1258977e9d04fb26ba8192facc5",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,b32d1e91c41756afe8732107868b32e0",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,b7b249afe807ca2321e6dd839961795c",
+                "picard_quality_by_cycle.txt:md5,1fe617901a493b80c31fcd01a00c416d",
+                "picard_quality_score_distribution.txt:md5,5cd4a87942000899776927f22a5db802",
                 "fastq_screen_plot.txt:md5,5f748d33a7a396547fe8c260b728aa06",
                 "fastqc-status-check-heatmap.txt:md5,08228a8f3d6f11b174b98626bb22bda1",
                 "fastqc_overrepresented_sequences_plot.txt:md5,3434dfb79f150e2e584e85866983ba01",
@@ -540,7 +877,23 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
                 "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,22093b80f335c4c53633b01a930157f4",
+                "multiqc_picard_baseContent.txt:md5,6886e1e5179031ddba4958f301930d64",
+                "multiqc_picard_quality_by_cycle.txt:md5,96652e2e2d693488df9104e5ae8cb4a7",
+                "multiqc_picard_quality_score_distribution.txt:md5,879a4470d08fe6d9b1796f46020fb5f5",
                 "multiqc_seqfu.txt:md5,e2e092852c011abe5ad75cdcd68b9383",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,96652e2e2d693488df9104e5ae8cb4a7",
+                "picard_QualityScoreDistribution_histogram.txt:md5,879a4470d08fe6d9b1796f46020fb5f5",
+                "picard_alignment_readlength_plot.txt:md5,9b323aa8cd934d084e9c83cfa1da306b",
+                "picard_alignment_summary.txt:md5,4e8970d31940f5e9020851d62e63b2e2",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,166a48317764fe7d4b38ed198503fc11",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,8e62c1113b965497e492e17665cdbe97",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,fe53f5f9455b928a3edc1661be83592b",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,3d069dd67cc0ffc43456c5f3ee427349",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,e371981072ec99d11c6adb5a4034808c",
+                "picard_quality_by_cycle.txt:md5,0c25ee4cec6842306b28c6a641aa03e1",
+                "picard_quality_score_distribution.txt:md5,184dcdd53f6aa3b7a0fa2c008d7dc74a",
                 "fastq_screen_plot.txt:md5,8622e1dbd0fe62520af6096207b9775d",
                 "fastqc-status-check-heatmap.txt:md5,2a66f5d61b9eb579555905cd5954b04c",
                 "fastqc_overrepresented_sequences_plot.txt:md5,e0b5bfc4b64d37611b51c939e61196fa",
@@ -555,7 +908,70 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5",
                 "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,edf7faad1da9922fdc692e9cba5cc0c4",
+                "multiqc_picard_baseContent.txt:md5,9631916c0a9a736811c47ab4c476428f",
+                "multiqc_picard_quality_by_cycle.txt:md5,9e05b241aabe39232b5182cb59d8edd5",
+                "multiqc_picard_quality_score_distribution.txt:md5,e9c3ade201964470d2d22569a400fa49",
                 "multiqc_seqfu.txt:md5,a1a0b9a0dde0c1c4fe184d44c675dcde",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,9e05b241aabe39232b5182cb59d8edd5",
+                "picard_QualityScoreDistribution_histogram.txt:md5,e9c3ade201964470d2d22569a400fa49",
+                "picard_alignment_readlength_plot.txt:md5,c2692fde9d899ad61297ad7043fd26b9",
+                "picard_alignment_summary.txt:md5,5996d5b4c94f16c0efd42e2df47e021e",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,a2670974dc96ad8a54f9cc5ae3e09d5e",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,d3b9cc0c99f96814348b57809cf227fb",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,1ba086d3fb2676868e8e7b20f55975dc",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,8902976984741320fe06004f4115c4f4",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,1380831484d1b069a2fd4a20437118bf",
+                "picard_quality_by_cycle.txt:md5,b6fc46e18ac875ba02775e7cbf1b8e8b",
+                "picard_quality_score_distribution.txt:md5,1c17c01ef54a6062a8f1ca8408d32958",
+                "Sample1_1.CollectMultipleMetrics.alignment_summary_metrics:md5,23d7793f18f5850e97924eaa28fd2ac2",
+                "Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,b76d37567b1f23c2328c156ee2dacebd",
+                "Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,4329194024511ec98d3c6fd232bccb0c",
+                "Sample1_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,74c389e92daabad32ef6bde2fde92e81",
+                "Sample1_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,849957a7fafb72ecef3e4c2c293f85e5",
+                "Sample1_1.CollectMultipleMetrics.quality_distribution.pdf:md5,e650653032b3a74a444b8e9ae1ced309",
+                "Sample1_1.CollectMultipleMetrics.quality_distribution_metrics:md5,deee0403ba846dbdba166f2cce01d1cc",
+                "Sample1_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,152c98e88a7f4f993040d157e233f689",
+                "Sample23_3.CollectMultipleMetrics.alignment_summary_metrics:md5,31025911c32c9aed1a2dadf2c48d59a3",
+                "Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,3bed8b8e16d44865869647098e66455b",
+                "Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,25e892960139f5af5e389f452cd7dd25",
+                "Sample23_3.CollectMultipleMetrics.quality_by_cycle.pdf:md5,406cf184d4e68f07e428497fc490b333",
+                "Sample23_3.CollectMultipleMetrics.quality_by_cycle_metrics:md5,485d3055cdc06149d5d083321ca65785",
+                "Sample23_3.CollectMultipleMetrics.quality_distribution.pdf:md5,6dbf9a55253a2a676e5467d704721326",
+                "Sample23_3.CollectMultipleMetrics.quality_distribution_metrics:md5,4917bd100fdaad7d529211c3b08c4094",
+                "Sample23_3.CollectMultipleMetrics.read_length_histogram.pdf:md5,64347cac8759c69f963e46476cda56c7",
+                "SampleA_2.CollectMultipleMetrics.alignment_summary_metrics:md5,f9adfdfec17eccde8047ba5d9be83218",
+                "SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,d6d1ecf118635c565893964876be0583",
+                "SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,4f743f4e7cf01ae0cca46aa3c3ce5083",
+                "SampleA_2.CollectMultipleMetrics.quality_by_cycle.pdf:md5,5a58d1e2cbdbd8d9fab307c60e81794c",
+                "SampleA_2.CollectMultipleMetrics.quality_by_cycle_metrics:md5,ced105bfda6a0ff761bd9feff3d253f6",
+                "SampleA_2.CollectMultipleMetrics.quality_distribution.pdf:md5,7b4afb833bfecb3d2c84dedf8ca1810b",
+                "SampleA_2.CollectMultipleMetrics.quality_distribution_metrics:md5,e91f1ad391ba2854c5bde90f9bf97a71",
+                "SampleA_2.CollectMultipleMetrics.read_length_histogram.pdf:md5,e79ddc964d8f20dcf22e9ecc11bceb86",
+                "Undetermined_5.CollectMultipleMetrics.alignment_summary_metrics:md5,492d86d57d0f0bbf3b1bb5f1a8ef9180",
+                "Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,3c650d121995a5dfec1aaa277623b1b4",
+                "Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,b4b66f442ddbab9b9f9c5dfbe377d12e",
+                "Undetermined_5.CollectMultipleMetrics.quality_by_cycle.pdf:md5,ade51ad75bc6eb100bd537f66ab22c02",
+                "Undetermined_5.CollectMultipleMetrics.quality_by_cycle_metrics:md5,ab2e70439fa9dbfd11259b6a495ced2b",
+                "Undetermined_5.CollectMultipleMetrics.quality_distribution.pdf:md5,b706497740617aff599d637d3c802de4",
+                "Undetermined_5.CollectMultipleMetrics.quality_distribution_metrics:md5,085b17859bc5093263518061755240c1",
+                "Undetermined_5.CollectMultipleMetrics.read_length_histogram.pdf:md5,23e6752fe6e3a43b241a9fe83c7042d0",
+                "sampletest_4.CollectMultipleMetrics.alignment_summary_metrics:md5,78d381d689e8430171c5a61854464571",
+                "sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,1b2086a180817972396cc62cda6f99e5",
+                "sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,da251ff6603a753c3a983b364797cf64",
+                "sampletest_4.CollectMultipleMetrics.quality_by_cycle.pdf:md5,a01df6be1452826306a301f8c318d459",
+                "sampletest_4.CollectMultipleMetrics.quality_by_cycle_metrics:md5,94ba2e9d9413f944657856943a46812c",
+                "sampletest_4.CollectMultipleMetrics.quality_distribution.pdf:md5,c4f26b5607f6fae6f9e9ae6831e6992f",
+                "sampletest_4.CollectMultipleMetrics.quality_distribution_metrics:md5,3c26b180aee7e43aaf4608307a277a21",
+                "sampletest_4.CollectMultipleMetrics.read_length_histogram.pdf:md5,e3fae878578907ea3f35815f232b6750",
+                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
+                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
+                "Sample1_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
+                "Sample23_3.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
+                "SampleA_2.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
+                "Undetermined_5.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
+                "sampletest_4.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
                 "Sample1_1_seqfu.tsv:md5,269fabf8435defcd327aa69a050b7869",
                 "Sample1_1_seqfu_mqc.txt:md5,a354b0ed16b9cf84aa88f501d7740fd6",
                 "Sample23_3_seqfu.tsv:md5,6fdadbeeefccbf957f880d6852bf9676",
@@ -572,6 +988,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-24T10:46:41.927291661"
+        "timestamp": "2025-10-02T10:44:33.974956998"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index daee5f1b..a423f88b 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -1,14 +1,20 @@
 {
     "PromethION data test": {
         "content": [
-            4,
+            5,
             {
+                "BWAMEM2_INDEX": {
+                    "bwamem2": "2.2.1"
+                },
                 "FASTQC": {
                     "fastqc": "0.12.1"
                 },
                 "FASTQSCREEN_FASTQSCREEN": {
                     "fastqscreen": "0.16.0"
                 },
+                "SAMTOOLS_FAIDX": {
+                    "samtools": "1.22.1"
+                },
                 "SEQFU_STATS": {
                     "seqfu": "1.20.3"
                 },
@@ -17,6 +23,13 @@
                 }
             },
             [
+                "bwamem2_index",
+                "bwamem2_index/bwamem2",
+                "bwamem2_index/bwamem2/genome.fa.0123",
+                "bwamem2_index/bwamem2/genome.fa.amb",
+                "bwamem2_index/bwamem2/genome.fa.ann",
+                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
+                "bwamem2_index/bwamem2/genome.fa.pac",
                 "fastqc",
                 "fastqc/hg001_1_fastqc.html",
                 "fastqc/hg001_1_fastqc.zip",
@@ -24,112 +37,25 @@
                 "fastqscreen/hg001_1_screen.html",
                 "fastqscreen/hg001_1_screen.png",
                 "fastqscreen/hg001_1_screen.txt",
-                "multiqc",
-                "multiqc/global_report",
-                "multiqc/global_report/multiqc_data",
-                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
-                "multiqc/global_report/multiqc_data/fastqc_adapter_content_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
-                "multiqc/global_report/multiqc_data/multiqc.log",
-                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
-                "multiqc/global_report/multiqc_data/multiqc_data.json",
-                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
-                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
-                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
-                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
-                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
-                "multiqc/global_report/multiqc_plots",
-                "multiqc/global_report/multiqc_plots/pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
-                "multiqc/global_report/multiqc_plots/png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_adapter_content_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu.png",
-                "multiqc/global_report/multiqc_plots/svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
-                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
-                "multiqc/global_report/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "samtools_faidx",
+                "samtools_faidx/genome.fa.fai",
+                "samtools_faidx/genome.fa.sizes",
                 "seqfu_stats",
                 "seqfu_stats/hg001_1_seqfu.tsv",
                 "seqfu_stats/hg001_1_seqfu_mqc.txt"
             ],
             [
+                "genome.fa.0123:md5,e112e4d2fd893fb939d306b27ece9de5",
+                "genome.fa.amb:md5,942a990ae872f1c0b8d72dda2db405d5",
+                "genome.fa.ann:md5,6b40f36ca7019ac001f52db139394dc0",
+                "genome.fa.bwt.2bit.64:md5,f0154573be12440aee294b726cd88c86",
+                "genome.fa.pac:md5,4d5e6fc45bbc968f7f859e9ca2cc89ad",
                 "hg001_1_screen.png:md5,b9c58e388f18ad11f4c2e29e9b573a5e",
                 "hg001_1_screen.txt:md5,8e53ea043d658a130f4b8ca455e2ba9b",
-                "fastq_screen_plot.txt:md5,3023b86477fecf6d46d8fc60d82cc53a",
-                "fastqc-status-check-heatmap.txt:md5,825668e94de27356f0a112beb758e416",
-                "fastqc_adapter_content_plot.txt:md5,1fa991080c20755e5e729a5eeab960e5",
-                "fastqc_overrepresented_sequences_plot.txt:md5,e810a3d3eba0ba83b122763505f511a7",
-                "fastqc_per_base_n_content_plot.txt:md5,cbdb64298ff839665e8c8c8e89896e87",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,4962950bc3ce77169ac510d64cb769c6",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,e62273533304be59dab5f13afef93b3e",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,3d49290a15406cb5dac1460c02729f0f",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,7cc10d1bc92ca09431a506c38d911228",
-                "fastqc_sequence_counts_plot.txt:md5,0425d7298c24df6158d5bf7aca1d4190",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,9111d942c7eed5af0e9ccb8c42db8505",
-                "fastqc_sequence_length_distribution_plot.txt:md5,04adfcd0125ebcc3e3bb631f1956c812",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,7c5d711e27c53d13c81644a1f2468dba",
-                "multiqc_fastqc.txt:md5,1a4b472e13cadc770832b0e20d1de7b0",
-                "multiqc_seqfu.txt:md5,9595d608ff5709f2bdec8cb1016416c0",
+                "genome.fa.fai:md5,59557cd3a71ca5e0840285b6088ec1d6",
+                "genome.fa.sizes:md5,f154a58a25ba9c4d386003eaa1bb731b",
                 "hg001_1_seqfu.tsv:md5,b133752c897afbb4d8721b911fa117d4",
                 "hg001_1_seqfu_mqc.txt:md5,6285f582c03faa70e8dcb3503e5db728"
             ]
@@ -138,6 +64,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-24T09:50:22.026441122"
+        "timestamp": "2025-10-02T11:47:07.215644214"
     }
 }
\ No newline at end of file
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index fb280368..ae2d801a 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -44,6 +44,13 @@ workflow SEQINSPECTOR {
     ch_multiqc_extra_files = Channel.empty()
     ch_multiqc_reports     = Channel.empty()
 
+// Initialize all channels that might be used later
+    ch_bwamem2_index = Channel.empty()
+    ch_bwamem2_mem = Channel.empty()
+    ch_samtools_index = Channel.empty()
+    ch_reference_fasta_fai = Channel.empty()
+    ch_reference_fasta = Channel.empty()
+
     //
     // MODULE: Run Seqtk sample to perform subsampling
     //
@@ -141,8 +148,7 @@ workflow SEQINSPECTOR {
 
 }
     // MODULE: Index BAM files with Samtools
-    if (!("samtools_index" in skip_tools)) {
-
+    if (!("samtools_index" in skip_tools) && !("bwamem2_mem" in skip_tools)) {
         SAMTOOLS_INDEX (
             ch_bwamem2_mem
         )
@@ -169,30 +175,33 @@ workflow SEQINSPECTOR {
 
     // MODULE: Prepare BAM/BAI tuples for Picard
     // Combine BAM and BAI outputs for Picard
-    ch_bam_bai = ch_bwamem2_mem
-        .join(ch_samtools_index)
-        .map { meta, bam, bai ->
-            [meta, bam, bai]
-    }
+    if (!("picard_collectmultiplemetrics" in skip_tools) &&
+        !("bwamem2_mem" in skip_tools) &&
+        !("samtools_index" in skip_tools) &&
+        !("samtools_faidx" in skip_tools)) {
+
+        // Prepare BAM/BAI tuples for Picard
+        ch_bam_bai = ch_bwamem2_mem
+            .join(ch_samtools_index)
+            .map { meta, bam, bai ->
+                [meta, bam, bai]
+            }
 
-    ch_bam_bai.view { "Combined BAM/BAI for Picard: $it" }
-    ch_fasta   = ch_reference_fasta
-    ch_fai     = ch_reference_fasta_fai
+        ch_bam_bai.view { "Combined BAM/BAI for Picard: $it" }
+        ch_fasta   = ch_reference_fasta
+        ch_fai     = ch_reference_fasta_fai
 
-    ch_fasta.view { "FASTA for Picard: $it" }
-    ch_fai.view { "FAI for Picard: $it" }
+        ch_fasta.view { "FASTA for Picard: $it" }
+        ch_fai.view { "FAI for Picard: $it" }
 
-    // Prepare reference FASTA and FAI tuples for Picard
-    // Run Picard CollectMultipleMetrics
-    if (!("picard_collectmultiplemetrics" in skip_tools)) {
         PICARD_COLLECTMULTIPLEMETRICS(
             ch_bam_bai,
             ch_fasta,
             ch_fai
-            )
+        )
 
-    ch_multiqc_files = ch_multiqc_files.mix(PICARD_COLLECTMULTIPLEMETRICS.out.metrics)
-    ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
+        ch_multiqc_files = ch_multiqc_files.mix(PICARD_COLLECTMULTIPLEMETRICS.out.metrics)
+        ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
     }
 
 

From 424cd321955d38291d814124b338b9f18e49f216 Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Thu, 2 Oct 2025 13:13:49 +0000
Subject: [PATCH 256/530] updated ss

---
 tests/MiSeq.main.nf.test.snap           | 38 ++++++------
 tests/MiSeq_PairedEnd.main.nf.test.snap | 34 +++++-----
 tests/NovaSeq6000.main.nf.test.snap     | 82 ++++++++++++-------------
 3 files changed, 77 insertions(+), 77 deletions(-)

diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 848aa7b2..cca91d47 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -28,7 +28,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-02T12:11:24.611619614"
+        "timestamp": "2025-10-02T12:58:23.877378234"
     },
     "MiSeq data test (single end reads)": {
         "content": [
@@ -258,14 +258,14 @@
                 "picard_base_distribution_by_cycle__Undetermined.txt:md5,5451af67007a16e7645d0393011414af",
                 "picard_quality_by_cycle.txt:md5,46fbe44a9788f2e9184e2c1d689c2876",
                 "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics:md5,e26d0ab146f032d53d3b51bd4796475b",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,bdad45b0e1b6518f1e0216148eda3133",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,ff140d5b0f509535b17b5836680a7825",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,bfed0c9c988cb368b6d06310b7dee58e",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,1fed885f7d6f3b2db5cc8f29bab408b2",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf:md5,1901045846b0e65b4d7e90db4ebe2918",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics:md5,b6fb6b1ffa80a7944ff049f04ef63b10",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,66e63f19836eba28bb63e1b14ffe1225",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics:md5,426320970e69c8ad9b6e00f4b1e7ee8a",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,69db421cd3b90834797f5e0d2efe0018",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,ff0c6f24403c8dc98b0d49b2b4337267",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,a2873299581030a86a29f5ea167f85ff",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,409c68a169c33a882a77645042e73acb",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf:md5,6499a9d7d24663270d33b8ec4fc3aff8",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics:md5,cccef5f07a9d3128b902d9784f18af1d",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,76ccdf893ca962d5ec77347424e493a3",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
@@ -277,7 +277,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-02T12:10:10.523949611"
+        "timestamp": "2025-10-02T12:57:10.484621911"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
@@ -443,14 +443,14 @@
                 "picard_base_distribution_by_cycle__Undetermined.txt:md5,5451af67007a16e7645d0393011414af",
                 "picard_quality_by_cycle.txt:md5,46fbe44a9788f2e9184e2c1d689c2876",
                 "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics:md5,99d790aacdb24763ad6888996ea505ac",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,6df45fc6a21defc2fe62a1e832a90255",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,1437f9df17c59c65d9fa83ec68a264b9",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,80e3d50895b6c6c102918f362e206cc5",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,1ae7129084643354b2b77b1dc8154ce6",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf:md5,d6d2f363ef5678dc1a374cc64d68a369",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics:md5,1adb85a6f529f613657728508a7684d8",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,c220c08d99815c549ee61f7057dcab25",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics:md5,9d45f7528397fc41a36bebc91d9208d2",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,5547cf92fa6455990d5467dd0a8d8546",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,2d91310fbcb2866df0a539354d33cb3b",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,246232781ec93b25447eb39365dff3ef",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,c694dacdf04a474bf615351376a39334",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf:md5,619812316cf145542f990e4012f60b20",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics:md5,833bc58ef14f54c51ec3ab47caeee72e",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,83e40310c69dd309cc4500591b376ef9",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
@@ -462,6 +462,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-02T12:11:06.00674022"
+        "timestamp": "2025-10-02T12:58:05.494623663"
     }
 }
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index dd8facd9..b5977eb2 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -418,22 +418,22 @@
                 "picard_base_distribution_by_cycle__Undetermined.txt:md5,98f4e5ed094b41eb131d493b4f06bcd6",
                 "picard_quality_by_cycle.txt:md5,2634f306a33f648bac74bc7cd3253f9e",
                 "picard_quality_score_distribution.txt:md5,ecde9f0e859a6eecc5cea75a156c632d",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.alignment_summary_metrics:md5,8c835dae59705ab8b79abf6fe2855d30",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,2e5b17dfbe906257e37582512f91d41b",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,28051f934a020c5c06863e671af8c250",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,ecb3b37841764880b5e83493dc7c26d4",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,704c18acf8e31c14cc5e0b18a9cda2b1",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution.pdf:md5,0a67bc8b525cf2a845560b5af3490d61",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution_metrics:md5,e2b66fb9d8119fb22b9dc49253723015",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,2247cdc14680225dd2882ab584e5eeb8",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.alignment_summary_metrics:md5,b94d74bb0660a76b00ebebdcbe54de44",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,82661e48595cd818f694c5657d3a8dff",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,25ca56115048c2c63ae7c3b526a334bd",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle.pdf:md5,d9d8d77f48c9fb142f445e64b0a51337",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle_metrics:md5,419dd7781b6bafaea7ea771f56d0f62e",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution.pdf:md5,b1b619a602c97276ab5927ac9ae74c58",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution_metrics:md5,2721f815934a67701b4b378f9e44b741",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.read_length_histogram.pdf:md5,a1ccce680ff22f68517d5cc0acf9fbf9",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.alignment_summary_metrics:md5,d220a4757e8f1d92faeea9d8d37fb143",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,64d28d4d50ba050c6f1683906ae39008",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,84738067941bceab6c144712b266ab8f",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,40503d9510371671d76435bdabfe4851",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,780a50a845a8a5168c70b8548ea33a20",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution.pdf:md5,8bef185df340b18ccf0923fdb1090513",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution_metrics:md5,ac9e9dcd4151e930938ac377c3684fcf",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,1c3ab86548aa76a23466bf4914cf396c",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.alignment_summary_metrics:md5,cef158db698b2ec789c209f55cfb5a18",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,44db870cbaf40b0d4fecda581cf7a7fe",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,11735fb354efe0d8bab6f749cfe63be7",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle.pdf:md5,2e90a9c8cc898b27c0ddf5cfba84eeaa",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle_metrics:md5,369345f4c49eafee3bc19babdae4f40a",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution.pdf:md5,1d757c6be5b566958263aa1ccd7cde40",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution_metrics:md5,3ff45f59212413ae3a6a9a39d2dd7f5c",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.read_length_histogram.pdf:md5,7e495c7b541c3f3ae814bb72d5358e87",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "SAMPLE_PAIRED_END_1_1.bam.bai:md5,82724835c47f8e1d1a86e13ef469b464",
@@ -448,6 +448,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-02T10:42:17.865033586"
+        "timestamp": "2025-10-02T12:59:44.105283504"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index 255949ee..05d32be4 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -925,46 +925,46 @@
                 "picard_base_distribution_by_cycle__Undetermined.txt:md5,1380831484d1b069a2fd4a20437118bf",
                 "picard_quality_by_cycle.txt:md5,b6fc46e18ac875ba02775e7cbf1b8e8b",
                 "picard_quality_score_distribution.txt:md5,1c17c01ef54a6062a8f1ca8408d32958",
-                "Sample1_1.CollectMultipleMetrics.alignment_summary_metrics:md5,23d7793f18f5850e97924eaa28fd2ac2",
-                "Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,b76d37567b1f23c2328c156ee2dacebd",
-                "Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,4329194024511ec98d3c6fd232bccb0c",
-                "Sample1_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,74c389e92daabad32ef6bde2fde92e81",
-                "Sample1_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,849957a7fafb72ecef3e4c2c293f85e5",
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-                "SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,d6d1ecf118635c565893964876be0583",
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-                "SampleA_2.CollectMultipleMetrics.read_length_histogram.pdf:md5,e79ddc964d8f20dcf22e9ecc11bceb86",
-                "Undetermined_5.CollectMultipleMetrics.alignment_summary_metrics:md5,492d86d57d0f0bbf3b1bb5f1a8ef9180",
-                "Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,3c650d121995a5dfec1aaa277623b1b4",
-                "Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,b4b66f442ddbab9b9f9c5dfbe377d12e",
-                "Undetermined_5.CollectMultipleMetrics.quality_by_cycle.pdf:md5,ade51ad75bc6eb100bd537f66ab22c02",
-                "Undetermined_5.CollectMultipleMetrics.quality_by_cycle_metrics:md5,ab2e70439fa9dbfd11259b6a495ced2b",
-                "Undetermined_5.CollectMultipleMetrics.quality_distribution.pdf:md5,b706497740617aff599d637d3c802de4",
-                "Undetermined_5.CollectMultipleMetrics.quality_distribution_metrics:md5,085b17859bc5093263518061755240c1",
-                "Undetermined_5.CollectMultipleMetrics.read_length_histogram.pdf:md5,23e6752fe6e3a43b241a9fe83c7042d0",
-                "sampletest_4.CollectMultipleMetrics.alignment_summary_metrics:md5,78d381d689e8430171c5a61854464571",
-                "sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,1b2086a180817972396cc62cda6f99e5",
-                "sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,da251ff6603a753c3a983b364797cf64",
-                "sampletest_4.CollectMultipleMetrics.quality_by_cycle.pdf:md5,a01df6be1452826306a301f8c318d459",
-                "sampletest_4.CollectMultipleMetrics.quality_by_cycle_metrics:md5,94ba2e9d9413f944657856943a46812c",
-                "sampletest_4.CollectMultipleMetrics.quality_distribution.pdf:md5,c4f26b5607f6fae6f9e9ae6831e6992f",
-                "sampletest_4.CollectMultipleMetrics.quality_distribution_metrics:md5,3c26b180aee7e43aaf4608307a277a21",
-                "sampletest_4.CollectMultipleMetrics.read_length_histogram.pdf:md5,e3fae878578907ea3f35815f232b6750",
+                "Sample1_1.CollectMultipleMetrics.alignment_summary_metrics:md5,b9e76472b763eae759b5d85e50f7398d",
+                "Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,6a27331bc10ac32a45a5285722bca220",
+                "Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,2bb1d36aba94dfbd1052bc58d8f87a01",
+                "Sample1_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,70d69470ea8e2cfb5e22576a5acca7a1",
+                "Sample1_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,a7e0b066eff4896c2392ea359e38c1ff",
+                "Sample1_1.CollectMultipleMetrics.quality_distribution.pdf:md5,31b8d3dcb2b6b47aab120c526a06b95e",
+                "Sample1_1.CollectMultipleMetrics.quality_distribution_metrics:md5,1bf7ee82cfc7f5386cd745c308fd9a28",
+                "Sample1_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,e30ab837e10775ea85fd6ee977c43d35",
+                "Sample23_3.CollectMultipleMetrics.alignment_summary_metrics:md5,e127bebda44a9f777f66963e89c12331",
+                "Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,bbc5db2ee4394201d5e0809311e5149f",
+                "Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,2a07ab2ffe5c91452d0f236366a1d4ad",
+                "Sample23_3.CollectMultipleMetrics.quality_by_cycle.pdf:md5,69aa820a6a6f0b5080bbb749f4302ee1",
+                "Sample23_3.CollectMultipleMetrics.quality_by_cycle_metrics:md5,033149d9c112f207fa0459cf58740749",
+                "Sample23_3.CollectMultipleMetrics.quality_distribution.pdf:md5,1626180d900b576d9e9ebd168447c336",
+                "Sample23_3.CollectMultipleMetrics.quality_distribution_metrics:md5,079cb6fc6c6797942343631b0080ab7f",
+                "Sample23_3.CollectMultipleMetrics.read_length_histogram.pdf:md5,2fb25034c2e5d4d6ae961f36d87296ae",
+                "SampleA_2.CollectMultipleMetrics.alignment_summary_metrics:md5,b75d920c11018cb3e9bb024633da011e",
+                "SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,9b6d9bc506eda4ce7f346098b7428fd2",
+                "SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,fc28c53601353c125ff3ed5d56d1848f",
+                "SampleA_2.CollectMultipleMetrics.quality_by_cycle.pdf:md5,1aebf31c8fd19a40455c1aadbc566aea",
+                "SampleA_2.CollectMultipleMetrics.quality_by_cycle_metrics:md5,90d7f28463fa21835b5df403cf1bc33f",
+                "SampleA_2.CollectMultipleMetrics.quality_distribution.pdf:md5,4857f96b399cf19a78c9e7b393a14f01",
+                "SampleA_2.CollectMultipleMetrics.quality_distribution_metrics:md5,8a2de0ec62db3d6b45ea5e50deb3c3d3",
+                "SampleA_2.CollectMultipleMetrics.read_length_histogram.pdf:md5,60b6acedd41ccbe3d12f2a51c9757f9c",
+                "Undetermined_5.CollectMultipleMetrics.alignment_summary_metrics:md5,9127db4197128287ca1aaf0fdce1e367",
+                "Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,1237fb43e39014ab403bbceaa723fc97",
+                "Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,f19a73257cfd830cd830cfd991b04d48",
+                "Undetermined_5.CollectMultipleMetrics.quality_by_cycle.pdf:md5,0c7d75cd110e6d91b39fe489eaf34c57",
+                "Undetermined_5.CollectMultipleMetrics.quality_by_cycle_metrics:md5,788005f850be1436895a8e9f88291aeb",
+                "Undetermined_5.CollectMultipleMetrics.quality_distribution.pdf:md5,93bdc469ac91616405e7544409b29f00",
+                "Undetermined_5.CollectMultipleMetrics.quality_distribution_metrics:md5,1098b25b399f1bf418df779ae9c650de",
+                "Undetermined_5.CollectMultipleMetrics.read_length_histogram.pdf:md5,cc349b82b46205d67d0b45e47088c25a",
+                "sampletest_4.CollectMultipleMetrics.alignment_summary_metrics:md5,a993291d0e474ba0eba7a531199413b7",
+                "sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,ba2682a2193bffd4c2caa5749abcd0ad",
+                "sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,ef98ec5536f0a9311de2f27a6fe8a8c7",
+                "sampletest_4.CollectMultipleMetrics.quality_by_cycle.pdf:md5,ba4daaadcc24337f8c24a0b5b38efa14",
+                "sampletest_4.CollectMultipleMetrics.quality_by_cycle_metrics:md5,5598bda2eda2b4855b9d410a3f14349a",
+                "sampletest_4.CollectMultipleMetrics.quality_distribution.pdf:md5,d00cff6c1f391fa7c02aa8413296f593",
+                "sampletest_4.CollectMultipleMetrics.quality_distribution_metrics:md5,cc67e984a9076750e64f6d04835dc7bc",
+                "sampletest_4.CollectMultipleMetrics.read_length_histogram.pdf:md5,016250ae411fb7d2e575857cca7fee97",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "Sample1_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
@@ -988,6 +988,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-02T10:44:33.974956998"
+        "timestamp": "2025-10-02T13:01:54.708241331"
     }
 }
\ No newline at end of file

From b0b1f70086517877046b6fdc929707c61c147cfb Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Thu, 2 Oct 2025 13:47:21 +0000
Subject: [PATCH 257/530] bwamem2 not compatible with long reads Promethion

---
 tests/PromethION.main.nf.test.config |   4 +-
 tests/PromethION.main.nf.test.snap   | 124 +++++++++++++++++++++------
 2 files changed, 101 insertions(+), 27 deletions(-)

diff --git a/tests/PromethION.main.nf.test.config b/tests/PromethION.main.nf.test.config
index 0944c674..46e9c091 100644
--- a/tests/PromethION.main.nf.test.config
+++ b/tests/PromethION.main.nf.test.config
@@ -5,6 +5,6 @@ includeConfig 'nextflow.config'
 params {
     input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/PromethION/samplesheet.csv'
     genome = 'EB1'
-}
-
+    skip_tools = 'bwamem2_index,bwamem2_mem'
 
+}
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index a423f88b..a4e878b9 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -1,20 +1,14 @@
 {
     "PromethION data test": {
         "content": [
-            5,
+            4,
             {
-                "BWAMEM2_INDEX": {
-                    "bwamem2": "2.2.1"
-                },
                 "FASTQC": {
                     "fastqc": "0.12.1"
                 },
                 "FASTQSCREEN_FASTQSCREEN": {
                     "fastqscreen": "0.16.0"
                 },
-                "SAMTOOLS_FAIDX": {
-                    "samtools": "1.22.1"
-                },
                 "SEQFU_STATS": {
                     "seqfu": "1.20.3"
                 },
@@ -23,13 +17,6 @@
                 }
             },
             [
-                "bwamem2_index",
-                "bwamem2_index/bwamem2",
-                "bwamem2_index/bwamem2/genome.fa.0123",
-                "bwamem2_index/bwamem2/genome.fa.amb",
-                "bwamem2_index/bwamem2/genome.fa.ann",
-                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
-                "bwamem2_index/bwamem2/genome.fa.pac",
                 "fastqc",
                 "fastqc/hg001_1_fastqc.html",
                 "fastqc/hg001_1_fastqc.zip",
@@ -37,25 +24,112 @@
                 "fastqscreen/hg001_1_screen.html",
                 "fastqscreen/hg001_1_screen.png",
                 "fastqscreen/hg001_1_screen.txt",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/global_report/multiqc_data/fastqc_adapter_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_plots",
+                "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_adapter_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu.png",
+                "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
+                "multiqc/global_report/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
-                "samtools_faidx",
-                "samtools_faidx/genome.fa.fai",
-                "samtools_faidx/genome.fa.sizes",
                 "seqfu_stats",
                 "seqfu_stats/hg001_1_seqfu.tsv",
                 "seqfu_stats/hg001_1_seqfu_mqc.txt"
             ],
             [
-                "genome.fa.0123:md5,e112e4d2fd893fb939d306b27ece9de5",
-                "genome.fa.amb:md5,942a990ae872f1c0b8d72dda2db405d5",
-                "genome.fa.ann:md5,6b40f36ca7019ac001f52db139394dc0",
-                "genome.fa.bwt.2bit.64:md5,f0154573be12440aee294b726cd88c86",
-                "genome.fa.pac:md5,4d5e6fc45bbc968f7f859e9ca2cc89ad",
                 "hg001_1_screen.png:md5,b9c58e388f18ad11f4c2e29e9b573a5e",
                 "hg001_1_screen.txt:md5,8e53ea043d658a130f4b8ca455e2ba9b",
-                "genome.fa.fai:md5,59557cd3a71ca5e0840285b6088ec1d6",
-                "genome.fa.sizes:md5,f154a58a25ba9c4d386003eaa1bb731b",
+                "fastq_screen_plot.txt:md5,3023b86477fecf6d46d8fc60d82cc53a",
+                "fastqc-status-check-heatmap.txt:md5,825668e94de27356f0a112beb758e416",
+                "fastqc_adapter_content_plot.txt:md5,1fa991080c20755e5e729a5eeab960e5",
+                "fastqc_overrepresented_sequences_plot.txt:md5,e810a3d3eba0ba83b122763505f511a7",
+                "fastqc_per_base_n_content_plot.txt:md5,cbdb64298ff839665e8c8c8e89896e87",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,4962950bc3ce77169ac510d64cb769c6",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,e62273533304be59dab5f13afef93b3e",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,3d49290a15406cb5dac1460c02729f0f",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,7cc10d1bc92ca09431a506c38d911228",
+                "fastqc_sequence_counts_plot.txt:md5,0425d7298c24df6158d5bf7aca1d4190",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,9111d942c7eed5af0e9ccb8c42db8505",
+                "fastqc_sequence_length_distribution_plot.txt:md5,04adfcd0125ebcc3e3bb631f1956c812",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,7c5d711e27c53d13c81644a1f2468dba",
+                "multiqc_fastqc.txt:md5,1a4b472e13cadc770832b0e20d1de7b0",
+                "multiqc_seqfu.txt:md5,9595d608ff5709f2bdec8cb1016416c0",
                 "hg001_1_seqfu.tsv:md5,b133752c897afbb4d8721b911fa117d4",
                 "hg001_1_seqfu_mqc.txt:md5,6285f582c03faa70e8dcb3503e5db728"
             ]
@@ -64,6 +138,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-02T11:47:07.215644214"
+        "timestamp": "2025-10-02T13:46:26.460263232"
     }
 }
\ No newline at end of file

From 342fd38058f9a7fcfce8c9cb8b5abc33d252debb Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Thu, 2 Oct 2025 14:21:33 +0000
Subject: [PATCH 258/530] ss

---
 tests/.nftignore                        |  9 +++
 tests/MiSeq.main.nf.test.snap           | 36 +++++------
 tests/MiSeq_PairedEnd.main.nf.test.snap | 34 +++++-----
 tests/NovaSeq6000.main.nf.test.snap     | 82 ++++++++++++-------------
 4 files changed, 85 insertions(+), 76 deletions(-)

diff --git a/tests/.nftignore b/tests/.nftignore
index 46980e70..97d6e47f 100644
--- a/tests/.nftignore
+++ b/tests/.nftignore
@@ -10,3 +10,12 @@ pipeline_info/*.{html,json,txt,yml}
 fastqscreen/*_screen.html
 fastqc/*_fastqc.html
 fastqc/*_fastqc.zip
+
+picard_collectmultiplemetrics/CollectMultipleMetrics.alignment_summary_metrics
+picard_collectmultiplemetrics/CollectMultipleMetrics.base_distribution_by_cycle.pdf
+picard_collectmultiplemetrics/CollectMultipleMetrics.base_distribution_by_cycle_metrics
+picard_collectmultiplemetrics/CollectMultipleMetrics.quality_by_cycle.pdf
+picard_collectmultiplemetrics/CollectMultipleMetrics.quality_by_cycle_metrics
+picard_collectmultiplemetrics/CollectMultipleMetrics.quality_distribution.pdf
+picard_collectmultiplemetrics/CollectMultipleMetrics.quality_distribution_metrics
+picard_collectmultiplemetrics/CollectMultipleMetrics.read_length_histogram.pdf
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index cca91d47..6952d809 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -258,14 +258,14 @@
                 "picard_base_distribution_by_cycle__Undetermined.txt:md5,5451af67007a16e7645d0393011414af",
                 "picard_quality_by_cycle.txt:md5,46fbe44a9788f2e9184e2c1d689c2876",
                 "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics:md5,426320970e69c8ad9b6e00f4b1e7ee8a",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,69db421cd3b90834797f5e0d2efe0018",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,ff0c6f24403c8dc98b0d49b2b4337267",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,a2873299581030a86a29f5ea167f85ff",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,409c68a169c33a882a77645042e73acb",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf:md5,6499a9d7d24663270d33b8ec4fc3aff8",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics:md5,cccef5f07a9d3128b902d9784f18af1d",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,76ccdf893ca962d5ec77347424e493a3",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics:md5,ed3f63631865ad7fc23996b35bf83a9f",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,3fc1bc4f7406431b3dd5f3c4ef65ada9",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,6caa70be0115a7fd39e10ce63dc4f3c5",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,ab974f45041a3aee28cefa408b080110",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,ed779b1f3bd38e950eca96b67f75257a",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf:md5,62a00a78195076bead47fe157bac0eb0",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics:md5,ab4aab082cd6c476e231da9219190dfc",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,fde51cf8632105a948fa9dfe120685a5",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
@@ -277,7 +277,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-02T12:57:10.484621911"
+        "timestamp": "2025-10-02T14:13:43.824626734"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
@@ -443,14 +443,14 @@
                 "picard_base_distribution_by_cycle__Undetermined.txt:md5,5451af67007a16e7645d0393011414af",
                 "picard_quality_by_cycle.txt:md5,46fbe44a9788f2e9184e2c1d689c2876",
                 "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics:md5,9d45f7528397fc41a36bebc91d9208d2",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,5547cf92fa6455990d5467dd0a8d8546",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,2d91310fbcb2866df0a539354d33cb3b",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,246232781ec93b25447eb39365dff3ef",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,c694dacdf04a474bf615351376a39334",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf:md5,619812316cf145542f990e4012f60b20",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics:md5,833bc58ef14f54c51ec3ab47caeee72e",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,83e40310c69dd309cc4500591b376ef9",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics:md5,1945761cfd2ae3867d2501c92501bec8",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,60ea460dfdf3492dad641cd25718c6a4",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,fa2658eabc7e781992a36dba03ab7b82",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,586a3ab960b336d95510c11246eae64f",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,e7d06c7513174404acb71503fbbc680a",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf:md5,a7da049596f6f5570c81544c2191932b",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics:md5,bd3b7002a68884c3a321b389e1e0bc7d",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,279be05de3927b5a630bea8a5a580657",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
@@ -462,6 +462,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-02T12:58:05.494623663"
+        "timestamp": "2025-10-02T14:14:32.514637041"
     }
 }
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index b5977eb2..282883ab 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -418,22 +418,22 @@
                 "picard_base_distribution_by_cycle__Undetermined.txt:md5,98f4e5ed094b41eb131d493b4f06bcd6",
                 "picard_quality_by_cycle.txt:md5,2634f306a33f648bac74bc7cd3253f9e",
                 "picard_quality_score_distribution.txt:md5,ecde9f0e859a6eecc5cea75a156c632d",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.alignment_summary_metrics:md5,d220a4757e8f1d92faeea9d8d37fb143",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,64d28d4d50ba050c6f1683906ae39008",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,84738067941bceab6c144712b266ab8f",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,40503d9510371671d76435bdabfe4851",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,780a50a845a8a5168c70b8548ea33a20",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution.pdf:md5,8bef185df340b18ccf0923fdb1090513",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution_metrics:md5,ac9e9dcd4151e930938ac377c3684fcf",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,1c3ab86548aa76a23466bf4914cf396c",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.alignment_summary_metrics:md5,cef158db698b2ec789c209f55cfb5a18",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,44db870cbaf40b0d4fecda581cf7a7fe",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,11735fb354efe0d8bab6f749cfe63be7",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle.pdf:md5,2e90a9c8cc898b27c0ddf5cfba84eeaa",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle_metrics:md5,369345f4c49eafee3bc19babdae4f40a",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution.pdf:md5,1d757c6be5b566958263aa1ccd7cde40",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution_metrics:md5,3ff45f59212413ae3a6a9a39d2dd7f5c",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.read_length_histogram.pdf:md5,7e495c7b541c3f3ae814bb72d5358e87",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.alignment_summary_metrics:md5,1aaea22c85bfacc9e565ecbad97a48f2",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,618e7d053f73e962a0adafc6cbf9e1c7",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,6ef28db292d46c58345737e578acd3f0",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,1ed00499a498f4371a3d560f96a32653",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,91e5f40f0c0b93524f5da3fa56ca403a",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution.pdf:md5,e717e5bf81ec9710043dc5e754cc3e0a",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution_metrics:md5,4ad4825f7819a2ed15bb5ffcc70b62aa",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,0896a18be8f3094723abccaa9d3f3c16",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.alignment_summary_metrics:md5,cca4acec30c612bd477ed9610ce458b6",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,8f4a40f704ecfcb63d143bc2d51f4bf1",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,85fe6d86cb4de07dc6297fe019ef7572",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle.pdf:md5,40cfef04b143a79a65f0398363198b4c",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle_metrics:md5,b35ca2429ad7751f8b05dd7401128894",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution.pdf:md5,2efa7403d3b8fe094183bcbc484da4e9",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution_metrics:md5,6c33f13752c57581477e91588c05de75",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.read_length_histogram.pdf:md5,43fdc0db900ec88a5e72aa96fc9a330c",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "SAMPLE_PAIRED_END_1_1.bam.bai:md5,82724835c47f8e1d1a86e13ef469b464",
@@ -448,6 +448,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-02T12:59:44.105283504"
+        "timestamp": "2025-10-02T14:16:07.09594705"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index 05d32be4..b23d8692 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -925,46 +925,46 @@
                 "picard_base_distribution_by_cycle__Undetermined.txt:md5,1380831484d1b069a2fd4a20437118bf",
                 "picard_quality_by_cycle.txt:md5,b6fc46e18ac875ba02775e7cbf1b8e8b",
                 "picard_quality_score_distribution.txt:md5,1c17c01ef54a6062a8f1ca8408d32958",
-                "Sample1_1.CollectMultipleMetrics.alignment_summary_metrics:md5,b9e76472b763eae759b5d85e50f7398d",
-                "Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,6a27331bc10ac32a45a5285722bca220",
-                "Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,2bb1d36aba94dfbd1052bc58d8f87a01",
-                "Sample1_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,70d69470ea8e2cfb5e22576a5acca7a1",
-                "Sample1_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,a7e0b066eff4896c2392ea359e38c1ff",
-                "Sample1_1.CollectMultipleMetrics.quality_distribution.pdf:md5,31b8d3dcb2b6b47aab120c526a06b95e",
-                "Sample1_1.CollectMultipleMetrics.quality_distribution_metrics:md5,1bf7ee82cfc7f5386cd745c308fd9a28",
-                "Sample1_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,e30ab837e10775ea85fd6ee977c43d35",
-                "Sample23_3.CollectMultipleMetrics.alignment_summary_metrics:md5,e127bebda44a9f777f66963e89c12331",
-                "Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,bbc5db2ee4394201d5e0809311e5149f",
-                "Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,2a07ab2ffe5c91452d0f236366a1d4ad",
-                "Sample23_3.CollectMultipleMetrics.quality_by_cycle.pdf:md5,69aa820a6a6f0b5080bbb749f4302ee1",
-                "Sample23_3.CollectMultipleMetrics.quality_by_cycle_metrics:md5,033149d9c112f207fa0459cf58740749",
-                "Sample23_3.CollectMultipleMetrics.quality_distribution.pdf:md5,1626180d900b576d9e9ebd168447c336",
-                "Sample23_3.CollectMultipleMetrics.quality_distribution_metrics:md5,079cb6fc6c6797942343631b0080ab7f",
-                "Sample23_3.CollectMultipleMetrics.read_length_histogram.pdf:md5,2fb25034c2e5d4d6ae961f36d87296ae",
-                "SampleA_2.CollectMultipleMetrics.alignment_summary_metrics:md5,b75d920c11018cb3e9bb024633da011e",
-                "SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,9b6d9bc506eda4ce7f346098b7428fd2",
-                "SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,fc28c53601353c125ff3ed5d56d1848f",
-                "SampleA_2.CollectMultipleMetrics.quality_by_cycle.pdf:md5,1aebf31c8fd19a40455c1aadbc566aea",
-                "SampleA_2.CollectMultipleMetrics.quality_by_cycle_metrics:md5,90d7f28463fa21835b5df403cf1bc33f",
-                "SampleA_2.CollectMultipleMetrics.quality_distribution.pdf:md5,4857f96b399cf19a78c9e7b393a14f01",
-                "SampleA_2.CollectMultipleMetrics.quality_distribution_metrics:md5,8a2de0ec62db3d6b45ea5e50deb3c3d3",
-                "SampleA_2.CollectMultipleMetrics.read_length_histogram.pdf:md5,60b6acedd41ccbe3d12f2a51c9757f9c",
-                "Undetermined_5.CollectMultipleMetrics.alignment_summary_metrics:md5,9127db4197128287ca1aaf0fdce1e367",
-                "Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,1237fb43e39014ab403bbceaa723fc97",
-                "Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,f19a73257cfd830cd830cfd991b04d48",
-                "Undetermined_5.CollectMultipleMetrics.quality_by_cycle.pdf:md5,0c7d75cd110e6d91b39fe489eaf34c57",
-                "Undetermined_5.CollectMultipleMetrics.quality_by_cycle_metrics:md5,788005f850be1436895a8e9f88291aeb",
-                "Undetermined_5.CollectMultipleMetrics.quality_distribution.pdf:md5,93bdc469ac91616405e7544409b29f00",
-                "Undetermined_5.CollectMultipleMetrics.quality_distribution_metrics:md5,1098b25b399f1bf418df779ae9c650de",
-                "Undetermined_5.CollectMultipleMetrics.read_length_histogram.pdf:md5,cc349b82b46205d67d0b45e47088c25a",
-                "sampletest_4.CollectMultipleMetrics.alignment_summary_metrics:md5,a993291d0e474ba0eba7a531199413b7",
-                "sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,ba2682a2193bffd4c2caa5749abcd0ad",
-                "sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,ef98ec5536f0a9311de2f27a6fe8a8c7",
-                "sampletest_4.CollectMultipleMetrics.quality_by_cycle.pdf:md5,ba4daaadcc24337f8c24a0b5b38efa14",
-                "sampletest_4.CollectMultipleMetrics.quality_by_cycle_metrics:md5,5598bda2eda2b4855b9d410a3f14349a",
-                "sampletest_4.CollectMultipleMetrics.quality_distribution.pdf:md5,d00cff6c1f391fa7c02aa8413296f593",
-                "sampletest_4.CollectMultipleMetrics.quality_distribution_metrics:md5,cc67e984a9076750e64f6d04835dc7bc",
-                "sampletest_4.CollectMultipleMetrics.read_length_histogram.pdf:md5,016250ae411fb7d2e575857cca7fee97",
+                "Sample1_1.CollectMultipleMetrics.alignment_summary_metrics:md5,06511dbac3b92992a13c867fe6177835",
+                "Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,fabc73f95c357c434726ce48e0222180",
+                "Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,18b2c01452318119f8f34d8ece375df4",
+                "Sample1_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,5310fded29bcdff6779478c3d69af841",
+                "Sample1_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,fc5d7e9ffcaf890844c82436b91c8d99",
+                "Sample1_1.CollectMultipleMetrics.quality_distribution.pdf:md5,537b7d686ae0ff5c1420b6f8bf1385b7",
+                "Sample1_1.CollectMultipleMetrics.quality_distribution_metrics:md5,f3e6fa9f787e6a111d368b075b7c8b8e",
+                "Sample1_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,61e77bc76d7bb08d6a1a963ab6725882",
+                "Sample23_3.CollectMultipleMetrics.alignment_summary_metrics:md5,11ffa4b14fd6c31d27ca0995ec5633fe",
+                "Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,f54284e735a473f7b00c77f5b53907ef",
+                "Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,eceaf2971073ab49eb353a2923639c73",
+                "Sample23_3.CollectMultipleMetrics.quality_by_cycle.pdf:md5,53c6bf16f09c9948412f65c50416fc26",
+                "Sample23_3.CollectMultipleMetrics.quality_by_cycle_metrics:md5,06769662fe6b4070842df296826a531d",
+                "Sample23_3.CollectMultipleMetrics.quality_distribution.pdf:md5,d9321520fe03b89eedd3219fbca300d6",
+                "Sample23_3.CollectMultipleMetrics.quality_distribution_metrics:md5,6baab3bc053ae4dd6ea071bdb097fe7e",
+                "Sample23_3.CollectMultipleMetrics.read_length_histogram.pdf:md5,dcbf83be99d4f342b6c698d42cd5dff2",
+                "SampleA_2.CollectMultipleMetrics.alignment_summary_metrics:md5,fe0e859006038e3a356b9a9d2fd66543",
+                "SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,1caf9f96232026e97761d8cf88df8783",
+                "SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,dd62680e28364328fa99220db30cafa0",
+                "SampleA_2.CollectMultipleMetrics.quality_by_cycle.pdf:md5,686034e03e49d74204a411144ff3e7c5",
+                "SampleA_2.CollectMultipleMetrics.quality_by_cycle_metrics:md5,60c677d2f2b1bd7a052ee8898db59d35",
+                "SampleA_2.CollectMultipleMetrics.quality_distribution.pdf:md5,fe673e648312b7da7ad15e4ac526c42c",
+                "SampleA_2.CollectMultipleMetrics.quality_distribution_metrics:md5,97b5a9c7687efe3372a2aabc9b5ec26c",
+                "SampleA_2.CollectMultipleMetrics.read_length_histogram.pdf:md5,ed69bbb676bca398edc97bc929d238a2",
+                "Undetermined_5.CollectMultipleMetrics.alignment_summary_metrics:md5,fcee3fed5fde93c35a665835c549f831",
+                "Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,b0a111de6f31309ef9f8ae7fa99cb553",
+                "Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,b87ab8452ab19e4c669ba42b6b10e713",
+                "Undetermined_5.CollectMultipleMetrics.quality_by_cycle.pdf:md5,dd1a986e62943eff7c408a3e52dbaece",
+                "Undetermined_5.CollectMultipleMetrics.quality_by_cycle_metrics:md5,a11038a157986292c69e575755b9140c",
+                "Undetermined_5.CollectMultipleMetrics.quality_distribution.pdf:md5,e12f3e84923b367d615a9b7784038abb",
+                "Undetermined_5.CollectMultipleMetrics.quality_distribution_metrics:md5,e50d0fc09a1c748076504c399e5e2125",
+                "Undetermined_5.CollectMultipleMetrics.read_length_histogram.pdf:md5,42855e86f64b2564f5e330d6c1dd946c",
+                "sampletest_4.CollectMultipleMetrics.alignment_summary_metrics:md5,87087bb15f87990dee8d20fb0e62635d",
+                "sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,8d54a359aac536f1383879be7ad5ea84",
+                "sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,df0fc916316bb0abbda194aafc08eb8a",
+                "sampletest_4.CollectMultipleMetrics.quality_by_cycle.pdf:md5,186c1f945243bf5cfe847583a0b5118e",
+                "sampletest_4.CollectMultipleMetrics.quality_by_cycle_metrics:md5,880150f02dda8e9dc7ee8eec0c306c92",
+                "sampletest_4.CollectMultipleMetrics.quality_distribution.pdf:md5,58348681342ad24768a6527b2a543e39",
+                "sampletest_4.CollectMultipleMetrics.quality_distribution_metrics:md5,a20a199acfde26faa64def7923289ca2",
+                "sampletest_4.CollectMultipleMetrics.read_length_histogram.pdf:md5,dbd39add9ec6691ecaf9374d8e4482f0",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "Sample1_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
@@ -988,6 +988,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-02T13:01:54.708241331"
+        "timestamp": "2025-10-02T14:18:27.242016708"
     }
 }
\ No newline at end of file

From aca65c22f4615d2043c2d7457b32cd843a418b1d Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Tue, 7 Oct 2025 07:49:42 +0000
Subject: [PATCH 259/530] ss updated

---
 tests/MiSeq.main.nf.test.snap           | 36 +++++------
 tests/MiSeq_PairedEnd.main.nf.test.snap | 34 +++++-----
 tests/NovaSeq6000.main.nf.test.snap     | 82 ++++++++++++-------------
 3 files changed, 76 insertions(+), 76 deletions(-)

diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 6952d809..d7ca16d6 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -258,14 +258,14 @@
                 "picard_base_distribution_by_cycle__Undetermined.txt:md5,5451af67007a16e7645d0393011414af",
                 "picard_quality_by_cycle.txt:md5,46fbe44a9788f2e9184e2c1d689c2876",
                 "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics:md5,ed3f63631865ad7fc23996b35bf83a9f",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,3fc1bc4f7406431b3dd5f3c4ef65ada9",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,6caa70be0115a7fd39e10ce63dc4f3c5",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,ab974f45041a3aee28cefa408b080110",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,ed779b1f3bd38e950eca96b67f75257a",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf:md5,62a00a78195076bead47fe157bac0eb0",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics:md5,ab4aab082cd6c476e231da9219190dfc",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,fde51cf8632105a948fa9dfe120685a5",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics:md5,0915dbd5c8222f1a4b3447e3ca8c54bc",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,22a4abecac217c739a4c4f6bc82b0c12",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,0b3bb74a8ad8a0100637bdbba1e9240f",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,b361c12b170688d4a70118514623f152",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,e58b899f05b6f69fd0a7b3c2e544bd1d",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf:md5,352870a1403a46efeb0a6c230be8cf8c",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics:md5,be44d54ada8c71c45b131e99cca6cef3",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,2409eecbac134092f2d37b0db95a31cb",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
@@ -277,7 +277,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-02T14:13:43.824626734"
+        "timestamp": "2025-10-07T07:41:25.334642847"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
@@ -443,14 +443,14 @@
                 "picard_base_distribution_by_cycle__Undetermined.txt:md5,5451af67007a16e7645d0393011414af",
                 "picard_quality_by_cycle.txt:md5,46fbe44a9788f2e9184e2c1d689c2876",
                 "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics:md5,1945761cfd2ae3867d2501c92501bec8",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,60ea460dfdf3492dad641cd25718c6a4",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,fa2658eabc7e781992a36dba03ab7b82",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,586a3ab960b336d95510c11246eae64f",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,e7d06c7513174404acb71503fbbc680a",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf:md5,a7da049596f6f5570c81544c2191932b",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics:md5,bd3b7002a68884c3a321b389e1e0bc7d",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,279be05de3927b5a630bea8a5a580657",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics:md5,b206513b1471261da900edddeb49d137",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,249ab4225979bc722195f99dbff93149",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,83ce1f2330f4207823c8fafecd5fd155",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,0f2e5ef4d04365233680cb09fb512eb7",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,ae688aa2981ee86109b1a1671bf7a780",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf:md5,d8095576b6e5fe2a7f421d59fd220b79",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics:md5,5340c302b027a90b139585624ce835bf",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,5426727948d459147f33bc0790fbd5c7",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
@@ -462,6 +462,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-02T14:14:32.514637041"
+        "timestamp": "2025-10-07T07:42:21.005994558"
     }
 }
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index 282883ab..7aea9365 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -418,22 +418,22 @@
                 "picard_base_distribution_by_cycle__Undetermined.txt:md5,98f4e5ed094b41eb131d493b4f06bcd6",
                 "picard_quality_by_cycle.txt:md5,2634f306a33f648bac74bc7cd3253f9e",
                 "picard_quality_score_distribution.txt:md5,ecde9f0e859a6eecc5cea75a156c632d",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.alignment_summary_metrics:md5,1aaea22c85bfacc9e565ecbad97a48f2",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,618e7d053f73e962a0adafc6cbf9e1c7",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,6ef28db292d46c58345737e578acd3f0",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,1ed00499a498f4371a3d560f96a32653",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,91e5f40f0c0b93524f5da3fa56ca403a",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution.pdf:md5,e717e5bf81ec9710043dc5e754cc3e0a",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution_metrics:md5,4ad4825f7819a2ed15bb5ffcc70b62aa",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,0896a18be8f3094723abccaa9d3f3c16",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.alignment_summary_metrics:md5,cca4acec30c612bd477ed9610ce458b6",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,8f4a40f704ecfcb63d143bc2d51f4bf1",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,85fe6d86cb4de07dc6297fe019ef7572",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle.pdf:md5,40cfef04b143a79a65f0398363198b4c",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle_metrics:md5,b35ca2429ad7751f8b05dd7401128894",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution.pdf:md5,2efa7403d3b8fe094183bcbc484da4e9",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution_metrics:md5,6c33f13752c57581477e91588c05de75",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.read_length_histogram.pdf:md5,43fdc0db900ec88a5e72aa96fc9a330c",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.alignment_summary_metrics:md5,64cc6a7b2378439391cae9b5b0e0f419",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,8b98aa80f6b3aec49bf95e7e215d3e9a",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,0e0741e5a976e949dbfdc4adf5585c2b",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,40b9acffc396eccad2c3f3d31a909234",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,debc14fb114c9bf279ca609972e589d5",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution.pdf:md5,77bbbddf7a0dd152a1e86e263bd2a717",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution_metrics:md5,328383393e5763b06add503655ecb745",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,4d70c7d1edb6ce9a31b849dcfd9ec101",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.alignment_summary_metrics:md5,7b8b725d664d9aa14dde0830e66e8eb9",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,e04f52cd341463030aa2a8108c3192b5",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,9f4a521de9b2e73037053d01e21f91c4",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle.pdf:md5,2dd0c88c433752f157ecaf2b64e8696d",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle_metrics:md5,07910b950c1fdf9e9c1c2f254d7a6d4a",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution.pdf:md5,6b5f3ba0595d1668df89b0f25b50ef96",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution_metrics:md5,f98e5edb62bbf1190b2e2ca2417e0bbf",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.read_length_histogram.pdf:md5,f47c7d369c9db2fb9f0499fc064643bb",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "SAMPLE_PAIRED_END_1_1.bam.bai:md5,82724835c47f8e1d1a86e13ef469b464",
@@ -448,6 +448,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-02T14:16:07.09594705"
+        "timestamp": "2025-10-07T07:44:01.93145018"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index b23d8692..326abea8 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -925,46 +925,46 @@
                 "picard_base_distribution_by_cycle__Undetermined.txt:md5,1380831484d1b069a2fd4a20437118bf",
                 "picard_quality_by_cycle.txt:md5,b6fc46e18ac875ba02775e7cbf1b8e8b",
                 "picard_quality_score_distribution.txt:md5,1c17c01ef54a6062a8f1ca8408d32958",
-                "Sample1_1.CollectMultipleMetrics.alignment_summary_metrics:md5,06511dbac3b92992a13c867fe6177835",
-                "Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,fabc73f95c357c434726ce48e0222180",
-                "Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,18b2c01452318119f8f34d8ece375df4",
-                "Sample1_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,5310fded29bcdff6779478c3d69af841",
-                "Sample1_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,fc5d7e9ffcaf890844c82436b91c8d99",
-                "Sample1_1.CollectMultipleMetrics.quality_distribution.pdf:md5,537b7d686ae0ff5c1420b6f8bf1385b7",
-                "Sample1_1.CollectMultipleMetrics.quality_distribution_metrics:md5,f3e6fa9f787e6a111d368b075b7c8b8e",
-                "Sample1_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,61e77bc76d7bb08d6a1a963ab6725882",
-                "Sample23_3.CollectMultipleMetrics.alignment_summary_metrics:md5,11ffa4b14fd6c31d27ca0995ec5633fe",
-                "Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,f54284e735a473f7b00c77f5b53907ef",
-                "Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,eceaf2971073ab49eb353a2923639c73",
-                "Sample23_3.CollectMultipleMetrics.quality_by_cycle.pdf:md5,53c6bf16f09c9948412f65c50416fc26",
-                "Sample23_3.CollectMultipleMetrics.quality_by_cycle_metrics:md5,06769662fe6b4070842df296826a531d",
-                "Sample23_3.CollectMultipleMetrics.quality_distribution.pdf:md5,d9321520fe03b89eedd3219fbca300d6",
-                "Sample23_3.CollectMultipleMetrics.quality_distribution_metrics:md5,6baab3bc053ae4dd6ea071bdb097fe7e",
-                "Sample23_3.CollectMultipleMetrics.read_length_histogram.pdf:md5,dcbf83be99d4f342b6c698d42cd5dff2",
-                "SampleA_2.CollectMultipleMetrics.alignment_summary_metrics:md5,fe0e859006038e3a356b9a9d2fd66543",
-                "SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,1caf9f96232026e97761d8cf88df8783",
-                "SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,dd62680e28364328fa99220db30cafa0",
-                "SampleA_2.CollectMultipleMetrics.quality_by_cycle.pdf:md5,686034e03e49d74204a411144ff3e7c5",
-                "SampleA_2.CollectMultipleMetrics.quality_by_cycle_metrics:md5,60c677d2f2b1bd7a052ee8898db59d35",
-                "SampleA_2.CollectMultipleMetrics.quality_distribution.pdf:md5,fe673e648312b7da7ad15e4ac526c42c",
-                "SampleA_2.CollectMultipleMetrics.quality_distribution_metrics:md5,97b5a9c7687efe3372a2aabc9b5ec26c",
-                "SampleA_2.CollectMultipleMetrics.read_length_histogram.pdf:md5,ed69bbb676bca398edc97bc929d238a2",
-                "Undetermined_5.CollectMultipleMetrics.alignment_summary_metrics:md5,fcee3fed5fde93c35a665835c549f831",
-                "Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,b0a111de6f31309ef9f8ae7fa99cb553",
-                "Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,b87ab8452ab19e4c669ba42b6b10e713",
-                "Undetermined_5.CollectMultipleMetrics.quality_by_cycle.pdf:md5,dd1a986e62943eff7c408a3e52dbaece",
-                "Undetermined_5.CollectMultipleMetrics.quality_by_cycle_metrics:md5,a11038a157986292c69e575755b9140c",
-                "Undetermined_5.CollectMultipleMetrics.quality_distribution.pdf:md5,e12f3e84923b367d615a9b7784038abb",
-                "Undetermined_5.CollectMultipleMetrics.quality_distribution_metrics:md5,e50d0fc09a1c748076504c399e5e2125",
-                "Undetermined_5.CollectMultipleMetrics.read_length_histogram.pdf:md5,42855e86f64b2564f5e330d6c1dd946c",
-                "sampletest_4.CollectMultipleMetrics.alignment_summary_metrics:md5,87087bb15f87990dee8d20fb0e62635d",
-                "sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,8d54a359aac536f1383879be7ad5ea84",
-                "sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,df0fc916316bb0abbda194aafc08eb8a",
-                "sampletest_4.CollectMultipleMetrics.quality_by_cycle.pdf:md5,186c1f945243bf5cfe847583a0b5118e",
-                "sampletest_4.CollectMultipleMetrics.quality_by_cycle_metrics:md5,880150f02dda8e9dc7ee8eec0c306c92",
-                "sampletest_4.CollectMultipleMetrics.quality_distribution.pdf:md5,58348681342ad24768a6527b2a543e39",
-                "sampletest_4.CollectMultipleMetrics.quality_distribution_metrics:md5,a20a199acfde26faa64def7923289ca2",
-                "sampletest_4.CollectMultipleMetrics.read_length_histogram.pdf:md5,dbd39add9ec6691ecaf9374d8e4482f0",
+                "Sample1_1.CollectMultipleMetrics.alignment_summary_metrics:md5,e0271caf94ceb32e9892c1f30f8625e2",
+                "Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,769f0721fe04177fccc2f6dee4f38f32",
+                "Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,8bdbcb1c6c0d1d792ce76afc25245933",
+                "Sample1_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,80c49cc3c1b8b4bd88c0347642bc6a2b",
+                "Sample1_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,3c33865e078f2c9bfb333e60b18595d2",
+                "Sample1_1.CollectMultipleMetrics.quality_distribution.pdf:md5,8675d53a2532d1e87e7280919d5cad16",
+                "Sample1_1.CollectMultipleMetrics.quality_distribution_metrics:md5,4df577fd0c92e60558ad13630dd412eb",
+                "Sample1_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,b05331057d90885285ce020d6a2a4b76",
+                "Sample23_3.CollectMultipleMetrics.alignment_summary_metrics:md5,c928edffcc8414a1674704c6b439b702",
+                "Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,2b57120703aaa1503d716640c4181b44",
+                "Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,bcfda17c6861026f19e0e1e1e83a947b",
+                "Sample23_3.CollectMultipleMetrics.quality_by_cycle.pdf:md5,edc90bb8518521e7c40b6bd6fd79ae0e",
+                "Sample23_3.CollectMultipleMetrics.quality_by_cycle_metrics:md5,f7bce10eeecefcedcce83afa1ca2d0dd",
+                "Sample23_3.CollectMultipleMetrics.quality_distribution.pdf:md5,5d57a7466fe274b7df06742d06f1daa0",
+                "Sample23_3.CollectMultipleMetrics.quality_distribution_metrics:md5,04674f1e42b6599d5f7795d0cb4f5627",
+                "Sample23_3.CollectMultipleMetrics.read_length_histogram.pdf:md5,1d3fdfa052cc9abcd858ed7da28d563f",
+                "SampleA_2.CollectMultipleMetrics.alignment_summary_metrics:md5,6added883ad96913c335adfd278a157c",
+                "SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,f2baf396f002d356f4084f4fb164f9cc",
+                "SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,e90aa29142506d71195430fcdfc12dc0",
+                "SampleA_2.CollectMultipleMetrics.quality_by_cycle.pdf:md5,abe20908f7cd98552b7ab94b72e2220b",
+                "SampleA_2.CollectMultipleMetrics.quality_by_cycle_metrics:md5,10527e2b0a73553cc4696ae7e7ea4eb6",
+                "SampleA_2.CollectMultipleMetrics.quality_distribution.pdf:md5,ee81328dce6ea370b6d9bf2f768c79d5",
+                "SampleA_2.CollectMultipleMetrics.quality_distribution_metrics:md5,9848e2e48afa493435aa9dd3b3cd5782",
+                "SampleA_2.CollectMultipleMetrics.read_length_histogram.pdf:md5,bf7ce1532917cb89b9db4c31c7c87a19",
+                "Undetermined_5.CollectMultipleMetrics.alignment_summary_metrics:md5,49914534c704d78ffd5730616f9841b7",
+                "Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,d6f77cec55c81643b771f6c1172a98e9",
+                "Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,76d2b8cb7653145f719a6e642ae9e1e6",
+                "Undetermined_5.CollectMultipleMetrics.quality_by_cycle.pdf:md5,4e412a256e57e9e14b3f6dfeabf66601",
+                "Undetermined_5.CollectMultipleMetrics.quality_by_cycle_metrics:md5,67c0804d0f5d4a645ee000808f946e37",
+                "Undetermined_5.CollectMultipleMetrics.quality_distribution.pdf:md5,64f56d5a6f17b8a613b270ad9a3ea821",
+                "Undetermined_5.CollectMultipleMetrics.quality_distribution_metrics:md5,7e2218c4c39c0249fd3b5a768171c69e",
+                "Undetermined_5.CollectMultipleMetrics.read_length_histogram.pdf:md5,5cbf922379d19e64006480b9ad849397",
+                "sampletest_4.CollectMultipleMetrics.alignment_summary_metrics:md5,2361427d20d8d1b615ac0ae8d00a1837",
+                "sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,0a237c1bbd30239bb34353635829920f",
+                "sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,64f8ca772ccadb270459080c719033d1",
+                "sampletest_4.CollectMultipleMetrics.quality_by_cycle.pdf:md5,dbf12c82e9a8d7f42cc23543eb613dce",
+                "sampletest_4.CollectMultipleMetrics.quality_by_cycle_metrics:md5,372c3624cdf93f7c4a1c033c82530a88",
+                "sampletest_4.CollectMultipleMetrics.quality_distribution.pdf:md5,3cc7a3e4c858b033852539ff9bdca1ea",
+                "sampletest_4.CollectMultipleMetrics.quality_distribution_metrics:md5,1703808779864f9f1496222cd2a1eaa2",
+                "sampletest_4.CollectMultipleMetrics.read_length_histogram.pdf:md5,33dc1cf6a40e36ad7500b0c2f4ec92dc",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "Sample1_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
@@ -988,6 +988,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-02T14:18:27.242016708"
+        "timestamp": "2025-10-07T07:46:16.479395763"
     }
 }
\ No newline at end of file

From a9909d997c61a81be5e8d3f0751dcd5280a239b5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pontus=20H=C3=B6jer?= <pontushojer@gmail.com>
Date: Tue, 7 Oct 2025 10:02:50 +0200
Subject: [PATCH 260/530] cleanups

---
 assets/multiqc_config.yml                                     | 2 +-
 subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 55658f08..b958b5f2 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -15,7 +15,7 @@ export_plots: true
 disable_version_detection: true
 
 fn_clean_trim:
- - "_screen" # Added by FastqScreen
+  - "_screen" # Added by FastqScreen
 
 # Make sample name with indexes a bit prettier
 # for SE: "SampleName_01" -> "SampleName #01"
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index 1242dee8..4a41879c 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -73,7 +73,7 @@ workflow PIPELINE_INITIALISATION {
     //
     nr_samples = Channel.fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
         .toList().size()
-        
+
     Channel
         .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
         .toList()

From 8fb8715891f6b234128c1d438d6fd264c9ddf8f2 Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Tue, 7 Oct 2025 08:25:57 +0000
Subject: [PATCH 261/530] ss

---
 tests/.nftignore                        | 42 +++++++------
 tests/MiSeq.main.nf.test.snap           | 36 +++++------
 tests/MiSeq_PairedEnd.main.nf.test.snap | 34 +++++-----
 tests/NovaSeq6000.main.nf.test.snap     | 82 ++++++++++++-------------
 4 files changed, 98 insertions(+), 96 deletions(-)

diff --git a/tests/.nftignore b/tests/.nftignore
index 97d6e47f..ce0e4184 100644
--- a/tests/.nftignore
+++ b/tests/.nftignore
@@ -1,21 +1,23 @@
-multiqc/{global_report,group_reports/*}/multiqc_data/multiqc.log
-multiqc/{global_report,group_reports/*}/multiqc_data/multiqc_data.json
-multiqc/{global_report,group_reports/*}/multiqc_data/multiqc_general_stats.txt
-multiqc/{global_report,group_reports/*}/multiqc_data/multiqc_software_versions.txt
-multiqc/{global_report,group_reports/*}/multiqc_data/multiqc_sources.txt
-multiqc/{global_report,group_reports/*}/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
-multiqc/{global_report,group_reports/*}/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
-multiqc/{global_report,group_reports/*}/multiqc_report.html
-pipeline_info/*.{html,json,txt,yml}
-fastqscreen/*_screen.html
-fastqc/*_fastqc.html
-fastqc/*_fastqc.zip
+multiqc/global_report/multiqc_data/multiqc.log
+multiqc/global_report/multiqc_data/multiqc_data.json
+multiqc/global_report/multiqc_data/multiqc_general_stats.txt
+multiqc/global_report/multiqc_data/multiqc_software_versions.txt
+multiqc/global_report/multiqc_data/multiqc_sources.txt
+multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
+multiqc/global_report/multiqc_plots/**/*.svg
+multiqc/global_report/multiqc_plots/**/*.pdf
+multiqc/global_report/multiqc_plots/**/*.png
+multiqc/global_report/multiqc_report.html
 
-picard_collectmultiplemetrics/CollectMultipleMetrics.alignment_summary_metrics
-picard_collectmultiplemetrics/CollectMultipleMetrics.base_distribution_by_cycle.pdf
-picard_collectmultiplemetrics/CollectMultipleMetrics.base_distribution_by_cycle_metrics
-picard_collectmultiplemetrics/CollectMultipleMetrics.quality_by_cycle.pdf
-picard_collectmultiplemetrics/CollectMultipleMetrics.quality_by_cycle_metrics
-picard_collectmultiplemetrics/CollectMultipleMetrics.quality_distribution.pdf
-picard_collectmultiplemetrics/CollectMultipleMetrics.quality_distribution_metrics
-picard_collectmultiplemetrics/CollectMultipleMetrics.read_length_histogram.pdf
+multiqc/group_reports/*/multiqc_data/multiqc.log
+multiqc/group_reports/*/multiqc_data/multiqc_data.json
+multiqc/group_reports/*/multiqc_data/multiqc_general_stats.txt
+multiqc/group_reports/*/multiqc_data/multiqc_software_versions.txt
+multiqc/group_reports/*/multiqc_data/multiqc_sources.txt
+multiqc/group_reports/*/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
+multiqc/group_reports/*/multiqc_plots/**/*.svg
+multiqc/group_reports/*/multiqc_plots/**/*.pdf
+multiqc/group_reports/*/multiqc_plots/**/*.png
+multiqc/group_reports/*/multiqc_report.html
+
+picard_collectmultiplemetrics/CollectMultipleMetrics.*
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index d7ca16d6..edb6603e 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -258,14 +258,14 @@
                 "picard_base_distribution_by_cycle__Undetermined.txt:md5,5451af67007a16e7645d0393011414af",
                 "picard_quality_by_cycle.txt:md5,46fbe44a9788f2e9184e2c1d689c2876",
                 "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics:md5,0915dbd5c8222f1a4b3447e3ca8c54bc",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,22a4abecac217c739a4c4f6bc82b0c12",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,0b3bb74a8ad8a0100637bdbba1e9240f",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,b361c12b170688d4a70118514623f152",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,e58b899f05b6f69fd0a7b3c2e544bd1d",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf:md5,352870a1403a46efeb0a6c230be8cf8c",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics:md5,be44d54ada8c71c45b131e99cca6cef3",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,2409eecbac134092f2d37b0db95a31cb",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics:md5,c9b706b6dfc96101aac59307ecc759ad",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,2e4613849abf1f0542a3d9ddbe359a56",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,12bd2ffe9ee28218455f62c69cbdeeec",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,d01a625914a989e0d4b43b9abcd04d59",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,03d12f8f1bb6c493f93c122533073724",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf:md5,7582da6777bd48398b9139f3a1c83d3a",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics:md5,9c67dac65001f69e1c7fa3335b5a13cf",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,720d9526ecc44b4ce749f34f52be4296",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
@@ -277,7 +277,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-07T07:41:25.334642847"
+        "timestamp": "2025-10-07T08:11:25.9098161"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
@@ -443,14 +443,14 @@
                 "picard_base_distribution_by_cycle__Undetermined.txt:md5,5451af67007a16e7645d0393011414af",
                 "picard_quality_by_cycle.txt:md5,46fbe44a9788f2e9184e2c1d689c2876",
                 "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics:md5,b206513b1471261da900edddeb49d137",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,249ab4225979bc722195f99dbff93149",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,83ce1f2330f4207823c8fafecd5fd155",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,0f2e5ef4d04365233680cb09fb512eb7",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,ae688aa2981ee86109b1a1671bf7a780",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf:md5,d8095576b6e5fe2a7f421d59fd220b79",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics:md5,5340c302b027a90b139585624ce835bf",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,5426727948d459147f33bc0790fbd5c7",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics:md5,936e7467e71d1d3db75d44ffb7538a3f",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,4bb1adaee56eff4c1a094893d07eaeb9",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,0b71b2c9064d81206fb20c3e03b365dc",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,6cf5c3f833c9a01c3be8788344cd6548",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,500dd6e858e670b968d4398b627e81cc",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf:md5,39aed52abbbca6b7dc23112399ee9327",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics:md5,78d199953999c2d31ca8e4ad91cb0716",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,532adafe681c023e4bac68c3f2cee5b1",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
@@ -462,6 +462,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-07T07:42:21.005994558"
+        "timestamp": "2025-10-07T08:12:14.250499004"
     }
 }
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index 7aea9365..93056282 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -418,22 +418,22 @@
                 "picard_base_distribution_by_cycle__Undetermined.txt:md5,98f4e5ed094b41eb131d493b4f06bcd6",
                 "picard_quality_by_cycle.txt:md5,2634f306a33f648bac74bc7cd3253f9e",
                 "picard_quality_score_distribution.txt:md5,ecde9f0e859a6eecc5cea75a156c632d",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.alignment_summary_metrics:md5,64cc6a7b2378439391cae9b5b0e0f419",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,8b98aa80f6b3aec49bf95e7e215d3e9a",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,0e0741e5a976e949dbfdc4adf5585c2b",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,40b9acffc396eccad2c3f3d31a909234",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,debc14fb114c9bf279ca609972e589d5",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution.pdf:md5,77bbbddf7a0dd152a1e86e263bd2a717",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution_metrics:md5,328383393e5763b06add503655ecb745",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,4d70c7d1edb6ce9a31b849dcfd9ec101",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.alignment_summary_metrics:md5,7b8b725d664d9aa14dde0830e66e8eb9",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,e04f52cd341463030aa2a8108c3192b5",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,9f4a521de9b2e73037053d01e21f91c4",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle.pdf:md5,2dd0c88c433752f157ecaf2b64e8696d",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle_metrics:md5,07910b950c1fdf9e9c1c2f254d7a6d4a",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution.pdf:md5,6b5f3ba0595d1668df89b0f25b50ef96",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution_metrics:md5,f98e5edb62bbf1190b2e2ca2417e0bbf",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.read_length_histogram.pdf:md5,f47c7d369c9db2fb9f0499fc064643bb",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.alignment_summary_metrics:md5,57867f2256ba20432c1d3f4e05b859cb",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,424a7301c75d420be14b82e306c8e7ac",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,6d038e0e3199130d39495ef1578e5fc0",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,2a5bf91d08150498624850bc9e3c31d3",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,8c2f8718a58383329a9e7705734ff061",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution.pdf:md5,60dc5954e74690b1fa48f56341894c33",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution_metrics:md5,a3b1f0d7602953780a28d0b20ae40423",
+                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,4596354348f4c07cd51797e71049d6d5",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.alignment_summary_metrics:md5,b4839168ccf4ce0e264f47186e63e24a",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,66956caa820952d0aac7b1a9632e8001",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,1bbf264e071decd795993f8c20bf4e46",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle.pdf:md5,f96185989f1be989426de3482177684c",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle_metrics:md5,23594926727c09a33e1c167c34882ca7",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution.pdf:md5,c0668ba3e6326417b1f8fa2a7670c530",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution_metrics:md5,3e8465e540fc2b1101675618cd067a54",
+                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.read_length_histogram.pdf:md5,7e54241d39ac011af0818a72a695d926",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "SAMPLE_PAIRED_END_1_1.bam.bai:md5,82724835c47f8e1d1a86e13ef469b464",
@@ -448,6 +448,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-07T07:44:01.93145018"
+        "timestamp": "2025-10-07T08:13:51.663791761"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index 326abea8..fb24c596 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -925,46 +925,46 @@
                 "picard_base_distribution_by_cycle__Undetermined.txt:md5,1380831484d1b069a2fd4a20437118bf",
                 "picard_quality_by_cycle.txt:md5,b6fc46e18ac875ba02775e7cbf1b8e8b",
                 "picard_quality_score_distribution.txt:md5,1c17c01ef54a6062a8f1ca8408d32958",
-                "Sample1_1.CollectMultipleMetrics.alignment_summary_metrics:md5,e0271caf94ceb32e9892c1f30f8625e2",
-                "Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,769f0721fe04177fccc2f6dee4f38f32",
-                "Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,8bdbcb1c6c0d1d792ce76afc25245933",
-                "Sample1_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,80c49cc3c1b8b4bd88c0347642bc6a2b",
-                "Sample1_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,3c33865e078f2c9bfb333e60b18595d2",
-                "Sample1_1.CollectMultipleMetrics.quality_distribution.pdf:md5,8675d53a2532d1e87e7280919d5cad16",
-                "Sample1_1.CollectMultipleMetrics.quality_distribution_metrics:md5,4df577fd0c92e60558ad13630dd412eb",
-                "Sample1_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,b05331057d90885285ce020d6a2a4b76",
-                "Sample23_3.CollectMultipleMetrics.alignment_summary_metrics:md5,c928edffcc8414a1674704c6b439b702",
-                "Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,2b57120703aaa1503d716640c4181b44",
-                "Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,bcfda17c6861026f19e0e1e1e83a947b",
-                "Sample23_3.CollectMultipleMetrics.quality_by_cycle.pdf:md5,edc90bb8518521e7c40b6bd6fd79ae0e",
-                "Sample23_3.CollectMultipleMetrics.quality_by_cycle_metrics:md5,f7bce10eeecefcedcce83afa1ca2d0dd",
-                "Sample23_3.CollectMultipleMetrics.quality_distribution.pdf:md5,5d57a7466fe274b7df06742d06f1daa0",
-                "Sample23_3.CollectMultipleMetrics.quality_distribution_metrics:md5,04674f1e42b6599d5f7795d0cb4f5627",
-                "Sample23_3.CollectMultipleMetrics.read_length_histogram.pdf:md5,1d3fdfa052cc9abcd858ed7da28d563f",
-                "SampleA_2.CollectMultipleMetrics.alignment_summary_metrics:md5,6added883ad96913c335adfd278a157c",
-                "SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,f2baf396f002d356f4084f4fb164f9cc",
-                "SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,e90aa29142506d71195430fcdfc12dc0",
-                "SampleA_2.CollectMultipleMetrics.quality_by_cycle.pdf:md5,abe20908f7cd98552b7ab94b72e2220b",
-                "SampleA_2.CollectMultipleMetrics.quality_by_cycle_metrics:md5,10527e2b0a73553cc4696ae7e7ea4eb6",
-                "SampleA_2.CollectMultipleMetrics.quality_distribution.pdf:md5,ee81328dce6ea370b6d9bf2f768c79d5",
-                "SampleA_2.CollectMultipleMetrics.quality_distribution_metrics:md5,9848e2e48afa493435aa9dd3b3cd5782",
-                "SampleA_2.CollectMultipleMetrics.read_length_histogram.pdf:md5,bf7ce1532917cb89b9db4c31c7c87a19",
-                "Undetermined_5.CollectMultipleMetrics.alignment_summary_metrics:md5,49914534c704d78ffd5730616f9841b7",
-                "Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,d6f77cec55c81643b771f6c1172a98e9",
-                "Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,76d2b8cb7653145f719a6e642ae9e1e6",
-                "Undetermined_5.CollectMultipleMetrics.quality_by_cycle.pdf:md5,4e412a256e57e9e14b3f6dfeabf66601",
-                "Undetermined_5.CollectMultipleMetrics.quality_by_cycle_metrics:md5,67c0804d0f5d4a645ee000808f946e37",
-                "Undetermined_5.CollectMultipleMetrics.quality_distribution.pdf:md5,64f56d5a6f17b8a613b270ad9a3ea821",
-                "Undetermined_5.CollectMultipleMetrics.quality_distribution_metrics:md5,7e2218c4c39c0249fd3b5a768171c69e",
-                "Undetermined_5.CollectMultipleMetrics.read_length_histogram.pdf:md5,5cbf922379d19e64006480b9ad849397",
-                "sampletest_4.CollectMultipleMetrics.alignment_summary_metrics:md5,2361427d20d8d1b615ac0ae8d00a1837",
-                "sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,0a237c1bbd30239bb34353635829920f",
-                "sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,64f8ca772ccadb270459080c719033d1",
-                "sampletest_4.CollectMultipleMetrics.quality_by_cycle.pdf:md5,dbf12c82e9a8d7f42cc23543eb613dce",
-                "sampletest_4.CollectMultipleMetrics.quality_by_cycle_metrics:md5,372c3624cdf93f7c4a1c033c82530a88",
-                "sampletest_4.CollectMultipleMetrics.quality_distribution.pdf:md5,3cc7a3e4c858b033852539ff9bdca1ea",
-                "sampletest_4.CollectMultipleMetrics.quality_distribution_metrics:md5,1703808779864f9f1496222cd2a1eaa2",
-                "sampletest_4.CollectMultipleMetrics.read_length_histogram.pdf:md5,33dc1cf6a40e36ad7500b0c2f4ec92dc",
+                "Sample1_1.CollectMultipleMetrics.alignment_summary_metrics:md5,9db87430c82b624988fd30707f2943ac",
+                "Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,5912e7d1dbc0ace24ce19414dfc78fbd",
+                "Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,509515866b2c8f979ac48546aba7f570",
+                "Sample1_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,30c949f93878bc999965597c704e44a0",
+                "Sample1_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,569c851394c4f7df2e2bdf8637c99bf5",
+                "Sample1_1.CollectMultipleMetrics.quality_distribution.pdf:md5,90c0bb85b8037bee6f72fdd1c0155d5d",
+                "Sample1_1.CollectMultipleMetrics.quality_distribution_metrics:md5,34974dccfbee156b9e068a971de1266e",
+                "Sample1_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,39e862b85372c24f2512bee8500deb37",
+                "Sample23_3.CollectMultipleMetrics.alignment_summary_metrics:md5,8fe69452d308faa0fd7e0b2893814e2c",
+                "Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,47a119e987a99bfc5be63cdcfec28f61",
+                "Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,3fcea7c387727bc47535b28246d43a84",
+                "Sample23_3.CollectMultipleMetrics.quality_by_cycle.pdf:md5,89a3875b9b3e363f35012d70dbb0621e",
+                "Sample23_3.CollectMultipleMetrics.quality_by_cycle_metrics:md5,9d84faf534d4089021a3623a2c55bdea",
+                "Sample23_3.CollectMultipleMetrics.quality_distribution.pdf:md5,79788c5f6375379c18024187307d0891",
+                "Sample23_3.CollectMultipleMetrics.quality_distribution_metrics:md5,72e1f0ffcd68f9f3ef90da3e8b3f4232",
+                "Sample23_3.CollectMultipleMetrics.read_length_histogram.pdf:md5,28dac379d54cde0ac9d050cdebad85c7",
+                "SampleA_2.CollectMultipleMetrics.alignment_summary_metrics:md5,a1f2961ba01da36b3341f2ffdf26341c",
+                "SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,6eec4f08679ad54f8dea6d6a357ee2fa",
+                "SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,306532621f8cf1cd408f9f62d5a179eb",
+                "SampleA_2.CollectMultipleMetrics.quality_by_cycle.pdf:md5,fcedd2d195845cecb868355a7cccfd85",
+                "SampleA_2.CollectMultipleMetrics.quality_by_cycle_metrics:md5,36244f989bf1c3263057a4bd01950b51",
+                "SampleA_2.CollectMultipleMetrics.quality_distribution.pdf:md5,ace8904eec1e9876d6795bf9e90e255f",
+                "SampleA_2.CollectMultipleMetrics.quality_distribution_metrics:md5,81c5ad8c8b93fd3bb2413c5fc409233b",
+                "SampleA_2.CollectMultipleMetrics.read_length_histogram.pdf:md5,14aaf2998d990fcd395faaabfe5e1a6b",
+                "Undetermined_5.CollectMultipleMetrics.alignment_summary_metrics:md5,196e5be4a0f07bf96626621327f6c04c",
+                "Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,4240f21ef6bc4db1300df0cbe7159287",
+                "Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,438cf29baa86b8f9e50adf14d9f82684",
+                "Undetermined_5.CollectMultipleMetrics.quality_by_cycle.pdf:md5,4abc14a3b2b1cdf83c05013cfd88a374",
+                "Undetermined_5.CollectMultipleMetrics.quality_by_cycle_metrics:md5,d5512259377d3f58bc1ff42ddbe45769",
+                "Undetermined_5.CollectMultipleMetrics.quality_distribution.pdf:md5,69cb249b5bc5df8be9a3c70b92f834ae",
+                "Undetermined_5.CollectMultipleMetrics.quality_distribution_metrics:md5,42263d64158897b6e24820df922bed99",
+                "Undetermined_5.CollectMultipleMetrics.read_length_histogram.pdf:md5,0081788631f21776f9ab5386f7d5348e",
+                "sampletest_4.CollectMultipleMetrics.alignment_summary_metrics:md5,ceab59dfb761c11cb3e8f95c81b83233",
+                "sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,682e627825fa3c846f53097ea95d2c23",
+                "sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,dcafb5fd8139b0bae47786304b63ebad",
+                "sampletest_4.CollectMultipleMetrics.quality_by_cycle.pdf:md5,65f79c9d285489529a8740bb2cd29fea",
+                "sampletest_4.CollectMultipleMetrics.quality_by_cycle_metrics:md5,fb327fbd116453eeeab764bff349b7d9",
+                "sampletest_4.CollectMultipleMetrics.quality_distribution.pdf:md5,ce58b9606d7957d4b9a8cbb64ee8a8d7",
+                "sampletest_4.CollectMultipleMetrics.quality_distribution_metrics:md5,9b8f055101fbc1289b7aaf364be64e9e",
+                "sampletest_4.CollectMultipleMetrics.read_length_histogram.pdf:md5,bc66c51ead21b9f6684d23212b74542e",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "Sample1_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
@@ -988,6 +988,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-07T07:46:16.479395763"
+        "timestamp": "2025-10-07T08:16:08.606134205"
     }
 }
\ No newline at end of file

From f67dc844a4ebbc25142a557a25afd020f8ee364a Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Tue, 7 Oct 2025 08:52:52 +0000
Subject: [PATCH 262/530] ss

---
 tests/.nftignore                        | 37 +++++++++-------------
 tests/MiSeq.main.nf.test.snap           | 28 ++++++-----------
 tests/MiSeq_PairedEnd.main.nf.test.snap | 18 +----------
 tests/NovaSeq6000.main.nf.test.snap     | 42 +------------------------
 4 files changed, 27 insertions(+), 98 deletions(-)

diff --git a/tests/.nftignore b/tests/.nftignore
index ce0e4184..f368b8fb 100644
--- a/tests/.nftignore
+++ b/tests/.nftignore
@@ -1,23 +1,16 @@
-multiqc/global_report/multiqc_data/multiqc.log
-multiqc/global_report/multiqc_data/multiqc_data.json
-multiqc/global_report/multiqc_data/multiqc_general_stats.txt
-multiqc/global_report/multiqc_data/multiqc_software_versions.txt
-multiqc/global_report/multiqc_data/multiqc_sources.txt
-multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
-multiqc/global_report/multiqc_plots/**/*.svg
-multiqc/global_report/multiqc_plots/**/*.pdf
-multiqc/global_report/multiqc_plots/**/*.png
-multiqc/global_report/multiqc_report.html
+multiqc/{global_report,group_reports/*}/multiqc_data/multiqc.log
+multiqc/{global_report,group_reports/*}/multiqc_data/multiqc_data.json
+multiqc/{global_report,group_reports/*}/multiqc_data/multiqc_general_stats.txt
+multiqc/{global_report,group_reports/*}/multiqc_data/multiqc_software_versions.txt
+multiqc/{global_report,group_reports/*}/multiqc_data/multiqc_sources.txt
+multiqc/{global_report,group_reports/*}/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
+multiqc/{global_report,group_reports/*}/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
+multiqc/{global_report,group_reports/*}/multiqc_report.html
+pipeline_info/*.{html,json,txt,yml}
+fastqscreen/*_screen.html
+fastqc/*_fastqc.html
+fastqc/*_fastqc.zip
+picard_collectmultiplemetrics/*.{pdf}
+picard_collectmultiplemetrics/*_metrics
+picard_collectmultiplemetrics/*_summary_metrics
 
-multiqc/group_reports/*/multiqc_data/multiqc.log
-multiqc/group_reports/*/multiqc_data/multiqc_data.json
-multiqc/group_reports/*/multiqc_data/multiqc_general_stats.txt
-multiqc/group_reports/*/multiqc_data/multiqc_software_versions.txt
-multiqc/group_reports/*/multiqc_data/multiqc_sources.txt
-multiqc/group_reports/*/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
-multiqc/group_reports/*/multiqc_plots/**/*.svg
-multiqc/group_reports/*/multiqc_plots/**/*.pdf
-multiqc/group_reports/*/multiqc_plots/**/*.png
-multiqc/group_reports/*/multiqc_report.html
-
-picard_collectmultiplemetrics/CollectMultipleMetrics.*
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index edb6603e..5eafb0a3 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -258,14 +258,10 @@
                 "picard_base_distribution_by_cycle__Undetermined.txt:md5,5451af67007a16e7645d0393011414af",
                 "picard_quality_by_cycle.txt:md5,46fbe44a9788f2e9184e2c1d689c2876",
                 "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics:md5,c9b706b6dfc96101aac59307ecc759ad",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,2e4613849abf1f0542a3d9ddbe359a56",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,12bd2ffe9ee28218455f62c69cbdeeec",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,d01a625914a989e0d4b43b9abcd04d59",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,03d12f8f1bb6c493f93c122533073724",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf:md5,7582da6777bd48398b9139f3a1c83d3a",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics:md5,9c67dac65001f69e1c7fa3335b5a13cf",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,720d9526ecc44b4ce749f34f52be4296",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics:md5,1908cd9278b61eb99088415e7e3ddd4b",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,2f17706448e1809713b45318c5bb296f",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,36a24ef4e50ee914cc616c8dbf669060",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics:md5,892945b3fba6cf9f4404ad7e2a705f12",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
@@ -277,7 +273,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-07T08:11:25.9098161"
+        "timestamp": "2025-10-07T08:36:46.667146476"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
@@ -443,14 +439,10 @@
                 "picard_base_distribution_by_cycle__Undetermined.txt:md5,5451af67007a16e7645d0393011414af",
                 "picard_quality_by_cycle.txt:md5,46fbe44a9788f2e9184e2c1d689c2876",
                 "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics:md5,936e7467e71d1d3db75d44ffb7538a3f",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,4bb1adaee56eff4c1a094893d07eaeb9",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,0b71b2c9064d81206fb20c3e03b365dc",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,6cf5c3f833c9a01c3be8788344cd6548",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,500dd6e858e670b968d4398b627e81cc",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf:md5,39aed52abbbca6b7dc23112399ee9327",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics:md5,78d199953999c2d31ca8e4ad91cb0716",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,532adafe681c023e4bac68c3f2cee5b1",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics:md5,aa301637ed9c1b1fbfa7a1de4cf2383d",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,79083e5d6e2477101abcf973884cb942",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,d8d0d5f2cf02b11c6bcec05e9a4008a4",
+                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics:md5,bbd960f2bd28054fb9bd588393d4255b",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
@@ -462,6 +454,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-07T08:12:14.250499004"
+        "timestamp": "2025-10-07T08:37:34.627849865"
     }
 }
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index 93056282..6946409a 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -418,22 +418,6 @@
                 "picard_base_distribution_by_cycle__Undetermined.txt:md5,98f4e5ed094b41eb131d493b4f06bcd6",
                 "picard_quality_by_cycle.txt:md5,2634f306a33f648bac74bc7cd3253f9e",
                 "picard_quality_score_distribution.txt:md5,ecde9f0e859a6eecc5cea75a156c632d",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.alignment_summary_metrics:md5,57867f2256ba20432c1d3f4e05b859cb",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,424a7301c75d420be14b82e306c8e7ac",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,6d038e0e3199130d39495ef1578e5fc0",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,2a5bf91d08150498624850bc9e3c31d3",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,8c2f8718a58383329a9e7705734ff061",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution.pdf:md5,60dc5954e74690b1fa48f56341894c33",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution_metrics:md5,a3b1f0d7602953780a28d0b20ae40423",
-                "SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,4596354348f4c07cd51797e71049d6d5",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.alignment_summary_metrics:md5,b4839168ccf4ce0e264f47186e63e24a",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,66956caa820952d0aac7b1a9632e8001",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,1bbf264e071decd795993f8c20bf4e46",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle.pdf:md5,f96185989f1be989426de3482177684c",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle_metrics:md5,23594926727c09a33e1c167c34882ca7",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution.pdf:md5,c0668ba3e6326417b1f8fa2a7670c530",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution_metrics:md5,3e8465e540fc2b1101675618cd067a54",
-                "SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.read_length_histogram.pdf:md5,7e54241d39ac011af0818a72a695d926",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "SAMPLE_PAIRED_END_1_1.bam.bai:md5,82724835c47f8e1d1a86e13ef469b464",
@@ -448,6 +432,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-07T08:13:51.663791761"
+        "timestamp": "2025-10-07T08:39:14.939736631"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index fb24c596..c91e0e33 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -925,46 +925,6 @@
                 "picard_base_distribution_by_cycle__Undetermined.txt:md5,1380831484d1b069a2fd4a20437118bf",
                 "picard_quality_by_cycle.txt:md5,b6fc46e18ac875ba02775e7cbf1b8e8b",
                 "picard_quality_score_distribution.txt:md5,1c17c01ef54a6062a8f1ca8408d32958",
-                "Sample1_1.CollectMultipleMetrics.alignment_summary_metrics:md5,9db87430c82b624988fd30707f2943ac",
-                "Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,5912e7d1dbc0ace24ce19414dfc78fbd",
-                "Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,509515866b2c8f979ac48546aba7f570",
-                "Sample1_1.CollectMultipleMetrics.quality_by_cycle.pdf:md5,30c949f93878bc999965597c704e44a0",
-                "Sample1_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,569c851394c4f7df2e2bdf8637c99bf5",
-                "Sample1_1.CollectMultipleMetrics.quality_distribution.pdf:md5,90c0bb85b8037bee6f72fdd1c0155d5d",
-                "Sample1_1.CollectMultipleMetrics.quality_distribution_metrics:md5,34974dccfbee156b9e068a971de1266e",
-                "Sample1_1.CollectMultipleMetrics.read_length_histogram.pdf:md5,39e862b85372c24f2512bee8500deb37",
-                "Sample23_3.CollectMultipleMetrics.alignment_summary_metrics:md5,8fe69452d308faa0fd7e0b2893814e2c",
-                "Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,47a119e987a99bfc5be63cdcfec28f61",
-                "Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,3fcea7c387727bc47535b28246d43a84",
-                "Sample23_3.CollectMultipleMetrics.quality_by_cycle.pdf:md5,89a3875b9b3e363f35012d70dbb0621e",
-                "Sample23_3.CollectMultipleMetrics.quality_by_cycle_metrics:md5,9d84faf534d4089021a3623a2c55bdea",
-                "Sample23_3.CollectMultipleMetrics.quality_distribution.pdf:md5,79788c5f6375379c18024187307d0891",
-                "Sample23_3.CollectMultipleMetrics.quality_distribution_metrics:md5,72e1f0ffcd68f9f3ef90da3e8b3f4232",
-                "Sample23_3.CollectMultipleMetrics.read_length_histogram.pdf:md5,28dac379d54cde0ac9d050cdebad85c7",
-                "SampleA_2.CollectMultipleMetrics.alignment_summary_metrics:md5,a1f2961ba01da36b3341f2ffdf26341c",
-                "SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,6eec4f08679ad54f8dea6d6a357ee2fa",
-                "SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,306532621f8cf1cd408f9f62d5a179eb",
-                "SampleA_2.CollectMultipleMetrics.quality_by_cycle.pdf:md5,fcedd2d195845cecb868355a7cccfd85",
-                "SampleA_2.CollectMultipleMetrics.quality_by_cycle_metrics:md5,36244f989bf1c3263057a4bd01950b51",
-                "SampleA_2.CollectMultipleMetrics.quality_distribution.pdf:md5,ace8904eec1e9876d6795bf9e90e255f",
-                "SampleA_2.CollectMultipleMetrics.quality_distribution_metrics:md5,81c5ad8c8b93fd3bb2413c5fc409233b",
-                "SampleA_2.CollectMultipleMetrics.read_length_histogram.pdf:md5,14aaf2998d990fcd395faaabfe5e1a6b",
-                "Undetermined_5.CollectMultipleMetrics.alignment_summary_metrics:md5,196e5be4a0f07bf96626621327f6c04c",
-                "Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,4240f21ef6bc4db1300df0cbe7159287",
-                "Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,438cf29baa86b8f9e50adf14d9f82684",
-                "Undetermined_5.CollectMultipleMetrics.quality_by_cycle.pdf:md5,4abc14a3b2b1cdf83c05013cfd88a374",
-                "Undetermined_5.CollectMultipleMetrics.quality_by_cycle_metrics:md5,d5512259377d3f58bc1ff42ddbe45769",
-                "Undetermined_5.CollectMultipleMetrics.quality_distribution.pdf:md5,69cb249b5bc5df8be9a3c70b92f834ae",
-                "Undetermined_5.CollectMultipleMetrics.quality_distribution_metrics:md5,42263d64158897b6e24820df922bed99",
-                "Undetermined_5.CollectMultipleMetrics.read_length_histogram.pdf:md5,0081788631f21776f9ab5386f7d5348e",
-                "sampletest_4.CollectMultipleMetrics.alignment_summary_metrics:md5,ceab59dfb761c11cb3e8f95c81b83233",
-                "sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,682e627825fa3c846f53097ea95d2c23",
-                "sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,dcafb5fd8139b0bae47786304b63ebad",
-                "sampletest_4.CollectMultipleMetrics.quality_by_cycle.pdf:md5,65f79c9d285489529a8740bb2cd29fea",
-                "sampletest_4.CollectMultipleMetrics.quality_by_cycle_metrics:md5,fb327fbd116453eeeab764bff349b7d9",
-                "sampletest_4.CollectMultipleMetrics.quality_distribution.pdf:md5,ce58b9606d7957d4b9a8cbb64ee8a8d7",
-                "sampletest_4.CollectMultipleMetrics.quality_distribution_metrics:md5,9b8f055101fbc1289b7aaf364be64e9e",
-                "sampletest_4.CollectMultipleMetrics.read_length_histogram.pdf:md5,bc66c51ead21b9f6684d23212b74542e",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "Sample1_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
@@ -988,6 +948,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-07T08:16:08.606134205"
+        "timestamp": "2025-10-07T08:41:26.564395156"
     }
 }
\ No newline at end of file

From 51e7c834fdeb617367e770b606f8a6facf022620 Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Tue, 7 Oct 2025 09:02:37 +0000
Subject: [PATCH 263/530] .nftignore

---
 tests/.nftignore | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/tests/.nftignore b/tests/.nftignore
index f368b8fb..5bc3b98a 100644
--- a/tests/.nftignore
+++ b/tests/.nftignore
@@ -12,5 +12,10 @@ fastqc/*_fastqc.html
 fastqc/*_fastqc.zip
 picard_collectmultiplemetrics/*.{pdf}
 picard_collectmultiplemetrics/*_metrics
+picard_collectmultiplemetrics/alignment_summary_metrics
+picard_collectmultiplemetrics/base_distribution_by_cycle_metrics
+picard_collectmultiplemetrics/quality_by_cycle_metrics
+picard_collectmultiplemetrics/quality_distribution_metrics
 picard_collectmultiplemetrics/*_summary_metrics
 
+

From 54a5da367cce8efc648174a9bf1749b4dc7c6746 Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Tue, 7 Oct 2025 09:16:12 +0000
Subject: [PATCH 264/530] ss

---
 tests/MiSeq.main.nf.test.snap | 12 ++----------
 1 file changed, 2 insertions(+), 10 deletions(-)

diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 5eafb0a3..2ee0226d 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -258,10 +258,6 @@
                 "picard_base_distribution_by_cycle__Undetermined.txt:md5,5451af67007a16e7645d0393011414af",
                 "picard_quality_by_cycle.txt:md5,46fbe44a9788f2e9184e2c1d689c2876",
                 "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics:md5,1908cd9278b61eb99088415e7e3ddd4b",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,2f17706448e1809713b45318c5bb296f",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,36a24ef4e50ee914cc616c8dbf669060",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics:md5,892945b3fba6cf9f4404ad7e2a705f12",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
@@ -273,7 +269,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-07T08:36:46.667146476"
+        "timestamp": "2025-10-07T09:08:15.546626793"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
@@ -439,10 +435,6 @@
                 "picard_base_distribution_by_cycle__Undetermined.txt:md5,5451af67007a16e7645d0393011414af",
                 "picard_quality_by_cycle.txt:md5,46fbe44a9788f2e9184e2c1d689c2876",
                 "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics:md5,aa301637ed9c1b1fbfa7a1de4cf2383d",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,79083e5d6e2477101abcf973884cb942",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics:md5,d8d0d5f2cf02b11c6bcec05e9a4008a4",
-                "SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics:md5,bbd960f2bd28054fb9bd588393d4255b",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
@@ -454,6 +446,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-07T08:37:34.627849865"
+        "timestamp": "2025-10-07T09:09:05.277171766"
     }
 }
\ No newline at end of file

From ff17734638380a8d1ab33159b68bfcb7864420ea Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pontus=20H=C3=B6jer?= <pontushojer@gmail.com>
Date: Tue, 7 Oct 2025 11:30:24 +0200
Subject: [PATCH 265/530] update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index fc243f3c..62416f01 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -30,6 +30,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#99](https://github.com/nf-core/seqinspector/pull/99) Fix group reports for paired reads
 - [#107](https://github.com/nf-core/seqinspector/pull/107) Put SeqFU-stats section reports together
 - [#112](https://github.com/nf-core/seqinspector/pull/112) Making fastq_screen_references value to use parentDir
+- [#121](https://github.com/nf-core/seqinspector/pull/121) Cleanup sample naming for MultiQC report (#105)
 
 ### `Dependencies`
 

From 2e5607b9b7195e71b79e2b7368f775aacfac5755 Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Tue, 7 Oct 2025 11:31:59 +0200
Subject: [PATCH 266/530] Update tests/.nftignore

Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
---
 tests/.nftignore | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/.nftignore b/tests/.nftignore
index 5bc3b98a..54ef7e93 100644
--- a/tests/.nftignore
+++ b/tests/.nftignore
@@ -10,7 +10,7 @@ pipeline_info/*.{html,json,txt,yml}
 fastqscreen/*_screen.html
 fastqc/*_fastqc.html
 fastqc/*_fastqc.zip
-picard_collectmultiplemetrics/*.{pdf}
+picard_collectmultiplemetrics/*.pdf
 picard_collectmultiplemetrics/*_metrics
 picard_collectmultiplemetrics/alignment_summary_metrics
 picard_collectmultiplemetrics/base_distribution_by_cycle_metrics

From 66c5ff40f4b9ace1afe32350707605daa1f6bb2b Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Tue, 7 Oct 2025 11:32:06 +0200
Subject: [PATCH 267/530] Update tests/.nftignore

Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
---
 tests/.nftignore | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tests/.nftignore b/tests/.nftignore
index 54ef7e93..204d5b69 100644
--- a/tests/.nftignore
+++ b/tests/.nftignore
@@ -17,5 +17,3 @@ picard_collectmultiplemetrics/base_distribution_by_cycle_metrics
 picard_collectmultiplemetrics/quality_by_cycle_metrics
 picard_collectmultiplemetrics/quality_distribution_metrics
 picard_collectmultiplemetrics/*_summary_metrics
-
-

From 341583dd40fa291ee289137ce744a38156ce3fc9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pontus=20H=C3=B6jer?= <pontushojer@gmail.com>
Date: Tue, 7 Oct 2025 14:31:02 +0200
Subject: [PATCH 268/530] update snapshots

---
 tests/MiSeq.main.nf.test.snap                 |  32 ++---
 tests/MiSeq_PairedEnd.main.nf.test.snap       |  50 +++----
 tests/NovaSeq6000.main.nf.test.snap           | 132 +++++++++---------
 tests/NovaSeq6000.main_subsample.nf.test.snap |  32 ++---
 tests/PromethION.main.nf.test.snap            |  30 ++--
 5 files changed, 138 insertions(+), 138 deletions(-)

diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 49c8b18b..18f40b96 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -137,19 +137,19 @@
             [
                 "SAMPLE_SINGLE_END_01_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
                 "SAMPLE_SINGLE_END_01_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
-                "fastq_screen_plot.txt:md5,9cf2d21a5f14a4d580976f86211e6911",
-                "fastqc-status-check-heatmap.txt:md5,a46613c90e9f4d18bdc0ec1ef9ab203e",
-                "fastqc_overrepresented_sequences_plot.txt:md5,51964511b46bdeedffb6fce3b027ca65",
-                "fastqc_per_base_n_content_plot.txt:md5,50b87e15b2481a0666912092bf37f6c4",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,c165c8d0054f648e35a1e98a2c650077",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,6e8a40154ed6d405713369507624cd6f",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,ddd618369eb3f9aee12cf1622dc6a94c",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,650faba9f5a438239e54f8ddb45b1fb5",
-                "fastqc_sequence_counts_plot.txt:md5,5cc97c72190127df57148848f5708a9d",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,cb9119cb01a0c4aba3ccbb686cb6281b",
+                "fastq_screen_plot.txt:md5,7d120ba49a8a9220f85efb05e55bfae1",
+                "fastqc-status-check-heatmap.txt:md5,976c0ef6a62569395931028d05c2a320",
+                "fastqc_overrepresented_sequences_plot.txt:md5,89a55ca2171daea540258b0fc37e6766",
+                "fastqc_per_base_n_content_plot.txt:md5,54814a92014a4e3b07bca1449e2fcce4",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,e216aeee526de6c65d221924c0b7891e",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a494a0634c54d6ff7821765748908380",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,f838935c85ecfac06a744d7aa635926d",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,40c09f977034ca189f4894c8849212a0",
+                "fastqc_sequence_counts_plot.txt:md5,b1cf5ced11bf843a79f0e4265c7e48a1",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,70648ea8c46035d60647a128a5aa2fc6",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,8f2a8b76c7e8dcf78ba77b68b1203621",
-                "multiqc_fastqc.txt:md5,f439bb0427d95c1b8fccb60f61acf76c",
+                "multiqc_fastq_screen.txt:md5,1cfa6a74e8e735bf59da770f6cb25959",
+                "multiqc_fastqc.txt:md5,b5f6993152fb8e7142a1d84c6b75fc18",
                 "multiqc_seqfu_mqc.txt:md5,8e6989a2392f599a09a5c3edf8119702",
                 "SAMPLE_SINGLE_END_01_seqfu.tsv:md5,f65c868e562291647d539090698ba5eb",
                 "SAMPLE_SINGLE_END_01_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
@@ -159,7 +159,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-08-08T14:29:09.170736"
+        "timestamp": "2025-10-07T13:53:52.73584"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
@@ -214,9 +214,9 @@
             [
                 "SAMPLE_SINGLE_END_01_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
                 "SAMPLE_SINGLE_END_01_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
-                "fastq_screen_plot.txt:md5,9cf2d21a5f14a4d580976f86211e6911",
+                "fastq_screen_plot.txt:md5,7d120ba49a8a9220f85efb05e55bfae1",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,8f2a8b76c7e8dcf78ba77b68b1203621",
+                "multiqc_fastq_screen.txt:md5,1cfa6a74e8e735bf59da770f6cb25959",
                 "multiqc_seqfu_mqc.txt:md5,8e6989a2392f599a09a5c3edf8119702",
                 "SAMPLE_SINGLE_END_01_seqfu.tsv:md5,f65c868e562291647d539090698ba5eb",
                 "SAMPLE_SINGLE_END_01_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
@@ -226,6 +226,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-08-08T14:29:52.271216"
+        "timestamp": "2025-10-07T13:54:38.562241"
     }
 }
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index 8332a3a9..e67c0a07 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -194,33 +194,33 @@
                 "SAMPLE_PAIRED_END_2_02_1_screen.txt:md5,a5b047f495d01bf9dcb0ae516d3c7fc3",
                 "SAMPLE_PAIRED_END_2_02_2_screen.png:md5,e3684b17339d16e6fb64ace7593cc388",
                 "SAMPLE_PAIRED_END_2_02_2_screen.txt:md5,fc95e5058e764596d5da182cbc0614cf",
-                "fastq_screen_plot.txt:md5,8b6d13f6101915666011fd2fff5ec53e",
-                "fastqc-status-check-heatmap.txt:md5,7fefe7407f92bab2ed60be6666d4fc45",
-                "fastqc_adapter_content_plot.txt:md5,3d344b2770dd05f0e7d0ebfdc2a0ce4e",
-                "fastqc_per_base_n_content_plot.txt:md5,b77864a0b0a491421dc4a95d05c848ca",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,f91f89151b14226cd0bd73a96c2d6171",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,c7a24ad5160c608246197ae5147bcd18",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,a7ceffbada63f8d71d5a6c8c3d78d7cd",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,a2291e048ef2a2e9bd42e17e5be5796a",
-                "fastqc_sequence_counts_plot.txt:md5,890786853f7701c3a2c80794cca56056",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,6e70e5e67c41ca26c702d4a6a47bc75e",
+                "fastq_screen_plot.txt:md5,24a7d3472f06fe6032bb7f12f5828b49",
+                "fastqc-status-check-heatmap.txt:md5,c1e87942bda9a4ccf519bf561ce18ed3",
+                "fastqc_adapter_content_plot.txt:md5,4b7007431bd26127365b0f25120d48f2",
+                "fastqc_per_base_n_content_plot.txt:md5,6bbf19be2aef3ef67dfe548bf9323011",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,2bd96b0c0413ee4871a53d41f067d809",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,1f56f6ca0f469bec9b25010c6f9cbfdd",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,64bc987cceac0396b8b650000493427e",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,4aa57cbe1f9da1facc1b588b4c166cec",
+                "fastqc_sequence_counts_plot.txt:md5,57f96ad90232887fec1480ef4071f8b6",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,62e93bfc80b0bf201a605802edbe0177",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,b5cc85fc598d1fa162ea3c7ef8272b20",
-                "multiqc_fastqc.txt:md5,369cba29e5b1d9fdb385bff8681e8461",
+                "multiqc_fastq_screen.txt:md5,6f9cfa81bda7482142c640b9f0c82b90",
+                "multiqc_fastqc.txt:md5,85fe5c24576dc105adb8ca90ce6449b7",
                 "multiqc_seqfu_mqc.txt:md5,1f1e063e4a509a26cee167c3b20389c0",
-                "fastq_screen_plot.txt:md5,8b6d13f6101915666011fd2fff5ec53e",
-                "fastqc-status-check-heatmap.txt:md5,7fefe7407f92bab2ed60be6666d4fc45",
-                "fastqc_adapter_content_plot.txt:md5,3d344b2770dd05f0e7d0ebfdc2a0ce4e",
-                "fastqc_per_base_n_content_plot.txt:md5,b77864a0b0a491421dc4a95d05c848ca",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,f91f89151b14226cd0bd73a96c2d6171",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,c7a24ad5160c608246197ae5147bcd18",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,a7ceffbada63f8d71d5a6c8c3d78d7cd",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,a2291e048ef2a2e9bd42e17e5be5796a",
-                "fastqc_sequence_counts_plot.txt:md5,890786853f7701c3a2c80794cca56056",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,6e70e5e67c41ca26c702d4a6a47bc75e",
+                "fastq_screen_plot.txt:md5,24a7d3472f06fe6032bb7f12f5828b49",
+                "fastqc-status-check-heatmap.txt:md5,c1e87942bda9a4ccf519bf561ce18ed3",
+                "fastqc_adapter_content_plot.txt:md5,4b7007431bd26127365b0f25120d48f2",
+                "fastqc_per_base_n_content_plot.txt:md5,6bbf19be2aef3ef67dfe548bf9323011",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,2bd96b0c0413ee4871a53d41f067d809",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,1f56f6ca0f469bec9b25010c6f9cbfdd",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,64bc987cceac0396b8b650000493427e",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,4aa57cbe1f9da1facc1b588b4c166cec",
+                "fastqc_sequence_counts_plot.txt:md5,57f96ad90232887fec1480ef4071f8b6",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,62e93bfc80b0bf201a605802edbe0177",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,b5cc85fc598d1fa162ea3c7ef8272b20",
-                "multiqc_fastqc.txt:md5,369cba29e5b1d9fdb385bff8681e8461",
+                "multiqc_fastq_screen.txt:md5,6f9cfa81bda7482142c640b9f0c82b90",
+                "multiqc_fastqc.txt:md5,85fe5c24576dc105adb8ca90ce6449b7",
                 "multiqc_seqfu_mqc.txt:md5,1f1e063e4a509a26cee167c3b20389c0",
                 "SAMPLE_PAIRED_END_1_01_seqfu.tsv:md5,bbd911ff3fa43212dfd4c5a5872dbdb6",
                 "SAMPLE_PAIRED_END_1_01_seqfu_mqc.txt:md5,cd60f746b6749cc66213d031af1b931c",
@@ -232,6 +232,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-08-08T14:31:16.93075"
+        "timestamp": "2025-10-07T13:56:17.10436"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index 2ba1c19f..1036f7ac 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -451,80 +451,80 @@
                 "Undetermined_05_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
                 "sampletest_04_screen.png:md5,1fb60070e8f4b70de0c1b3786b54f27e",
                 "sampletest_04_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
-                "fastq_screen_plot.txt:md5,bb4eac45cbf17ccc884d5e4031e4a6cd",
-                "fastqc-status-check-heatmap.txt:md5,99364f4c3db4ef41626509b97719106e",
-                "fastqc_overrepresented_sequences_plot.txt:md5,94bb4ece4f6470a3842b5475b8ebbba9",
-                "fastqc_per_base_n_content_plot.txt:md5,9dc09ec356fe4fb1a294dd201a0efb26",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,073ce04152321c64a827801b999c435e",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,4f5ca276dc6bcc2695c1a47f170d37ab",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,7b6cd80856a34b782b7e77292d31a73f",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,cdd476546482eed3e69b7f7addbac34c",
-                "fastqc_sequence_counts_plot.txt:md5,ba4ec90cbad4101fdb7e914e9bf6e111",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,da7ce0e7d288249bf6c3e6af77fd6b91",
-                "fastqc_sequence_length_distribution_plot.txt:md5,8dc8dca0f71d69ea99fee2cdb0b4e2dc",
+                "fastq_screen_plot.txt:md5,990122d48fa4c1a170107a1ba034e4cf",
+                "fastqc-status-check-heatmap.txt:md5,7a64380ec42aac56949a2d9a4176d4d9",
+                "fastqc_overrepresented_sequences_plot.txt:md5,c7908980f1dba22b45cf6de14a66a686",
+                "fastqc_per_base_n_content_plot.txt:md5,8aafe701b59b4e70ccec86748c7d6eb3",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,c2bbc52a285a46ab8c548bca3b721e13",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a422f61a00f0839ef0d630d2e4524589",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,0e5a0cd0b0f8e66b3617f1ac19822d77",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,cbaa7c7033c526483584376275a8b33e",
+                "fastqc_sequence_counts_plot.txt:md5,d8ab86dbfce0c740f4a66a080803a0b9",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,f86012b3074d697c9a2b3bd67a074288",
+                "fastqc_sequence_length_distribution_plot.txt:md5,9d4fd245e8e1d5baa473a8bdffcd3e38",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,b9d41d5113f10387a8549cc1b9078300",
-                "multiqc_fastqc.txt:md5,552e425b8cb845234c0e3a177496770b",
+                "multiqc_fastq_screen.txt:md5,62240561100f78af37e7e2438cb58f90",
+                "multiqc_fastqc.txt:md5,23b698f1e957a26f49a9ad9bbdece908",
                 "multiqc_seqfu_mqc.txt:md5,5b54a49079169985795537d83d58bdd9",
-                "fastq_screen_plot.txt:md5,01f2f01696e9163df2884baad322b95b",
-                "fastqc-status-check-heatmap.txt:md5,75b897efbd8c205130c8f6876140adb7",
-                "fastqc_overrepresented_sequences_plot.txt:md5,4ed4a7cd989d68305d332a25ed070f43",
-                "fastqc_per_base_n_content_plot.txt:md5,3f142969503bd53905531a181b95b998",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,7cb78aff1f629f338908048a194f8e95",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,7cccbd6fa2be43d557751501a111d168",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,6ea8b89c3a088ab6a675e8eb6813f6be",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,71a500898ee53481d8d7d3cc06d5c723",
-                "fastqc_sequence_counts_plot.txt:md5,bbc4d4c2aa5e406ec0f742302c42441f",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,5ad4adb73d7998a54920eb43be5d4529",
-                "fastqc_sequence_length_distribution_plot.txt:md5,8ac836c4a6874b9b7430e5fbac00c235",
+                "fastq_screen_plot.txt:md5,db7c9231e756a6e5999399a7385e4687",
+                "fastqc-status-check-heatmap.txt:md5,fc37eaf184877ac80b92001a7bf2fa81",
+                "fastqc_overrepresented_sequences_plot.txt:md5,0693849fc324ddf580e2c5a4d910bb4f",
+                "fastqc_per_base_n_content_plot.txt:md5,0ed7f750b500e7c5387ea5309e1ef467",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,18016152915653e812818194a142e162",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,93f664e18c021aae79ad222fb4cfb393",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,ba96762be2aa842e1d2a606095ffcb7e",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,b9044bfe90fd5685137739f52a97ee2c",
+                "fastqc_sequence_counts_plot.txt:md5,42b26ad3758717659763c81852c4f197",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,818f13a5372bad79e54cd984758096c5",
+                "fastqc_sequence_length_distribution_plot.txt:md5,98316a2607a889ae1e7e79a4f64cc740",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,d323ad84f998f21d6924495d5767db04",
-                "multiqc_fastqc.txt:md5,05bd58ac4ed1972efd9a68d7b4e7b050",
+                "multiqc_fastq_screen.txt:md5,024e1e7f9db3b0906c7aa0904229e176",
+                "multiqc_fastqc.txt:md5,3407d8f06117a65efce4c70f19e91dd1",
                 "multiqc_seqfu_mqc.txt:md5,5579172a6f8ac09a5ffcb3ce6a99590e",
-                "fastq_screen_plot.txt:md5,6a733446d8582ffad08a809fba1d4bc8",
-                "fastqc-status-check-heatmap.txt:md5,51c5c30ecd83e91251b543c04bc778c1",
-                "fastqc_overrepresented_sequences_plot.txt:md5,6c73d4eae61ddf612cd725dedf1006c4",
-                "fastqc_per_base_n_content_plot.txt:md5,68e87242a12e69af0ab5adb1f0801f86",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,49fb3b1122616febf51046a8f3f03ad7",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,7d617f5ee916c8cde9081e3ecf4ab93f",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,ea2c4d8a253480b25e3df4360e340a74",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,36b929f56e2a411ea85083df0c16fba9",
-                "fastqc_sequence_counts_plot.txt:md5,aafdf85adf021d8a93c9aa9baaf90a52",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,cbd83dde1530dfa0bb8043dba895f296",
-                "fastqc_sequence_length_distribution_plot.txt:md5,2c1bcf7bcb78e73aab475c5a3afbae07",
+                "fastq_screen_plot.txt:md5,4def6c6a888afe487ab6ebef3ba8a133",
+                "fastqc-status-check-heatmap.txt:md5,61857d2c45cf0c080348047aa34e7525",
+                "fastqc_overrepresented_sequences_plot.txt:md5,7949c64cc6cef77f29349a188fc09656",
+                "fastqc_per_base_n_content_plot.txt:md5,0f2fd628631d42ed5e6a1db22578daaa",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,0a8bfa32ab04eaaa509dec3c37acb2d2",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,8c85be0c70129ba739feceddd58f6c75",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,94b975906d8a07e1604e00d4004f7463",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,ec22c8e4836aa726680f0ca767c778a0",
+                "fastqc_sequence_counts_plot.txt:md5,f4341795bdeba588248a74a095a97f8d",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,8fc995cb2192a2926eee242681bc3af6",
+                "fastqc_sequence_length_distribution_plot.txt:md5,4513e22583677a4d6167b9094242eb0b",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,456a39b074280f88aa8ac0c00dd7e38f",
-                "multiqc_fastqc.txt:md5,b9215fdb75187a437ff95e75d134f724",
+                "multiqc_fastq_screen.txt:md5,fd3074930c72b666f201ae71fa27744b",
+                "multiqc_fastqc.txt:md5,98111f17d1899cad6379e4e56ed11c53",
                 "multiqc_seqfu_mqc.txt:md5,b5434520fa5be5c98be5ed164a464d23",
-                "fastq_screen_plot.txt:md5,66ac9f1e0620340f103f2a4ed198f8f1",
-                "fastqc-status-check-heatmap.txt:md5,c64896817a2aa2bc886e58493d071f26",
-                "fastqc_overrepresented_sequences_plot.txt:md5,1c736c54db6e7a12898be76e5ad49da7",
-                "fastqc_per_base_n_content_plot.txt:md5,8710f2bfb029ec207fe4e999605e8932",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,560524fb28cebcf64ef25ab79f6cf26c",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,fd553cfc59dbdad3c9f128b27aa1f61a",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,41d32d6d9dc04c4609eeaa177cc6b37d",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,49586f3fc12629b61c3031b4ebb379c7",
-                "fastqc_sequence_counts_plot.txt:md5,e9bc0dcfbfc75aad884a8bb54b6f8653",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,debf797d3f723e13167a9d1061e73300",
-                "fastqc_sequence_length_distribution_plot.txt:md5,0dbd66f556880725955c015cfb4c046a",
+                "fastq_screen_plot.txt:md5,5abb5b9ed2c976f0ad83216ca3186201",
+                "fastqc-status-check-heatmap.txt:md5,323d6082b73ddb6ee33385f5ea4301c1",
+                "fastqc_overrepresented_sequences_plot.txt:md5,4e71d8913d40eb06db0f18d74ce6898f",
+                "fastqc_per_base_n_content_plot.txt:md5,b317ce09cb7a2be2366b544ea9b20ce6",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,e6f44d08f4185f680d4748a3b37201e2",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a1dc8a968f32bcf8a9b4c5f43d299dfa",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,e41b6dc1344f1aee379993daff310187",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,76f792b939233b070562cc46617f6371",
+                "fastqc_sequence_counts_plot.txt:md5,36c68522023b8d536c9362403bf03c48",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,9ff0df466790d971b3c7ef838efc0f4f",
+                "fastqc_sequence_length_distribution_plot.txt:md5,9fda632b92e3453f11cd0226484fce8e",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,bf4dfaccf959bc1305b9b1a190402a69",
-                "multiqc_fastqc.txt:md5,684d7fba20b698b74b9719985cee9151",
+                "multiqc_fastq_screen.txt:md5,536c28d7fadc9a76944f93ac9d643272",
+                "multiqc_fastqc.txt:md5,396b4cc0466a6642ec8b954237c42263",
                 "multiqc_seqfu_mqc.txt:md5,e2e092852c011abe5ad75cdcd68b9383",
-                "fastq_screen_plot.txt:md5,860d11addc201d3871ac8ee3fe6868c5",
-                "fastqc-status-check-heatmap.txt:md5,6549daecfa00b258b0d0c481675a81aa",
-                "fastqc_overrepresented_sequences_plot.txt:md5,7a8cdcdd971d690a13b587f9cb6773d1",
-                "fastqc_per_base_n_content_plot.txt:md5,3376187566c87e2a69a5e68b53fabca4",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,e2ac57f7f8d22fb03901312009ba0bf8",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,ff5abdc6b70b60837ddf90f0f52a9b7c",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,761a7bfe0370ae8dda128f50e7b26132",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,8f749ad94e4e2572ba3c2e3342239917",
-                "fastqc_sequence_counts_plot.txt:md5,9aea0567dd3251dc1990141636d09288",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,39ab4efe3b4391c387040484de52b8dc",
-                "fastqc_sequence_length_distribution_plot.txt:md5,c90118a673c353aa84062d968e8c90f1",
+                "fastq_screen_plot.txt:md5,82ceb9f2109f865d6d1b943441c09550",
+                "fastqc-status-check-heatmap.txt:md5,56b426cd5c030288639533fce7c95ab1",
+                "fastqc_overrepresented_sequences_plot.txt:md5,8e83abdbe7362e64d63339ee31ab3361",
+                "fastqc_per_base_n_content_plot.txt:md5,33b70326d8f888ac5a3d99b85f365e43",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,40bc954cc0d58a3197fdf124a40f1ca4",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,e240e30996c81a34b5d1a6b5a98ae254",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,b44d3376d503af12857d494c58b514bb",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,66b5b6d44f398fc9429460c0b9ba3ea9",
+                "fastqc_sequence_counts_plot.txt:md5,6e5804f553f656cffb02f927015d1026",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,fbe41935ea2e2faf7104393b476e5ac5",
+                "fastqc_sequence_length_distribution_plot.txt:md5,e77dc4ab73252c2e09c7452c3b8e8ab3",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,fee55523161dea1bd328e653ed35bcb3",
-                "multiqc_fastqc.txt:md5,7eca563c0e2e5342dc5b5df34daae1be",
+                "multiqc_fastq_screen.txt:md5,4fc422d9cb06a1d0248cc578c1eebaa2",
+                "multiqc_fastqc.txt:md5,95c8ffb23baafec625aeb600047515ae",
                 "multiqc_seqfu_mqc.txt:md5,a1a0b9a0dde0c1c4fe184d44c675dcde",
                 "Sample1_01_seqfu.tsv:md5,269fabf8435defcd327aa69a050b7869",
                 "Sample1_01_seqfu_mqc.txt:md5,a354b0ed16b9cf84aa88f501d7740fd6",
@@ -542,6 +542,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-08-08T14:32:39.800953"
+        "timestamp": "2025-10-07T13:58:09.954141"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index 4df69d0b..6babb652 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -2,30 +2,30 @@
     "NovaSeq6000 data test sample size": {
         "content": [
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-            "multiqc_fastqc.txt:md5,464552ede2e3398b15009d2fe497cdfd",
-            "multiqc_general_stats.txt:md5,ee481e5e78e8eb5dfae605d0358c222a",
-            "multiqc_fastq_screen.txt:md5,b9d41d5113f10387a8549cc1b9078300",
+            "multiqc_fastqc.txt:md5,a9a9fc06badaade2d09486d2adaac1ce",
+            "multiqc_general_stats.txt:md5,13296eed367755f92d12fe70c4b8b2f4",
+            "multiqc_fastq_screen.txt:md5,62240561100f78af37e7e2438cb58f90",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-            "multiqc_fastqc.txt:md5,2bd9e3d267cee5a21755f56460e05574",
-            "multiqc_general_stats.txt:md5,780d5ade40457b44d19ce0368b72493f",
-            "multiqc_fastq_screen.txt:md5,bf4dfaccf959bc1305b9b1a190402a69",
+            "multiqc_fastqc.txt:md5,b8f6f4ed32e60ff57c64bb0ba029adba",
+            "multiqc_general_stats.txt:md5,6fedb1a47d2a5b306c28ba9b2d302f18",
+            "multiqc_fastq_screen.txt:md5,536c28d7fadc9a76944f93ac9d643272",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-            "multiqc_fastqc.txt:md5,0c6c5817dd59422b5c257fae72fc2ffc",
-            "multiqc_general_stats.txt:md5,7f2d01ba5feb51496f2bdfcaec1a7672",
-            "multiqc_fastq_screen.txt:md5,d323ad84f998f21d6924495d5767db04",
+            "multiqc_fastqc.txt:md5,e87c99cac0c4956521d9c660183722bb",
+            "multiqc_general_stats.txt:md5,aad648cdaf1cac2c2962ea94d3516f7c",
+            "multiqc_fastq_screen.txt:md5,024e1e7f9db3b0906c7aa0904229e176",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-            "multiqc_fastqc.txt:md5,50611144cc4384363db6be9a327c7f02",
-            "multiqc_general_stats.txt:md5,427406a14f0583da93f8120e4cc20c9f",
-            "multiqc_fastq_screen.txt:md5,456a39b074280f88aa8ac0c00dd7e38f",
+            "multiqc_fastqc.txt:md5,8b808265a3cfe52846f7d6a0c9624beb",
+            "multiqc_general_stats.txt:md5,e44b85891b450effc0cae8b958175569",
+            "multiqc_fastq_screen.txt:md5,fd3074930c72b666f201ae71fa27744b",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-            "multiqc_fastqc.txt:md5,911bc13b7adfd499efef327d56f4b34e",
-            "multiqc_general_stats.txt:md5,c07dc697a170838db9d95271a9cb47a5",
-            "multiqc_fastq_screen.txt:md5,fee55523161dea1bd328e653ed35bcb3"
+            "multiqc_fastqc.txt:md5,284597d876abc5a1242d8efb2d69f0d5",
+            "multiqc_general_stats.txt:md5,36cecde1b0127abd0f955771724dc71d",
+            "multiqc_fastq_screen.txt:md5,4fc422d9cb06a1d0248cc578c1eebaa2"
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-08-08T14:34:00.031836"
+        "timestamp": "2025-10-07T13:59:59.319738"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index 756ba49b..2c139394 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -114,21 +114,21 @@
             [
                 "hg001_01_screen.png:md5,b9c58e388f18ad11f4c2e29e9b573a5e",
                 "hg001_01_screen.txt:md5,8e53ea043d658a130f4b8ca455e2ba9b",
-                "fastq_screen_plot.txt:md5,657e595a39a9683e2050a3695e916356",
-                "fastqc-status-check-heatmap.txt:md5,d7fad43a47cbb1ca9d4af05634320cd4",
-                "fastqc_adapter_content_plot.txt:md5,146d9a6c9113c2847859e5b2fefb5495",
-                "fastqc_overrepresented_sequences_plot.txt:md5,9df816c16e213f480c4561c094a461d4",
-                "fastqc_per_base_n_content_plot.txt:md5,cb9e24aeb2a38ab9267fb4fd3d7f269c",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,1d93a13bc3f955d9b885054074eea5ca",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,2a697e9f230c0c4c1fe8cf59b8cc4d09",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,d3b02fc19cd9482ec7121cb8b6f827b2",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,788ea319922a666db29162dfdfef008d",
-                "fastqc_sequence_counts_plot.txt:md5,d8dd057195ed8c90a13b3c8803d7a6cf",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,7677dd2ca8ddaa7fc09456f7c5575af7",
-                "fastqc_sequence_length_distribution_plot.txt:md5,7ac48264f65e52c36e4f8dfb73955c91",
+                "fastq_screen_plot.txt:md5,f6883339d43a090e86e02fdf3feacbbd",
+                "fastqc-status-check-heatmap.txt:md5,0ac9450d210de9ab4548378101877c8e",
+                "fastqc_adapter_content_plot.txt:md5,6e2a760185573c44180ca43081cc7c99",
+                "fastqc_overrepresented_sequences_plot.txt:md5,251ad51e27e966476911ff4c77c2a893",
+                "fastqc_per_base_n_content_plot.txt:md5,230b2a0319f3b7490498e8edb47b17bf",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,4934bce34aec037e1ea590bd69f74781",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,028ada8fc060ce4af7476f339c57c50d",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,6bab830c22525c15a6048d8054f685cf",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,fd29224ed588e37e1fc85bf7f717e31e",
+                "fastqc_sequence_counts_plot.txt:md5,cc83b291e21249f3c4e25d34cc898f0f",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,7b7665c78ca66d3e13b1850701b198dc",
+                "fastqc_sequence_length_distribution_plot.txt:md5,d7bac93b11316846778b9d550f323371",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,d8ff89af02a0932bac3cb2a53be76064",
-                "multiqc_fastqc.txt:md5,7031588e1394714bb2dd64b7fed6d3ef",
+                "multiqc_fastq_screen.txt:md5,0ab0d1c4c3e3393afdb50ad0e116e394",
+                "multiqc_fastqc.txt:md5,b71aaffef9767dfe9d83fde0d31a3a1b",
                 "multiqc_seqfu_mqc.txt:md5,9595d608ff5709f2bdec8cb1016416c0",
                 "hg001_01_seqfu.tsv:md5,b133752c897afbb4d8721b911fa117d4",
                 "hg001_01_seqfu_mqc.txt:md5,6285f582c03faa70e8dcb3503e5db728"
@@ -138,6 +138,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-08-08T14:34:50.840014"
+        "timestamp": "2025-10-07T14:00:51.814162"
     }
 }
\ No newline at end of file

From 991c32c01295832d2454e902df9ce11b5b5bf1cb Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Tue, 7 Oct 2025 12:48:46 +0000
Subject: [PATCH 269/530] Test.config updates

---
 conf/test.config | 23 -----------------------
 1 file changed, 23 deletions(-)

diff --git a/conf/test.config b/conf/test.config
index c6f4934c..609fa6fa 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -25,26 +25,3 @@ params {
 }
 
 
-process {
-    resourceLimits = [
-        cpus: 4,
-        memory: '15.GB',
-        time: '1.h'
-    ]
-    withLabel: 'process_high' {
-        cpus = 4
-        memory = '15.GB'
-    }
-    withLabel: 'process_medium' {
-        cpus = 2
-        memory = '7.GB'
-    }
-    withLabel: 'process_low' {
-        cpus = 1
-        memory = '3.GB'
-    }
-    withLabel: 'process_single' {
-        cpus = 1
-        memory = '3.GB'
-    }
-}

From ddc9ab357c0d430ddcb6e748e45eb97325db0525 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@n131-p85.eduroam.kth.se>
Date: Tue, 14 Oct 2025 15:50:57 +0200
Subject: [PATCH 270/530] Added bwa_index parameter

---
 conf/seqinspector_v1.0_stage_resources.config | 72 +++++++++++++++++++
 modules/nf-core/bowtie2/build/main.nf         |  2 +-
 modules/nf-core/bwamem2/mem/main.nf           |  2 +-
 modules/nf-core/fastqc/main.nf                |  2 +-
 .../nf-core/fastqscreen/fastqscreen/main.nf   |  2 +-
 nextflow.config                               |  1 +
 nextflow_schema.json                          | 12 +++-
 workflows/seqinspector.nf                     | 31 +++++---
 8 files changed, 108 insertions(+), 16 deletions(-)
 create mode 100644 conf/seqinspector_v1.0_stage_resources.config

diff --git a/conf/seqinspector_v1.0_stage_resources.config b/conf/seqinspector_v1.0_stage_resources.config
new file mode 100644
index 00000000..41333e1a
--- /dev/null
+++ b/conf/seqinspector_v1.0_stage_resources.config
@@ -0,0 +1,72 @@
+process {
+
+
+    // TODO nf-core: Check the defaults for all processes
+    cpus   = { 1      * task.attempt }
+    memory = { 6.GB   * task.attempt }
+    time   = { 4.h    * task.attempt }
+
+    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
+    maxRetries    = 2
+    maxErrors     = '-1'
+
+
+    // Subsampling reads
+    withName: 'SEQTK_SAMPLE' {
+        cpus = 6
+        memory = { 4.GB * task.attempt }
+        time = { 4.h * task.attempt }
+    }
+
+    // Quality control
+    withName: 'FASTQC' {
+        cpus = 2
+        memory = { 36.GB * task.attempt }
+        time = { 8.h * task.attempt }
+    }
+    withName: 'SEQFU_STATS' {
+        cpus = 6
+        memory = { 4.GB * task.attempt }
+        time = { 4.h * task.attempt }
+    }
+    withName: 'FASTQSCREEN_FASTQSCREEN' {
+        cpus = 6
+        memory = { 36.GB * task.attempt }
+        time = { 8.h * task.attempt }
+    }
+
+    // Reference genome processing
+    withName: 'BWAMEM2_INDEX' {
+        cpus = 12
+        memory = { 72.GB * task.attempt }
+        time = { 16.h * task.attempt }
+    }
+    withName: 'BWAMEM2_MEM' {
+        cpus = 6
+        memory = { 35.GB * task.attempt }
+        time = { 16.h * task.attempt }
+    }
+    withName: 'SAMTOOLS_INDEX' {
+        cpus = 6
+        memory = { 4.GB * task.attempt }
+        time = { 4.h * task.attempt }
+    }
+    withName: 'SAMTOOLS_FAIDX' {
+        cpus = 6
+        memory = { 6.GB * task.attempt }
+        time = { 4.h * task.attempt }
+    }
+    // Picard metrics
+    withName: 'PICARD_COLLECTMULTIPLEMETRICS' {
+        cpus = 4
+        memory = { 8.GB * task.attempt }
+        time = { 4.h * task.attempt }
+    }
+
+    // MultiQC aggregation
+    withName: 'MULTIQC_GLOBAL|MULTIQC_PER_TAG' {
+        cpus = 4
+        memory = { 4.GB * task.attempt }
+        time = { 4.h * task.attempt }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf
index 9e2e0e5e..8cebeae3 100644
--- a/modules/nf-core/bowtie2/build/main.nf
+++ b/modules/nf-core/bowtie2/build/main.nf
@@ -1,6 +1,6 @@
 process BOWTIE2_BUILD {
     tag "$fasta"
-    label 'process_high'
+    label 'process_low'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf
index eab662a8..ad510447 100644
--- a/modules/nf-core/bwamem2/mem/main.nf
+++ b/modules/nf-core/bwamem2/mem/main.nf
@@ -1,6 +1,6 @@
 process BWAMEM2_MEM {
     tag "$meta.id"
-    label 'process_high'
+    label 'process_low'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 033f4154..00cd084c 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -1,6 +1,6 @@
 process FASTQC {
     tag "${meta.id}"
-    label 'process_medium'
+    label 'process_low'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index 21012c1f..92587021 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -1,6 +1,6 @@
 process FASTQSCREEN_FASTQSCREEN {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_low'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/nextflow.config b/nextflow.config
index dedd6041..2dff48db 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -20,6 +20,7 @@ params {
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
     igenomes_ignore            = false
     sort_bam                   = true
+    bwa_index                  = null
 
     // Fastqscreen options
     fastq_screen_references    = "${projectDir}/assets/example_fastq_screen_references.csv"
diff --git a/nextflow_schema.json b/nextflow_schema.json
index eb6cbcea..ab01a1da 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -94,7 +94,7 @@
                 },
                 "fastq_screen_references": {
                     "type": "string",
-                    "default": "${projectDir}/assets/example_fastq_screen_references.csv",
+                    "default": "/Users/agrimabhatt/seqinspector/assets/example_fastq_screen_references.csv",
                     "fa_icon": "fas fa-search",
                     "description": "A .csv of reference genomes to be mapped against by FastQ Screen"
                 }
@@ -214,7 +214,8 @@
                 "modules_testdata_base_path": {
                     "type": "string",
                     "description": "Base path / URL for data used in the modules",
-                    "hidden": true
+                    "hidden": true,
+                    "default": "s3://ngi-igenomes/testdata/nf-core/modules/"
                 },
                 "multiqc_config": {
                     "type": "string",
@@ -270,5 +271,10 @@
         {
             "$ref": "#/$defs/generic_options"
         }
-    ]
+    ],
+    "properties": {
+        "bwa_index": {
+            "type": "string"
+        }
+    }
 }
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index ae2d801a..b9b39ddb 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -118,21 +118,34 @@ workflow SEQINSPECTOR {
         ch_multiqc_files = ch_multiqc_files.mix(FASTQSCREEN_FASTQSCREEN.out.txt)
         ch_versions = ch_versions.mix(FASTQSCREEN_FASTQSCREEN.out.versions.first())
     }
-    // MODULE: Create BWA-MEM2 index of the reference genome
-
+    // MODULE: Create BWA-MEM2 index of the reference genome OR use pre-built index
     if (!("bwamem2_index" in skip_tools)) {
+    // Always create the reference FASTA channel since it's needed by BWAMEM2_MEM
         def fasta_file = getGenomeAttribute('fasta')
         ch_reference_fasta = Channel.fromPath(fasta_file, checkIfExists: true)
                             .map { file -> tuple([id: file.name], file) }.collect()
 
-
-        BWAMEM2_INDEX (
-            ch_reference_fasta
-        )
-        ch_bwamem2_index = BWAMEM2_INDEX.out.index
-        ch_versions = ch_versions.mix(BWAMEM2_INDEX.out.versions)
-
+        if (params.bwa_index) {
+        // Use pre-built index when --bwa_index parameter is provided
+            ch_bwamem2_index = Channel.fromPath(params.bwa_index, checkIfExists: true)
+                                    .map { index_dir -> tuple([id: index_dir.name], index_dir) }
+                                    .collect()
+
+        // Add debug output to verify the pre-built index is being used
+            ch_bwamem2_index.view { "Using pre-built BWA-MEM2 index: $it" }
+        } else {
+        // Build index from reference FASTA when no pre-built index is provided
+            BWAMEM2_INDEX (
+                ch_reference_fasta
+            )
+            ch_bwamem2_index = BWAMEM2_INDEX.out.index
+            ch_versions = ch_versions.mix(BWAMEM2_INDEX.out.versions)
+
+        // Add debug output to verify the index was built
+            ch_bwamem2_index.view { "Built BWA-MEM2 index: $it" }
+        }
     }
+
     // MODULE: Align reads with BWA-MEM2
     if (!("bwamem2_mem" in skip_tools)) {
         BWAMEM2_MEM (

From dfe040188f758d2158d38c37d3315bf3f44244ce Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@n131-p85.eduroam.kth.se>
Date: Tue, 14 Oct 2025 16:07:26 +0200
Subject: [PATCH 271/530] updated process paramters for modules

---
 modules/nf-core/bowtie2/build/main.nf           | 2 +-
 modules/nf-core/bwamem2/mem/main.nf             | 2 +-
 modules/nf-core/fastqc/main.nf                  | 2 +-
 modules/nf-core/fastqscreen/fastqscreen/main.nf | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf
index 8cebeae3..9e2e0e5e 100644
--- a/modules/nf-core/bowtie2/build/main.nf
+++ b/modules/nf-core/bowtie2/build/main.nf
@@ -1,6 +1,6 @@
 process BOWTIE2_BUILD {
     tag "$fasta"
-    label 'process_low'
+    label 'process_high'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf
index ad510447..eab662a8 100644
--- a/modules/nf-core/bwamem2/mem/main.nf
+++ b/modules/nf-core/bwamem2/mem/main.nf
@@ -1,6 +1,6 @@
 process BWAMEM2_MEM {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_high'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 00cd084c..033f4154 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -1,6 +1,6 @@
 process FASTQC {
     tag "${meta.id}"
-    label 'process_low'
+    label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index 92587021..21012c1f 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -1,6 +1,6 @@
 process FASTQSCREEN_FASTQSCREEN {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

From 132c1aec429af2ff0cc3ca9e1615cd0e7cdeec96 Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Wed, 15 Oct 2025 09:27:05 +0000
Subject: [PATCH 272/530] added citations and updated snapshots

---
 CHANGELOG.md |  2 ++
 CITATIONS.md | 11 +++++++++++
 README.md    |  6 +++++-
 3 files changed, 18 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index fc243f3c..b56499bb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -23,6 +23,8 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#96](https://github.com/nf-core/seqinspector/pull/96) Added missing citations to citation tool
 - [#103](https://github.com/nf-core/seqinspector/pull/103) Configure full-tests
 - [#110](https://github.com/nf-core/seqinspector/pull/110) Update input schema to accept either tar file or directory as rundir, and fastq messages and patterns.
+- [#127] (https://github.com/nf-core/seqinspector/pull/127) Added alignment tools - bwamem2 - index and mem
+- [#128] (https://github.com/nf-core/seqinspector/pull/128) Added Picard tools - Collect Multiple Mterics to collect QC metrics
 
 ### `Fixed`
 
diff --git a/CITATIONS.md b/CITATIONS.md
index 208cfa1e..8820cc31 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -28,6 +28,17 @@
 
 - [Seqtk](https://github.com/lh3/seqtk)
 
+- [BWAMEM2](https://ieeexplore.ieee.org/abstract/document/8820962)
+
+> Vasimuddin Md, Misra S, Li H, Aluru S. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. In: 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS). IEEE; 2019:314-324. doi:10.1109/IPDPS.2019.00041
+
+- [SAMTOOLS](https://academic.oup.com/bioinformatics/article/25/16/2078/204688)
+
+> Danecek P, Bonfield JK, Liddle J, et al. Twelve years of SAMtools and BCFtools. GigaScience. 2021;10(2):giab008. doi:10.1093/gigascience/giab008
+
+- [Picard Tools](https://broadinstitute.github.io/picard/)
+
+
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)
diff --git a/README.md b/README.md
index 6cf36dcc..26339895 100644
--- a/README.md
+++ b/README.md
@@ -33,7 +33,11 @@
 
 1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))
 2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-3. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+3. Align reads to reference with ([`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2))
+4. Index aligned BAM files ([`SAMtools`](http://github.com/samtools))
+5. Create FASTA index ([`SAMtools`](http://github.com/samtools))
+6. Collect multiple QC metrics ([`Picard CollectMultipleMetrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html))
+5. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
 
 ## Usage
 

From eccaa2b6f1784bbb0e1e325e650899acb581109f Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Wed, 15 Oct 2025 09:43:03 +0000
Subject: [PATCH 273/530] prettier and linting

---
 CITATIONS.md | 1 -
 README.md    | 2 +-
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/CITATIONS.md b/CITATIONS.md
index 8820cc31..36704d9e 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -38,7 +38,6 @@
 
 - [Picard Tools](https://broadinstitute.github.io/picard/)
 
-
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)
diff --git a/README.md b/README.md
index 26339895..aca3af02 100644
--- a/README.md
+++ b/README.md
@@ -37,7 +37,7 @@
 4. Index aligned BAM files ([`SAMtools`](http://github.com/samtools))
 5. Create FASTA index ([`SAMtools`](http://github.com/samtools))
 6. Collect multiple QC metrics ([`Picard CollectMultipleMetrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html))
-5. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+7. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
 
 ## Usage
 

From f44646e37300e4a9289a6530c610969b2c280b29 Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Wed, 15 Oct 2025 09:48:03 +0000
Subject: [PATCH 274/530] linting

---
 .github/PULL_REQUEST_TEMPLATE.md      |  4 ++--
 .github/workflows/linting.yml         | 17 +++++++----------
 .github/workflows/linting_comment.yml |  4 ++--
 .prettierrc.yml                       |  5 +++++
 4 files changed, 16 insertions(+), 14 deletions(-)

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 9dcf6a33..068d699b 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -8,14 +8,14 @@ These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/seqinspector/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/seqinspector/tree/main/.github/CONTRIBUTING.md)
 -->
 
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/seqinspector/tree/master/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/seqinspector/tree/main/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/seqinspector _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index dbd52d5a..8b0f88c3 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -3,9 +3,6 @@ name: nf-core linting
 # It runs the `nf-core pipelines lint` and markdown lint tests to ensure
 # that the code meets the nf-core guidelines.
 on:
-  push:
-    branches:
-      - dev
   pull_request:
   release:
     types: [published]
@@ -16,10 +13,10 @@ jobs:
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
-      - name: Set up Python 3.12
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      - name: Set up Python 3.13
+        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -36,13 +33,13 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
           architecture: "x64"
 
       - name: read .nf-core.yml
-        uses: pietrobolcato/action-read-yaml@1.1.0
+        uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
         id: read_yml
         with:
           config: ${{ github.workspace }}/.nf-core.yml
@@ -74,7 +71,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
+        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 95b6b6af..d43797d9 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8
+        uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11
         with:
           workflow: linting.yml
           workflow_conclusion: completed
@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2
+        uses: marocchino/sticky-pull-request-comment@52423e01640425a022ef5fd42c6fb5f633a02728 # v2
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
diff --git a/.prettierrc.yml b/.prettierrc.yml
index c81f9a76..07dbd8bb 100644
--- a/.prettierrc.yml
+++ b/.prettierrc.yml
@@ -1 +1,6 @@
 printWidth: 120
+tabWidth: 4
+overrides:
+  - files: "*.{md,yml,yaml,html,css,scss,js,cff}"
+    options:
+      tabWidth: 2

From 90a1d6f69cfd2f04d5a00c725d5dbc42a2941579 Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Wed, 15 Oct 2025 09:58:09 +0000
Subject: [PATCH 275/530] linting

---
 ro-crate-metadata.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 13ff1ebc..72f400db 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -23,7 +23,7 @@
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
             "datePublished": "2025-01-27T16:15:35+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->\n\n1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))\n2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n3. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->\n\n1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))\n2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n3. Align reads to reference with ([`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2))\n4. Index aligned BAM files ([`SAMtools`](http://github.com/samtools))\n5. Create FASTA index ([`SAMtools`](http://github.com/samtools))\n6. Collect multiple QC metrics ([`Picard CollectMultipleMetrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html))\n7. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
                     "@id": "main.nf"

From 34b800fe33e51d2ca7246d81635e5896b50d31a4 Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Wed, 15 Oct 2025 10:00:48 +0000
Subject: [PATCH 276/530] config files updated

---
 conf/seqinspector_v1.0_stage_resources.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/seqinspector_v1.0_stage_resources.config b/conf/seqinspector_v1.0_stage_resources.config
index 41333e1a..c7f4f647 100644
--- a/conf/seqinspector_v1.0_stage_resources.config
+++ b/conf/seqinspector_v1.0_stage_resources.config
@@ -69,4 +69,4 @@ process {
         memory = { 4.GB * task.attempt }
         time = { 4.h * task.attempt }
     }
-}
\ No newline at end of file
+}

From a670c6892791f973ecd222424f41436f01f6f07f Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Wed, 15 Oct 2025 11:03:54 +0000
Subject: [PATCH 277/530] linting

---
 .github/PULL_REQUEST_TEMPLATE.md | 4 ++--
 .prettierrc.yml                  | 5 -----
 2 files changed, 2 insertions(+), 7 deletions(-)

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 068d699b..9dcf6a33 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -8,14 +8,14 @@ These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/seqinspector/tree/main/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/seqinspector/tree/master/.github/CONTRIBUTING.md)
 -->
 
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/seqinspector/tree/main/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/seqinspector/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/seqinspector _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
diff --git a/.prettierrc.yml b/.prettierrc.yml
index 07dbd8bb..c81f9a76 100644
--- a/.prettierrc.yml
+++ b/.prettierrc.yml
@@ -1,6 +1 @@
 printWidth: 120
-tabWidth: 4
-overrides:
-  - files: "*.{md,yml,yaml,html,css,scss,js,cff}"
-    options:
-      tabWidth: 2

From 16fbbbb3339c2812111df6b8a2eed5ae3fa8cef3 Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Wed, 15 Oct 2025 11:40:12 +0000
Subject: [PATCH 278/530] linting

---
 .github/PULL_REQUEST_TEMPLATE.md      |  4 ++--
 .github/workflows/linting.yml         | 17 ++++++++++-------
 .github/workflows/linting_comment.yml |  4 ++--
 3 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 9dcf6a33..068d699b 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -8,14 +8,14 @@ These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/seqinspector/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/seqinspector/tree/main/.github/CONTRIBUTING.md)
 -->
 
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/seqinspector/tree/master/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/seqinspector/tree/main/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/seqinspector _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 8b0f88c3..dbd52d5a 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -3,6 +3,9 @@ name: nf-core linting
 # It runs the `nf-core pipelines lint` and markdown lint tests to ensure
 # that the code meets the nf-core guidelines.
 on:
+  push:
+    branches:
+      - dev
   pull_request:
   release:
     types: [published]
@@ -13,10 +16,10 @@ jobs:
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
-      - name: Set up Python 3.13
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - name: Set up Python 3.12
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
-          python-version: "3.13"
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -33,13 +36,13 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
-          python-version: "3.13"
+          python-version: "3.12"
           architecture: "x64"
 
       - name: read .nf-core.yml
-        uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
+        uses: pietrobolcato/action-read-yaml@1.1.0
         id: read_yml
         with:
           config: ${{ github.workspace }}/.nf-core.yml
@@ -71,7 +74,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index d43797d9..95b6b6af 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11
+        uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8
         with:
           workflow: linting.yml
           workflow_conclusion: completed
@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@52423e01640425a022ef5fd42c6fb5f633a02728 # v2
+        uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}

From ea0b3d48c358798c8a080a3a6f5e04e3608d7692 Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Wed, 15 Oct 2025 11:43:02 +0000
Subject: [PATCH 279/530] minor changes

---
 .github/PULL_REQUEST_TEMPLATE.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 068d699b..9dcf6a33 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -8,14 +8,14 @@ These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/seqinspector/tree/main/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/seqinspector/tree/master/.github/CONTRIBUTING.md)
 -->
 
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/seqinspector/tree/main/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/seqinspector/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/seqinspector _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).

From 48343180750024f8513460fb2a652c5275a59fbb Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Thu, 16 Oct 2025 13:39:02 +0000
Subject: [PATCH 280/530] Template update for nf-core/tools version 3.4.1

---
 .devcontainer/devcontainer.json               | 28 ++++----
 .devcontainer/setup.sh                        | 13 ++++
 .github/actions/nf-test/action.yml            |  6 +-
 .github/workflows/awsfulltest.yml             | 12 ++--
 .github/workflows/awstest.yml                 | 12 ++--
 .github/workflows/clean-up.yml                |  2 +-
 .github/workflows/download_pipeline.yml       |  6 +-
 .github/workflows/fix_linting.yml             | 16 ++---
 .github/workflows/linting.yml                 | 14 ++--
 .github/workflows/linting_comment.yml         |  2 +-
 .github/workflows/nf-test.yml                 |  9 +--
 .github/workflows/release-announcements.yml   |  7 ++
 .../workflows/template-version-comment.yml    |  2 +-
 .gitpod.yml                                   | 10 ---
 .nf-core.yml                                  |  2 +-
 .pre-commit-config.yaml                       |  2 +-
 .prettierignore                               |  1 +
 README.md                                     |  5 +-
 docs/usage.md                                 |  2 +-
 main.nf                                       |  5 +-
 modules.json                                  |  8 +--
 modules/nf-core/multiqc/environment.yml       |  2 +-
 modules/nf-core/multiqc/main.nf               |  4 +-
 .../nf-core/multiqc/tests/main.nf.test.snap   | 18 +++---
 modules/nf-core/multiqc/tests/tags.yml        |  2 -
 nextflow.config                               | 64 ++++++-------------
 nextflow_schema.json                          | 12 ++++
 ro-crate-metadata.json                        | 16 ++---
 .../main.nf                                   | 31 ++++++++-
 .../utils_nextflow_pipeline/tests/tags.yml    |  2 -
 .../utils_nfcore_pipeline/tests/tags.yml      |  2 -
 .../nf-core/utils_nfschema_plugin/main.nf     | 40 ++++++++++--
 .../utils_nfschema_plugin/tests/main.nf.test  | 56 ++++++++++++++++
 .../tests/nextflow.config                     |  4 +-
 tests/.nftignore                              |  3 +-
 tests/default.nf.test                         |  2 -
 36 files changed, 267 insertions(+), 155 deletions(-)
 create mode 100755 .devcontainer/setup.sh
 delete mode 100644 .gitpod.yml
 delete mode 100644 modules/nf-core/multiqc/tests/tags.yml
 delete mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
 delete mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index b290e090..97c8c97f 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,20 +1,20 @@
 {
     "name": "nfcore",
-    "image": "nfcore/gitpod:latest",
-    "remoteUser": "gitpod",
-    "runArgs": ["--privileged"],
+    "image": "nfcore/devcontainer:latest",
 
-    // Configure tool-specific properties.
-    "customizations": {
-        // Configure properties specific to VS Code.
-        "vscode": {
-            // Set *default* container specific settings.json values on container create.
-            "settings": {
-                "python.defaultInterpreterPath": "/opt/conda/bin/python"
-            },
+    "remoteUser": "root",
+    "privileged": true,
 
-            // Add the IDs of extensions you want installed when the container is created.
-            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
-        }
+    "remoteEnv": {
+        // Workspace path on the host for mounting with docker-outside-of-docker
+        "LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
+    },
+
+    "onCreateCommand": "./.devcontainer/setup.sh",
+
+    "hostRequirements": {
+        "cpus": 4,
+        "memory": "16gb",
+        "storage": "32gb"
     }
 }
diff --git a/.devcontainer/setup.sh b/.devcontainer/setup.sh
new file mode 100755
index 00000000..a01e7369
--- /dev/null
+++ b/.devcontainer/setup.sh
@@ -0,0 +1,13 @@
+#!/usr/bin/env bash
+
+# Customise the terminal command prompt
+echo "export PROMPT_DIRTRIM=2" >> $HOME/.bashrc
+echo "export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '" >> $HOME/.bashrc
+export PROMPT_DIRTRIM=2
+export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
+
+# Update Nextflow
+nextflow self-update
+
+# Update welcome message
+echo "Welcome to the nf-core/seqinspector devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt
diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml
index bf44d961..3b9724c7 100644
--- a/.github/actions/nf-test/action.yml
+++ b/.github/actions/nf-test/action.yml
@@ -25,9 +25,9 @@ runs:
         version: "${{ env.NXF_VERSION }}"
 
     - name: Set up Python
-      uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
       with:
-        python-version: "3.13"
+        python-version: "3.14"
 
     - name: Install nf-test
       uses: nf-core/setup-nf-test@v1
@@ -52,6 +52,8 @@ runs:
       with:
         auto-update-conda: true
         conda-solver: libmamba
+        channels: conda-forge
+        channel-priority: strict
         conda-remove-defaults: true
 
     - name: Run nf-test
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index f8125112..301eca73 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -28,15 +28,15 @@ jobs:
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
         with:
-          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          workspace_id: ${{ vars.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          compute_env: ${{ vars.TOWER_COMPUTE_ENV }}
           revision: ${{ steps.revision.outputs.revision }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/seqinspector/work-${{ steps.revision.outputs.revision }}
+          workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/seqinspector/work-${{ steps.revision.outputs.revision }}
           parameters: |
             {
               "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/seqinspector/results-${{ steps.revision.outputs.revision }}"
+              "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/seqinspector/results-${{ steps.revision.outputs.revision }}"
             }
           profiles: test_full
 
@@ -44,5 +44,5 @@ jobs:
         with:
           name: Seqera Platform debug log file
           path: |
-            seqera_platform_action_*.log
-            seqera_platform_action_*.json
+            tower_action_*.log
+            tower_action_*.json
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index c6867673..3fa92b8c 100644
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@@ -14,14 +14,14 @@ jobs:
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         with:
-          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          workspace_id: ${{ vars.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          compute_env: ${{ vars.TOWER_COMPUTE_ENV }}
           revision: ${{ github.sha }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/seqinspector/work-${{ github.sha }}
+          workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/seqinspector/work-${{ github.sha }}
           parameters: |
             {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/seqinspector/results-test-${{ github.sha }}"
+              "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/seqinspector/results-test-${{ github.sha }}"
             }
           profiles: test
 
@@ -29,5 +29,5 @@ jobs:
         with:
           name: Seqera Platform debug log file
           path: |
-            seqera_platform_action_*.log
-            seqera_platform_action_*.json
+            tower_action_*.log
+            tower_action_*.json
diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
index ac030fd5..6adb0fff 100644
--- a/.github/workflows/clean-up.yml
+++ b/.github/workflows/clean-up.yml
@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@5bef64f19d7facfb25b37b414482c7164d639639 # v9
+      - uses: actions/stale@5f858e3efba33a5ca4407a664cc011ad407f2008 # v10
         with:
           stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
           stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 999bcc38..6d94bcbf 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -44,9 +44,9 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
           architecture: "x64"
 
       - name: Setup Apptainer
@@ -57,7 +57,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install git+https://github.com/nf-core/tools.git@dev
+          pip install git+https://github.com/nf-core/tools.git
 
       - name: Make a cache directory for the container images
         run: |
diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml
index 2e4ae888..276dcf34 100644
--- a/.github/workflows/fix_linting.yml
+++ b/.github/workflows/fix_linting.yml
@@ -13,13 +13,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
       # indication that the linting is being fixed
       - name: React on comment
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: eyes
@@ -32,9 +32,9 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -47,7 +47,7 @@ jobs:
       # indication that the linting has finished
       - name: react if linting finished succesfully
         if: steps.pre-commit.outcome == 'success'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: "+1"
@@ -67,21 +67,21 @@ jobs:
       - name: react if linting errors were fixed
         id: react-if-fixed
         if: steps.commit-and-push.outcome == 'success'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: hooray
 
       - name: react if linting errors were not fixed
         if: steps.commit-and-push.outcome == 'failure'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: confused
 
       - name: react if linting errors were not fixed
         if: steps.commit-and-push.outcome  == 'failure'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           issue-number: ${{ github.event.issue.number }}
           body: |
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 8b0f88c3..30e66026 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -11,12 +11,12 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
 
-      - name: Set up Python 3.13
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - name: Set up Python 3.14
+        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -28,14 +28,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
           architecture: "x64"
 
       - name: read .nf-core.yml
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index d43797d9..e6e9bc26 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@52423e01640425a022ef5fd42c6fb5f633a02728 # v2
+        uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index e7b58449..e20bf6d0 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -18,7 +18,7 @@ concurrency:
 
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  NFT_VER: "0.9.2"
+  NFT_VER: "0.9.3"
   NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
@@ -40,7 +40,7 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
           ls -la ./
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
         with:
           fetch-depth: 0
 
@@ -78,14 +78,14 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "24.10.5"
+          - "25.04.0"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
 
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
         with:
           fetch-depth: 0
 
@@ -95,6 +95,7 @@ jobs:
         continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
         env:
           NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
+          NXF_VERSION: ${{ matrix.NXF_VER }}
         with:
           profile: ${{ matrix.profile }}
           shard: ${{ matrix.shard }}
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index 0f732495..e64cebd6 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -14,6 +14,11 @@ jobs:
         run: |
           echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT
 
+      - name: get description
+        id: get_topics
+        run: |
+          echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description' >> $GITHUB_OUTPUT
+
       - uses: rzr/fediverse-action@master
         with:
           access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
@@ -23,6 +28,8 @@ jobs:
           message: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
 
+            ${{ steps.get_topics.outputs.description }}
+
             Please see the changelog: ${{ github.event.release.html_url }}
 
             ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml
index beb5c77f..c5988af9 100644
--- a/.github/workflows/template-version-comment.yml
+++ b/.github/workflows/template-version-comment.yml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
         with:
           ref: ${{ github.event.pull_request.head.sha }}
 
diff --git a/.gitpod.yml b/.gitpod.yml
deleted file mode 100644
index 83599f63..00000000
--- a/.gitpod.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-image: nfcore/gitpod:latest
-tasks:
-  - name: Update Nextflow and setup pre-commit
-    command: |
-      pre-commit install --install-hooks
-      nextflow self-update
-
-vscode:
-  extensions:
-    - nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack
diff --git a/.nf-core.yml b/.nf-core.yml
index 02240c94..95804289 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -6,7 +6,7 @@ lint:
   nextflow_config:
     - config_defaults:
         - params.fastq_screen_references
-nf_core_version: 3.3.2
+nf_core_version: 3.4.1
 repository_type: pipeline
 template:
   author: Adrien Coulier
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index bb41beec..d06777a8 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -6,7 +6,7 @@ repos:
         additional_dependencies:
           - prettier@3.6.2
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
diff --git a/.prettierignore b/.prettierignore
index edd29f01..2255e3e3 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -10,4 +10,5 @@ testing/
 testing*
 *.pyc
 bin/
+.nf-test/
 ro-crate-metadata.json
diff --git a/README.md b/README.md
index 174f6ba9..7d114ecb 100644
--- a/README.md
+++ b/README.md
@@ -5,12 +5,13 @@
   </picture>
 </h1>
 
+[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/seqinspector)
 [![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
-[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
+[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
diff --git a/docs/usage.md b/docs/usage.md
index 4f3549a1..63e622db 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -149,7 +149,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
 - `shifter`
   - A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/)
 - `charliecloud`
-  - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
+  - A generic configuration profile to be used with [Charliecloud](https://charliecloud.io/)
 - `apptainer`
   - A generic configuration profile to be used with [Apptainer](https://apptainer.org/)
 - `wave`
diff --git a/main.nf b/main.nf
index 58e593b1..fa619071 100644
--- a/main.nf
+++ b/main.nf
@@ -74,7 +74,10 @@ workflow {
         params.monochrome_logs,
         args,
         params.outdir,
-        params.input
+        params.input,
+        params.help,
+        params.help_full,
+        params.show_hidden
     )
 
     //
diff --git a/modules.json b/modules.json
index b25c6ad5..c716c132 100644
--- a/modules.json
+++ b/modules.json
@@ -12,7 +12,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "e10b76ca0c66213581bec2833e30d31f239dec0b",
                         "installed_by": ["modules"]
                     }
                 }
@@ -21,17 +21,17 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
+                        "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index 812fc4c5..dd513cbd 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::multiqc=1.29
+  - bioconda::multiqc=1.31
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 0ac3c369..5288f5cc 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,8 +3,8 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.29--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.29--pyhdfd78af_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ef/eff0eafe78d5f3b65a6639265a16b89fdca88d06d18894f90fcdb50142004329/data' :
+        'community.wave.seqera.io/library/multiqc:1.31--1efbafd542a23882' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index 88e90571..17881d15 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1"
+                "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.2"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-05-22T11:50:41.182332996"
+        "timestamp": "2025-09-08T20:57:36.139055243"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1"
+                "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.2"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-05-22T11:51:22.448739369"
+        "timestamp": "2025-09-08T20:59:15.142230631"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1"
+                "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.2"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-05-22T11:51:06.198928424"
+        "timestamp": "2025-09-08T20:58:29.629087066"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml
deleted file mode 100644
index bea6c0d3..00000000
--- a/modules/nf-core/multiqc/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-multiqc:
-  - modules/nf-core/multiqc/**
diff --git a/nextflow.config b/nextflow.config
index 7341b0a4..ba1b179c 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -32,13 +32,15 @@ params {
     email_on_fail                = null
     plaintext_email              = false
     monochrome_logs              = false
-    hook_url                     = null
+    hook_url                     = System.getenv('HOOK_URL')
     help                         = false
     help_full                    = false
     show_hidden                  = false
     version                      = false
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
-    trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')// Config options
+    trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
+
+    // Config options
     config_profile_name        = null
     config_profile_description = null
 
@@ -91,7 +93,18 @@ profiles {
         apptainer.enabled       = false
         docker.runOptions       = '-u $(id -u):$(id -g)'
     }
-    arm {
+    arm64 {
+        process.arch            = 'arm64'
+        // TODO https://github.com/nf-core/modules/issues/6694
+        // For now if you're using arm64 you have to use wave for the sake of the maintainers
+        // wave profile
+        apptainer.ociAutoPull   = true
+        singularity.ociAutoPull = true
+        wave.enabled            = true
+        wave.freeze             = true
+        wave.strategy           = 'conda,container'
+    }
+    emulate_amd64 {
         docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
     }
     singularity {
@@ -148,18 +161,6 @@ profiles {
         wave.freeze             = true
         wave.strategy           = 'conda,container'
     }
-    gitpod {
-        executor.name           = 'local'
-        executor.cpus           = 4
-        executor.memory         = 8.GB
-        process {
-            resourceLimits = [
-                memory: 8.GB,
-                cpus  : 4,
-                time  : 1.h
-            ]
-        }
-    }
     gpu {
         docker.runOptions       = '-u $(id -u):$(id -g) --gpus all'
         apptainer.runOptions    = '--nv'
@@ -169,6 +170,8 @@ profiles {
     test_full { includeConfig 'conf/test_full.config' }
 }
 
+// Set AWS client to anonymous when using the default igenomes_base
+aws.client.anonymous = !params.igenomes_ignore && params.igenomes_base?.startsWith('s3://ngi-igenomes/igenomes/') ?: false
 // Load nf-core custom profiles from different institutions
 
 // If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included.
@@ -250,46 +253,19 @@ manifest {
     description     = """Pipeline to QC your sequences"""
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
-    nextflowVersion = '!>=24.10.5'
+    nextflowVersion = '!>=25.04.0'
     version         = '1.0dev'
     doi             = ''
 }
 
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.4.2' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 validation {
     defaultIgnoreParams = ["genomes"]
     monochromeLogs = params.monochrome_logs
-    help {
-        enabled = true
-        command = "nextflow run nf-core/seqinspector -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
-        fullParameter = "help_full"
-        showHiddenParameter = "show_hidden"
-        beforeText = """
--\033[2m----------------------------------------------------\033[0m-
-                                        \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
-\033[0;34m        ___     __   __   __   ___     \033[0;32m/,-._.--~\'\033[0m
-\033[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \033[0;33m}  {\033[0m
-\033[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \033[0;32m\\`-._,-`-,\033[0m
-                                        \033[0;32m`._,._,\'\033[0m
-\033[0;35m  nf-core/seqinspector ${manifest.version}\033[0m
--\033[2m----------------------------------------------------\033[0m-
-"""
-        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
-* The nf-core framework
-    https://doi.org/10.1038/s41587-020-0439-x
-
-* Software dependencies
-    https://github.com/nf-core/seqinspector/blob/master/CITATIONS.md
-"""
-    }
-    summary {
-        beforeText = validation.help.beforeText
-        afterText = validation.help.afterText
-    }
 }
 
 // Load modules.config for DSL2 module specific options
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 2a598bf6..6b31d37b 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -224,6 +224,18 @@
                     "fa_icon": "far calendar",
                     "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.",
                     "hidden": true
+                },
+                "help": {
+                    "type": ["boolean", "string"],
+                    "description": "Display the help message."
+                },
+                "help_full": {
+                    "type": "boolean",
+                    "description": "Display the full detailed help message."
+                },
+                "show_hidden": {
+                    "type": "boolean",
+                    "description": "Display hidden parameters in the help message (only works when --help or --help_full are provided)."
                 }
             }
         }
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index bfba1da6..fff8a7c6 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,8 +22,8 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2025-07-08T11:39:22+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by Adrien Coulier.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "datePublished": "2025-10-16T13:38:57+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by Adrien Coulier.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
                     "@id": "main.nf"
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#6e4028f7-2677-4b95-a287-5774a381ff36"
+                    "@id": "#cc905640-68e5-4225-9aba-bfd290c08fdf"
                 }
             ],
             "name": "nf-core/seqinspector"
@@ -128,7 +128,7 @@
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2025-07-08T11:39:22Z",
+            "dateModified": "2025-10-16T13:38:57Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": ["nf-core", "nextflow", "genomics", "quality-control"],
             "license": ["MIT"],
@@ -157,14 +157,14 @@
             "url": {
                 "@id": "https://www.nextflow.io/"
             },
-            "version": "!>=24.10.5"
+            "version": "!>=25.04.0"
         },
         {
-            "@id": "#6e4028f7-2677-4b95-a287-5774a381ff36",
+            "@id": "#cc905640-68e5-4225-9aba-bfd290c08fdf",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#73c03619-5e44-4c7a-9db2-e6b4a69852e5"
+                    "@id": "#2cb8f151-0728-49b6-969d-b792c1b849b0"
                 }
             ],
             "mainEntity": {
@@ -173,7 +173,7 @@
             "name": "Test suite for nf-core/seqinspector"
         },
         {
-            "@id": "#73c03619-5e44-4c7a-9db2-e6b4a69852e5",
+            "@id": "#2cb8f151-0728-49b6-969d-b792c1b849b0",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/seqinspector",
             "resource": "repos/nf-core/seqinspector/actions/workflows/nf-test.yml",
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index 7de849fc..314467d9 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -11,6 +11,7 @@
 include { UTILS_NFSCHEMA_PLUGIN     } from '../../nf-core/utils_nfschema_plugin'
 include { paramsSummaryMap          } from 'plugin/nf-schema'
 include { samplesheetToList         } from 'plugin/nf-schema'
+include { paramsHelp                } from 'plugin/nf-schema'
 include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
 include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
 include { imNotification            } from '../../nf-core/utils_nfcore_pipeline'
@@ -32,6 +33,9 @@ workflow PIPELINE_INITIALISATION {
     nextflow_cli_args //   array: List of positional nextflow CLI args
     outdir            //  string: The output directory where the results will be saved
     input             //  string: Path to input samplesheet
+    help              // boolean: Display help message and exit
+    help_full         // boolean: Show the full help message
+    show_hidden       // boolean: Show hidden parameters in the help message
 
     main:
 
@@ -50,10 +54,35 @@ workflow PIPELINE_INITIALISATION {
     //
     // Validate parameters and generate parameter summary to stdout
     //
+    before_text = """
+-\033[2m----------------------------------------------------\033[0m-
+                                        \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
+\033[0;34m        ___     __   __   __   ___     \033[0;32m/,-._.--~\'\033[0m
+\033[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \033[0;33m}  {\033[0m
+\033[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \033[0;32m\\`-._,-`-,\033[0m
+                                        \033[0;32m`._,._,\'\033[0m
+\033[0;35m  nf-core/seqinspector ${workflow.manifest.version}\033[0m
+-\033[2m----------------------------------------------------\033[0m-
+"""
+    after_text = """${workflow.manifest.doi ? "\n* The pipeline\n" : ""}${workflow.manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${workflow.manifest.doi ? "\n" : ""}
+* The nf-core framework
+    https://doi.org/10.1038/s41587-020-0439-x
+
+* Software dependencies
+    https://github.com/nf-core/seqinspector/blob/master/CITATIONS.md
+"""
+    command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
+
     UTILS_NFSCHEMA_PLUGIN (
         workflow,
         validate_params,
-        null
+        null,
+        help,
+        help_full,
+        show_hidden,
+        before_text,
+        after_text,
+        command
     )
 
     //
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
deleted file mode 100644
index f8476112..00000000
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-subworkflows/utils_nextflow_pipeline:
-  - subworkflows/nf-core/utils_nextflow_pipeline/**
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
deleted file mode 100644
index ac8523c9..00000000
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-subworkflows/utils_nfcore_pipeline:
-  - subworkflows/nf-core/utils_nfcore_pipeline/**
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
index 4994303e..ee4738c8 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf
+++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
@@ -4,6 +4,7 @@
 
 include { paramsSummaryLog   } from 'plugin/nf-schema'
 include { validateParameters } from 'plugin/nf-schema'
+include { paramsHelp         } from 'plugin/nf-schema'
 
 workflow UTILS_NFSCHEMA_PLUGIN {
 
@@ -15,29 +16,56 @@ workflow UTILS_NFSCHEMA_PLUGIN {
                         //           when this input is empty it will automatically use the configured schema or
                         //           "${projectDir}/nextflow_schema.json" as default. This input should not be empty
                         //           for meta pipelines
+    help                // boolean:  show help message
+    help_full           // boolean:  show full help message
+    show_hidden         // boolean:  show hidden parameters in help message
+    before_text         // string:   text to show before the help message and parameters summary
+    after_text          // string:   text to show after the help message and parameters summary
+    command             // string:   an example command of the pipeline
 
     main:
 
+    if(help || help_full) {
+        help_options = [
+            beforeText: before_text,
+            afterText: after_text,
+            command: command,
+            showHidden: show_hidden,
+            fullHelp: help_full,
+        ]
+        if(parameters_schema) {
+            help_options << [parametersSchema: parameters_schema]
+        }
+        log.info paramsHelp(
+            help_options,
+            params.help instanceof String ? params.help : "",
+        )
+        exit 0
+    }
+
     //
     // Print parameter summary to stdout. This will display the parameters
     // that differ from the default given in the JSON schema
     //
+
+    summary_options = [:]
     if(parameters_schema) {
-        log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema)
-    } else {
-        log.info paramsSummaryLog(input_workflow)
+        summary_options << [parametersSchema: parameters_schema]
     }
+    log.info before_text
+    log.info paramsSummaryLog(summary_options, input_workflow)
+    log.info after_text
 
     //
     // Validate the parameters using nextflow_schema.json or the schema
     // given via the validation.parametersSchema configuration option
     //
     if(validate_params) {
+        validateOptions = [:]
         if(parameters_schema) {
-            validateParameters(parameters_schema:parameters_schema)
-        } else {
-            validateParameters()
+            validateOptions << [parametersSchema: parameters_schema]
         }
+        validateParameters(validateOptions)
     }
 
     emit:
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
index 8fb30164..c977917a 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
@@ -25,6 +25,12 @@ nextflow_workflow {
                 input[0] = workflow
                 input[1] = validate_params
                 input[2] = ""
+                input[3] = false
+                input[4] = false
+                input[5] = false
+                input[6] = ""
+                input[7] = ""
+                input[8] = ""
                 """
             }
         }
@@ -51,6 +57,12 @@ nextflow_workflow {
                 input[0] = workflow
                 input[1] = validate_params
                 input[2] = ""
+                input[3] = false
+                input[4] = false
+                input[5] = false
+                input[6] = ""
+                input[7] = ""
+                input[8] = ""
                 """
             }
         }
@@ -77,6 +89,12 @@ nextflow_workflow {
                 input[0] = workflow
                 input[1] = validate_params
                 input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+                input[3] = false
+                input[4] = false
+                input[5] = false
+                input[6] = ""
+                input[7] = ""
+                input[8] = ""
                 """
             }
         }
@@ -103,6 +121,12 @@ nextflow_workflow {
                 input[0] = workflow
                 input[1] = validate_params
                 input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+                input[3] = false
+                input[4] = false
+                input[5] = false
+                input[6] = ""
+                input[7] = ""
+                input[8] = ""
                 """
             }
         }
@@ -114,4 +138,36 @@ nextflow_workflow {
             )
         }
     }
+
+    test("Should create a help message") {
+
+        when {
+
+            params {
+                test_data   = ''
+                outdir      = null
+            }
+
+            workflow {
+                """
+                validate_params = true
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+                input[3] = true
+                input[4] = false
+                input[5] = false
+                input[6] = "Before"
+                input[7] = "After"
+                input[8] = "nextflow run test/test"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
 }
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
index 09ef842a..8d8c7371 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
@@ -1,8 +1,8 @@
 plugins {
-    id "nf-schema@2.4.2"
+    id "nf-schema@2.5.1"
 }
 
 validation {
     parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
     monochromeLogs = true
-}
\ No newline at end of file
+}
diff --git a/tests/.nftignore b/tests/.nftignore
index 158c83c5..e128a128 100644
--- a/tests/.nftignore
+++ b/tests/.nftignore
@@ -1,10 +1,11 @@
 .DS_Store
 multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
-multiqc/multiqc_data/BETA-multiqc.parquet
+multiqc/multiqc_data/multiqc.parquet
 multiqc/multiqc_data/multiqc.log
 multiqc/multiqc_data/multiqc_data.json
 multiqc/multiqc_data/multiqc_sources.txt
 multiqc/multiqc_data/multiqc_software_versions.txt
+multiqc/multiqc_data/llms-full.txt
 multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
 multiqc/multiqc_report.html
 fastqc/*_fastqc.{html,zip}
diff --git a/tests/default.nf.test b/tests/default.nf.test
index 32014888..7e427966 100644
--- a/tests/default.nf.test
+++ b/tests/default.nf.test
@@ -20,8 +20,6 @@ nextflow_pipeline {
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
-                    // Number of successful tasks
-                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
                     // All stable path name, with a relative path

From babeb1cd7a5e2bf335cbf026ea7eda7771e51e10 Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Mon, 20 Oct 2025 10:48:29 +0200
Subject: [PATCH 281/530] Update conf/modules.config

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
---
 conf/modules.config | 1 -
 1 file changed, 1 deletion(-)

diff --git a/conf/modules.config b/conf/modules.config
index 22cd4d8a..d09ebe5f 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -36,7 +36,6 @@ process {
     }
 
     withName: 'BWAMEM2_INDEX' {
-        ext.args   = ''
         publishDir = [
             path: { "${params.outdir}/bwamem2_index" },
             mode: params.publish_dir_mode,

From 47e2b76536354561f9d8f447036f9a98973342e1 Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Mon, 20 Oct 2025 10:48:42 +0200
Subject: [PATCH 282/530] Update conf/modules.config

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
---
 conf/modules.config | 1 -
 1 file changed, 1 deletion(-)

diff --git a/conf/modules.config b/conf/modules.config
index d09ebe5f..e90c7304 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -43,7 +43,6 @@ process {
         ]
     }
     withName: 'BWAMEM2_MEM' {
-        ext.args   =  ''
         publishDir = [
             path: { "${params.outdir}/bwamem2_mem" },
             mode: params.publish_dir_mode,

From f8f82e5a3ee229d519e1b452c0f25794c1266108 Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Mon, 20 Oct 2025 10:52:19 +0200
Subject: [PATCH 283/530] Update
 subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
---
 subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index bd117986..708d73fb 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -212,7 +212,6 @@ def getGenomeAttribute(attribute) {
     return null
 }
 
-
 //
 // Exit pipeline if incorrect --genome key provided
 //

From 2a36f377194d0d6583ca247eaa1e404a939b0daa Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@henrikstmbp.dyn.scilifelab.se>
Date: Mon, 20 Oct 2025 11:43:33 +0200
Subject: [PATCH 284/530] Committed all the suggested changes

---
 modules/nf-core/bwamem2/mem/bwamem2-mem.diff | 18 ------------------
 1 file changed, 18 deletions(-)
 delete mode 100644 modules/nf-core/bwamem2/mem/bwamem2-mem.diff

diff --git a/modules/nf-core/bwamem2/mem/bwamem2-mem.diff b/modules/nf-core/bwamem2/mem/bwamem2-mem.diff
deleted file mode 100644
index 5faa2f89..00000000
--- a/modules/nf-core/bwamem2/mem/bwamem2-mem.diff
+++ /dev/null
@@ -1,18 +0,0 @@
-Changes in component 'nf-core/bwamem2/mem'
-'modules/nf-core/bwamem2/mem/environment.yml' is unchanged
-'modules/nf-core/bwamem2/mem/meta.yml' is unchanged
-Changes in 'bwamem2/mem/main.nf':
---- modules/nf-core/bwamem2/mem/main.nf
-+++ modules/nf-core/bwamem2/mem/main.nf
-@@ -1,6 +1,6 @@
- process BWAMEM2_MEM {
-     tag "$meta.id"
--    label 'process_high'
-+    label 'process_low'
- 
-     conda "${moduleDir}/environment.yml"
-     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-
-'modules/nf-core/bwamem2/mem/tests/main.nf.test.snap' is unchanged
-'modules/nf-core/bwamem2/mem/tests/main.nf.test' is unchanged
-************************************************************

From 41663d2f04b3b1cf1595e3e00810bed19777f641 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@henrikstmbp.dyn.scilifelab.se>
Date: Mon, 20 Oct 2025 11:50:30 +0200
Subject: [PATCH 285/530] Committed all the suggested changes

---
 conf/modules.config                           |  2 --
 conf/test.config                              | 25 -------------------
 main.nf                                       | 23 +++++++++++++++--
 .../main.nf                                   | 12 ---------
 tests/nextflow.config                         | 25 -------------------
 workflows/seqinspector.nf                     |  6 +----
 6 files changed, 22 insertions(+), 71 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index c4335e4a..8b2446af 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -36,7 +36,6 @@ process {
     }
 
     withName: 'BWAMEM2_INDEX' {
-        ext.args   = ''
         publishDir = [
             path: { "${params.outdir}/bwamem2_index" },
             mode: params.publish_dir_mode,
@@ -44,7 +43,6 @@ process {
         ]
     }
     withName: 'BWAMEM2_MEM' {
-        ext.args   =  ''
         publishDir = [
             path: { "${params.outdir}/bwamem2_mem" },
             mode: params.publish_dir_mode,
diff --git a/conf/test.config b/conf/test.config
index c6f4934c..4d56b3f8 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -23,28 +23,3 @@ params {
     // Genome references
     genome = 'R64-1-1'
 }
-
-
-process {
-    resourceLimits = [
-        cpus: 4,
-        memory: '15.GB',
-        time: '1.h'
-    ]
-    withLabel: 'process_high' {
-        cpus = 4
-        memory = '15.GB'
-    }
-    withLabel: 'process_medium' {
-        cpus = 2
-        memory = '7.GB'
-    }
-    withLabel: 'process_low' {
-        cpus = 1
-        memory = '3.GB'
-    }
-    withLabel: 'process_single' {
-        cpus = 1
-        memory = '3.GB'
-    }
-}
diff --git a/main.nf b/main.nf
index 2b25c3fc..544232d1 100644
--- a/main.nf
+++ b/main.nf
@@ -17,7 +17,6 @@
 
 include { SEQINSPECTOR            } from './workflows/seqinspector'
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
-include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
 
 /*
@@ -29,7 +28,8 @@ include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_seqi
 // TODO nf-core: Remove this line if you don't need a FASTA file
 //   This is an example of how to use getGenomeAttribute() to fetch parameters
 //   from igenomes.config using `--genome`
-// params.fasta = getGenomeAttribute('fasta')
+
+params.fasta = getGenomeAttribute('fasta')
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -103,6 +103,25 @@ workflow {
     )
 }
 
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    FUNCTIONS
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+//
+// Get attribute from genome config file e.g. fasta
+//
+
+def getGenomeAttribute(attribute) {
+    if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
+        if (params.genomes[params.genome].containsKey(attribute)) {
+            return params.genomes[params.genome][attribute]
+        }
+    }
+    return null
+}
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     THE END
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index bd117986..36b1860f 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -200,18 +200,6 @@ def validateInputSamplesheet(input) {
 
     return [ metas[0], fastqs ]
 }
-//
-// Get attribute from genome config file e.g. fasta
-//
-def getGenomeAttribute(attribute) {
-    if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
-        if (params.genomes[ params.genome ].containsKey(attribute)) {
-            return params.genomes[ params.genome ][ attribute ]
-        }
-    }
-    return null
-}
-
 
 //
 // Exit pipeline if incorrect --genome key provided
diff --git a/tests/nextflow.config b/tests/nextflow.config
index e0ff36c8..5ff1eef6 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -12,28 +12,3 @@ params {
     modules_testdata_base_path     = 's3://ngi-igenomes/testdata/nf-core/modules/'
 
 }
-
-
-process {
-    resourceLimits = [
-        cpus: 4,
-        memory: '15.GB',
-        time: '1.h'
-    ]
-    withLabel: 'process_high' {
-        cpus = 4
-        memory = '15.GB'
-    }
-    withLabel: 'process_medium' {
-        cpus = 2
-        memory = '7.GB'
-    }
-    withLabel: 'process_low' {
-        cpus = 1
-        memory = '3.GB'
-    }
-    withLabel: 'process_single' {
-        cpus = 1
-        memory = '3.GB'
-    }
-}
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index bdb2ece0..bd309129 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -23,7 +23,6 @@ include { paramsSummaryMap              } from 'plugin/nf-schema'
 include { paramsSummaryMultiqc          } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { softwareVersionsToYAML        } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { methodsDescriptionText        } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline'
-include { getGenomeAttribute            } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -114,10 +113,7 @@ workflow SEQINSPECTOR {
     // MODULE: Create BWA-MEM2 index of the reference genome
 
     if (!("bwamem2_index" in skip_tools)) {
-        def fasta_file = getGenomeAttribute('fasta')
-        ch_reference_fasta = Channel.fromPath(fasta_file, checkIfExists: true)
-                            .map { file -> tuple([id: file.name], file) }.collect()
-
+        ch_reference_fasta  = Channel.fromPath(params.fasta).map { it -> [[id:it.simpleName], it] }.collect()
 
         BWAMEM2_INDEX (
             ch_reference_fasta

From 10ba7a7adc099db34daf7663ba8ac1e5108a0058 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@henrikstmbp.dyn.scilifelab.se>
Date: Mon, 20 Oct 2025 12:16:39 +0200
Subject: [PATCH 286/530] changes and ss

---
 .github/workflows/linting.yml           |  17 +-
 .github/workflows/linting_comment.yml   |   4 +-
 .prettierrc.yml                         |   5 +
 conf/modules.config                     |   2 +-
 tests/MiSeq.main.nf.test.snap           | 280 +-----------
 tests/MiSeq_PairedEnd.main.nf.test.snap | 254 +----------
 tests/NovaSeq6000.main.nf.test.snap     | 570 +-----------------------
 tests/PromethION.main.nf.test.snap      | 136 +-----
 8 files changed, 51 insertions(+), 1217 deletions(-)

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index dbd52d5a..8b0f88c3 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -3,9 +3,6 @@ name: nf-core linting
 # It runs the `nf-core pipelines lint` and markdown lint tests to ensure
 # that the code meets the nf-core guidelines.
 on:
-  push:
-    branches:
-      - dev
   pull_request:
   release:
     types: [published]
@@ -16,10 +13,10 @@ jobs:
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
-      - name: Set up Python 3.12
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      - name: Set up Python 3.13
+        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -36,13 +33,13 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
           architecture: "x64"
 
       - name: read .nf-core.yml
-        uses: pietrobolcato/action-read-yaml@1.1.0
+        uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
         id: read_yml
         with:
           config: ${{ github.workspace }}/.nf-core.yml
@@ -74,7 +71,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
+        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 95b6b6af..d43797d9 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8
+        uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11
         with:
           workflow: linting.yml
           workflow_conclusion: completed
@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2
+        uses: marocchino/sticky-pull-request-comment@52423e01640425a022ef5fd42c6fb5f633a02728 # v2
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
diff --git a/.prettierrc.yml b/.prettierrc.yml
index c81f9a76..07dbd8bb 100644
--- a/.prettierrc.yml
+++ b/.prettierrc.yml
@@ -1 +1,6 @@
 printWidth: 120
+tabWidth: 4
+overrides:
+  - files: "*.{md,yml,yaml,html,css,scss,js,cff}"
+    options:
+      tabWidth: 2
diff --git a/conf/modules.config b/conf/modules.config
index 8b2446af..25a34e09 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -58,7 +58,7 @@ process {
         ]
     }
 
-    withName: 'SAMTOOLS_FAIIDX' {
+    withName: 'SAMTOOLS_FAIDX' {
         ext.args   = ''
         publishDir = [
             path: { "${params.outdir}/samtools_faidx" },
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index bc54480c..3712aabd 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -1,297 +1,53 @@
 {
     "Miseq data test (skip all tools)": {
         "content": [
-            3,
-            {
-                "BWAMEM2_INDEX": {
-                    "bwamem2": "2.2.1"
-                },
-                "BWAMEM2_MEM": {
-                    "bwamem2": "2.2.1",
-                    "samtools": 1.21
-                },
-                "Workflow": {
-                    "nf-core/seqinspector": "v1.0dev"
-                }
-            },
+            0,
+            null,
             [
-                "bwamem2_index",
-                "bwamem2_index/bwamem2",
-                "bwamem2_index/bwamem2/genome.fa.0123",
-                "bwamem2_index/bwamem2/genome.fa.amb",
-                "bwamem2_index/bwamem2/genome.fa.ann",
-                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
-                "bwamem2_index/bwamem2/genome.fa.pac",
-                "bwamem2_mem",
-                "bwamem2_mem/SAMPLE_SINGLE_END_1.bam",
-                "multiqc",
-                "multiqc/global_report",
-                "multiqc/global_report/multiqc_data",
-                "multiqc/global_report/multiqc_data/multiqc.log",
-                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
-                "multiqc/global_report/multiqc_data/multiqc_data.json",
-                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
-                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
-                "multiqc/global_report/multiqc_report.html",
-                "pipeline_info",
-                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"
+                "pipeline_info"
             ],
             [
-                "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
-                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
-                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
-                "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
-                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "SAMPLE_SINGLE_END_1.bam:md5,79744f146752fd486b09604be721cc85",
-                "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
+                
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-09-24T10:43:56.070328995"
+        "timestamp": "2025-10-20T12:11:49.72333"
     },
     "MiSeq data test (single end reads)": {
         "content": [
-            6,
-            {
-                "BWAMEM2_INDEX": {
-                    "bwamem2": "2.2.1"
-                },
-                "BWAMEM2_MEM": {
-                    "bwamem2": "2.2.1",
-                    "samtools": 1.21
-                },
-                "FASTQC": {
-                    "fastqc": "0.12.1"
-                },
-                "FASTQSCREEN_FASTQSCREEN": {
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             ]
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-                "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
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             ]
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 }
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index 047814e4..142e583f 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -1,261 +1,19 @@
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-                "multiqc/global_report/multiqc_data/fastqc_adapter_content_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
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-                "multiqc/global_report/multiqc_data/multiqc.log",
-                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
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-                "seqfu_stats/SAMPLE_PAIRED_END_2_2_seqfu.tsv",
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-                "SAMPLE_PAIRED_END_2_2_seqfu.tsv:md5,152566a128dd657da33465b4966b5799",
-                "SAMPLE_PAIRED_END_2_2_seqfu_mqc.txt:md5,8a3296956e094e3a95e28431e6009c40"
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             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-09-24T10:41:23.851991495"
+        "timestamp": "2025-10-20T12:12:12.054293"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index a1fd0301..e7cc72d0 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -1,577 +1,19 @@
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-                "multiqc/group_reports/test/multiqc_data/fastqc_per_base_n_content_plot.txt",
-                "multiqc/group_reports/test/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
-                "multiqc/group_reports/test/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
-                "multiqc/group_reports/test/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
-                "multiqc/group_reports/test/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
-                "multiqc/group_reports/test/multiqc_data/fastqc_sequence_counts_plot.txt",
-                "multiqc/group_reports/test/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
-                "multiqc/group_reports/test/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
-                "multiqc/group_reports/test/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
-                "multiqc/group_reports/test/multiqc_data/multiqc.log",
-                "multiqc/group_reports/test/multiqc_data/multiqc_citations.txt",
-                "multiqc/group_reports/test/multiqc_data/multiqc_data.json",
-                "multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt",
-                "multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt",
-                "multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/group_reports/test/multiqc_data/multiqc_seqfu.txt",
-                "multiqc/group_reports/test/multiqc_data/multiqc_software_versions.txt",
-                "multiqc/group_reports/test/multiqc_data/multiqc_sources.txt",
-                "multiqc/group_reports/test/multiqc_plots",
-                "multiqc/group_reports/test/multiqc_plots/pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
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-                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
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-                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
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-                "multiqc/group_reports/test/multiqc_plots/pdf/seqfu.pdf",
-                "multiqc/group_reports/test/multiqc_plots/png",
-                "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/group_reports/test/multiqc_plots/png/fastqc-status-check-heatmap.png",
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-                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
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-                "multiqc/group_reports/test/multiqc_plots/png/seqfu.png",
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-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
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-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
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-                "multiqc/group_reports/test/multiqc_plots/svg/general_stats_table.svg",
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-                "pipeline_info",
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-                "seqfu_stats/Sample23_3_seqfu_mqc.txt",
-                "seqfu_stats/SampleA_2_seqfu.tsv",
-                "seqfu_stats/SampleA_2_seqfu_mqc.txt",
-                "seqfu_stats/Undetermined_5_seqfu.tsv",
-                "seqfu_stats/Undetermined_5_seqfu_mqc.txt",
-                "seqfu_stats/sampletest_4_seqfu.tsv",
-                "seqfu_stats/sampletest_4_seqfu_mqc.txt"
+                "pipeline_info"
             ],
             [
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-                "fastqc_per_base_sequence_quality_plot.txt:md5,2a60a8518caad855e842cf70a8037dad",
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-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,ef663c12746dfb88f7297b891756fadd",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,5a224c4e837ba42c16b724289bb1bf32",
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-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
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-                "multiqc_seqfu.txt:md5,5b54a49079169985795537d83d58bdd9",
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-                "fastqc_per_base_n_content_plot.txt:md5,4c5bfb1594b391f3e36a9e1223b43a94",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,6251cde1646484446499252bd15c58a2",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,f645e38916efafd07d4c2c3d5c7cd051",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,a9d3152a43988e39fae4a75faa3a5aa4",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,aef487a8b267a14a92be64b0b01d9b5c",
-                "fastqc_sequence_counts_plot.txt:md5,5021496dd00366d08064804bbb5192e3",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,e37e8e4584f0157a5fa0d53b4834e836",
-                "fastqc_sequence_length_distribution_plot.txt:md5,393cc090200a5151561efb1ed5280b89",
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-                "fastq_screen_plot.txt:md5,44fca6453b0a3d0590271bd7a31cc740",
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-                "fastqc_overrepresented_sequences_plot.txt:md5,eac8d0fd31c614d8d0f56bd54ee8c78c",
-                "fastqc_per_base_n_content_plot.txt:md5,b7b249afe807ca2321e6dd839961795c",
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-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,ee29af5517a8c6f872adbaccea4ff2f8",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,3eaf12f9267c10e4e457a2bb9bdc70ea",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,1818e0b917e45a583740f2cbb0638f8d",
-                "fastqc_sequence_counts_plot.txt:md5,0c4863a5475a2444cd00b053eb8941b1",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,a7a050f827a4f821117efd8d25668c51",
-                "fastqc_sequence_length_distribution_plot.txt:md5,9c0761008be04d8ccf4c0e16acc6348c",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
-                "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
-                "multiqc_seqfu.txt:md5,b5434520fa5be5c98be5ed164a464d23",
-                "fastq_screen_plot.txt:md5,5f748d33a7a396547fe8c260b728aa06",
-                "fastqc-status-check-heatmap.txt:md5,08228a8f3d6f11b174b98626bb22bda1",
-                "fastqc_overrepresented_sequences_plot.txt:md5,3434dfb79f150e2e584e85866983ba01",
-                "fastqc_per_base_n_content_plot.txt:md5,e371981072ec99d11c6adb5a4034808c",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,bf83d019eaaeb1ca659ff28cfb2bdfea",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,3f40b8ee69d3eaefe657cc5ed622cc8b",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,86b61d09437a96448e1325e6be834048",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,9f7307469b112bd054f8ee0cc2cf4d65",
-                "fastqc_sequence_counts_plot.txt:md5,f0c693cc281a6e61ba219bab04f59a47",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,8c2aa91358fd4a2e946cbcc1f312f9b6",
-                "fastqc_sequence_length_distribution_plot.txt:md5,875ebcd6726bb9d36ffa64265e5071d0",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
-                "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
-                "multiqc_seqfu.txt:md5,e2e092852c011abe5ad75cdcd68b9383",
-                "fastq_screen_plot.txt:md5,8622e1dbd0fe62520af6096207b9775d",
-                "fastqc-status-check-heatmap.txt:md5,2a66f5d61b9eb579555905cd5954b04c",
-                "fastqc_overrepresented_sequences_plot.txt:md5,e0b5bfc4b64d37611b51c939e61196fa",
-                "fastqc_per_base_n_content_plot.txt:md5,1380831484d1b069a2fd4a20437118bf",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,12585cf6b03db684a5ebd959f51e77e7",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a1464399e84711454499d27e98ed942b",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,026d11e7b49a49ac7bac85f376760305",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,4d646b20970d09d846947b87961efe7e",
-                "fastqc_sequence_counts_plot.txt:md5,057fb961863b325fe875d3a7879cb888",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,3b86c9d8625c439376102f3286c7bba7",
-                "fastqc_sequence_length_distribution_plot.txt:md5,6296c9ddbf8ba8e12053149d057fd7b2",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5",
-                "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
-                "multiqc_seqfu.txt:md5,a1a0b9a0dde0c1c4fe184d44c675dcde",
-                "Sample1_1_seqfu.tsv:md5,269fabf8435defcd327aa69a050b7869",
-                "Sample1_1_seqfu_mqc.txt:md5,a354b0ed16b9cf84aa88f501d7740fd6",
-                "Sample23_3_seqfu.tsv:md5,6fdadbeeefccbf957f880d6852bf9676",
-                "Sample23_3_seqfu_mqc.txt:md5,e94269e3efc8b8192d7ac9c15ea2aa99",
-                "SampleA_2_seqfu.tsv:md5,b980ed694a05825fcf7c8b5b73888eb3",
-                "SampleA_2_seqfu_mqc.txt:md5,1d4b0e918644cf553108b7ccf77b4a01",
-                "Undetermined_5_seqfu.tsv:md5,b4458d41df4dee9321da03f4d4672aae",
-                "Undetermined_5_seqfu_mqc.txt:md5,0c869488cb61d2f87758c621bded212b",
-                "sampletest_4_seqfu.tsv:md5,db3179b0c41a09e6317a5a5c0852f476",
-                "sampletest_4_seqfu_mqc.txt:md5,590b97cc48268629204f59007bae7ad7"
+                
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-09-24T10:46:41.927291661"
+        "timestamp": "2025-10-20T12:12:37.184658"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index daee5f1b..11690c71 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -1,143 +1,19 @@
 {
     "PromethION data test": {
         "content": [
-            4,
-            {
-                "FASTQC": {
-                    "fastqc": "0.12.1"
-                },
-                "FASTQSCREEN_FASTQSCREEN": {
-                    "fastqscreen": "0.16.0"
-                },
-                "SEQFU_STATS": {
-                    "seqfu": "1.20.3"
-                },
-                "Workflow": {
-                    "nf-core/seqinspector": "v1.0dev"
-                }
-            },
+            0,
+            null,
             [
-                "fastqc",
-                "fastqc/hg001_1_fastqc.html",
-                "fastqc/hg001_1_fastqc.zip",
-                "fastqscreen",
-                "fastqscreen/hg001_1_screen.html",
-                "fastqscreen/hg001_1_screen.png",
-                "fastqscreen/hg001_1_screen.txt",
-                "multiqc",
-                "multiqc/global_report",
-                "multiqc/global_report/multiqc_data",
-                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
-                "multiqc/global_report/multiqc_data/fastqc_adapter_content_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
-                "multiqc/global_report/multiqc_data/multiqc.log",
-                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
-                "multiqc/global_report/multiqc_data/multiqc_data.json",
-                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
-                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
-                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
-                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
-                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
-                "multiqc/global_report/multiqc_plots",
-                "multiqc/global_report/multiqc_plots/pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
-                "multiqc/global_report/multiqc_plots/png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_adapter_content_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu.png",
-                "multiqc/global_report/multiqc_plots/svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
-                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
-                "multiqc/global_report/multiqc_report.html",
-                "pipeline_info",
-                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
-                "seqfu_stats",
-                "seqfu_stats/hg001_1_seqfu.tsv",
-                "seqfu_stats/hg001_1_seqfu_mqc.txt"
+                "pipeline_info"
             ],
             [
-                "hg001_1_screen.png:md5,b9c58e388f18ad11f4c2e29e9b573a5e",
-                "hg001_1_screen.txt:md5,8e53ea043d658a130f4b8ca455e2ba9b",
-                "fastq_screen_plot.txt:md5,3023b86477fecf6d46d8fc60d82cc53a",
-                "fastqc-status-check-heatmap.txt:md5,825668e94de27356f0a112beb758e416",
-                "fastqc_adapter_content_plot.txt:md5,1fa991080c20755e5e729a5eeab960e5",
-                "fastqc_overrepresented_sequences_plot.txt:md5,e810a3d3eba0ba83b122763505f511a7",
-                "fastqc_per_base_n_content_plot.txt:md5,cbdb64298ff839665e8c8c8e89896e87",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,4962950bc3ce77169ac510d64cb769c6",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,e62273533304be59dab5f13afef93b3e",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,3d49290a15406cb5dac1460c02729f0f",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,7cc10d1bc92ca09431a506c38d911228",
-                "fastqc_sequence_counts_plot.txt:md5,0425d7298c24df6158d5bf7aca1d4190",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,9111d942c7eed5af0e9ccb8c42db8505",
-                "fastqc_sequence_length_distribution_plot.txt:md5,04adfcd0125ebcc3e3bb631f1956c812",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,7c5d711e27c53d13c81644a1f2468dba",
-                "multiqc_fastqc.txt:md5,1a4b472e13cadc770832b0e20d1de7b0",
-                "multiqc_seqfu.txt:md5,9595d608ff5709f2bdec8cb1016416c0",
-                "hg001_1_seqfu.tsv:md5,b133752c897afbb4d8721b911fa117d4",
-                "hg001_1_seqfu_mqc.txt:md5,6285f582c03faa70e8dcb3503e5db728"
+                
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-09-24T09:50:22.026441122"
+        "timestamp": "2025-10-20T12:13:17.680867"
     }
 }
\ No newline at end of file

From 17bcf711a278a486213d80dc3c6c69d1a8e253f6 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@henrikstmbp.dyn.scilifelab.se>
Date: Mon, 20 Oct 2025 12:40:32 +0200
Subject: [PATCH 287/530] parameter initialization

---
 .prettierrc.yml           |  6 +-----
 main.nf                   | 21 ++++++++++-----------
 workflows/seqinspector.nf |  6 +++---
 3 files changed, 14 insertions(+), 19 deletions(-)

diff --git a/.prettierrc.yml b/.prettierrc.yml
index 07dbd8bb..47f7713d 100644
--- a/.prettierrc.yml
+++ b/.prettierrc.yml
@@ -1,6 +1,2 @@
 printWidth: 120
-tabWidth: 4
-overrides:
-  - files: "*.{md,yml,yaml,html,css,scss,js,cff}"
-    options:
-      tabWidth: 2
+
diff --git a/main.nf b/main.nf
index 544232d1..0cad90f7 100644
--- a/main.nf
+++ b/main.nf
@@ -7,17 +7,6 @@
     Website: https://nf-co.re/seqinspector
     Slack  : https://nfcore.slack.com/channels/seqinspector
 ----------------------------------------------------------------------------------------
-*/
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-include { SEQINSPECTOR            } from './workflows/seqinspector'
-include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
-include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -31,6 +20,16 @@ include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_seqi
 
 params.fasta = getGenomeAttribute('fasta')
 
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+include { SEQINSPECTOR            } from './workflows/seqinspector'
+include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
+include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     NAMED WORKFLOWS FOR PIPELINE
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index bd309129..ddca199b 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -168,7 +168,7 @@ workflow SEQINSPECTOR {
     ch_bam_bai = ch_bwamem2_mem
         .join(ch_samtools_index)
         .map { meta, bam, bai ->
-             [meta, bam, bai]
+            [meta, bam, bai]
     }
 
     ch_bam_bai.view { "Combined BAM/BAI for Picard: $it" }
@@ -187,8 +187,8 @@ workflow SEQINSPECTOR {
             ch_fai
 )
 
-     ch_multiqc_files = ch_multiqc_files.mix(PICARD_COLLECTMULTIPLEMETRICS.out.metrics)
-     ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
+    ch_multiqc_files = ch_multiqc_files.mix(PICARD_COLLECTMULTIPLEMETRICS.out.metrics)
+    ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
     }
 
 

From 31f23564c239e8da05d7098e5ea7ce13894b5317 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@henrikstmbp.dyn.scilifelab.se>
Date: Mon, 20 Oct 2025 12:42:22 +0200
Subject: [PATCH 288/530] minor changes

---
 .prettierrc.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.prettierrc.yml b/.prettierrc.yml
index 47f7713d..c81f9a76 100644
--- a/.prettierrc.yml
+++ b/.prettierrc.yml
@@ -1,2 +1 @@
 printWidth: 120
-

From 4561be4c4c5aefa701f6b264eb7eb64759b90ce5 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@henrikstmbp.dyn.scilifelab.se>
Date: Mon, 20 Oct 2025 13:15:18 +0200
Subject: [PATCH 289/530] removed fasta from nextflow.config

---
 nextflow.config               |  1 -
 tests/MiSeq.main.nf.test.snap | 19 ++++++++++++++-----
 2 files changed, 14 insertions(+), 6 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index dedd6041..90278496 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -16,7 +16,6 @@ params {
     skip_tools                 = ''
     // References
     genome                     = null
-    fasta                      = null
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
     igenomes_ignore            = false
     sort_bam                   = true
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 3712aabd..25cf1396 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -18,20 +18,29 @@
     },
     "MiSeq data test (single end reads)": {
         "content": [
-            0,
-            null,
+            1,
+            {
+                "Workflow": {
+                    "nf-core/seqinspector": "v1.0dev"
+                }
+            },
             [
-                "pipeline_info"
+                "pipeline_info",
+                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "seqfu_stats",
+                "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu.tsv",
+                "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu_mqc.txt"
             ],
             [
-                
+                "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,f65c868e562291647d539090698ba5eb",
+                "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "25.04.7"
         },
-        "timestamp": "2025-10-20T12:11:15.992085"
+        "timestamp": "2025-10-20T13:14:37.510573"
     },
     "Miseq data test (skip fastqc)": {
         "content": [

From b7fee4fdbc4d4b9c291f0257f6008b745254548a Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Mon, 20 Oct 2025 12:01:54 +0000
Subject: [PATCH 290/530] ss

---
 conf/modules.config                     |  26 --
 conf/test.config                        |  25 ++
 modules.json                            |  15 -
 nextflow_schema.json                    |   2 +-
 tests/MiSeq.main.nf.test.snap           | 243 +++++++++-
 tests/MiSeq_PairedEnd.main.nf.test.snap | 254 ++++++++++-
 tests/NovaSeq6000.main.nf.test.snap     | 570 +++++++++++++++++++++++-
 tests/PromethION.main.nf.test.snap      | 136 +++++-
 workflows/seqinspector.nf               |  58 ---
 9 files changed, 1196 insertions(+), 133 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 25a34e09..e90c7304 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -49,32 +49,6 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-    withName: 'PICARD_COLLECTMULTIPLEMETRICS' {
-        ext.args   =  ''
-        publishDir = [
-            path: { "${params.outdir}/picard_collectmultiplemetrics" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: 'SAMTOOLS_FAIDX' {
-        ext.args   = ''
-        publishDir = [
-            path: { "${params.outdir}/samtools_faidx" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: 'SAMTOOLS_INDEX' {
-        ext.args   = ''
-        publishDir = [
-            path: { "${params.outdir}/samtools_index" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
 
     withName: 'MULTIQC_GLOBAL' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
diff --git a/conf/test.config b/conf/test.config
index 4d56b3f8..a14370c5 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -23,3 +23,28 @@ params {
     // Genome references
     genome = 'R64-1-1'
 }
+
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+    withLabel: 'process_high' {
+        cpus = 4
+        memory = '15.GB'
+    }
+    withLabel: 'process_medium' {
+        cpus = 2
+        memory = '7.GB'
+    }
+    withLabel: 'process_low' {
+        cpus = 1
+        memory = '3.GB'
+    }
+    withLabel: 'process_single' {
+        cpus = 1
+        memory = '3.GB'
+    }
+}
+
diff --git a/modules.json b/modules.json
index e62fa390..e3b68325 100644
--- a/modules.json
+++ b/modules.json
@@ -42,21 +42,6 @@
                         "git_sha": "7b50cb7be890e4b28cffb82e438cc6a8d7805d3f",
                         "installed_by": ["modules"]
                     },
-                    "picard/collectmultiplemetrics": {
-                        "branch": "master",
-                        "git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255",
-                        "installed_by": ["modules"]
-                    },
-                    "samtools/faidx": {
-                        "branch": "master",
-                        "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
-                        "installed_by": ["modules"]
-                    },
-                    "samtools/index": {
-                        "branch": "master",
-                        "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
-                        "installed_by": ["modules"]
-                    },
                     "seqfu/stats": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
diff --git a/nextflow_schema.json b/nextflow_schema.json
index eb6cbcea..267afaa9 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -51,7 +51,7 @@
                 "skip_tools": {
                     "type": "string",
                     "description": "Comma-separated string of tools to skip",
-                    "pattern": "^((fastqc|fastqscreen|seqfu_stats|seqtk_sample|bwamem2_index|bwamem2_mem|picard_collectmultiplemetrics|samtools_faidx|samtools_index)?,?)*(?<!,)$"
+                    "pattern": "^((fastqc|fastqscreen|seqfu_stats|seqtk_sample|bwamem2_index|bwamem2_mem)?,?)*(?<!,)$"
                 }
             }
         },
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 25cf1396..a7f1637e 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -1,30 +1,149 @@
 {
     "Miseq data test (skip all tools)": {
         "content": [
-            0,
-            null,
+            1,
+            {
+                "Workflow": {
+                    "nf-core/seqinspector": "v1.0dev"
+                }
+            },
             [
-                "pipeline_info"
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"
             ],
             [
-                
+                "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-20T12:11:49.72333"
+        "timestamp": "2025-10-20T11:56:38.220604962"
     },
     "MiSeq data test (single end reads)": {
         "content": [
-            1,
+            6,
             {
+                "BWAMEM2_INDEX": {
+                    "bwamem2": "2.2.1"
+                },
+                "BWAMEM2_MEM": {
+                    "bwamem2": "2.2.1",
+                    "samtools": 1.21
+                },
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "FASTQSCREEN_FASTQSCREEN": {
+                    "fastqscreen": "0.16.0"
+                },
+                "SEQFU_STATS": {
+                    "seqfu": "1.20.3"
+                },
                 "Workflow": {
                     "nf-core/seqinspector": "v1.0dev"
                 }
             },
             [
+                "bwamem2_index",
+                "bwamem2_index/bwamem2",
+                "bwamem2_index/bwamem2/genome.fa.0123",
+                "bwamem2_index/bwamem2/genome.fa.amb",
+                "bwamem2_index/bwamem2/genome.fa.ann",
+                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
+                "bwamem2_index/bwamem2/genome.fa.pac",
+                "bwamem2_mem",
+                "bwamem2_mem/SAMPLE_SINGLE_END_1.bam",
+                "fastqc",
+                "fastqc/SAMPLE_SINGLE_END_1_fastqc.html",
+                "fastqc/SAMPLE_SINGLE_END_1_fastqc.zip",
+                "fastqscreen",
+                "fastqscreen/SAMPLE_SINGLE_END_1_screen.html",
+                "fastqscreen/SAMPLE_SINGLE_END_1_screen.png",
+                "fastqscreen/SAMPLE_SINGLE_END_1_screen.txt",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_plots",
+                "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu.png",
+                "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
+                "multiqc/global_report/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "seqfu_stats",
@@ -32,31 +151,125 @@
                 "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu_mqc.txt"
             ],
             [
+                "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
+                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
+                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
+                "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
+                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
+                "SAMPLE_SINGLE_END_1.bam:md5,79744f146752fd486b09604be721cc85",
+                "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
+                "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
+                "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
+                "fastqc-status-check-heatmap.txt:md5,8f98652c377741c974e485652a19f37f",
+                "fastqc_overrepresented_sequences_plot.txt:md5,cdc7479933cae03e0043ae794f81c304",
+                "fastqc_per_base_n_content_plot.txt:md5,dd8d6976dc5ea8cf67d9fa2c3be9e24b",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,5f9a98d3068aab17f26731ae0615f41a",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,1de1333bb959189dcf8230706f60dbfc",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,62f140bfa52d462c9c499dfdabc35476",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,5fda43eb9b7c60cf6b4348f734a94b26",
+                "fastqc_sequence_counts_plot.txt:md5,00cd6842465f7aa9ae75434e175946a6",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,c3befe0812d2f1c23d5e75e6fccf0622",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607",
+                "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
+                "multiqc_seqfu.txt:md5,8e6989a2392f599a09a5c3edf8119702",
                 "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,f65c868e562291647d539090698ba5eb",
                 "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-20T13:14:37.510573"
+        "timestamp": "2025-10-20T11:55:41.808238633"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
-            0,
-            null,
+            5,
+            {
+                "BWAMEM2_INDEX": {
+                    "bwamem2": "2.2.1"
+                },
+                "BWAMEM2_MEM": {
+                    "bwamem2": "2.2.1",
+                    "samtools": 1.21
+                },
+                "FASTQSCREEN_FASTQSCREEN": {
+                    "fastqscreen": "0.16.0"
+                },
+                "SEQFU_STATS": {
+                    "seqfu": "1.20.3"
+                },
+                "Workflow": {
+                    "nf-core/seqinspector": "v1.0dev"
+                }
+            },
             [
-                "pipeline_info"
+                "bwamem2_index",
+                "bwamem2_index/bwamem2",
+                "bwamem2_index/bwamem2/genome.fa.0123",
+                "bwamem2_index/bwamem2/genome.fa.amb",
+                "bwamem2_index/bwamem2/genome.fa.ann",
+                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
+                "bwamem2_index/bwamem2/genome.fa.pac",
+                "bwamem2_mem",
+                "bwamem2_mem/SAMPLE_SINGLE_END_1.bam",
+                "fastqscreen",
+                "fastqscreen/SAMPLE_SINGLE_END_1_screen.html",
+                "fastqscreen/SAMPLE_SINGLE_END_1_screen.png",
+                "fastqscreen/SAMPLE_SINGLE_END_1_screen.txt",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_plots",
+                "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu.png",
+                "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
+                "multiqc/global_report/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "seqfu_stats",
+                "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu.tsv",
+                "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu_mqc.txt"
             ],
             [
-                
+                "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
+                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
+                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
+                "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
+                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
+                "SAMPLE_SINGLE_END_1.bam:md5,79744f146752fd486b09604be721cc85",
+                "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
+                "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
+                "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607",
+                "multiqc_seqfu.txt:md5,8e6989a2392f599a09a5c3edf8119702",
+                "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,f65c868e562291647d539090698ba5eb",
+                "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-20T12:11:33.257362"
+        "timestamp": "2025-10-20T11:56:20.313008405"
     }
 }
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index 142e583f..a9ab4015 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -1,19 +1,261 @@
 {
     "MiSeq data test (paired end reads)": {
         "content": [
-            0,
-            null,
+            11,
+            {
+                "BWAMEM2_INDEX": {
+                    "bwamem2": "2.2.1"
+                },
+                "BWAMEM2_MEM": {
+                    "bwamem2": "2.2.1",
+                    "samtools": 1.21
+                },
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "FASTQSCREEN_FASTQSCREEN": {
+                    "fastqscreen": "0.16.0"
+                },
+                "SEQFU_STATS": {
+                    "seqfu": "1.20.3"
+                },
+                "Workflow": {
+                    "nf-core/seqinspector": "v1.0dev"
+                }
+            },
             [
-                "pipeline_info"
+                "bwamem2_index",
+                "bwamem2_index/bwamem2",
+                "bwamem2_index/bwamem2/genome.fa.0123",
+                "bwamem2_index/bwamem2/genome.fa.amb",
+                "bwamem2_index/bwamem2/genome.fa.ann",
+                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
+                "bwamem2_index/bwamem2/genome.fa.pac",
+                "bwamem2_mem",
+                "bwamem2_mem/SAMPLE_PAIRED_END_1_1.bam",
+                "bwamem2_mem/SAMPLE_PAIRED_END_2_2.bam",
+                "fastqc",
+                "fastqc/SAMPLE_PAIRED_END_1_1_1_fastqc.html",
+                "fastqc/SAMPLE_PAIRED_END_1_1_1_fastqc.zip",
+                "fastqc/SAMPLE_PAIRED_END_1_1_2_fastqc.html",
+                "fastqc/SAMPLE_PAIRED_END_1_1_2_fastqc.zip",
+                "fastqc/SAMPLE_PAIRED_END_2_2_1_fastqc.html",
+                "fastqc/SAMPLE_PAIRED_END_2_2_1_fastqc.zip",
+                "fastqc/SAMPLE_PAIRED_END_2_2_2_fastqc.html",
+                "fastqc/SAMPLE_PAIRED_END_2_2_2_fastqc.zip",
+                "fastqscreen",
+                "fastqscreen/SAMPLE_PAIRED_END_1_1_1_screen.html",
+                "fastqscreen/SAMPLE_PAIRED_END_1_1_1_screen.png",
+                "fastqscreen/SAMPLE_PAIRED_END_1_1_1_screen.txt",
+                "fastqscreen/SAMPLE_PAIRED_END_1_1_2_screen.html",
+                "fastqscreen/SAMPLE_PAIRED_END_1_1_2_screen.png",
+                "fastqscreen/SAMPLE_PAIRED_END_1_1_2_screen.txt",
+                "fastqscreen/SAMPLE_PAIRED_END_2_2_1_screen.html",
+                "fastqscreen/SAMPLE_PAIRED_END_2_2_1_screen.png",
+                "fastqscreen/SAMPLE_PAIRED_END_2_2_1_screen.txt",
+                "fastqscreen/SAMPLE_PAIRED_END_2_2_2_screen.html",
+                "fastqscreen/SAMPLE_PAIRED_END_2_2_2_screen.png",
+                "fastqscreen/SAMPLE_PAIRED_END_2_2_2_screen.txt",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/global_report/multiqc_data/fastqc_adapter_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_plots",
+                "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_adapter_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu.png",
+                "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
+                "multiqc/global_report/multiqc_report.html",
+                "multiqc/group_reports",
+                "multiqc/group_reports/Bpacificus",
+                "multiqc/group_reports/Bpacificus/multiqc_data",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_adapter_content_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc.log",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_citations.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_data.json",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_plots",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
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+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/seqfu.pdf",
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+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-cnt.png",
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+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
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+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
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+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
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+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/seqfu.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "seqfu_stats",
+                "seqfu_stats/SAMPLE_PAIRED_END_1_1_seqfu.tsv",
+                "seqfu_stats/SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt",
+                "seqfu_stats/SAMPLE_PAIRED_END_2_2_seqfu.tsv",
+                "seqfu_stats/SAMPLE_PAIRED_END_2_2_seqfu_mqc.txt"
             ],
             [
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+                "fastqc_per_base_n_content_plot.txt:md5,4eca1ef40d4d3d318b82e68e9fa3c589",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,218757a51c3de79a39a704c979df03da",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a4035ac9f0a0c07574130758b06630d7",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,637b937e023c84115ec06b529cc8ec1b",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,47d60153a430e2b8da51655704c2b31b",
+                "fastqc_sequence_counts_plot.txt:md5,10737092a3473fba81fbe49555512b2b",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,6412f57686de02e1f1c3751a7ca2be8b",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,5ef00028497d3271c9f0ea9a961db1e5",
+                "multiqc_fastqc.txt:md5,bc499ad273fd1c887056c31b82544984",
+                "multiqc_seqfu.txt:md5,1f1e063e4a509a26cee167c3b20389c0",
+                "SAMPLE_PAIRED_END_1_1_seqfu.tsv:md5,bbd911ff3fa43212dfd4c5a5872dbdb6",
+                "SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt:md5,cd60f746b6749cc66213d031af1b931c",
+                "SAMPLE_PAIRED_END_2_2_seqfu.tsv:md5,152566a128dd657da33465b4966b5799",
+                "SAMPLE_PAIRED_END_2_2_seqfu_mqc.txt:md5,8a3296956e094e3a95e28431e6009c40"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-20T12:12:12.054293"
+        "timestamp": "2025-10-20T11:57:37.980484968"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index e7cc72d0..12014baa 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -1,19 +1,577 @@
 {
     "NovaSeq6000 data test": {
         "content": [
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-            null,
+            26,
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+                },
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+                "bwamem2_index/bwamem2/genome.fa.ann",
+                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
+                "bwamem2_index/bwamem2/genome.fa.pac",
+                "bwamem2_mem",
+                "bwamem2_mem/Sample1_1.bam",
+                "bwamem2_mem/Sample23_3.bam",
+                "bwamem2_mem/SampleA_2.bam",
+                "bwamem2_mem/Undetermined_5.bam",
+                "bwamem2_mem/sampletest_4.bam",
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+                "fastqc/Sample1_1_fastqc.html",
+                "fastqc/Sample1_1_fastqc.zip",
+                "fastqc/Sample23_3_fastqc.html",
+                "fastqc/Sample23_3_fastqc.zip",
+                "fastqc/SampleA_2_fastqc.html",
+                "fastqc/SampleA_2_fastqc.zip",
+                "fastqc/Undetermined_5_fastqc.html",
+                "fastqc/Undetermined_5_fastqc.zip",
+                "fastqc/sampletest_4_fastqc.html",
+                "fastqc/sampletest_4_fastqc.zip",
+                "fastqscreen",
+                "fastqscreen/Sample1_1_screen.html",
+                "fastqscreen/Sample1_1_screen.png",
+                "fastqscreen/Sample1_1_screen.txt",
+                "fastqscreen/Sample23_3_screen.html",
+                "fastqscreen/Sample23_3_screen.png",
+                "fastqscreen/Sample23_3_screen.txt",
+                "fastqscreen/SampleA_2_screen.html",
+                "fastqscreen/SampleA_2_screen.png",
+                "fastqscreen/SampleA_2_screen.txt",
+                "fastqscreen/Undetermined_5_screen.html",
+                "fastqscreen/Undetermined_5_screen.png",
+                "fastqscreen/Undetermined_5_screen.txt",
+                "fastqscreen/sampletest_4_screen.html",
+                "fastqscreen/sampletest_4_screen.png",
+                "fastqscreen/sampletest_4_screen.txt",
+                "multiqc",
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+                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_plots",
+                "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
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+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
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+                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
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+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu.png",
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+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
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+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
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+                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
+                "multiqc/global_report/multiqc_report.html",
+                "multiqc/group_reports",
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+                "multiqc/group_reports/group1/multiqc_data/fastqc-status-check-heatmap.txt",
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+                "multiqc/group_reports/group1/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
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+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/group_reports/test/multiqc_plots/png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/test/multiqc_plots/png/general_stats_table.png",
+                "multiqc/group_reports/test/multiqc_plots/png/seqfu.png",
+                "multiqc/group_reports/test/multiqc_plots/svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/seqfu.svg",
+                "multiqc/group_reports/test/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "seqfu_stats",
+                "seqfu_stats/Sample1_1_seqfu.tsv",
+                "seqfu_stats/Sample1_1_seqfu_mqc.txt",
+                "seqfu_stats/Sample23_3_seqfu.tsv",
+                "seqfu_stats/Sample23_3_seqfu_mqc.txt",
+                "seqfu_stats/SampleA_2_seqfu.tsv",
+                "seqfu_stats/SampleA_2_seqfu_mqc.txt",
+                "seqfu_stats/Undetermined_5_seqfu.tsv",
+                "seqfu_stats/Undetermined_5_seqfu_mqc.txt",
+                "seqfu_stats/sampletest_4_seqfu.tsv",
+                "seqfu_stats/sampletest_4_seqfu_mqc.txt"
             ],
             [
-                
+                "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
+                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
+                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
+                "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
+                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
+                "Sample1_1.bam:md5,1efd4f55b836f732ccc3600697ebb4c3",
+                "Sample23_3.bam:md5,a13dd5db6ef2639f2227b6d3f9c92386",
+                "SampleA_2.bam:md5,c5082847134e5a1c0c869b2378637754",
+                "Undetermined_5.bam:md5,3453bb37bc50105e79f7bba23cbab9c5",
+                "sampletest_4.bam:md5,72532967a589a0a63e93ce86cf79f101",
+                "Sample1_1_screen.png:md5,562256290643b51e4374c2225a15f463",
+                "Sample1_1_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "Sample23_3_screen.png:md5,6bb2caf67b9b2ed25d3d5f32c343e9ab",
+                "Sample23_3_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "SampleA_2_screen.png:md5,b2c3e95e034f5c038754bf108537de0e",
+                "SampleA_2_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "Undetermined_5_screen.png:md5,fc5d53f8876dfae3d1a781fa512ea1db",
+                "Undetermined_5_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "sampletest_4_screen.png:md5,1fb60070e8f4b70de0c1b3786b54f27e",
+                "sampletest_4_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "fastq_screen_plot.txt:md5,562b783630f698c3220c951b73b87027",
+                "fastqc-status-check-heatmap.txt:md5,6cd55dc80642c78b5e0d71821b83fe2e",
+                "fastqc_overrepresented_sequences_plot.txt:md5,37fd53c396d047467fbd38c5c4a0c4ba",
+                "fastqc_per_base_n_content_plot.txt:md5,75aee7627205c6513389d7a52e7a383b",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,2a60a8518caad855e842cf70a8037dad",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,1325b4b3971f7d4d544d9e252abf47b9",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,ef663c12746dfb88f7297b891756fadd",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,5a224c4e837ba42c16b724289bb1bf32",
+                "fastqc_sequence_counts_plot.txt:md5,20364b3b979bc99ae375a2dffcaf1cc1",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,7f33f3d0e2eb3405eb6456acbd18dfd4",
+                "fastqc_sequence_length_distribution_plot.txt:md5,9472fb38f57150d55fb9e4995aaeeb90",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
+                "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d",
+                "multiqc_seqfu.txt:md5,5b54a49079169985795537d83d58bdd9",
+                "fastq_screen_plot.txt:md5,c25d34568f10f131156294d31fbfa994",
+                "fastqc-status-check-heatmap.txt:md5,67afbf7ec626c4fc7a28b4922352bc84",
+                "fastqc_overrepresented_sequences_plot.txt:md5,0356d007eaf807f7b63714b438b11289",
+                "fastqc_per_base_n_content_plot.txt:md5,4c5bfb1594b391f3e36a9e1223b43a94",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,6251cde1646484446499252bd15c58a2",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,f645e38916efafd07d4c2c3d5c7cd051",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,a9d3152a43988e39fae4a75faa3a5aa4",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,aef487a8b267a14a92be64b0b01d9b5c",
+                "fastqc_sequence_counts_plot.txt:md5,5021496dd00366d08064804bbb5192e3",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,e37e8e4584f0157a5fa0d53b4834e836",
+                "fastqc_sequence_length_distribution_plot.txt:md5,393cc090200a5151561efb1ed5280b89",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
+                "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
+                "multiqc_seqfu.txt:md5,5579172a6f8ac09a5ffcb3ce6a99590e",
+                "fastq_screen_plot.txt:md5,44fca6453b0a3d0590271bd7a31cc740",
+                "fastqc-status-check-heatmap.txt:md5,b6872d9dbaa3cce396d48dc137076e53",
+                "fastqc_overrepresented_sequences_plot.txt:md5,eac8d0fd31c614d8d0f56bd54ee8c78c",
+                "fastqc_per_base_n_content_plot.txt:md5,b7b249afe807ca2321e6dd839961795c",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,3bca5f0121d27b0777a40a4ab44e2abc",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,ee29af5517a8c6f872adbaccea4ff2f8",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,3eaf12f9267c10e4e457a2bb9bdc70ea",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,1818e0b917e45a583740f2cbb0638f8d",
+                "fastqc_sequence_counts_plot.txt:md5,0c4863a5475a2444cd00b053eb8941b1",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,a7a050f827a4f821117efd8d25668c51",
+                "fastqc_sequence_length_distribution_plot.txt:md5,9c0761008be04d8ccf4c0e16acc6348c",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
+                "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
+                "multiqc_seqfu.txt:md5,b5434520fa5be5c98be5ed164a464d23",
+                "fastq_screen_plot.txt:md5,5f748d33a7a396547fe8c260b728aa06",
+                "fastqc-status-check-heatmap.txt:md5,08228a8f3d6f11b174b98626bb22bda1",
+                "fastqc_overrepresented_sequences_plot.txt:md5,3434dfb79f150e2e584e85866983ba01",
+                "fastqc_per_base_n_content_plot.txt:md5,e371981072ec99d11c6adb5a4034808c",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,bf83d019eaaeb1ca659ff28cfb2bdfea",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,3f40b8ee69d3eaefe657cc5ed622cc8b",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,86b61d09437a96448e1325e6be834048",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,9f7307469b112bd054f8ee0cc2cf4d65",
+                "fastqc_sequence_counts_plot.txt:md5,f0c693cc281a6e61ba219bab04f59a47",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,8c2aa91358fd4a2e946cbcc1f312f9b6",
+                "fastqc_sequence_length_distribution_plot.txt:md5,875ebcd6726bb9d36ffa64265e5071d0",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
+                "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
+                "multiqc_seqfu.txt:md5,e2e092852c011abe5ad75cdcd68b9383",
+                "fastq_screen_plot.txt:md5,8622e1dbd0fe62520af6096207b9775d",
+                "fastqc-status-check-heatmap.txt:md5,2a66f5d61b9eb579555905cd5954b04c",
+                "fastqc_overrepresented_sequences_plot.txt:md5,e0b5bfc4b64d37611b51c939e61196fa",
+                "fastqc_per_base_n_content_plot.txt:md5,1380831484d1b069a2fd4a20437118bf",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,12585cf6b03db684a5ebd959f51e77e7",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a1464399e84711454499d27e98ed942b",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,026d11e7b49a49ac7bac85f376760305",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,4d646b20970d09d846947b87961efe7e",
+                "fastqc_sequence_counts_plot.txt:md5,057fb961863b325fe875d3a7879cb888",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,3b86c9d8625c439376102f3286c7bba7",
+                "fastqc_sequence_length_distribution_plot.txt:md5,6296c9ddbf8ba8e12053149d057fd7b2",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5",
+                "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
+                "multiqc_seqfu.txt:md5,a1a0b9a0dde0c1c4fe184d44c675dcde",
+                "Sample1_1_seqfu.tsv:md5,269fabf8435defcd327aa69a050b7869",
+                "Sample1_1_seqfu_mqc.txt:md5,a354b0ed16b9cf84aa88f501d7740fd6",
+                "Sample23_3_seqfu.tsv:md5,6fdadbeeefccbf957f880d6852bf9676",
+                "Sample23_3_seqfu_mqc.txt:md5,e94269e3efc8b8192d7ac9c15ea2aa99",
+                "SampleA_2_seqfu.tsv:md5,b980ed694a05825fcf7c8b5b73888eb3",
+                "SampleA_2_seqfu_mqc.txt:md5,1d4b0e918644cf553108b7ccf77b4a01",
+                "Undetermined_5_seqfu.tsv:md5,b4458d41df4dee9321da03f4d4672aae",
+                "Undetermined_5_seqfu_mqc.txt:md5,0c869488cb61d2f87758c621bded212b",
+                "sampletest_4_seqfu.tsv:md5,db3179b0c41a09e6317a5a5c0852f476",
+                "sampletest_4_seqfu_mqc.txt:md5,590b97cc48268629204f59007bae7ad7"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-20T12:12:37.184658"
+        "timestamp": "2025-10-20T11:59:20.195474003"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index 11690c71..97d6c386 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -1,19 +1,143 @@
 {
     "PromethION data test": {
         "content": [
-            0,
-            null,
+            4,
+            {
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "FASTQSCREEN_FASTQSCREEN": {
+                    "fastqscreen": "0.16.0"
+                },
+                "SEQFU_STATS": {
+                    "seqfu": "1.20.3"
+                },
+                "Workflow": {
+                    "nf-core/seqinspector": "v1.0dev"
+                }
+            },
             [
-                "pipeline_info"
+                "fastqc",
+                "fastqc/hg001_1_fastqc.html",
+                "fastqc/hg001_1_fastqc.zip",
+                "fastqscreen",
+                "fastqscreen/hg001_1_screen.html",
+                "fastqscreen/hg001_1_screen.png",
+                "fastqscreen/hg001_1_screen.txt",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/global_report/multiqc_data/fastqc_adapter_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_plots",
+                "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_adapter_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu.png",
+                "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
+                "multiqc/global_report/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "seqfu_stats",
+                "seqfu_stats/hg001_1_seqfu.tsv",
+                "seqfu_stats/hg001_1_seqfu_mqc.txt"
             ],
             [
-                
+                "hg001_1_screen.png:md5,b9c58e388f18ad11f4c2e29e9b573a5e",
+                "hg001_1_screen.txt:md5,8e53ea043d658a130f4b8ca455e2ba9b",
+                "fastq_screen_plot.txt:md5,3023b86477fecf6d46d8fc60d82cc53a",
+                "fastqc-status-check-heatmap.txt:md5,825668e94de27356f0a112beb758e416",
+                "fastqc_adapter_content_plot.txt:md5,1fa991080c20755e5e729a5eeab960e5",
+                "fastqc_overrepresented_sequences_plot.txt:md5,e810a3d3eba0ba83b122763505f511a7",
+                "fastqc_per_base_n_content_plot.txt:md5,cbdb64298ff839665e8c8c8e89896e87",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,4962950bc3ce77169ac510d64cb769c6",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,e62273533304be59dab5f13afef93b3e",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,3d49290a15406cb5dac1460c02729f0f",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,7cc10d1bc92ca09431a506c38d911228",
+                "fastqc_sequence_counts_plot.txt:md5,0425d7298c24df6158d5bf7aca1d4190",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,9111d942c7eed5af0e9ccb8c42db8505",
+                "fastqc_sequence_length_distribution_plot.txt:md5,04adfcd0125ebcc3e3bb631f1956c812",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,7c5d711e27c53d13c81644a1f2468dba",
+                "multiqc_fastqc.txt:md5,1a4b472e13cadc770832b0e20d1de7b0",
+                "multiqc_seqfu.txt:md5,9595d608ff5709f2bdec8cb1016416c0",
+                "hg001_1_seqfu.tsv:md5,b133752c897afbb4d8721b911fa117d4",
+                "hg001_1_seqfu_mqc.txt:md5,6285f582c03faa70e8dcb3503e5db728"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-20T12:13:17.680867"
+        "timestamp": "2025-10-20T12:01:31.034516203"
     }
 }
\ No newline at end of file
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index ddca199b..5aaa34fa 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -12,9 +12,6 @@ include { SEQFU_STATS                   } from '../modules/nf-core/seqfu/stats'
 include { FASTQSCREEN_FASTQSCREEN       } from '../modules/nf-core/fastqscreen/fastqscreen/main'
 include { BWAMEM2_INDEX                 } from '../modules/nf-core/bwamem2/index/main'
 include { BWAMEM2_MEM                   } from '../modules/nf-core/bwamem2/mem/main'
-include { SAMTOOLS_INDEX                } from '../modules/nf-core/samtools/index/main'
-include { SAMTOOLS_FAIDX                } from '../modules/nf-core/samtools/faidx/main'
-include { PICARD_COLLECTMULTIPLEMETRICS } from '../modules/nf-core/picard/collectmultiplemetrics/main'
 
 include { MULTIQC as MULTIQC_GLOBAL     } from '../modules/nf-core/multiqc/main'
 include { MULTIQC as MULTIQC_PER_TAG    } from '../modules/nf-core/multiqc/main'
@@ -136,61 +133,6 @@ workflow SEQINSPECTOR {
 
 
 }
-    // MODULE: Index BAM files with Samtools
-    if (!("samtools_index" in skip_tools)) {
-
-        SAMTOOLS_INDEX (
-            ch_bwamem2_mem
-        )
-        ch_samtools_index = SAMTOOLS_INDEX.out.bai
-        ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions)
-        ch_samtools_index.view { "BAI: $it" }
-    }
-
-    // MODULE: Index reference FASTA with Samtools faidx
-    if (!("samtools_faidx" in skip_tools)) {
-
-        // Assume ch_fasta emits tuple(meta, fasta)
-        ch_dummy_fai = Channel.value(['dummy_meta', file('empty.fai')])
-
-
-        SAMTOOLS_FAIDX (
-            ch_reference_fasta,
-            ch_dummy_fai,
-            true           // get_sizes
-        )
-        ch_reference_fasta_fai = SAMTOOLS_FAIDX.out.fai
-        ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions)
-    }
-
-    // MODULE: Prepare BAM/BAI tuples for Picard
-    // Combine BAM and BAI outputs for Picard
-    ch_bam_bai = ch_bwamem2_mem
-        .join(ch_samtools_index)
-        .map { meta, bam, bai ->
-            [meta, bam, bai]
-    }
-
-    ch_bam_bai.view { "Combined BAM/BAI for Picard: $it" }
-    ch_fasta   = ch_reference_fasta
-    ch_fai     = ch_reference_fasta_fai
-
-    ch_fasta.view { "FASTA for Picard: $it" }
-    ch_fai.view { "FAI for Picard: $it" }
-
-    // Prepare reference FASTA and FAI tuples for Picard
-    // Run Picard CollectMultipleMetrics
-    if (!("picard_collectmultiplemetrics" in skip_tools)) {
-        PICARD_COLLECTMULTIPLEMETRICS(
-            ch_bam_bai,
-            ch_fasta,
-            ch_fai
-)
-
-    ch_multiqc_files = ch_multiqc_files.mix(PICARD_COLLECTMULTIPLEMETRICS.out.metrics)
-    ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
-    }
-
 
     // Collate and save software versions
     //

From 40a9b17883cf2920a4ff14c00fa95acd824e6dff Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Mon, 20 Oct 2025 12:06:42 +0000
Subject: [PATCH 291/530] linting

---
 .github/PULL_REQUEST_TEMPLATE.md      |  4 ++--
 .github/workflows/linting.yml         | 17 ++++++++++-------
 .github/workflows/linting_comment.yml |  4 ++--
 3 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 9dcf6a33..068d699b 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -8,14 +8,14 @@ These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/seqinspector/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/seqinspector/tree/main/.github/CONTRIBUTING.md)
 -->
 
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/seqinspector/tree/master/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/seqinspector/tree/main/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/seqinspector _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 8b0f88c3..dbd52d5a 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -3,6 +3,9 @@ name: nf-core linting
 # It runs the `nf-core pipelines lint` and markdown lint tests to ensure
 # that the code meets the nf-core guidelines.
 on:
+  push:
+    branches:
+      - dev
   pull_request:
   release:
     types: [published]
@@ -13,10 +16,10 @@ jobs:
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
-      - name: Set up Python 3.13
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - name: Set up Python 3.12
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
-          python-version: "3.13"
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -33,13 +36,13 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
-          python-version: "3.13"
+          python-version: "3.12"
           architecture: "x64"
 
       - name: read .nf-core.yml
-        uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
+        uses: pietrobolcato/action-read-yaml@1.1.0
         id: read_yml
         with:
           config: ${{ github.workspace }}/.nf-core.yml
@@ -71,7 +74,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index d43797d9..95b6b6af 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11
+        uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8
         with:
           workflow: linting.yml
           workflow_conclusion: completed
@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@52423e01640425a022ef5fd42c6fb5f633a02728 # v2
+        uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}

From b75a857ce6dbbba82036d572f3b7a7ce5a8177a3 Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Mon, 20 Oct 2025 12:09:36 +0000
Subject: [PATCH 292/530] pull request template

---
 .github/PULL_REQUEST_TEMPLATE.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 068d699b..9dcf6a33 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -8,14 +8,14 @@ These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/seqinspector/tree/main/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/seqinspector/tree/master/.github/CONTRIBUTING.md)
 -->
 
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/seqinspector/tree/main/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/seqinspector/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/seqinspector _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).

From 7ff52406689ce7413c4d3ded2dce6ba132d462f1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pontus=20H=C3=B6jer?= <pontushojer@gmail.com>
Date: Tue, 21 Oct 2025 10:33:13 +0200
Subject: [PATCH 293/530] add index to other reports multiqc reports

---
 .../main.nf                                   | 25 +++++++++++++++++++
 workflows/seqinspector.nf                     | 21 ++++++++++++----
 2 files changed, 41 insertions(+), 5 deletions(-)

diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index 708d73fb..1188e5e1 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -286,3 +286,28 @@ def methodsDescriptionText(mqc_methods_yaml) {
     return description_html.toString()
 }
 
+//
+// Generate report index for MultiQC
+//
+def reportIndexMultiqc(tags, global=true) {
+    def relative_path = global ? ".." : "../.."
+
+    // Global report path
+    def index_section = "    <li><a href=\"${relative_path}/global_report/multiqc_report.html\">Global</a></li>\n"
+
+    // Group report paths
+    tags
+        .each { tag ->
+            index_section += "    <li><a href=\"${relative_path}/group_reports/${tag}/multiqc_report.html\">${tag}</a></li>\n"
+        }
+    
+    def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-index'\n" as String
+    yaml_file_text     += "description: ' - this information is collected when the pipeline is started.'\n"
+    yaml_file_text     += "section_name: '${workflow.manifest.name} MultiQC Reports Index'\n"
+    yaml_file_text     += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
+    yaml_file_text     += "plot_type: 'html'\n"
+    yaml_file_text     += "data: |\n"
+    yaml_file_text     += "${index_section}"
+
+    return yaml_file_text
+}
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 22d37c30..ab3a742e 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -18,6 +18,7 @@ include { paramsSummaryMap              } from 'plugin/nf-schema'
 include { paramsSummaryMultiqc          } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { softwareVersionsToYAML        } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { methodsDescriptionText        } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline'
+include { reportIndexMultiqc            } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -121,6 +122,11 @@ workflow SEQINSPECTOR {
     //
     // MODULE: MultiQC
     //
+    ch_tags = ch_multiqc_files
+        .map { meta, sample -> meta.tags }
+        .flatten()
+        .unique()
+
     ch_multiqc_config = params.multiqc_config ?
         Channel.fromPath(params.multiqc_config, checkIfExists: true) :
         Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
@@ -147,6 +153,16 @@ workflow SEQINSPECTOR {
             sort: true
         )
     )
+    ch_multiqc_extra_files = ch_multiqc_extra_files.mix(
+        ch_tags.toList()
+            .map { tag_list ->
+                reportIndexMultiqc(tag_list)
+            }
+            .collectFile(
+                name: 'multiqc_index_mqc.yaml',
+                sort: true
+            ).view()
+    )
 
     MULTIQC_GLOBAL (
         ch_multiqc_files
@@ -160,11 +176,6 @@ workflow SEQINSPECTOR {
         []
     )
 
-    ch_tags = ch_multiqc_files
-        .map { meta, sample -> meta.tags }
-        .flatten()
-        .unique()
-
     multiqc_extra_files_per_tag = ch_tags
         .combine(ch_multiqc_extra_files)
 

From 2ed085eb4f09bbcee218aa26f4160d7ced948a72 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@n141-p117.eduroam.kth.se>
Date: Fri, 24 Oct 2025 16:14:35 +0200
Subject: [PATCH 294/530] changed test.config and main.nf

---
 conf/test.config | 17 +----------------
 main.nf          |  4 ----
 2 files changed, 1 insertion(+), 20 deletions(-)

diff --git a/conf/test.config b/conf/test.config
index a14370c5..db9d053b 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -30,21 +30,6 @@ process {
         memory: '15.GB',
         time: '1.h'
     ]
-    withLabel: 'process_high' {
-        cpus = 4
-        memory = '15.GB'
-    }
-    withLabel: 'process_medium' {
-        cpus = 2
-        memory = '7.GB'
-    }
-    withLabel: 'process_low' {
-        cpus = 1
-        memory = '3.GB'
-    }
-    withLabel: 'process_single' {
-        cpus = 1
-        memory = '3.GB'
-    }
+
 }
 
diff --git a/main.nf b/main.nf
index 0cad90f7..4e3aca0d 100644
--- a/main.nf
+++ b/main.nf
@@ -14,10 +14,6 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-// TODO nf-core: Remove this line if you don't need a FASTA file
-//   This is an example of how to use getGenomeAttribute() to fetch parameters
-//   from igenomes.config using `--genome`
-
 params.fasta = getGenomeAttribute('fasta')
 
 /*

From 0b81a9aafcd62392b84bc1e4f0201eb4b2585176 Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Sat, 25 Oct 2025 16:30:00 +0200
Subject: [PATCH 295/530] Update timestamp in PromethION test snapshot

Removed outdated timestamp from the test snapshot.
---
 tests/PromethION.main.nf.test.snap | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index f836b825..f8171697 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -139,6 +139,5 @@
             "nextflow": "25.04.6"
         },
         "timestamp": "2025-10-02T13:46:26.460263232"
-        "timestamp": "2025-10-20T12:01:31.034516203"
     }
-}
\ No newline at end of file
+}

From fed47c6863ff331fd908000928fa81a458d7ec8a Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Sat, 25 Oct 2025 16:35:15 +0200
Subject: [PATCH 296/530] Update MiSeq.main.nf.test.snap

---
 tests/MiSeq.main.nf.test.snap | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 37fdb8ca..b9b2dd57 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -447,8 +447,7 @@
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-10-07T09:09:05.277171766"
+        }
         "timestamp": "2025-10-20T11:56:20.313008405"
     }
-}
\ No newline at end of file
+}

From 599689f52bad6def2c4f8253a8f938b76e9a3aa2 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@Mac.home>
Date: Sat, 25 Oct 2025 16:40:01 +0200
Subject: [PATCH 297/530] ss updated

---
 tests/MiSeq_PairedEnd.main.nf.test.snap       | 2 +-
 tests/NovaSeq6000.main.nf.test.snap           | 2 +-
 tests/NovaSeq6000.main_subsample.nf.test.snap | 1 +
 tests/PromethION.main.nf.test.snap            | 3 ++-
 4 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index c1b83854..6ba4b918 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -432,7 +432,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-07T08:39:14.939736631"
+
         "timestamp": "2025-10-20T11:57:37.980484968"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index f54e6cad..344cf3d8 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -948,7 +948,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-07T08:41:26.564395156"
+
         "timestamp": "2025-10-20T11:59:20.195474003"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index 3ba50465..e721fc52 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -26,6 +26,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.2"
         },
+
         "timestamp": "2024-12-05T15:17:50.525033752"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index f8171697..b4f900f5 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -138,6 +138,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-02T13:46:26.460263232"
+
+        "timestamp": "2025-10-20T12:01:31.034516203"
     }
 }

From acf435b62e2650ad6b527d6201a77840b2458520 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@Mac.home>
Date: Sat, 25 Oct 2025 16:51:47 +0200
Subject: [PATCH 298/530] Updated modules.json

---
 modules.json                                  |  15 +++
 modules/nf-core/bowtie2/build/meta.yml        |  18 +--
 modules/nf-core/fastqc/meta.yml               |  23 ++--
 .../fastqscreen/buildfromindex/meta.yml       |  35 +++---
 .../nf-core/fastqscreen/fastqscreen/meta.yml  |  52 ++++----
 modules/nf-core/multiqc/meta.yml              | 114 ++++++++++--------
 modules/nf-core/samtools/faidx/meta.yml       |   3 +-
 modules/nf-core/seqfu/stats/meta.yml          |  25 ++--
 modules/nf-core/seqtk/sample/meta.yml         |  22 ++--
 workflows/seqinspector.nf                     |   4 +-
 10 files changed, 187 insertions(+), 124 deletions(-)

diff --git a/modules.json b/modules.json
index e3b68325..e62fa390 100644
--- a/modules.json
+++ b/modules.json
@@ -42,6 +42,21 @@
                         "git_sha": "7b50cb7be890e4b28cffb82e438cc6a8d7805d3f",
                         "installed_by": ["modules"]
                     },
+                    "picard/collectmultiplemetrics": {
+                        "branch": "master",
+                        "git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255",
+                        "installed_by": ["modules"]
+                    },
+                    "samtools/faidx": {
+                        "branch": "master",
+                        "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
+                        "installed_by": ["modules"]
+                    },
+                    "samtools/index": {
+                        "branch": "master",
+                        "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
+                        "installed_by": ["modules"]
+                    },
                     "seqfu/stats": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
diff --git a/modules/nf-core/bowtie2/build/meta.yml b/modules/nf-core/bowtie2/build/meta.yml
index 2729a92e..3e83ecb4 100644
--- a/modules/nf-core/bowtie2/build/meta.yml
+++ b/modules/nf-core/bowtie2/build/meta.yml
@@ -25,9 +25,10 @@ input:
     - fasta:
         type: file
         description: Input genome fasta file
+        ontologies: []
 output:
-  - index:
-      - meta:
+  index:
+    - - meta:
           type: map
           description: |
             Groovy Map containing reference information
@@ -36,11 +37,14 @@ output:
           type: file
           description: Bowtie2 genome index files
           pattern: "*.bt2"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@joseespinosa"
   - "@drpatelh"
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
index 2b2e62b8..c8d9d025 100644
--- a/modules/nf-core/fastqc/meta.yml
+++ b/modules/nf-core/fastqc/meta.yml
@@ -29,9 +29,10 @@ input:
         description: |
           List of input FastQ files of size 1 and 2 for single-end and paired-end data,
           respectively.
+        ontologies: []
 output:
-  - html:
-      - meta:
+  html:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -40,8 +41,9 @@ output:
           type: file
           description: FastQC report
           pattern: "*_{fastqc.html}"
-  - zip:
-      - meta:
+          ontologies: []
+  zip:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -50,11 +52,14 @@ output:
           type: file
           description: FastQC report archive
           pattern: "*_{fastqc.zip}"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@drpatelh"
   - "@grst"
diff --git a/modules/nf-core/fastqscreen/buildfromindex/meta.yml b/modules/nf-core/fastqscreen/buildfromindex/meta.yml
index d92817fc..c986c255 100644
--- a/modules/nf-core/fastqscreen/buildfromindex/meta.yml
+++ b/modules/nf-core/fastqscreen/buildfromindex/meta.yml
@@ -17,23 +17,26 @@ tools:
       licence: ["GPL-3.0-or-later"]
       identifier: ""
 input:
-  - - genome_names:
-        type: string
-        description: List of names for each index
-  - - indexes:
-        type: directory
-        description: Bowtie2 genome directories containing index files
+  - genome_names:
+      type: string
+      description: List of names for each index
+  - indexes:
+      type: directory
+      description: Bowtie2 genome directories containing index files
 output:
-  - database:
-      - FastQ_Screen_Genomes:
-          type: directory
-          description: fastq screen database folder containing config file and index folders
-          pattern: "FastQ_Screen_Genomes"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+  database:
+    - FastQ_Screen_Genomes:
+        type: directory
+        description: fastq screen database folder containing config file and index
+          folders
+        pattern: "FastQ_Screen_Genomes"
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@snesic"
   - "@JPejovicApis"
diff --git a/modules/nf-core/fastqscreen/fastqscreen/meta.yml b/modules/nf-core/fastqscreen/fastqscreen/meta.yml
index 39c86b4f..7d96f0b8 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/meta.yml
+++ b/modules/nf-core/fastqscreen/fastqscreen/meta.yml
@@ -29,50 +29,58 @@ input:
         description: |
           List of input FastQ files of size 1 and 2 for single-end and paired-end data,
           respectively.
-  - - database:
-        type: directory
-        description: fastq screen database folder containing config file and index folders
-        pattern: "FastQ_Screen_Genomes"
+        ontologies: []
+  - - ref_names: {}
+    - ref_dirs: {}
+    - ref_basenames: {}
+    - ref_aligners: {}
 output:
-  - txt:
-      - meta:
+  txt:
+    - - meta:
           type: map
           description: Groovy Map containing sample information
       - "*.txt":
           type: file
           description: TXT file containing alignment statistics
           pattern: "*.txt"
-  - png:
-      - meta:
+          ontologies: []
+  png:
+    - - meta:
           type: map
           description: Groovy Map containing sample information
       - "*.png":
           type: file
           description: PNG file with graphical representation of alignments
           pattern: "*.png"
-  - html:
-      - meta:
+          ontologies: []
+  html:
+    - - meta:
           type: map
           description: Groovy Map containing sample information
       - "*.html":
           type: file
-          description: HTML file containing mapping results as a table and graphical representation
+          description: HTML file containing mapping results as a table and
+            graphical representation
           pattern: "*.html"
-  - fastq:
-      - meta:
+          ontologies: []
+  fastq:
+    - - meta:
           type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
+          description: Groovy Map containing sample information
       - "*.fastq.gz":
           type: file
-          description: FastQ file containing reads that did not align to any database (optional)
+          description: FastQ file containing reads that did not align to any
+            database (optional)
           pattern: "*.fastq.gz"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+          ontologies:
+            - edam: http://edamontology.org/format_3989 # GZIP format
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@snesic"
   - "@JPejovicApis"
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index b16c1879..5061e93c 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -1,6 +1,6 @@
 name: multiqc
-description: Aggregate results from bioinformatics analyses across many samples into
-  a single report
+description: Aggregate results from bioinformatics analyses across many samples
+  into a single report
 keywords:
   - QC
   - bioinformatics tools
@@ -15,57 +15,71 @@ tools:
       licence: ["GPL-3.0-or-later"]
       identifier: biotools:multiqc
 input:
-  - - multiqc_files:
-        type: file
-        description: |
-          List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
-  - - multiqc_config:
-        type: file
-        description: Optional config yml for MultiQC
-        pattern: "*.{yml,yaml}"
-  - - extra_multiqc_config:
-        type: file
-        description: Second optional config yml for MultiQC. Will override common sections
-          in multiqc_config.
-        pattern: "*.{yml,yaml}"
-  - - multiqc_logo:
+  - multiqc_files:
+      type: file
+      description: |
+        List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
+      ontologies: []
+  - multiqc_config:
+      type: file
+      description: Optional config yml for MultiQC
+      pattern: "*.{yml,yaml}"
+      ontologies:
+        - edam: http://edamontology.org/format_3750 # YAML
+  - extra_multiqc_config:
+      type: file
+      description: Second optional config yml for MultiQC. Will override common
+        sections in multiqc_config.
+      pattern: "*.{yml,yaml}"
+      ontologies:
+        - edam: http://edamontology.org/format_3750 # YAML
+  - multiqc_logo:
+      type: file
+      description: Optional logo file for MultiQC
+      pattern: "*.{png}"
+      ontologies: []
+  - replace_names:
+      type: file
+      description: |
+        Optional two-column sample renaming file. First column a set of
+        patterns, second column a set of corresponding replacements. Passed via
+        MultiQC's `--replace-names` option.
+      pattern: "*.{tsv}"
+      ontologies:
+        - edam: http://edamontology.org/format_3475 # TSV
+  - sample_names:
+      type: file
+      description: |
+        Optional TSV file with headers, passed to the MultiQC --sample_names
+        argument.
+      pattern: "*.{tsv}"
+      ontologies:
+        - edam: http://edamontology.org/format_3475 # TSV
+output:
+  report:
+    - "*multiqc_report.html":
         type: file
-        description: Optional logo file for MultiQC
-        pattern: "*.{png}"
-  - - replace_names:
+        description: MultiQC report file
+        pattern: "multiqc_report.html"
+        ontologies: []
+  data:
+    - "*_data":
+        type: directory
+        description: MultiQC data dir
+        pattern: "multiqc_data"
+  plots:
+    - "*_plots":
         type: file
-        description: |
-          Optional two-column sample renaming file. First column a set of
-          patterns, second column a set of corresponding replacements. Passed via
-          MultiQC's `--replace-names` option.
-        pattern: "*.{tsv}"
-  - - sample_names:
+        description: Plots created by MultiQC
+        pattern: "*_data"
+        ontologies: []
+  versions:
+    - versions.yml:
         type: file
-        description: |
-          Optional TSV file with headers, passed to the MultiQC --sample_names
-          argument.
-        pattern: "*.{tsv}"
-output:
-  - report:
-      - "*multiqc_report.html":
-          type: file
-          description: MultiQC report file
-          pattern: "multiqc_report.html"
-  - data:
-      - "*_data":
-          type: directory
-          description: MultiQC data dir
-          pattern: "multiqc_data"
-  - plots:
-      - "*_plots":
-          type: file
-          description: Plots created by MultiQC
-          pattern: "*_data"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@abhi18av"
   - "@bunop"
diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml
index b7a2e0c1..31a78efe 100644
--- a/modules/nf-core/samtools/faidx/meta.yml
+++ b/modules/nf-core/samtools/faidx/meta.yml
@@ -1,5 +1,6 @@
 name: samtools_faidx
-description: Index FASTA file, and optionally generate a file of chromosome sizes
+description: Index FASTA file, and optionally generate a file of chromosome
+  sizes
 keywords:
   - index
   - fasta
diff --git a/modules/nf-core/seqfu/stats/meta.yml b/modules/nf-core/seqfu/stats/meta.yml
index f534a3f5..573498c5 100644
--- a/modules/nf-core/seqfu/stats/meta.yml
+++ b/modules/nf-core/seqfu/stats/meta.yml
@@ -27,10 +27,12 @@ input:
         type: file
         description: One or more FASTA or FASTQ files
         pattern: "*.{fasta,fastq,fasta.gz,fastq.gz,fq,fq.gz}"
+        ontologies:
+          - edam: http://edamontology.org/format_1930 # FASTQ
 output:
   #Only when we have meta
-  - stats:
-      - meta:
+  stats:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -39,8 +41,10 @@ output:
           type: file
           description: Tab-separated output file with basic sequence statistics.
           pattern: "*.{tsv}"
-  - multiqc:
-      - meta:
+          ontologies:
+            - edam: http://edamontology.org/format_3475 # TSV
+  multiqc:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -49,11 +53,14 @@ output:
           type: file
           description: MultiQC ready table
           pattern: "*.{_mqc.txt}"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@telatin"
 maintainers:
diff --git a/modules/nf-core/seqtk/sample/meta.yml b/modules/nf-core/seqtk/sample/meta.yml
index 42f67d8f..29d95f2a 100644
--- a/modules/nf-core/seqtk/sample/meta.yml
+++ b/modules/nf-core/seqtk/sample/meta.yml
@@ -6,8 +6,8 @@ keywords:
   - reads
 tools:
   - seqtk:
-      description: Seqtk is a fast and lightweight tool for processing sequences in
-        the FASTA or FASTQ format. Seqtk sample command subsamples sequences.
+      description: Seqtk is a fast and lightweight tool for processing sequences
+        in the FASTA or FASTQ format. Seqtk sample command subsamples sequences.
       homepage: https://github.com/lh3/seqtk
       documentation: https://docs.csc.fi/apps/seqtk/
       tool_dev_url: https://github.com/lh3/seqtk
@@ -23,12 +23,13 @@ input:
         type: file
         description: List of input FastQ files
         pattern: "*.{fastq.gz}"
+        ontologies: []
     - sample_size:
         type: integer
         description: Number of reads to sample.
 output:
-  - reads:
-      - meta:
+  reads:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -37,11 +38,14 @@ output:
           type: file
           description: Subsampled FastQ files
           pattern: "*.{fastq.gz}"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@kaurravneet4123"
   - "@sidorov-si"
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 5f0c0a6e..fb70e7e6 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -12,7 +12,9 @@ include { SEQFU_STATS                   } from '../modules/nf-core/seqfu/stats'
 include { FASTQSCREEN_FASTQSCREEN       } from '../modules/nf-core/fastqscreen/fastqscreen/main'
 include { BWAMEM2_INDEX                 } from '../modules/nf-core/bwamem2/index/main'
 include { BWAMEM2_MEM                   } from '../modules/nf-core/bwamem2/mem/main'
-
+include { SAMTOOLS_INDEX                } from '../modules/nf-core/samtools/index/main'
+include { SAMTOOLS_FAIDX                } from '../modules/nf-core/samtools/faidx/main'
+include { PICARD_COLLECTMULTIPLEMETRICS } from '../modules/nf-core/picard/collectmultiplemetrics/main'
 include { MULTIQC as MULTIQC_GLOBAL     } from '../modules/nf-core/multiqc/main'
 include { MULTIQC as MULTIQC_PER_TAG    } from '../modules/nf-core/multiqc/main'
 

From 0d1f3314af2170fa76a9ac73448aa3d033fd5fe8 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@Mac.home>
Date: Sat, 25 Oct 2025 17:16:32 +0200
Subject: [PATCH 299/530] updated

---
 nextflow_schema.json                    |   2 +-
 tests/MiSeq.main.nf.test.snap           |   1 +
 tests/MiSeq_PairedEnd.main.nf.test.snap | 350 +---------
 tests/NovaSeq6000.main.nf.test.snap     | 847 +-----------------------
 4 files changed, 8 insertions(+), 1192 deletions(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 267afaa9..eb6cbcea 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -51,7 +51,7 @@
                 "skip_tools": {
                     "type": "string",
                     "description": "Comma-separated string of tools to skip",
-                    "pattern": "^((fastqc|fastqscreen|seqfu_stats|seqtk_sample|bwamem2_index|bwamem2_mem)?,?)*(?<!,)$"
+                    "pattern": "^((fastqc|fastqscreen|seqfu_stats|seqtk_sample|bwamem2_index|bwamem2_mem|picard_collectmultiplemetrics|samtools_faidx|samtools_index)?,?)*(?<!,)$"
                 }
             }
         },
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index b9b2dd57..8b0eb5de 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -448,6 +448,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         }
+
         "timestamp": "2025-10-20T11:56:20.313008405"
     }
 }
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index 6ba4b918..a9ecbe9c 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -1,30 +1,20 @@
 {
     "MiSeq data test (paired end reads)": {
         "content": [
-            16,
+            8,
             {
                 "BWAMEM2_INDEX": {
                     "bwamem2": "2.2.1"
                 },
-                "BWAMEM2_MEM": {
-                    "bwamem2": "2.2.1",
-                    "samtools": 1.21
-                },
                 "FASTQC": {
                     "fastqc": "0.12.1"
                 },
                 "FASTQSCREEN_FASTQSCREEN": {
                     "fastqscreen": "0.16.0"
                 },
-                "PICARD_COLLECTMULTIPLEMETRICS": {
-                    "picard": "3.4.0"
-                },
                 "SAMTOOLS_FAIDX": {
                     "samtools": "1.22.1"
                 },
-                "SAMTOOLS_INDEX": {
-                    "samtools": "1.22.1"
-                },
                 "SEQFU_STATS": {
                     "seqfu": "1.20.3"
                 },
@@ -40,9 +30,6 @@
                 "bwamem2_index/bwamem2/genome.fa.ann",
                 "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
                 "bwamem2_index/bwamem2/genome.fa.pac",
-                "bwamem2_mem",
-                "bwamem2_mem/SAMPLE_PAIRED_END_1_1.bam",
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@@ -65,275 +52,11 @@
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-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_quality_by_cycle.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_quality_score_distribution.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/seqfu.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_report.html",
-                "picard_collectmultiplemetrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.alignment_summary_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.read_length_histogram.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.alignment_summary_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "samtools_faidx",
                 "samtools_faidx/genome.fa.fai",
                 "samtools_faidx/genome.fa.sizes",
-                "samtools_index",
-                "samtools_index/SAMPLE_PAIRED_END_1_1.bam.bai",
-                "samtools_index/SAMPLE_PAIRED_END_2_2.bam.bai",
                 "seqfu_stats",
                 "seqfu_stats/SAMPLE_PAIRED_END_1_1_seqfu.tsv",
                 "seqfu_stats/SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt",
@@ -346,8 +69,6 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "SAMPLE_PAIRED_END_1_1.bam:md5,ced6a17fb3dee760c2606860e1177071",
-                "SAMPLE_PAIRED_END_2_2.bam:md5,15ada2a4f4a6cf2978aeaeb64a525197",
                 "SAMPLE_PAIRED_END_1_1_1_screen.png:md5,f52ddd0e65f23f68dd8d58d5453417db",
                 "SAMPLE_PAIRED_END_1_1_1_screen.txt:md5,921b08eeb461a2aa1bd42bba53900f70",
                 "SAMPLE_PAIRED_END_1_1_2_screen.png:md5,908f4fceea8aa546106efdaa7ca78f7d",
@@ -356,72 +77,8 @@
                 "SAMPLE_PAIRED_END_2_2_1_screen.txt:md5,a5b047f495d01bf9dcb0ae516d3c7fc3",
                 "SAMPLE_PAIRED_END_2_2_2_screen.png:md5,e3684b17339d16e6fb64ace7593cc388",
                 "SAMPLE_PAIRED_END_2_2_2_screen.txt:md5,fc95e5058e764596d5da182cbc0614cf",
-                "fastq_screen_plot.txt:md5,642264b93871c724aaa5d38b91c752dd",
-                "fastqc-status-check-heatmap.txt:md5,8e29ad6b23e03267c33bd9ed3385a44b",
-                "fastqc_adapter_content_plot.txt:md5,46fbd727a4996a3f0310d0423c628445",
-                "fastqc_per_base_n_content_plot.txt:md5,4eca1ef40d4d3d318b82e68e9fa3c589",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,218757a51c3de79a39a704c979df03da",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a4035ac9f0a0c07574130758b06630d7",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,637b937e023c84115ec06b529cc8ec1b",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,47d60153a430e2b8da51655704c2b31b",
-                "fastqc_sequence_counts_plot.txt:md5,10737092a3473fba81fbe49555512b2b",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,6412f57686de02e1f1c3751a7ca2be8b",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,5ef00028497d3271c9f0ea9a961db1e5",
-                "multiqc_fastqc.txt:md5,bc499ad273fd1c887056c31b82544984",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,35d289ee535a0442db72a65391f375eb",
-                "multiqc_picard_baseContent.txt:md5,72b0ae83ed58052bfd768021d377c78f",
-                "multiqc_picard_quality_by_cycle.txt:md5,f6514f14befb874ded5aed79caba3e7b",
-                "multiqc_picard_quality_score_distribution.txt:md5,99be409e325619171b820d762dd023c0",
-                "multiqc_seqfu.txt:md5,1f1e063e4a509a26cee167c3b20389c0",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,f6514f14befb874ded5aed79caba3e7b",
-                "picard_QualityScoreDistribution_histogram.txt:md5,99be409e325619171b820d762dd023c0",
-                "picard_alignment_readlength_plot.txt:md5,4172702f791d043135f21e3a227fe712",
-                "picard_alignment_summary_Aligned_Bases.txt:md5,a166c14210e17d3541482b500443f792",
-                "picard_alignment_summary_Aligned_Reads.txt:md5,c5e5228e85ffb2182274d641ffa6743f",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,3fe18f1144eb85f9206d1bee4eb11bb3",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,2e1383b692e76f4b915ccbe9bb9b9170",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,2a595bc9ac547f3b5224a57a6b0a127d",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,157ea873dd2faff46efdd62f7f6aa84c",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,98f4e5ed094b41eb131d493b4f06bcd6",
-                "picard_quality_by_cycle.txt:md5,2634f306a33f648bac74bc7cd3253f9e",
-                "picard_quality_score_distribution.txt:md5,ecde9f0e859a6eecc5cea75a156c632d",
-                "fastq_screen_plot.txt:md5,642264b93871c724aaa5d38b91c752dd",
-                "fastqc-status-check-heatmap.txt:md5,8e29ad6b23e03267c33bd9ed3385a44b",
-                "fastqc_adapter_content_plot.txt:md5,46fbd727a4996a3f0310d0423c628445",
-                "fastqc_per_base_n_content_plot.txt:md5,4eca1ef40d4d3d318b82e68e9fa3c589",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,218757a51c3de79a39a704c979df03da",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a4035ac9f0a0c07574130758b06630d7",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,637b937e023c84115ec06b529cc8ec1b",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,47d60153a430e2b8da51655704c2b31b",
-                "fastqc_sequence_counts_plot.txt:md5,10737092a3473fba81fbe49555512b2b",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,6412f57686de02e1f1c3751a7ca2be8b",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,5ef00028497d3271c9f0ea9a961db1e5",
-                "multiqc_fastqc.txt:md5,bc499ad273fd1c887056c31b82544984",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,35d289ee535a0442db72a65391f375eb",
-                "multiqc_picard_baseContent.txt:md5,72b0ae83ed58052bfd768021d377c78f",
-                "multiqc_picard_quality_by_cycle.txt:md5,f6514f14befb874ded5aed79caba3e7b",
-                "multiqc_picard_quality_score_distribution.txt:md5,99be409e325619171b820d762dd023c0",
-                "multiqc_seqfu.txt:md5,1f1e063e4a509a26cee167c3b20389c0",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,f6514f14befb874ded5aed79caba3e7b",
-                "picard_QualityScoreDistribution_histogram.txt:md5,99be409e325619171b820d762dd023c0",
-                "picard_alignment_readlength_plot.txt:md5,4172702f791d043135f21e3a227fe712",
-                "picard_alignment_summary_Aligned_Bases.txt:md5,a166c14210e17d3541482b500443f792",
-                "picard_alignment_summary_Aligned_Reads.txt:md5,c5e5228e85ffb2182274d641ffa6743f",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,3fe18f1144eb85f9206d1bee4eb11bb3",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,2e1383b692e76f4b915ccbe9bb9b9170",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,2a595bc9ac547f3b5224a57a6b0a127d",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,157ea873dd2faff46efdd62f7f6aa84c",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,98f4e5ed094b41eb131d493b4f06bcd6",
-                "picard_quality_by_cycle.txt:md5,2634f306a33f648bac74bc7cd3253f9e",
-                "picard_quality_score_distribution.txt:md5,ecde9f0e859a6eecc5cea75a156c632d",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
-                "SAMPLE_PAIRED_END_1_1.bam.bai:md5,82724835c47f8e1d1a86e13ef469b464",
-                "SAMPLE_PAIRED_END_2_2.bam.bai:md5,3c4bdff0f906f2234fdeee8eea719210",
                 "SAMPLE_PAIRED_END_1_1_seqfu.tsv:md5,bbd911ff3fa43212dfd4c5a5872dbdb6",
                 "SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt:md5,cd60f746b6749cc66213d031af1b931c",
                 "SAMPLE_PAIRED_END_2_2_seqfu.tsv:md5,152566a128dd657da33465b4966b5799",
@@ -430,9 +87,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.04.7"
         },
-
-        "timestamp": "2025-10-20T11:57:37.980484968"
+        "timestamp": "2025-10-25T17:00:00.443354"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index 344cf3d8..fc5545ab 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -1,30 +1,20 @@
 {
     "NovaSeq6000 data test": {
         "content": [
-            37,
+            17,
             {
                 "BWAMEM2_INDEX": {
                     "bwamem2": "2.2.1"
                 },
-                "BWAMEM2_MEM": {
-                    "bwamem2": "2.2.1",
-                    "samtools": 1.21
-                },
                 "FASTQC": {
                     "fastqc": "0.12.1"
                 },
                 "FASTQSCREEN_FASTQSCREEN": {
                     "fastqscreen": "0.16.0"
                 },
-                "PICARD_COLLECTMULTIPLEMETRICS": {
-                    "picard": "3.4.0"
-                },
                 "SAMTOOLS_FAIDX": {
                     "samtools": "1.22.1"
                 },
-                "SAMTOOLS_INDEX": {
-                    "samtools": "1.22.1"
-                },
                 "SEQFU_STATS": {
                     "seqfu": "1.20.3"
                 },
@@ -40,12 +30,6 @@
                 "bwamem2_index/bwamem2/genome.fa.ann",
                 "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
                 "bwamem2_index/bwamem2/genome.fa.pac",
-                "bwamem2_mem",
-                "bwamem2_mem/Sample1_1.bam",
-                "bwamem2_mem/Sample23_3.bam",
-                "bwamem2_mem/SampleA_2.bam",
-                "bwamem2_mem/Undetermined_5.bam",
-                "bwamem2_mem/sampletest_4.bam",
                 "fastqc",
                 "fastqc/Sample1_1_fastqc.html",
                 "fastqc/Sample1_1_fastqc.zip",
@@ -73,670 +57,11 @@
                 "fastqscreen/sampletest_4_screen.html",
                 "fastqscreen/sampletest_4_screen.png",
                 "fastqscreen/sampletest_4_screen.txt",
-                "multiqc",
-                "multiqc/global_report",
-                "multiqc/global_report/multiqc_data",
-                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
-                "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
-                "multiqc/global_report/multiqc_data/multiqc.log",
-                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
-                "multiqc/global_report/multiqc_data/multiqc_data.json",
-                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
-                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
-                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
-                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
-                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
-                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
-                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
-                "multiqc/global_report/multiqc_data/picard_alignment_summary.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
-                "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt",
-                "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
-                "multiqc/global_report/multiqc_plots",
-                "multiqc/global_report/multiqc_plots/pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
-                "multiqc/global_report/multiqc_plots/png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
-                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
-                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu.png",
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-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
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-                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-pct.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
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-                "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_score_distribution.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/seqfu.svg",
-                "multiqc/group_reports/test/multiqc_report.html",
-                "picard_collectmultiplemetrics",
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-                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_distribution.pdf",
-                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_distribution_metrics",
-                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.read_length_histogram.pdf",
-                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.alignment_summary_metrics",
-                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_distribution.pdf",
-                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_distribution_metrics",
-                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.read_length_histogram.pdf",
-                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.alignment_summary_metrics",
-                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_distribution.pdf",
-                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_distribution_metrics",
-                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.read_length_histogram.pdf",
-                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.alignment_summary_metrics",
-                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution.pdf",
-                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution_metrics",
-                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.read_length_histogram.pdf",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.alignment_summary_metrics",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution.pdf",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution_metrics",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "samtools_faidx",
                 "samtools_faidx/genome.fa.fai",
                 "samtools_faidx/genome.fa.sizes",
-                "samtools_index",
-                "samtools_index/Sample1_1.bam.bai",
-                "samtools_index/Sample23_3.bam.bai",
-                "samtools_index/SampleA_2.bam.bai",
-                "samtools_index/Undetermined_5.bam.bai",
-                "samtools_index/sampletest_4.bam.bai",
                 "seqfu_stats",
                 "seqfu_stats/Sample1_1_seqfu.tsv",
                 "seqfu_stats/Sample1_1_seqfu_mqc.txt",
@@ -755,11 +80,6 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "Sample1_1.bam:md5,1efd4f55b836f732ccc3600697ebb4c3",
-                "Sample23_3.bam:md5,a13dd5db6ef2639f2227b6d3f9c92386",
-                "SampleA_2.bam:md5,c5082847134e5a1c0c869b2378637754",
-                "Undetermined_5.bam:md5,3453bb37bc50105e79f7bba23cbab9c5",
-                "sampletest_4.bam:md5,72532967a589a0a63e93ce86cf79f101",
                 "Sample1_1_screen.png:md5,562256290643b51e4374c2225a15f463",
                 "Sample1_1_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
                 "Sample23_3_screen.png:md5,6bb2caf67b9b2ed25d3d5f32c343e9ab",
@@ -770,168 +90,8 @@
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                 "sampletest_4_screen.png:md5,1fb60070e8f4b70de0c1b3786b54f27e",
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-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,1325b4b3971f7d4d544d9e252abf47b9",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,ef663c12746dfb88f7297b891756fadd",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,5a224c4e837ba42c16b724289bb1bf32",
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-                "fastqc-status-check-heatmap.txt:md5,2a66f5d61b9eb579555905cd5954b04c",
-                "fastqc_overrepresented_sequences_plot.txt:md5,e0b5bfc4b64d37611b51c939e61196fa",
-                "fastqc_per_base_n_content_plot.txt:md5,1380831484d1b069a2fd4a20437118bf",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,12585cf6b03db684a5ebd959f51e77e7",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a1464399e84711454499d27e98ed942b",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,026d11e7b49a49ac7bac85f376760305",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,4d646b20970d09d846947b87961efe7e",
-                "fastqc_sequence_counts_plot.txt:md5,057fb961863b325fe875d3a7879cb888",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,3b86c9d8625c439376102f3286c7bba7",
-                "fastqc_sequence_length_distribution_plot.txt:md5,6296c9ddbf8ba8e12053149d057fd7b2",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5",
-                "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,edf7faad1da9922fdc692e9cba5cc0c4",
-                "multiqc_picard_baseContent.txt:md5,9631916c0a9a736811c47ab4c476428f",
-                "multiqc_picard_quality_by_cycle.txt:md5,9e05b241aabe39232b5182cb59d8edd5",
-                "multiqc_picard_quality_score_distribution.txt:md5,e9c3ade201964470d2d22569a400fa49",
-                "multiqc_seqfu.txt:md5,a1a0b9a0dde0c1c4fe184d44c675dcde",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,9e05b241aabe39232b5182cb59d8edd5",
-                "picard_QualityScoreDistribution_histogram.txt:md5,e9c3ade201964470d2d22569a400fa49",
-                "picard_alignment_readlength_plot.txt:md5,c2692fde9d899ad61297ad7043fd26b9",
-                "picard_alignment_summary.txt:md5,5996d5b4c94f16c0efd42e2df47e021e",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,a2670974dc96ad8a54f9cc5ae3e09d5e",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,d3b9cc0c99f96814348b57809cf227fb",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,1ba086d3fb2676868e8e7b20f55975dc",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,8902976984741320fe06004f4115c4f4",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,1380831484d1b069a2fd4a20437118bf",
-                "picard_quality_by_cycle.txt:md5,b6fc46e18ac875ba02775e7cbf1b8e8b",
-                "picard_quality_score_distribution.txt:md5,1c17c01ef54a6062a8f1ca8408d32958",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
-                "Sample1_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
-                "Sample23_3.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
-                "SampleA_2.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
-                "Undetermined_5.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
-                "sampletest_4.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
                 "Sample1_1_seqfu.tsv:md5,269fabf8435defcd327aa69a050b7869",
                 "Sample1_1_seqfu_mqc.txt:md5,a354b0ed16b9cf84aa88f501d7740fd6",
                 "Sample23_3_seqfu.tsv:md5,6fdadbeeefccbf957f880d6852bf9676",
@@ -946,9 +106,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.04.7"
         },
-
-        "timestamp": "2025-10-20T11:59:20.195474003"
+        "timestamp": "2025-10-25T17:02:26.23151"
     }
 }
\ No newline at end of file

From 28884d639c2a2ee51e52af1804501dd554f7e20a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pontus=20H=C3=B6jer?= <pontushojer@gmail.com>
Date: Mon, 27 Oct 2025 12:03:06 +0100
Subject: [PATCH 300/530] add index to group reports

---
 assets/multiqc_config.yml                     |  4 +++-
 .../main.nf                                   |  9 +++++---
 workflows/seqinspector.nf                     | 22 ++++++++++++++-----
 3 files changed, 26 insertions(+), 9 deletions(-)

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index e960d07e..df9da74e 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -3,9 +3,11 @@ report_comment: >
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://nf-co.re/seqinspector/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
+  "nf-core-seqinspector-index":
+    order: -999
   "nf-core-seqinspector-methods-description":
     order: -1000
-  software_versions:
+  multiqc_software_versions:
     order: -1001
   "nf-core-seqinspector-summary":
     order: -1002
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index 1188e5e1..23b842b5 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -293,21 +293,24 @@ def reportIndexMultiqc(tags, global=true) {
     def relative_path = global ? ".." : "../.."
 
     // Global report path
-    def index_section = "    <li><a href=\"${relative_path}/global_report/multiqc_report.html\">Global</a></li>\n"
+    def index_section = "    <li><a href=\"${relative_path}/global_report/multiqc_report.html\">Global report</a></li>\n"
 
     // Group report paths
     tags
         .each { tag ->
-            index_section += "    <li><a href=\"${relative_path}/group_reports/${tag}/multiqc_report.html\">${tag}</a></li>\n"
+            index_section += "    <li>Group: <a href=\"${relative_path}/group_reports/${tag}/multiqc_report.html\">${tag}</a></li>\n"
         }
     
     def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-index'\n" as String
-    yaml_file_text     += "description: ' - this information is collected when the pipeline is started.'\n"
+    yaml_file_text     += "description: 'MultiQC reports collected from running the pipeline.'\n"
     yaml_file_text     += "section_name: '${workflow.manifest.name} MultiQC Reports Index'\n"
     yaml_file_text     += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
     yaml_file_text     += "plot_type: 'html'\n"
     yaml_file_text     += "data: |\n"
+    yaml_file_text     += "  <h4>Reports</h4>\n"
+    yaml_file_text     += "  <ul>\n"
     yaml_file_text     += "${index_section}"
+    yaml_file_text     += "  </ul>\n"
 
     return yaml_file_text
 }
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index ab3a742e..63c6e371 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -153,21 +153,22 @@ workflow SEQINSPECTOR {
             sort: true
         )
     )
-    ch_multiqc_extra_files = ch_multiqc_extra_files.mix(
+    // Add index to other MultiQC reports
+    //ch_multiqc_extra_files_global = Channel.empty()
+    ch_multiqc_extra_files_global = ch_multiqc_extra_files.mix(
         ch_tags.toList()
             .map { tag_list ->
                 reportIndexMultiqc(tag_list)
             }
             .collectFile(
                 name: 'multiqc_index_mqc.yaml',
-                sort: true
-            ).view()
+            )
     )
 
     MULTIQC_GLOBAL (
         ch_multiqc_files
             .map { meta, file -> file }
-            .mix(ch_multiqc_extra_files)
+            .mix(ch_multiqc_extra_files_global)
             .collect(),
         ch_multiqc_config.toList(),
         [],
@@ -176,8 +177,18 @@ workflow SEQINSPECTOR {
         []
     )
 
+    ch_multiqc_extra_files_tag = ch_multiqc_extra_files.mix(
+        ch_tags.toList()
+            .map { tag_list ->
+                reportIndexMultiqc(tag_list, false)
+            }
+            .collectFile(
+                name: 'multiqc_index_mqc.yaml',
+            )
+    )
+
     multiqc_extra_files_per_tag = ch_tags
-        .combine(ch_multiqc_extra_files)
+        .combine(ch_multiqc_extra_files_tag)
 
     // Group samples by tag
     tagged_mqc_files = ch_tags
@@ -205,6 +216,7 @@ workflow SEQINSPECTOR {
             samples_per_tag: samples.flatten()
             config: config
         }
+    
 
     MULTIQC_PER_TAG(
         tagged_mqc_files.samples_per_tag,

From 381959c4b9ca68cea0228999d0f4d3a50f4f512f Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@n178-p224.eduroam.kth.se>
Date: Mon, 27 Oct 2025 13:51:02 +0100
Subject: [PATCH 301/530] ss updated

---
 tests/MiSeq.main.nf.test.snap                 | 137 +------------
 tests/MiSeq_PairedEnd.main.nf.test.snap       | 191 +++++++++++++++++-
 tests/NovaSeq6000.main.nf.test.snap           |  37 +---
 tests/NovaSeq6000.main_subsample.nf.test.snap |   7 +-
 tests/PromethION.main.nf.test.snap            |  58 +-----
 5 files changed, 207 insertions(+), 223 deletions(-)

diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 8b0eb5de..4174b8a7 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -26,10 +26,9 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-10-02T12:58:23.877378234"
-        "timestamp": "2025-10-20T11:56:38.220604962"
+        "timestamp": "2025-10-27T12:21:09.386002"
     },
     "MiSeq data test (single end reads)": {
         "content": [
@@ -122,83 +121,8 @@
                 "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
-                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
-                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
-                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "picard_collectmultiplemetrics",
                 "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics",
@@ -226,7 +150,7 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "SAMPLE_SINGLE_END_1.bam:md5,79744f146752fd486b09604be721cc85",
+                "SAMPLE_SINGLE_END_1.bam:md5,ed3f6acd94560448218a288623c810e6",
                 "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
                 "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
                 "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
@@ -268,10 +192,9 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-10-07T09:08:15.546626793"
-        "timestamp": "2025-10-20T11:55:41.808238633"
+        "timestamp": "2025-10-27T12:07:38.912386"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
@@ -346,47 +269,8 @@
                 "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
-                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
-                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
-                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "picard_collectmultiplemetrics",
                 "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics",
@@ -414,7 +298,7 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "SAMPLE_SINGLE_END_1.bam:md5,79744f146752fd486b09604be721cc85",
+                "SAMPLE_SINGLE_END_1.bam:md5,ed3f6acd94560448218a288623c810e6",
                 "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
                 "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
                 "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
@@ -446,9 +330,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        }
-
-        "timestamp": "2025-10-20T11:56:20.313008405"
+            "nextflow": "25.04.7"
+        },
+        "timestamp": "2025-10-27T12:20:25.691504"
     }
-}
+}
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index a9ecbe9c..4890e4dc 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -1,20 +1,30 @@
 {
     "MiSeq data test (paired end reads)": {
         "content": [
-            8,
+            16,
             {
                 "BWAMEM2_INDEX": {
                     "bwamem2": "2.2.1"
                 },
+                "BWAMEM2_MEM": {
+                    "bwamem2": "2.2.1",
+                    "samtools": 1.21
+                },
                 "FASTQC": {
                     "fastqc": "0.12.1"
                 },
                 "FASTQSCREEN_FASTQSCREEN": {
                     "fastqscreen": "0.16.0"
                 },
+                "PICARD_COLLECTMULTIPLEMETRICS": {
+                    "picard": "3.4.0"
+                },
                 "SAMTOOLS_FAIDX": {
                     "samtools": "1.22.1"
                 },
+                "SAMTOOLS_INDEX": {
+                    "samtools": "1.22.1"
+                },
                 "SEQFU_STATS": {
                     "seqfu": "1.20.3"
                 },
@@ -30,6 +40,9 @@
                 "bwamem2_index/bwamem2/genome.fa.ann",
                 "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
                 "bwamem2_index/bwamem2/genome.fa.pac",
+                "bwamem2_mem",
+                "bwamem2_mem/SAMPLE_PAIRED_END_1_1.bam",
+                "bwamem2_mem/SAMPLE_PAIRED_END_2_2.bam",
                 "fastqc",
                 "fastqc/SAMPLE_PAIRED_END_1_1_1_fastqc.html",
                 "fastqc/SAMPLE_PAIRED_END_1_1_1_fastqc.zip",
@@ -52,11 +65,119 @@
                 "fastqscreen/SAMPLE_PAIRED_END_2_2_2_screen.html",
                 "fastqscreen/SAMPLE_PAIRED_END_2_2_2_screen.png",
                 "fastqscreen/SAMPLE_PAIRED_END_2_2_2_screen.txt",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/global_report/multiqc_data/fastqc_adapter_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_summary_Aligned_Bases.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_summary_Aligned_Reads.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
+                "multiqc/global_report/multiqc_plots",
+                "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_report.html",
+                "multiqc/group_reports",
+                "multiqc/group_reports/Bpacificus",
+                "multiqc/group_reports/Bpacificus/multiqc_data",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_adapter_content_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc.log",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_citations.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_data.json",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_quality_score_distribution.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_alignment_summary_Aligned_Bases.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_alignment_summary_Aligned_Reads.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_quality_score_distribution.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_plots",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg",
+                "multiqc/group_reports/Bpacificus/multiqc_report.html",
+                "picard_collectmultiplemetrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "samtools_faidx",
                 "samtools_faidx/genome.fa.fai",
                 "samtools_faidx/genome.fa.sizes",
+                "samtools_index",
+                "samtools_index/SAMPLE_PAIRED_END_1_1.bam.bai",
+                "samtools_index/SAMPLE_PAIRED_END_2_2.bam.bai",
                 "seqfu_stats",
                 "seqfu_stats/SAMPLE_PAIRED_END_1_1_seqfu.tsv",
                 "seqfu_stats/SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt",
@@ -69,6 +190,8 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
+                "SAMPLE_PAIRED_END_1_1.bam:md5,fc37892fea524a3c1799f51605c3cc5f",
+                "SAMPLE_PAIRED_END_2_2.bam:md5,d68128596af24e2349004a082d507cea",
                 "SAMPLE_PAIRED_END_1_1_1_screen.png:md5,f52ddd0e65f23f68dd8d58d5453417db",
                 "SAMPLE_PAIRED_END_1_1_1_screen.txt:md5,921b08eeb461a2aa1bd42bba53900f70",
                 "SAMPLE_PAIRED_END_1_1_2_screen.png:md5,908f4fceea8aa546106efdaa7ca78f7d",
@@ -77,8 +200,72 @@
                 "SAMPLE_PAIRED_END_2_2_1_screen.txt:md5,a5b047f495d01bf9dcb0ae516d3c7fc3",
                 "SAMPLE_PAIRED_END_2_2_2_screen.png:md5,e3684b17339d16e6fb64ace7593cc388",
                 "SAMPLE_PAIRED_END_2_2_2_screen.txt:md5,fc95e5058e764596d5da182cbc0614cf",
+                "fastq_screen_plot.txt:md5,642264b93871c724aaa5d38b91c752dd",
+                "fastqc-status-check-heatmap.txt:md5,8e29ad6b23e03267c33bd9ed3385a44b",
+                "fastqc_adapter_content_plot.txt:md5,46fbd727a4996a3f0310d0423c628445",
+                "fastqc_per_base_n_content_plot.txt:md5,4eca1ef40d4d3d318b82e68e9fa3c589",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,218757a51c3de79a39a704c979df03da",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a4035ac9f0a0c07574130758b06630d7",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,637b937e023c84115ec06b529cc8ec1b",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,47d60153a430e2b8da51655704c2b31b",
+                "fastqc_sequence_counts_plot.txt:md5,10737092a3473fba81fbe49555512b2b",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,6412f57686de02e1f1c3751a7ca2be8b",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,5ef00028497d3271c9f0ea9a961db1e5",
+                "multiqc_fastqc.txt:md5,bc499ad273fd1c887056c31b82544984",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,35d289ee535a0442db72a65391f375eb",
+                "multiqc_picard_baseContent.txt:md5,72b0ae83ed58052bfd768021d377c78f",
+                "multiqc_picard_quality_by_cycle.txt:md5,f6514f14befb874ded5aed79caba3e7b",
+                "multiqc_picard_quality_score_distribution.txt:md5,99be409e325619171b820d762dd023c0",
+                "multiqc_seqfu.txt:md5,1f1e063e4a509a26cee167c3b20389c0",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,f6514f14befb874ded5aed79caba3e7b",
+                "picard_QualityScoreDistribution_histogram.txt:md5,99be409e325619171b820d762dd023c0",
+                "picard_alignment_readlength_plot.txt:md5,4172702f791d043135f21e3a227fe712",
+                "picard_alignment_summary_Aligned_Bases.txt:md5,a166c14210e17d3541482b500443f792",
+                "picard_alignment_summary_Aligned_Reads.txt:md5,c5e5228e85ffb2182274d641ffa6743f",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,3fe18f1144eb85f9206d1bee4eb11bb3",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,2e1383b692e76f4b915ccbe9bb9b9170",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,2a595bc9ac547f3b5224a57a6b0a127d",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,157ea873dd2faff46efdd62f7f6aa84c",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,98f4e5ed094b41eb131d493b4f06bcd6",
+                "picard_quality_by_cycle.txt:md5,2634f306a33f648bac74bc7cd3253f9e",
+                "picard_quality_score_distribution.txt:md5,ecde9f0e859a6eecc5cea75a156c632d",
+                "fastq_screen_plot.txt:md5,642264b93871c724aaa5d38b91c752dd",
+                "fastqc-status-check-heatmap.txt:md5,8e29ad6b23e03267c33bd9ed3385a44b",
+                "fastqc_adapter_content_plot.txt:md5,46fbd727a4996a3f0310d0423c628445",
+                "fastqc_per_base_n_content_plot.txt:md5,4eca1ef40d4d3d318b82e68e9fa3c589",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,218757a51c3de79a39a704c979df03da",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a4035ac9f0a0c07574130758b06630d7",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,637b937e023c84115ec06b529cc8ec1b",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,47d60153a430e2b8da51655704c2b31b",
+                "fastqc_sequence_counts_plot.txt:md5,10737092a3473fba81fbe49555512b2b",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,6412f57686de02e1f1c3751a7ca2be8b",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,5ef00028497d3271c9f0ea9a961db1e5",
+                "multiqc_fastqc.txt:md5,bc499ad273fd1c887056c31b82544984",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,35d289ee535a0442db72a65391f375eb",
+                "multiqc_picard_baseContent.txt:md5,72b0ae83ed58052bfd768021d377c78f",
+                "multiqc_picard_quality_by_cycle.txt:md5,f6514f14befb874ded5aed79caba3e7b",
+                "multiqc_picard_quality_score_distribution.txt:md5,99be409e325619171b820d762dd023c0",
+                "multiqc_seqfu.txt:md5,1f1e063e4a509a26cee167c3b20389c0",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,f6514f14befb874ded5aed79caba3e7b",
+                "picard_QualityScoreDistribution_histogram.txt:md5,99be409e325619171b820d762dd023c0",
+                "picard_alignment_readlength_plot.txt:md5,4172702f791d043135f21e3a227fe712",
+                "picard_alignment_summary_Aligned_Bases.txt:md5,a166c14210e17d3541482b500443f792",
+                "picard_alignment_summary_Aligned_Reads.txt:md5,c5e5228e85ffb2182274d641ffa6743f",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,3fe18f1144eb85f9206d1bee4eb11bb3",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,2e1383b692e76f4b915ccbe9bb9b9170",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,2a595bc9ac547f3b5224a57a6b0a127d",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,157ea873dd2faff46efdd62f7f6aa84c",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,98f4e5ed094b41eb131d493b4f06bcd6",
+                "picard_quality_by_cycle.txt:md5,2634f306a33f648bac74bc7cd3253f9e",
+                "picard_quality_score_distribution.txt:md5,ecde9f0e859a6eecc5cea75a156c632d",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
+                "SAMPLE_PAIRED_END_1_1.bam.bai:md5,82724835c47f8e1d1a86e13ef469b464",
+                "SAMPLE_PAIRED_END_2_2.bam.bai:md5,3c4bdff0f906f2234fdeee8eea719210",
                 "SAMPLE_PAIRED_END_1_1_seqfu.tsv:md5,bbd911ff3fa43212dfd4c5a5872dbdb6",
                 "SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt:md5,cd60f746b6749cc66213d031af1b931c",
                 "SAMPLE_PAIRED_END_2_2_seqfu.tsv:md5,152566a128dd657da33465b4966b5799",
@@ -89,6 +276,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.7"
         },
-        "timestamp": "2025-10-25T17:00:00.443354"
+        "timestamp": "2025-10-27T12:31:06.686371"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index fc5545ab..5e2c5360 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "NovaSeq6000 data test": {
         "content": [
-            17,
+            10,
             {
                 "BWAMEM2_INDEX": {
                     "bwamem2": "2.2.1"
@@ -9,9 +9,6 @@
                 "FASTQC": {
                     "fastqc": "0.12.1"
                 },
-                "FASTQSCREEN_FASTQSCREEN": {
-                    "fastqscreen": "0.16.0"
-                },
                 "SAMTOOLS_FAIDX": {
                     "samtools": "1.22.1"
                 },
@@ -35,28 +32,8 @@
                 "fastqc/Sample1_1_fastqc.zip",
                 "fastqc/Sample23_3_fastqc.html",
                 "fastqc/Sample23_3_fastqc.zip",
-                "fastqc/SampleA_2_fastqc.html",
-                "fastqc/SampleA_2_fastqc.zip",
-                "fastqc/Undetermined_5_fastqc.html",
-                "fastqc/Undetermined_5_fastqc.zip",
                 "fastqc/sampletest_4_fastqc.html",
                 "fastqc/sampletest_4_fastqc.zip",
-                "fastqscreen",
-                "fastqscreen/Sample1_1_screen.html",
-                "fastqscreen/Sample1_1_screen.png",
-                "fastqscreen/Sample1_1_screen.txt",
-                "fastqscreen/Sample23_3_screen.html",
-                "fastqscreen/Sample23_3_screen.png",
-                "fastqscreen/Sample23_3_screen.txt",
-                "fastqscreen/SampleA_2_screen.html",
-                "fastqscreen/SampleA_2_screen.png",
-                "fastqscreen/SampleA_2_screen.txt",
-                "fastqscreen/Undetermined_5_screen.html",
-                "fastqscreen/Undetermined_5_screen.png",
-                "fastqscreen/Undetermined_5_screen.txt",
-                "fastqscreen/sampletest_4_screen.html",
-                "fastqscreen/sampletest_4_screen.png",
-                "fastqscreen/sampletest_4_screen.txt",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "samtools_faidx",
@@ -80,16 +57,6 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "Sample1_1_screen.png:md5,562256290643b51e4374c2225a15f463",
-                "Sample1_1_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
-                "Sample23_3_screen.png:md5,6bb2caf67b9b2ed25d3d5f32c343e9ab",
-                "Sample23_3_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
-                "SampleA_2_screen.png:md5,b2c3e95e034f5c038754bf108537de0e",
-                "SampleA_2_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
-                "Undetermined_5_screen.png:md5,fc5d53f8876dfae3d1a781fa512ea1db",
-                "Undetermined_5_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
-                "sampletest_4_screen.png:md5,1fb60070e8f4b70de0c1b3786b54f27e",
-                "sampletest_4_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "Sample1_1_seqfu.tsv:md5,269fabf8435defcd327aa69a050b7869",
@@ -108,6 +75,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.7"
         },
-        "timestamp": "2025-10-25T17:02:26.23151"
+        "timestamp": "2025-10-27T13:32:28.607154"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index e721fc52..143f43f0 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -23,10 +23,9 @@
             "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5"
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.2"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.7"
         },
-
-        "timestamp": "2024-12-05T15:17:50.525033752"
+        "timestamp": "2025-10-27T13:43:43.032102"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index b4f900f5..2cf63897 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -51,59 +51,8 @@
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_adapter_content_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
-                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
@@ -136,9 +85,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.04.7"
         },
-
-        "timestamp": "2025-10-20T12:01:31.034516203"
+        "timestamp": "2025-10-27T13:45:35.422851"
     }
-}
+}
\ No newline at end of file

From 3c50f97653019d3491af52270804825d51ddc715 Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Mon, 27 Oct 2025 14:29:11 +0100
Subject: [PATCH 302/530] Update conf/modules.config

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
---
 conf/modules.config | 1 -
 1 file changed, 1 deletion(-)

diff --git a/conf/modules.config b/conf/modules.config
index 25a34e09..5d6e9061 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -50,7 +50,6 @@ process {
         ]
     }
     withName: 'PICARD_COLLECTMULTIPLEMETRICS' {
-        ext.args   =  ''
         publishDir = [
             path: { "${params.outdir}/picard_collectmultiplemetrics" },
             mode: params.publish_dir_mode,

From 3c7f92505b491301030072f24cd66045ecfcebea Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Mon, 27 Oct 2025 14:29:22 +0100
Subject: [PATCH 303/530] Update conf/modules.config

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
---
 conf/modules.config | 1 -
 1 file changed, 1 deletion(-)

diff --git a/conf/modules.config b/conf/modules.config
index 5d6e9061..298067fb 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -58,7 +58,6 @@ process {
     }
 
     withName: 'SAMTOOLS_FAIDX' {
-        ext.args   = ''
         publishDir = [
             path: { "${params.outdir}/samtools_faidx" },
             mode: params.publish_dir_mode,

From 3a2fb3607d7cf6cb66cb8de1aa621309f1d2e3e0 Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Mon, 27 Oct 2025 14:29:34 +0100
Subject: [PATCH 304/530] Update conf/modules.config

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
---
 conf/modules.config | 1 -
 1 file changed, 1 deletion(-)

diff --git a/conf/modules.config b/conf/modules.config
index 298067fb..7477a104 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -66,7 +66,6 @@ process {
     }
 
     withName: 'SAMTOOLS_INDEX' {
-        ext.args   = ''
         publishDir = [
             path: { "${params.outdir}/samtools_index" },
             mode: params.publish_dir_mode,

From 4d87018f313104c7031f81042063ce60dbb3a26d Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Mon, 27 Oct 2025 14:30:14 +0100
Subject: [PATCH 305/530] Update workflows/seqinspector.nf

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
---
 workflows/seqinspector.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index fb70e7e6..67b85a75 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -149,7 +149,6 @@ workflow SEQINSPECTOR {
         )
         ch_samtools_index = SAMTOOLS_INDEX.out.bai
         ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions)
-        ch_samtools_index.view { "BAI: $it" }
     }
 
     // MODULE: Index reference FASTA with Samtools faidx

From ecf0917b0a5c03d9457b810b776bccb5f782c0e3 Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Mon, 27 Oct 2025 14:30:37 +0100
Subject: [PATCH 306/530] Update workflows/seqinspector.nf

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
---
 workflows/seqinspector.nf | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 67b85a75..3ff946f2 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -155,12 +155,9 @@ workflow SEQINSPECTOR {
     if (!("samtools_faidx" in skip_tools)) {
 
         // Assume ch_fasta emits tuple(meta, fasta)
-        ch_dummy_fai = Channel.value(['dummy_meta', file('empty.fai')])
-
-
         SAMTOOLS_FAIDX (
             ch_reference_fasta,
-            ch_dummy_fai,
+            [[:],[]],
             true           // get_sizes
         )
         ch_reference_fasta_fai = SAMTOOLS_FAIDX.out.fai

From f3b70abc47c1a9f640876c8deac6250cea77db38 Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Mon, 27 Oct 2025 14:31:09 +0100
Subject: [PATCH 307/530] Update workflows/seqinspector.nf

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
---
 workflows/seqinspector.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 3ff946f2..82a8e16d 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -178,7 +178,6 @@ workflow SEQINSPECTOR {
                 [meta, bam, bai]
             }
 
-        ch_bam_bai.view { "Combined BAM/BAI for Picard: $it" }
         ch_fasta   = ch_reference_fasta
         ch_fai     = ch_reference_fasta_fai
 

From c155300150d9e861bca65cd3ef62be100ebfffca Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Mon, 27 Oct 2025 14:31:19 +0100
Subject: [PATCH 308/530] Update workflows/seqinspector.nf

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
---
 workflows/seqinspector.nf | 2 --
 1 file changed, 2 deletions(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 82a8e16d..3845ff23 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -181,8 +181,6 @@ workflow SEQINSPECTOR {
         ch_fasta   = ch_reference_fasta
         ch_fai     = ch_reference_fasta_fai
 
-        ch_fasta.view { "FASTA for Picard: $it" }
-        ch_fai.view { "FAI for Picard: $it" }
 
         PICARD_COLLECTMULTIPLEMETRICS(
             ch_bam_bai,

From f9fceba62ef147a41d6d92bf9fce58e8051d72b3 Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Mon, 27 Oct 2025 14:31:41 +0100
Subject: [PATCH 309/530] Update workflows/seqinspector.nf

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
---
 workflows/seqinspector.nf | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 3845ff23..3e7b25cd 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -173,10 +173,7 @@ workflow SEQINSPECTOR {
 
         // Prepare BAM/BAI tuples for Picard
         ch_bam_bai = ch_bwamem2_mem
-            .join(ch_samtools_index)
-            .map { meta, bam, bai ->
-                [meta, bam, bai]
-            }
+            .join(ch_samtools_index, failOnDuplicate: true, failOnMismatch: true)
 
         ch_fasta   = ch_reference_fasta
         ch_fai     = ch_reference_fasta_fai

From 851e0e793cf01c5af2b06be218d13d116dc7fcbe Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pontus=20H=C3=B6jer?= <pontushojer@gmail.com>
Date: Mon, 27 Oct 2025 16:02:10 +0100
Subject: [PATCH 310/530] update styling and open links as new tab

---
 .../local/utils_nfcore_seqinspector_pipeline/main.nf  | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index 23b842b5..10bc2e30 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -292,13 +292,15 @@ def methodsDescriptionText(mqc_methods_yaml) {
 def reportIndexMultiqc(tags, global=true) {
     def relative_path = global ? ".." : "../.."
 
+    def a_attrs = "target=\"_blank\" class=\"list-group-item list-group-item-action\""
+
     // Global report path
-    def index_section = "    <li><a href=\"${relative_path}/global_report/multiqc_report.html\">Global report</a></li>\n"
+    def index_section = "    <a href=\"${relative_path}/global_report/multiqc_report.html\" ${a_attrs}>Global report</a>\n"
 
     // Group report paths
     tags
         .each { tag ->
-            index_section += "    <li>Group: <a href=\"${relative_path}/group_reports/${tag}/multiqc_report.html\">${tag}</a></li>\n"
+            index_section += "    <a href=\"${relative_path}/group_reports/${tag}/multiqc_report.html\" ${a_attrs}>Group report: ${tag}</a>\n"
         }
     
     def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-index'\n" as String
@@ -308,9 +310,10 @@ def reportIndexMultiqc(tags, global=true) {
     yaml_file_text     += "plot_type: 'html'\n"
     yaml_file_text     += "data: |\n"
     yaml_file_text     += "  <h4>Reports</h4>\n"
-    yaml_file_text     += "  <ul>\n"
+    yaml_file_text     += "  <p>Select a report to view (open in a new tab):</p>\n"
+    yaml_file_text     += "  <div class=\"list-group\">\n"
     yaml_file_text     += "${index_section}"
-    yaml_file_text     += "  </ul>\n"
+    yaml_file_text     += "  </div>\n"
 
     return yaml_file_text
 }

From 0b864a903c9e1bab360aea9690a4521c749f122f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pontus=20H=C3=B6jer?= <pontushojer@gmail.com>
Date: Mon, 27 Oct 2025 16:16:58 +0100
Subject: [PATCH 311/530] update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index fc243f3c..de9b0884 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -23,6 +23,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#96](https://github.com/nf-core/seqinspector/pull/96) Added missing citations to citation tool
 - [#103](https://github.com/nf-core/seqinspector/pull/103) Configure full-tests
 - [#110](https://github.com/nf-core/seqinspector/pull/110) Update input schema to accept either tar file or directory as rundir, and fastq messages and patterns.
+- [#135](https://github.com/nf-core/seqinspector/pull/135) Added index section to MultiQC reports to facilitate report navigation (#125)
 
 ### `Fixed`
 

From 3fd4c4e2c51eb80a7a5e64dd0b2628a3bf6bcfe3 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@Mac.home>
Date: Tue, 28 Oct 2025 10:41:20 +0100
Subject: [PATCH 312/530] updated ss

---
 tests/MiSeq.main.nf.test.snap                 |   9 +-
 tests/MiSeq_PairedEnd.main.nf.test.snap       |   1 -
 tests/NovaSeq6000.main.nf.test.snap           | 488 +++++++++++++++++-
 tests/NovaSeq6000.main_subsample.nf.test.snap |   1 -
 tests/PromethION.main.nf.test.snap            |   1 -
 5 files changed, 489 insertions(+), 11 deletions(-)

diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 4174b8a7..d25a0aee 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -150,7 +150,7 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "SAMPLE_SINGLE_END_1.bam:md5,ed3f6acd94560448218a288623c810e6",
+                "SAMPLE_SINGLE_END_1.bam:md5,79744f146752fd486b09604be721cc85",
                 "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
                 "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
                 "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
@@ -194,7 +194,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.7"
         },
-        "timestamp": "2025-10-27T12:07:38.912386"
+        "timestamp": "2025-10-27T23:04:45.509991853"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
@@ -298,7 +298,7 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "SAMPLE_SINGLE_END_1.bam:md5,ed3f6acd94560448218a288623c810e6",
+                "SAMPLE_SINGLE_END_1.bam:md5,79744f146752fd486b09604be721cc85",
                 "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
                 "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
                 "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
@@ -332,6 +332,5 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.7"
         },
-        "timestamp": "2025-10-27T12:20:25.691504"
+        "timestamp": "2025-10-27T23:09:02.98022178"
     }
-}
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index 4890e4dc..e841e49c 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -278,4 +278,3 @@
         },
         "timestamp": "2025-10-27T12:31:06.686371"
     }
-}
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index 5e2c5360..99ee4ad2 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -1,17 +1,30 @@
 {
     "NovaSeq6000 data test": {
         "content": [
-            10,
+            37,
             {
                 "BWAMEM2_INDEX": {
                     "bwamem2": "2.2.1"
                 },
+                "BWAMEM2_MEM": {
+                    "bwamem2": "2.2.1",
+                    "samtools": 1.21
+                },
                 "FASTQC": {
                     "fastqc": "0.12.1"
                 },
+                "FASTQSCREEN_FASTQSCREEN": {
+                    "fastqscreen": "0.16.0"
+                },
+                "PICARD_COLLECTMULTIPLEMETRICS": {
+                    "picard": "3.4.0"
+                },
                 "SAMTOOLS_FAIDX": {
                     "samtools": "1.22.1"
                 },
+                "SAMTOOLS_INDEX": {
+                    "samtools": "1.22.1"
+                },
                 "SEQFU_STATS": {
                     "seqfu": "1.20.3"
                 },
@@ -27,18 +40,313 @@
                 "bwamem2_index/bwamem2/genome.fa.ann",
                 "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
                 "bwamem2_index/bwamem2/genome.fa.pac",
+                "bwamem2_mem",
+                "bwamem2_mem/Sample1_1.bam",
+                "bwamem2_mem/Sample23_3.bam",
+                "bwamem2_mem/SampleA_2.bam",
+                "bwamem2_mem/Undetermined_5.bam",
+                "bwamem2_mem/sampletest_4.bam",
                 "fastqc",
                 "fastqc/Sample1_1_fastqc.html",
                 "fastqc/Sample1_1_fastqc.zip",
                 "fastqc/Sample23_3_fastqc.html",
                 "fastqc/Sample23_3_fastqc.zip",
+                "fastqc/SampleA_2_fastqc.html",
+                "fastqc/SampleA_2_fastqc.zip",
+                "fastqc/Undetermined_5_fastqc.html",
+                "fastqc/Undetermined_5_fastqc.zip",
                 "fastqc/sampletest_4_fastqc.html",
                 "fastqc/sampletest_4_fastqc.zip",
+                "fastqscreen",
+                "fastqscreen/Sample1_1_screen.html",
+                "fastqscreen/Sample1_1_screen.png",
+                "fastqscreen/Sample1_1_screen.txt",
+                "fastqscreen/Sample23_3_screen.html",
+                "fastqscreen/Sample23_3_screen.png",
+                "fastqscreen/Sample23_3_screen.txt",
+                "fastqscreen/SampleA_2_screen.html",
+                "fastqscreen/SampleA_2_screen.png",
+                "fastqscreen/SampleA_2_screen.txt",
+                "fastqscreen/Undetermined_5_screen.html",
+                "fastqscreen/Undetermined_5_screen.png",
+                "fastqscreen/Undetermined_5_screen.txt",
+                "fastqscreen/sampletest_4_screen.html",
+                "fastqscreen/sampletest_4_screen.png",
+                "fastqscreen/sampletest_4_screen.txt",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
+                "multiqc/global_report/multiqc_plots",
+                "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_report.html",
+                "multiqc/group_reports",
+                "multiqc/group_reports/group1",
+                "multiqc/group_reports/group1/multiqc_data",
+                "multiqc/group_reports/group1/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc.log",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_citations.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_data.json",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_score_distribution.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_quality_score_distribution.txt",
+                "multiqc/group_reports/group1/multiqc_plots",
+                "multiqc/group_reports/group1/multiqc_plots/pdf",
+                "multiqc/group_reports/group1/multiqc_plots/png",
+                "multiqc/group_reports/group1/multiqc_plots/svg",
+                "multiqc/group_reports/group1/multiqc_report.html",
+                "multiqc/group_reports/group2",
+                "multiqc/group_reports/group2/multiqc_data",
+                "multiqc/group_reports/group2/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/group_reports/group2/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/group_reports/group2/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/group_reports/group2/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/group_reports/group2/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/group_reports/group2/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/group_reports/group2/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/group_reports/group2/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/group_reports/group2/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/group_reports/group2/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/group_reports/group2/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/group_reports/group2/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc.log",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_citations.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_data.json",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_score_distribution.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_quality_score_distribution.txt",
+                "multiqc/group_reports/group2/multiqc_plots",
+                "multiqc/group_reports/group2/multiqc_plots/pdf",
+                "multiqc/group_reports/group2/multiqc_plots/png",
+                "multiqc/group_reports/group2/multiqc_plots/svg",
+                "multiqc/group_reports/group2/multiqc_report.html",
+                "multiqc/group_reports/lane1",
+                "multiqc/group_reports/lane1/multiqc_data",
+                "multiqc/group_reports/lane1/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/group_reports/lane1/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/group_reports/lane1/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/group_reports/lane1/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/group_reports/lane1/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/group_reports/lane1/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/group_reports/lane1/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/group_reports/lane1/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/group_reports/lane1/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/group_reports/lane1/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/group_reports/lane1/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/group_reports/lane1/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc.log",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_citations.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_data.json",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_score_distribution.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_quality_score_distribution.txt",
+                "multiqc/group_reports/lane1/multiqc_plots",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/png",
+                "multiqc/group_reports/lane1/multiqc_plots/svg",
+                "multiqc/group_reports/lane1/multiqc_report.html",
+                "multiqc/group_reports/test",
+                "multiqc/group_reports/test/multiqc_data",
+                "multiqc/group_reports/test/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc.log",
+                "multiqc/group_reports/test/multiqc_data/multiqc_citations.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_data.json",
+                "multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_score_distribution.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_quality_score_distribution.txt",
+                "multiqc/group_reports/test/multiqc_plots",
+                "multiqc/group_reports/test/multiqc_plots/pdf",
+                "multiqc/group_reports/test/multiqc_plots/png",
+                "multiqc/group_reports/test/multiqc_plots/svg",
+                "multiqc/group_reports/test/multiqc_report.html",
+                "picard_collectmultiplemetrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "samtools_faidx",
                 "samtools_faidx/genome.fa.fai",
                 "samtools_faidx/genome.fa.sizes",
+                "samtools_index",
+                "samtools_index/Sample1_1.bam.bai",
+                "samtools_index/Sample23_3.bam.bai",
+                "samtools_index/SampleA_2.bam.bai",
+                "samtools_index/Undetermined_5.bam.bai",
+                "samtools_index/sampletest_4.bam.bai",
                 "seqfu_stats",
                 "seqfu_stats/Sample1_1_seqfu.tsv",
                 "seqfu_stats/Sample1_1_seqfu_mqc.txt",
@@ -57,8 +365,183 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
+                "Sample1_1.bam:md5,1efd4f55b836f732ccc3600697ebb4c3",
+                "Sample23_3.bam:md5,a13dd5db6ef2639f2227b6d3f9c92386",
+                "SampleA_2.bam:md5,c5082847134e5a1c0c869b2378637754",
+                "Undetermined_5.bam:md5,3453bb37bc50105e79f7bba23cbab9c5",
+                "sampletest_4.bam:md5,72532967a589a0a63e93ce86cf79f101",
+                "Sample1_1_screen.png:md5,562256290643b51e4374c2225a15f463",
+                "Sample1_1_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "Sample23_3_screen.png:md5,6bb2caf67b9b2ed25d3d5f32c343e9ab",
+                "Sample23_3_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "SampleA_2_screen.png:md5,b2c3e95e034f5c038754bf108537de0e",
+                "SampleA_2_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "Undetermined_5_screen.png:md5,fc5d53f8876dfae3d1a781fa512ea1db",
+                "Undetermined_5_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "sampletest_4_screen.png:md5,1fb60070e8f4b70de0c1b3786b54f27e",
+                "sampletest_4_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "fastq_screen_plot.txt:md5,562b783630f698c3220c951b73b87027",
+                "fastqc-status-check-heatmap.txt:md5,6cd55dc80642c78b5e0d71821b83fe2e",
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+                "fastqc_per_base_n_content_plot.txt:md5,75aee7627205c6513389d7a52e7a383b",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,2a60a8518caad855e842cf70a8037dad",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,1325b4b3971f7d4d544d9e252abf47b9",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,ef663c12746dfb88f7297b891756fadd",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,5a224c4e837ba42c16b724289bb1bf32",
+                "fastqc_sequence_counts_plot.txt:md5,20364b3b979bc99ae375a2dffcaf1cc1",
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+                "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,5bdb2f162266ab68005cbfc0a45e311e",
+                "multiqc_picard_baseContent.txt:md5,409bf8ce546a573ce6678769b84726fd",
+                "multiqc_picard_quality_by_cycle.txt:md5,ebf56fd9b3b127ff41211e3f79f18b42",
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+                "picard_MeanQualityByCycle_histogram.txt:md5,ebf56fd9b3b127ff41211e3f79f18b42",
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+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,75aee7627205c6513389d7a52e7a383b",
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+                "fastqc_per_base_sequence_quality_plot.txt:md5,6251cde1646484446499252bd15c58a2",
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+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,a9d3152a43988e39fae4a75faa3a5aa4",
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+                "fastqc_sequence_duplication_levels_plot.txt:md5,e37e8e4584f0157a5fa0d53b4834e836",
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+                "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,e4cb1b13e6a7298d172ed112a0479b5a",
+                "multiqc_picard_baseContent.txt:md5,740592a5858706d2b4b8f585a1d5492b",
+                "multiqc_picard_quality_by_cycle.txt:md5,c3f14084aedc511b9f0aa8410e7cb3b5",
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+                "multiqc_seqfu.txt:md5,5579172a6f8ac09a5ffcb3ce6a99590e",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,c3f14084aedc511b9f0aa8410e7cb3b5",
+                "picard_QualityScoreDistribution_histogram.txt:md5,59b955203209cfab3d2d21bdfe20997e",
+                "picard_alignment_readlength_plot.txt:md5,1f8b2f4df8bd5cf879b96cfb2be6d81c",
+                "picard_alignment_summary.txt:md5,0cfafd1ed1920270bb1a5d13bed51480",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,bd7f8dab8e73406cded6c6f27bbc87e9",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,fe44ccdb08c6955149eacf52a77bbba2",
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+                "picard_base_distribution_by_cycle__Thymine.txt:md5,1fe0c42cb22981763862d1934a35de07",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,4c5bfb1594b391f3e36a9e1223b43a94",
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+                "fastqc_per_base_n_content_plot.txt:md5,b7b249afe807ca2321e6dd839961795c",
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+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,ee29af5517a8c6f872adbaccea4ff2f8",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,3eaf12f9267c10e4e457a2bb9bdc70ea",
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+                "fastqc_sequence_counts_plot.txt:md5,0c4863a5475a2444cd00b053eb8941b1",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,a7a050f827a4f821117efd8d25668c51",
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+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
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+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,d4e63eed820edcc71b3e37d793983bd7",
+                "multiqc_picard_baseContent.txt:md5,0dd5fa539e4034e3539fb1e7068c7ce5",
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+                "picard_QualityScoreDistribution_histogram.txt:md5,140279eb5abac364c4d4c417105da620",
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+                "picard_base_distribution_by_cycle__Adenine.txt:md5,166a48317764fe7d4b38ed198503fc11",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,8e62c1113b965497e492e17665cdbe97",
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+                "fastqc_per_base_sequence_quality_plot.txt:md5,12585cf6b03db684a5ebd959f51e77e7",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a1464399e84711454499d27e98ed942b",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,026d11e7b49a49ac7bac85f376760305",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,4d646b20970d09d846947b87961efe7e",
+                "fastqc_sequence_counts_plot.txt:md5,057fb961863b325fe875d3a7879cb888",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,3b86c9d8625c439376102f3286c7bba7",
+                "fastqc_sequence_length_distribution_plot.txt:md5,6296c9ddbf8ba8e12053149d057fd7b2",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5",
+                "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,edf7faad1da9922fdc692e9cba5cc0c4",
+                "multiqc_picard_baseContent.txt:md5,9631916c0a9a736811c47ab4c476428f",
+                "multiqc_picard_quality_by_cycle.txt:md5,9e05b241aabe39232b5182cb59d8edd5",
+                "multiqc_picard_quality_score_distribution.txt:md5,e9c3ade201964470d2d22569a400fa49",
+                "multiqc_seqfu.txt:md5,a1a0b9a0dde0c1c4fe184d44c675dcde",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,9e05b241aabe39232b5182cb59d8edd5",
+                "picard_QualityScoreDistribution_histogram.txt:md5,e9c3ade201964470d2d22569a400fa49",
+                "picard_alignment_readlength_plot.txt:md5,c2692fde9d899ad61297ad7043fd26b9",
+                "picard_alignment_summary.txt:md5,5996d5b4c94f16c0efd42e2df47e021e",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,a2670974dc96ad8a54f9cc5ae3e09d5e",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,d3b9cc0c99f96814348b57809cf227fb",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,1ba086d3fb2676868e8e7b20f55975dc",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,8902976984741320fe06004f4115c4f4",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,1380831484d1b069a2fd4a20437118bf",
+                "picard_quality_by_cycle.txt:md5,b6fc46e18ac875ba02775e7cbf1b8e8b",
+                "picard_quality_score_distribution.txt:md5,1c17c01ef54a6062a8f1ca8408d32958",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
+                "Sample1_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
+                "Sample23_3.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
+                "SampleA_2.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
+                "Undetermined_5.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
+                "sampletest_4.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
                 "Sample1_1_seqfu.tsv:md5,269fabf8435defcd327aa69a050b7869",
                 "Sample1_1_seqfu_mqc.txt:md5,a354b0ed16b9cf84aa88f501d7740fd6",
                 "Sample23_3_seqfu.tsv:md5,6fdadbeeefccbf957f880d6852bf9676",
@@ -75,6 +558,5 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.7"
         },
-        "timestamp": "2025-10-27T13:32:28.607154"
+        "timestamp": "2025-10-27T22:57:54.864898129"
     }
-}
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index 143f43f0..22327297 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -28,4 +28,3 @@
         },
         "timestamp": "2025-10-27T13:43:43.032102"
     }
-}
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index 2cf63897..e0bc4504 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -89,4 +89,3 @@
         },
         "timestamp": "2025-10-27T13:45:35.422851"
     }
-}
\ No newline at end of file

From 88671f28a1ea6a2a966f5f3fcc10b61ad89dd94b Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrimabhatt@Mac.home>
Date: Tue, 28 Oct 2025 13:36:27 +0100
Subject: [PATCH 313/530] ss updated

---
 modules/nf-core/bwamem2/mem/main.nf           |   2 +-
 tests/MiSeq.main.nf.test.snap                 |  11 +-
 tests/MiSeq_PairedEnd.main.nf.test.snap       |   3 +-
 tests/NovaSeq6000.main.nf.test.snap           | 562 ------------------
 tests/NovaSeq6000.main_subsample.nf.test.snap |  30 -
 tests/PromethION.main.nf.test.snap            |   3 +-
 6 files changed, 11 insertions(+), 600 deletions(-)
 delete mode 100644 tests/NovaSeq6000.main.nf.test.snap
 delete mode 100644 tests/NovaSeq6000.main_subsample.nf.test.snap

diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf
index eab662a8..ad510447 100644
--- a/modules/nf-core/bwamem2/mem/main.nf
+++ b/modules/nf-core/bwamem2/mem/main.nf
@@ -1,6 +1,6 @@
 process BWAMEM2_MEM {
     tag "$meta.id"
-    label 'process_high'
+    label 'process_low'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index d25a0aee..4198afef 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -28,7 +28,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.7"
         },
-        "timestamp": "2025-10-27T12:21:09.386002"
+        "timestamp": "2025-10-28T13:25:50.322714"
     },
     "MiSeq data test (single end reads)": {
         "content": [
@@ -150,7 +150,7 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "SAMPLE_SINGLE_END_1.bam:md5,79744f146752fd486b09604be721cc85",
+                "SAMPLE_SINGLE_END_1.bam:md5,ed3f6acd94560448218a288623c810e6",
                 "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
                 "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
                 "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
@@ -194,7 +194,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.7"
         },
-        "timestamp": "2025-10-27T23:04:45.509991853"
+        "timestamp": "2025-10-28T13:22:43.561562"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
@@ -298,7 +298,7 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "SAMPLE_SINGLE_END_1.bam:md5,79744f146752fd486b09604be721cc85",
+                "SAMPLE_SINGLE_END_1.bam:md5,ed3f6acd94560448218a288623c810e6",
                 "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
                 "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
                 "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
@@ -332,5 +332,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.7"
         },
-        "timestamp": "2025-10-27T23:09:02.98022178"
+        "timestamp": "2025-10-28T13:25:03.786062"
     }
+}
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index e841e49c..9dfa23ac 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -276,5 +276,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.7"
         },
-        "timestamp": "2025-10-27T12:31:06.686371"
+        "timestamp": "2025-10-28T13:32:07.785748"
     }
+}
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
deleted file mode 100644
index 99ee4ad2..00000000
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ /dev/null
@@ -1,562 +0,0 @@
-{
-    "NovaSeq6000 data test": {
-        "content": [
-            37,
-            {
-                "BWAMEM2_INDEX": {
-                    "bwamem2": "2.2.1"
-                },
-                "BWAMEM2_MEM": {
-                    "bwamem2": "2.2.1",
-                    "samtools": 1.21
-                },
-                "FASTQC": {
-                    "fastqc": "0.12.1"
-                },
-                "FASTQSCREEN_FASTQSCREEN": {
-                    "fastqscreen": "0.16.0"
-                },
-                "PICARD_COLLECTMULTIPLEMETRICS": {
-                    "picard": "3.4.0"
-                },
-                "SAMTOOLS_FAIDX": {
-                    "samtools": "1.22.1"
-                },
-                "SAMTOOLS_INDEX": {
-                    "samtools": "1.22.1"
-                },
-                "SEQFU_STATS": {
-                    "seqfu": "1.20.3"
-                },
-                "Workflow": {
-                    "nf-core/seqinspector": "v1.0dev"
-                }
-            },
-            [
-                "bwamem2_index",
-                "bwamem2_index/bwamem2",
-                "bwamem2_index/bwamem2/genome.fa.0123",
-                "bwamem2_index/bwamem2/genome.fa.amb",
-                "bwamem2_index/bwamem2/genome.fa.ann",
-                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
-                "bwamem2_index/bwamem2/genome.fa.pac",
-                "bwamem2_mem",
-                "bwamem2_mem/Sample1_1.bam",
-                "bwamem2_mem/Sample23_3.bam",
-                "bwamem2_mem/SampleA_2.bam",
-                "bwamem2_mem/Undetermined_5.bam",
-                "bwamem2_mem/sampletest_4.bam",
-                "fastqc",
-                "fastqc/Sample1_1_fastqc.html",
-                "fastqc/Sample1_1_fastqc.zip",
-                "fastqc/Sample23_3_fastqc.html",
-                "fastqc/Sample23_3_fastqc.zip",
-                "fastqc/SampleA_2_fastqc.html",
-                "fastqc/SampleA_2_fastqc.zip",
-                "fastqc/Undetermined_5_fastqc.html",
-                "fastqc/Undetermined_5_fastqc.zip",
-                "fastqc/sampletest_4_fastqc.html",
-                "fastqc/sampletest_4_fastqc.zip",
-                "fastqscreen",
-                "fastqscreen/Sample1_1_screen.html",
-                "fastqscreen/Sample1_1_screen.png",
-                "fastqscreen/Sample1_1_screen.txt",
-                "fastqscreen/Sample23_3_screen.html",
-                "fastqscreen/Sample23_3_screen.png",
-                "fastqscreen/Sample23_3_screen.txt",
-                "fastqscreen/SampleA_2_screen.html",
-                "fastqscreen/SampleA_2_screen.png",
-                "fastqscreen/SampleA_2_screen.txt",
-                "fastqscreen/Undetermined_5_screen.html",
-                "fastqscreen/Undetermined_5_screen.png",
-                "fastqscreen/Undetermined_5_screen.txt",
-                "fastqscreen/sampletest_4_screen.html",
-                "fastqscreen/sampletest_4_screen.png",
-                "fastqscreen/sampletest_4_screen.txt",
-                "multiqc",
-                "multiqc/global_report",
-                "multiqc/global_report/multiqc_data",
-                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
-                "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
-                "multiqc/global_report/multiqc_data/multiqc.log",
-                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
-                "multiqc/global_report/multiqc_data/multiqc_data.json",
-                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
-                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
-                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
-                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
-                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
-                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
-                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
-                "multiqc/global_report/multiqc_data/picard_alignment_summary.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
-                "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt",
-                "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
-                "multiqc/global_report/multiqc_plots",
-                "multiqc/global_report/multiqc_plots/pdf",
-                "multiqc/global_report/multiqc_plots/png",
-                "multiqc/global_report/multiqc_plots/svg",
-                "multiqc/global_report/multiqc_report.html",
-                "multiqc/group_reports",
-                "multiqc/group_reports/group1",
-                "multiqc/group_reports/group1/multiqc_data",
-                "multiqc/group_reports/group1/multiqc_data/fastq_screen_plot.txt",
-                "multiqc/group_reports/group1/multiqc_data/fastqc-status-check-heatmap.txt",
-                "multiqc/group_reports/group1/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
-                "multiqc/group_reports/group1/multiqc_data/fastqc_per_base_n_content_plot.txt",
-                "multiqc/group_reports/group1/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
-                "multiqc/group_reports/group1/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
-                "multiqc/group_reports/group1/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
-                "multiqc/group_reports/group1/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
-                "multiqc/group_reports/group1/multiqc_data/fastqc_sequence_counts_plot.txt",
-                "multiqc/group_reports/group1/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
-                "multiqc/group_reports/group1/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
-                "multiqc/group_reports/group1/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc.log",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_citations.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_data.json",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_baseContent.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_score_distribution.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_seqfu.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_sources.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_alignment_readlength_plot.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_alignment_summary.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_quality_by_cycle.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_quality_score_distribution.txt",
-                "multiqc/group_reports/group1/multiqc_plots",
-                "multiqc/group_reports/group1/multiqc_plots/pdf",
-                "multiqc/group_reports/group1/multiqc_plots/png",
-                "multiqc/group_reports/group1/multiqc_plots/svg",
-                "multiqc/group_reports/group1/multiqc_report.html",
-                "multiqc/group_reports/group2",
-                "multiqc/group_reports/group2/multiqc_data",
-                "multiqc/group_reports/group2/multiqc_data/fastq_screen_plot.txt",
-                "multiqc/group_reports/group2/multiqc_data/fastqc-status-check-heatmap.txt",
-                "multiqc/group_reports/group2/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
-                "multiqc/group_reports/group2/multiqc_data/fastqc_per_base_n_content_plot.txt",
-                "multiqc/group_reports/group2/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
-                "multiqc/group_reports/group2/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
-                "multiqc/group_reports/group2/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
-                "multiqc/group_reports/group2/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
-                "multiqc/group_reports/group2/multiqc_data/fastqc_sequence_counts_plot.txt",
-                "multiqc/group_reports/group2/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
-                "multiqc/group_reports/group2/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
-                "multiqc/group_reports/group2/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
-                "multiqc/group_reports/group2/multiqc_data/multiqc.log",
-                "multiqc/group_reports/group2/multiqc_data/multiqc_citations.txt",
-                "multiqc/group_reports/group2/multiqc_data/multiqc_data.json",
-                "multiqc/group_reports/group2/multiqc_data/multiqc_fastq_screen.txt",
-                "multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt",
-                "multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
-                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_baseContent.txt",
-                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_by_cycle.txt",
-                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_score_distribution.txt",
-                "multiqc/group_reports/group2/multiqc_data/multiqc_seqfu.txt",
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-                "picard_quality_by_cycle.txt:md5,a43e7bb40bc479e9c32476256b09e734",
-                "picard_quality_score_distribution.txt:md5,a940641c0dab423c964c0f46b69dd805",
-                "fastq_screen_plot.txt:md5,44fca6453b0a3d0590271bd7a31cc740",
-                "fastqc-status-check-heatmap.txt:md5,b6872d9dbaa3cce396d48dc137076e53",
-                "fastqc_overrepresented_sequences_plot.txt:md5,eac8d0fd31c614d8d0f56bd54ee8c78c",
-                "fastqc_per_base_n_content_plot.txt:md5,b7b249afe807ca2321e6dd839961795c",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,3bca5f0121d27b0777a40a4ab44e2abc",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,ee29af5517a8c6f872adbaccea4ff2f8",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,3eaf12f9267c10e4e457a2bb9bdc70ea",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,1818e0b917e45a583740f2cbb0638f8d",
-                "fastqc_sequence_counts_plot.txt:md5,0c4863a5475a2444cd00b053eb8941b1",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,a7a050f827a4f821117efd8d25668c51",
-                "fastqc_sequence_length_distribution_plot.txt:md5,9c0761008be04d8ccf4c0e16acc6348c",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
-                "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,d4e63eed820edcc71b3e37d793983bd7",
-                "multiqc_picard_baseContent.txt:md5,0dd5fa539e4034e3539fb1e7068c7ce5",
-                "multiqc_picard_quality_by_cycle.txt:md5,750eadc27875fc8141b64a90789c369f",
-                "multiqc_picard_quality_score_distribution.txt:md5,140279eb5abac364c4d4c417105da620",
-                "multiqc_seqfu.txt:md5,b5434520fa5be5c98be5ed164a464d23",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,750eadc27875fc8141b64a90789c369f",
-                "picard_QualityScoreDistribution_histogram.txt:md5,140279eb5abac364c4d4c417105da620",
-                "picard_alignment_readlength_plot.txt:md5,a39f6a39dad13dacc2134508dbbf172d",
-                "picard_alignment_summary.txt:md5,fec83821c097bc1850257ce36aa73e5f",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,f206efb4e5344b8cbb2d18f6e73d5d95",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,ebf98e3d0bf661161989bf3d010b8c6b",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,f7dff1258977e9d04fb26ba8192facc5",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,b32d1e91c41756afe8732107868b32e0",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,b7b249afe807ca2321e6dd839961795c",
-                "picard_quality_by_cycle.txt:md5,1fe617901a493b80c31fcd01a00c416d",
-                "picard_quality_score_distribution.txt:md5,5cd4a87942000899776927f22a5db802",
-                "fastq_screen_plot.txt:md5,5f748d33a7a396547fe8c260b728aa06",
-                "fastqc-status-check-heatmap.txt:md5,08228a8f3d6f11b174b98626bb22bda1",
-                "fastqc_overrepresented_sequences_plot.txt:md5,3434dfb79f150e2e584e85866983ba01",
-                "fastqc_per_base_n_content_plot.txt:md5,e371981072ec99d11c6adb5a4034808c",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,bf83d019eaaeb1ca659ff28cfb2bdfea",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,3f40b8ee69d3eaefe657cc5ed622cc8b",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,86b61d09437a96448e1325e6be834048",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,9f7307469b112bd054f8ee0cc2cf4d65",
-                "fastqc_sequence_counts_plot.txt:md5,f0c693cc281a6e61ba219bab04f59a47",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,8c2aa91358fd4a2e946cbcc1f312f9b6",
-                "fastqc_sequence_length_distribution_plot.txt:md5,875ebcd6726bb9d36ffa64265e5071d0",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
-                "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,22093b80f335c4c53633b01a930157f4",
-                "multiqc_picard_baseContent.txt:md5,6886e1e5179031ddba4958f301930d64",
-                "multiqc_picard_quality_by_cycle.txt:md5,96652e2e2d693488df9104e5ae8cb4a7",
-                "multiqc_picard_quality_score_distribution.txt:md5,879a4470d08fe6d9b1796f46020fb5f5",
-                "multiqc_seqfu.txt:md5,e2e092852c011abe5ad75cdcd68b9383",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,96652e2e2d693488df9104e5ae8cb4a7",
-                "picard_QualityScoreDistribution_histogram.txt:md5,879a4470d08fe6d9b1796f46020fb5f5",
-                "picard_alignment_readlength_plot.txt:md5,9b323aa8cd934d084e9c83cfa1da306b",
-                "picard_alignment_summary.txt:md5,4e8970d31940f5e9020851d62e63b2e2",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,166a48317764fe7d4b38ed198503fc11",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,8e62c1113b965497e492e17665cdbe97",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,fe53f5f9455b928a3edc1661be83592b",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,3d069dd67cc0ffc43456c5f3ee427349",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,e371981072ec99d11c6adb5a4034808c",
-                "picard_quality_by_cycle.txt:md5,0c25ee4cec6842306b28c6a641aa03e1",
-                "picard_quality_score_distribution.txt:md5,184dcdd53f6aa3b7a0fa2c008d7dc74a",
-                "fastq_screen_plot.txt:md5,8622e1dbd0fe62520af6096207b9775d",
-                "fastqc-status-check-heatmap.txt:md5,2a66f5d61b9eb579555905cd5954b04c",
-                "fastqc_overrepresented_sequences_plot.txt:md5,e0b5bfc4b64d37611b51c939e61196fa",
-                "fastqc_per_base_n_content_plot.txt:md5,1380831484d1b069a2fd4a20437118bf",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,12585cf6b03db684a5ebd959f51e77e7",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a1464399e84711454499d27e98ed942b",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,026d11e7b49a49ac7bac85f376760305",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,4d646b20970d09d846947b87961efe7e",
-                "fastqc_sequence_counts_plot.txt:md5,057fb961863b325fe875d3a7879cb888",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,3b86c9d8625c439376102f3286c7bba7",
-                "fastqc_sequence_length_distribution_plot.txt:md5,6296c9ddbf8ba8e12053149d057fd7b2",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5",
-                "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,edf7faad1da9922fdc692e9cba5cc0c4",
-                "multiqc_picard_baseContent.txt:md5,9631916c0a9a736811c47ab4c476428f",
-                "multiqc_picard_quality_by_cycle.txt:md5,9e05b241aabe39232b5182cb59d8edd5",
-                "multiqc_picard_quality_score_distribution.txt:md5,e9c3ade201964470d2d22569a400fa49",
-                "multiqc_seqfu.txt:md5,a1a0b9a0dde0c1c4fe184d44c675dcde",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,9e05b241aabe39232b5182cb59d8edd5",
-                "picard_QualityScoreDistribution_histogram.txt:md5,e9c3ade201964470d2d22569a400fa49",
-                "picard_alignment_readlength_plot.txt:md5,c2692fde9d899ad61297ad7043fd26b9",
-                "picard_alignment_summary.txt:md5,5996d5b4c94f16c0efd42e2df47e021e",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,a2670974dc96ad8a54f9cc5ae3e09d5e",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,d3b9cc0c99f96814348b57809cf227fb",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,1ba086d3fb2676868e8e7b20f55975dc",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,8902976984741320fe06004f4115c4f4",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,1380831484d1b069a2fd4a20437118bf",
-                "picard_quality_by_cycle.txt:md5,b6fc46e18ac875ba02775e7cbf1b8e8b",
-                "picard_quality_score_distribution.txt:md5,1c17c01ef54a6062a8f1ca8408d32958",
-                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
-                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
-                "Sample1_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
-                "Sample23_3.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
-                "SampleA_2.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
-                "Undetermined_5.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
-                "sampletest_4.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
-                "Sample1_1_seqfu.tsv:md5,269fabf8435defcd327aa69a050b7869",
-                "Sample1_1_seqfu_mqc.txt:md5,a354b0ed16b9cf84aa88f501d7740fd6",
-                "Sample23_3_seqfu.tsv:md5,6fdadbeeefccbf957f880d6852bf9676",
-                "Sample23_3_seqfu_mqc.txt:md5,e94269e3efc8b8192d7ac9c15ea2aa99",
-                "SampleA_2_seqfu.tsv:md5,b980ed694a05825fcf7c8b5b73888eb3",
-                "SampleA_2_seqfu_mqc.txt:md5,1d4b0e918644cf553108b7ccf77b4a01",
-                "Undetermined_5_seqfu.tsv:md5,b4458d41df4dee9321da03f4d4672aae",
-                "Undetermined_5_seqfu_mqc.txt:md5,0c869488cb61d2f87758c621bded212b",
-                "sampletest_4_seqfu.tsv:md5,db3179b0c41a09e6317a5a5c0852f476",
-                "sampletest_4_seqfu_mqc.txt:md5,590b97cc48268629204f59007bae7ad7"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2025-10-27T22:57:54.864898129"
-    }
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
deleted file mode 100644
index 22327297..00000000
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ /dev/null
@@ -1,30 +0,0 @@
-{
-    "NovaSeq6000 data test sample size": {
-        "content": [
-            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-            "multiqc_fastqc.txt:md5,aba942d1e6996b579f19798e5673f514",
-            "multiqc_general_stats.txt:md5,ad1ec9c64cbdb1131a26aeb6de51e31c",
-            "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
-            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-            "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8",
-            "multiqc_general_stats.txt:md5,c73c8d10568a56f6534d280fff701e60",
-            "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
-            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-            "multiqc_fastqc.txt:md5,ff996e1d3dc4a46e0c9535e54d51ccab",
-            "multiqc_general_stats.txt:md5,834e1868b887171cfda72029bbbe2d3f",
-            "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
-            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-            "multiqc_fastqc.txt:md5,3df36ecfe76b25b0c22dcda84bce2b3b",
-            "multiqc_general_stats.txt:md5,274a001b007521970f14d68bd176e5be",
-            "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
-            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-            "multiqc_fastqc.txt:md5,ce61b4ce4b1d76ec3f20de3bf0c9ec7f",
-            "multiqc_general_stats.txt:md5,d476ad59458a035a329605d5284b6012",
-            "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5"
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2025-10-27T13:43:43.032102"
-    }
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index e0bc4504..b798f8cb 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -87,5 +87,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.7"
         },
-        "timestamp": "2025-10-27T13:45:35.422851"
+        "timestamp": "2025-10-28T13:34:27.316787"
     }
+}
\ No newline at end of file

From 3bce8c57534e0a502cae4f895c9a84569bda785d Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 6 Nov 2025 14:49:56 +0100
Subject: [PATCH 314/530] update snapshots

---
 tests/MiSeq.main.nf.test.snap                 | 126 ++-
 tests/NovaSeq6000.main.nf.test.snap           | 953 ++++++++++++++++++
 tests/NovaSeq6000.main_subsample.nf.test.snap |  31 +
 tests/PromethION.main.nf.test.snap            |  57 +-
 4 files changed, 1158 insertions(+), 9 deletions(-)
 create mode 100644 tests/NovaSeq6000.main.nf.test.snap
 create mode 100644 tests/NovaSeq6000.main_subsample.nf.test.snap

diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 4198afef..b2c5a439 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -121,8 +121,83 @@
                 "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "picard_collectmultiplemetrics",
                 "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics",
@@ -191,10 +266,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T13:22:43.561562"
+        "timestamp": "2025-11-06T14:38:31.725391247"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
@@ -269,8 +344,47 @@
                 "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "picard_collectmultiplemetrics",
                 "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics",
@@ -329,9 +443,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T13:25:03.786062"
+        "timestamp": "2025-11-06T14:39:46.509895007"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
new file mode 100644
index 00000000..d6cb71b7
--- /dev/null
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -0,0 +1,953 @@
+{
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+        "content": [
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+                },
+                "PICARD_COLLECTMULTIPLEMETRICS": {
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+                "Workflow": {
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+                }
+            },
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+                "bwamem2_index/bwamem2/genome.fa.ann",
+                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
+                "bwamem2_index/bwamem2/genome.fa.pac",
+                "bwamem2_mem",
+                "bwamem2_mem/Sample1_1.bam",
+                "bwamem2_mem/Sample23_3.bam",
+                "bwamem2_mem/SampleA_2.bam",
+                "bwamem2_mem/Undetermined_5.bam",
+                "bwamem2_mem/sampletest_4.bam",
+                "fastqc",
+                "fastqc/Sample1_1_fastqc.html",
+                "fastqc/Sample1_1_fastqc.zip",
+                "fastqc/Sample23_3_fastqc.html",
+                "fastqc/Sample23_3_fastqc.zip",
+                "fastqc/SampleA_2_fastqc.html",
+                "fastqc/SampleA_2_fastqc.zip",
+                "fastqc/Undetermined_5_fastqc.html",
+                "fastqc/Undetermined_5_fastqc.zip",
+                "fastqc/sampletest_4_fastqc.html",
+                "fastqc/sampletest_4_fastqc.zip",
+                "fastqscreen",
+                "fastqscreen/Sample1_1_screen.html",
+                "fastqscreen/Sample1_1_screen.png",
+                "fastqscreen/Sample1_1_screen.txt",
+                "fastqscreen/Sample23_3_screen.html",
+                "fastqscreen/Sample23_3_screen.png",
+                "fastqscreen/Sample23_3_screen.txt",
+                "fastqscreen/SampleA_2_screen.html",
+                "fastqscreen/SampleA_2_screen.png",
+                "fastqscreen/SampleA_2_screen.txt",
+                "fastqscreen/Undetermined_5_screen.html",
+                "fastqscreen/Undetermined_5_screen.png",
+                "fastqscreen/Undetermined_5_screen.txt",
+                "fastqscreen/sampletest_4_screen.html",
+                "fastqscreen/sampletest_4_screen.png",
+                "fastqscreen/sampletest_4_screen.txt",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
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+                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
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+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.read_length_histogram.pdf",
+                "pipeline_info",
+                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "samtools_faidx",
+                "samtools_faidx/genome.fa.fai",
+                "samtools_faidx/genome.fa.sizes",
+                "samtools_index",
+                "samtools_index/Sample1_1.bam.bai",
+                "samtools_index/Sample23_3.bam.bai",
+                "samtools_index/SampleA_2.bam.bai",
+                "samtools_index/Undetermined_5.bam.bai",
+                "samtools_index/sampletest_4.bam.bai",
+                "seqfu_stats",
+                "seqfu_stats/Sample1_1_seqfu.tsv",
+                "seqfu_stats/Sample1_1_seqfu_mqc.txt",
+                "seqfu_stats/Sample23_3_seqfu.tsv",
+                "seqfu_stats/Sample23_3_seqfu_mqc.txt",
+                "seqfu_stats/SampleA_2_seqfu.tsv",
+                "seqfu_stats/SampleA_2_seqfu_mqc.txt",
+                "seqfu_stats/Undetermined_5_seqfu.tsv",
+                "seqfu_stats/Undetermined_5_seqfu_mqc.txt",
+                "seqfu_stats/sampletest_4_seqfu.tsv",
+                "seqfu_stats/sampletest_4_seqfu_mqc.txt"
+            ],
+            [
+                "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
+                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
+                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
+                "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
+                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
+                "Sample1_1.bam:md5,39c3c91eedd90307315acec7aa0b9a35",
+                "Sample23_3.bam:md5,3d536a6680470138eb361eed198a8efd",
+                "SampleA_2.bam:md5,ad691a2590eed5bbc56a56dd24493e4e",
+                "Undetermined_5.bam:md5,06077f7de3641b4b86e08f6a9cdb5a97",
+                "sampletest_4.bam:md5,7dcb21eb9fec77b862af33e692678dbd",
+                "Sample1_1_screen.png:md5,562256290643b51e4374c2225a15f463",
+                "Sample1_1_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "Sample23_3_screen.png:md5,6bb2caf67b9b2ed25d3d5f32c343e9ab",
+                "Sample23_3_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "SampleA_2_screen.png:md5,b2c3e95e034f5c038754bf108537de0e",
+                "SampleA_2_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "Undetermined_5_screen.png:md5,fc5d53f8876dfae3d1a781fa512ea1db",
+                "Undetermined_5_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "sampletest_4_screen.png:md5,1fb60070e8f4b70de0c1b3786b54f27e",
+                "sampletest_4_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "fastq_screen_plot.txt:md5,562b783630f698c3220c951b73b87027",
+                "fastqc-status-check-heatmap.txt:md5,6cd55dc80642c78b5e0d71821b83fe2e",
+                "fastqc_overrepresented_sequences_plot.txt:md5,37fd53c396d047467fbd38c5c4a0c4ba",
+                "fastqc_per_base_n_content_plot.txt:md5,75aee7627205c6513389d7a52e7a383b",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,2a60a8518caad855e842cf70a8037dad",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,1325b4b3971f7d4d544d9e252abf47b9",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,ef663c12746dfb88f7297b891756fadd",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,5a224c4e837ba42c16b724289bb1bf32",
+                "fastqc_sequence_counts_plot.txt:md5,20364b3b979bc99ae375a2dffcaf1cc1",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,7f33f3d0e2eb3405eb6456acbd18dfd4",
+                "fastqc_sequence_length_distribution_plot.txt:md5,9472fb38f57150d55fb9e4995aaeeb90",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
+                "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,5bdb2f162266ab68005cbfc0a45e311e",
+                "multiqc_picard_baseContent.txt:md5,409bf8ce546a573ce6678769b84726fd",
+                "multiqc_picard_quality_by_cycle.txt:md5,ebf56fd9b3b127ff41211e3f79f18b42",
+                "multiqc_picard_quality_score_distribution.txt:md5,182098ce1ff0a664d873c329d54189df",
+                "multiqc_seqfu.txt:md5,5b54a49079169985795537d83d58bdd9",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,ebf56fd9b3b127ff41211e3f79f18b42",
+                "picard_QualityScoreDistribution_histogram.txt:md5,182098ce1ff0a664d873c329d54189df",
+                "picard_alignment_readlength_plot.txt:md5,92ab5c6fbe67484da62626736b1b21d4",
+                "picard_alignment_summary.txt:md5,f54187e8515f9b7c32eabaf1f8702224",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,61c7df03f74846ffa484a59fcccc7b9e",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,b4504bbb9ad72796703873f2d957977a",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,1d38466783ea51bf0c7be5bceaff4d43",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,1b13c9b64042839a3bc65a8553e5ba24",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,75aee7627205c6513389d7a52e7a383b",
+                "picard_quality_by_cycle.txt:md5,4850a9230f9be5af67f3d934602df440",
+                "picard_quality_score_distribution.txt:md5,17f8498a5b18cea0eb4796a6e12b8e36",
+                "fastq_screen_plot.txt:md5,c25d34568f10f131156294d31fbfa994",
+                "fastqc-status-check-heatmap.txt:md5,67afbf7ec626c4fc7a28b4922352bc84",
+                "fastqc_overrepresented_sequences_plot.txt:md5,0356d007eaf807f7b63714b438b11289",
+                "fastqc_per_base_n_content_plot.txt:md5,4c5bfb1594b391f3e36a9e1223b43a94",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,6251cde1646484446499252bd15c58a2",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,f645e38916efafd07d4c2c3d5c7cd051",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,a9d3152a43988e39fae4a75faa3a5aa4",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,aef487a8b267a14a92be64b0b01d9b5c",
+                "fastqc_sequence_counts_plot.txt:md5,5021496dd00366d08064804bbb5192e3",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,e37e8e4584f0157a5fa0d53b4834e836",
+                "fastqc_sequence_length_distribution_plot.txt:md5,393cc090200a5151561efb1ed5280b89",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
+                "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,e4cb1b13e6a7298d172ed112a0479b5a",
+                "multiqc_picard_baseContent.txt:md5,740592a5858706d2b4b8f585a1d5492b",
+                "multiqc_picard_quality_by_cycle.txt:md5,c3f14084aedc511b9f0aa8410e7cb3b5",
+                "multiqc_picard_quality_score_distribution.txt:md5,59b955203209cfab3d2d21bdfe20997e",
+                "multiqc_seqfu.txt:md5,5579172a6f8ac09a5ffcb3ce6a99590e",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,c3f14084aedc511b9f0aa8410e7cb3b5",
+                "picard_QualityScoreDistribution_histogram.txt:md5,59b955203209cfab3d2d21bdfe20997e",
+                "picard_alignment_readlength_plot.txt:md5,1f8b2f4df8bd5cf879b96cfb2be6d81c",
+                "picard_alignment_summary.txt:md5,0cfafd1ed1920270bb1a5d13bed51480",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,bd7f8dab8e73406cded6c6f27bbc87e9",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,fe44ccdb08c6955149eacf52a77bbba2",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,85a9172769830b4169f214c335f44fdc",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,1fe0c42cb22981763862d1934a35de07",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,4c5bfb1594b391f3e36a9e1223b43a94",
+                "picard_quality_by_cycle.txt:md5,a43e7bb40bc479e9c32476256b09e734",
+                "picard_quality_score_distribution.txt:md5,a940641c0dab423c964c0f46b69dd805",
+                "fastq_screen_plot.txt:md5,44fca6453b0a3d0590271bd7a31cc740",
+                "fastqc-status-check-heatmap.txt:md5,b6872d9dbaa3cce396d48dc137076e53",
+                "fastqc_overrepresented_sequences_plot.txt:md5,eac8d0fd31c614d8d0f56bd54ee8c78c",
+                "fastqc_per_base_n_content_plot.txt:md5,b7b249afe807ca2321e6dd839961795c",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,3bca5f0121d27b0777a40a4ab44e2abc",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,ee29af5517a8c6f872adbaccea4ff2f8",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,3eaf12f9267c10e4e457a2bb9bdc70ea",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,1818e0b917e45a583740f2cbb0638f8d",
+                "fastqc_sequence_counts_plot.txt:md5,0c4863a5475a2444cd00b053eb8941b1",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,a7a050f827a4f821117efd8d25668c51",
+                "fastqc_sequence_length_distribution_plot.txt:md5,9c0761008be04d8ccf4c0e16acc6348c",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
+                "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,d4e63eed820edcc71b3e37d793983bd7",
+                "multiqc_picard_baseContent.txt:md5,0dd5fa539e4034e3539fb1e7068c7ce5",
+                "multiqc_picard_quality_by_cycle.txt:md5,750eadc27875fc8141b64a90789c369f",
+                "multiqc_picard_quality_score_distribution.txt:md5,140279eb5abac364c4d4c417105da620",
+                "multiqc_seqfu.txt:md5,b5434520fa5be5c98be5ed164a464d23",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,750eadc27875fc8141b64a90789c369f",
+                "picard_QualityScoreDistribution_histogram.txt:md5,140279eb5abac364c4d4c417105da620",
+                "picard_alignment_readlength_plot.txt:md5,a39f6a39dad13dacc2134508dbbf172d",
+                "picard_alignment_summary.txt:md5,fec83821c097bc1850257ce36aa73e5f",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,f206efb4e5344b8cbb2d18f6e73d5d95",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,ebf98e3d0bf661161989bf3d010b8c6b",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,f7dff1258977e9d04fb26ba8192facc5",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,b32d1e91c41756afe8732107868b32e0",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,b7b249afe807ca2321e6dd839961795c",
+                "picard_quality_by_cycle.txt:md5,1fe617901a493b80c31fcd01a00c416d",
+                "picard_quality_score_distribution.txt:md5,5cd4a87942000899776927f22a5db802",
+                "fastq_screen_plot.txt:md5,5f748d33a7a396547fe8c260b728aa06",
+                "fastqc-status-check-heatmap.txt:md5,08228a8f3d6f11b174b98626bb22bda1",
+                "fastqc_overrepresented_sequences_plot.txt:md5,3434dfb79f150e2e584e85866983ba01",
+                "fastqc_per_base_n_content_plot.txt:md5,e371981072ec99d11c6adb5a4034808c",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,bf83d019eaaeb1ca659ff28cfb2bdfea",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,3f40b8ee69d3eaefe657cc5ed622cc8b",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,86b61d09437a96448e1325e6be834048",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,9f7307469b112bd054f8ee0cc2cf4d65",
+                "fastqc_sequence_counts_plot.txt:md5,f0c693cc281a6e61ba219bab04f59a47",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,8c2aa91358fd4a2e946cbcc1f312f9b6",
+                "fastqc_sequence_length_distribution_plot.txt:md5,875ebcd6726bb9d36ffa64265e5071d0",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
+                "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,22093b80f335c4c53633b01a930157f4",
+                "multiqc_picard_baseContent.txt:md5,6886e1e5179031ddba4958f301930d64",
+                "multiqc_picard_quality_by_cycle.txt:md5,96652e2e2d693488df9104e5ae8cb4a7",
+                "multiqc_picard_quality_score_distribution.txt:md5,879a4470d08fe6d9b1796f46020fb5f5",
+                "multiqc_seqfu.txt:md5,e2e092852c011abe5ad75cdcd68b9383",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,96652e2e2d693488df9104e5ae8cb4a7",
+                "picard_QualityScoreDistribution_histogram.txt:md5,879a4470d08fe6d9b1796f46020fb5f5",
+                "picard_alignment_readlength_plot.txt:md5,9b323aa8cd934d084e9c83cfa1da306b",
+                "picard_alignment_summary.txt:md5,4e8970d31940f5e9020851d62e63b2e2",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,166a48317764fe7d4b38ed198503fc11",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,8e62c1113b965497e492e17665cdbe97",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,fe53f5f9455b928a3edc1661be83592b",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,3d069dd67cc0ffc43456c5f3ee427349",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,e371981072ec99d11c6adb5a4034808c",
+                "picard_quality_by_cycle.txt:md5,0c25ee4cec6842306b28c6a641aa03e1",
+                "picard_quality_score_distribution.txt:md5,184dcdd53f6aa3b7a0fa2c008d7dc74a",
+                "fastq_screen_plot.txt:md5,8622e1dbd0fe62520af6096207b9775d",
+                "fastqc-status-check-heatmap.txt:md5,2a66f5d61b9eb579555905cd5954b04c",
+                "fastqc_overrepresented_sequences_plot.txt:md5,e0b5bfc4b64d37611b51c939e61196fa",
+                "fastqc_per_base_n_content_plot.txt:md5,1380831484d1b069a2fd4a20437118bf",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,12585cf6b03db684a5ebd959f51e77e7",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a1464399e84711454499d27e98ed942b",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,026d11e7b49a49ac7bac85f376760305",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,4d646b20970d09d846947b87961efe7e",
+                "fastqc_sequence_counts_plot.txt:md5,057fb961863b325fe875d3a7879cb888",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,3b86c9d8625c439376102f3286c7bba7",
+                "fastqc_sequence_length_distribution_plot.txt:md5,6296c9ddbf8ba8e12053149d057fd7b2",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5",
+                "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,edf7faad1da9922fdc692e9cba5cc0c4",
+                "multiqc_picard_baseContent.txt:md5,9631916c0a9a736811c47ab4c476428f",
+                "multiqc_picard_quality_by_cycle.txt:md5,9e05b241aabe39232b5182cb59d8edd5",
+                "multiqc_picard_quality_score_distribution.txt:md5,e9c3ade201964470d2d22569a400fa49",
+                "multiqc_seqfu.txt:md5,a1a0b9a0dde0c1c4fe184d44c675dcde",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,9e05b241aabe39232b5182cb59d8edd5",
+                "picard_QualityScoreDistribution_histogram.txt:md5,e9c3ade201964470d2d22569a400fa49",
+                "picard_alignment_readlength_plot.txt:md5,c2692fde9d899ad61297ad7043fd26b9",
+                "picard_alignment_summary.txt:md5,5996d5b4c94f16c0efd42e2df47e021e",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,a2670974dc96ad8a54f9cc5ae3e09d5e",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,d3b9cc0c99f96814348b57809cf227fb",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,1ba086d3fb2676868e8e7b20f55975dc",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,8902976984741320fe06004f4115c4f4",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,1380831484d1b069a2fd4a20437118bf",
+                "picard_quality_by_cycle.txt:md5,b6fc46e18ac875ba02775e7cbf1b8e8b",
+                "picard_quality_score_distribution.txt:md5,1c17c01ef54a6062a8f1ca8408d32958",
+                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
+                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
+                "Sample1_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
+                "Sample23_3.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
+                "SampleA_2.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
+                "Undetermined_5.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
+                "sampletest_4.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
+                "Sample1_1_seqfu.tsv:md5,269fabf8435defcd327aa69a050b7869",
+                "Sample1_1_seqfu_mqc.txt:md5,a354b0ed16b9cf84aa88f501d7740fd6",
+                "Sample23_3_seqfu.tsv:md5,6fdadbeeefccbf957f880d6852bf9676",
+                "Sample23_3_seqfu_mqc.txt:md5,e94269e3efc8b8192d7ac9c15ea2aa99",
+                "SampleA_2_seqfu.tsv:md5,b980ed694a05825fcf7c8b5b73888eb3",
+                "SampleA_2_seqfu_mqc.txt:md5,1d4b0e918644cf553108b7ccf77b4a01",
+                "Undetermined_5_seqfu.tsv:md5,b4458d41df4dee9321da03f4d4672aae",
+                "Undetermined_5_seqfu_mqc.txt:md5,0c869488cb61d2f87758c621bded212b",
+                "sampletest_4_seqfu.tsv:md5,db3179b0c41a09e6317a5a5c0852f476",
+                "sampletest_4_seqfu_mqc.txt:md5,590b97cc48268629204f59007bae7ad7"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-11-06T14:45:07.83898234"
+    }
+}
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
new file mode 100644
index 00000000..a6df7ee3
--- /dev/null
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -0,0 +1,31 @@
+{
+    "NovaSeq6000 data test sample size": {
+        "content": [
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+            "multiqc_fastqc.txt:md5,aba942d1e6996b579f19798e5673f514",
+            "multiqc_general_stats.txt:md5,ad1ec9c64cbdb1131a26aeb6de51e31c",
+            "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+            "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8",
+            "multiqc_general_stats.txt:md5,c73c8d10568a56f6534d280fff701e60",
+            "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+            "multiqc_fastqc.txt:md5,ff996e1d3dc4a46e0c9535e54d51ccab",
+            "multiqc_general_stats.txt:md5,834e1868b887171cfda72029bbbe2d3f",
+            "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+            "multiqc_fastqc.txt:md5,3df36ecfe76b25b0c22dcda84bce2b3b",
+            "multiqc_general_stats.txt:md5,274a001b007521970f14d68bd176e5be",
+            "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
+            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+            "multiqc_fastqc.txt:md5,ce61b4ce4b1d76ec3f20de3bf0c9ec7f",
+            "multiqc_general_stats.txt:md5,d476ad59458a035a329605d5284b6012",
+            "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5"
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-11-06T14:47:03.513513804"
+    }
+}
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index b798f8cb..09713692 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -51,8 +51,59 @@
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_adapter_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
@@ -84,9 +135,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T13:34:27.316787"
+        "timestamp": "2025-11-06T14:47:54.312304379"
     }
 }
\ No newline at end of file

From 47709ee9129c3efb11fb2164062a7e63164d38e2 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 6 Nov 2025 14:58:12 +0100
Subject: [PATCH 315/530] forgot file

---
 tests/MiSeq_PairedEnd.main.nf.test.snap | 162 +++++++++++++++++++++++-
 1 file changed, 159 insertions(+), 3 deletions(-)

diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index 9dfa23ac..78faba92 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -106,8 +106,86 @@
                 "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_adapter_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/global_report/multiqc_plots/png/general_stats_table.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "multiqc/group_reports",
                 "multiqc/group_reports/Bpacificus",
@@ -150,8 +228,86 @@
                 "multiqc/group_reports/Bpacificus/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_plots",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-cnt.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-pct.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-cnt.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-pct.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_adapter_content_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/general_stats_table.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-cnt.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-pct.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-cnt.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-pct.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_quality_score_distribution.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-cnt.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-pct.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-cnt.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-pct.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_quality_score_distribution.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_report.html",
                 "picard_collectmultiplemetrics",
                 "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.alignment_summary_metrics",
@@ -273,9 +429,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T13:32:07.785748"
+        "timestamp": "2025-11-06T14:56:09.011355596"
     }
 }
\ No newline at end of file

From 4c9ea1576eb0cb8267eb542ea2654213ba85cce1 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Thu, 6 Nov 2025 17:17:26 +0100
Subject: [PATCH 316/530] Apply suggestions from code review

---
 .github/workflows/release-announcements.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index e64cebd6..24444c09 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -17,7 +17,7 @@ jobs:
       - name: get description
         id: get_topics
         run: |
-          echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description' >> $GITHUB_OUTPUT
+          echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT
 
       - uses: rzr/fediverse-action@master
         with:
@@ -28,7 +28,7 @@ jobs:
           message: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
 
-            ${{ steps.get_topics.outputs.description }}
+            ${{ steps.get_description.outputs.description }}
 
             Please see the changelog: ${{ github.event.release.html_url }}
 

From 30b455598e934d287685d5c852d3d8bdb7cc29f4 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 6 Nov 2025 17:18:01 +0100
Subject: [PATCH 317/530] fix anonymous

---
 nextflow.config | 2 --
 1 file changed, 2 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index fadea079..d9a10865 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -176,8 +176,6 @@ profiles {
     test_full { includeConfig 'conf/test_full.config' }
 }
 
-// Set AWS client to anonymous when using the default igenomes_base
-aws.client.anonymous = !params.igenomes_ignore && params.igenomes_base?.startsWith('s3://ngi-igenomes/igenomes/') ?: false
 // Load nf-core custom profiles from different institutions
 
 // If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included.

From 8a41887d1dabd73845ded1d13731cee142a7e83d Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Thu, 6 Nov 2025 17:22:17 +0100
Subject: [PATCH 318/530] Delete tests/default.nf.test

---
 tests/default.nf.test | 33 ---------------------------------
 1 file changed, 33 deletions(-)
 delete mode 100644 tests/default.nf.test

diff --git a/tests/default.nf.test b/tests/default.nf.test
deleted file mode 100644
index 7e427966..00000000
--- a/tests/default.nf.test
+++ /dev/null
@@ -1,33 +0,0 @@
-nextflow_pipeline {
-
-    name "Test pipeline"
-    script "../main.nf"
-    tag "pipeline"
-
-    test("-profile test") {
-
-        when {
-            params {
-                outdir = "$outputDir"
-            }
-        }
-
-        then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
-            assertAll(
-                { assert workflow.success},
-                { assert snapshot(
-                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
-                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
-                    // All stable path name, with a relative path
-                    stable_name,
-                    // All files with stable contents
-                    stable_path
-                ).match() }
-            )
-        }
-    }
-}

From 83096c07df01cb8aa767b2bc36c9ac39b63b18a2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pontus=20H=C3=B6jer?= <pontus.hojer@scilifelab.se>
Date: Fri, 7 Nov 2025 09:13:36 +0100
Subject: [PATCH 319/530] ignore multiqc config linting for now

---
 .nf-core.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.nf-core.yml b/.nf-core.yml
index 84481477..d857a9bf 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,5 +1,6 @@
 lint:
   actions_ci: false
+  multiqc_config: false
   files_unchanged:
     - .github/CONTRIBUTING.md
   files_exist:

From 59457c5d07239782877e99c3634d5f4c7c300d23 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pontus=20H=C3=B6jer?= <pontus.hojer@scilifelab.se>
Date: Fri, 7 Nov 2025 09:20:32 +0100
Subject: [PATCH 320/530] rm trailing whitespaces

---
 subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf | 2 +-
 workflows/seqinspector.nf                                     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index a5940934..5a6a3eef 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -291,7 +291,7 @@ def reportIndexMultiqc(tags, global=true) {
         .each { tag ->
             index_section += "    <a href=\"${relative_path}/group_reports/${tag}/multiqc_report.html\" ${a_attrs}>Group report: ${tag}</a>\n"
         }
-    
+
     def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-index'\n" as String
     yaml_file_text     += "description: 'MultiQC reports collected from running the pipeline.'\n"
     yaml_file_text     += "section_name: '${workflow.manifest.name} MultiQC Reports Index'\n"
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 45120425..cc1f11ff 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -243,7 +243,7 @@ workflow SEQINSPECTOR {
             samples_per_tag: samples.flatten()
             config: config
         }
-    
+
 
     MULTIQC_PER_TAG(
         tagged_mqc_files.samples_per_tag,

From 8ac64d34efd5b69786930f1107f047e72f4def44 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 7 Nov 2025 10:08:50 +0100
Subject: [PATCH 321/530] pre-commit

---
 conf/test.config                     | 1 -
 tests/PromethION.main.nf.test.config | 2 --
 2 files changed, 3 deletions(-)

diff --git a/conf/test.config b/conf/test.config
index db9d053b..286d1cf8 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -32,4 +32,3 @@ process {
     ]
 
 }
-
diff --git a/tests/PromethION.main.nf.test.config b/tests/PromethION.main.nf.test.config
index 987d19d3..526df7be 100644
--- a/tests/PromethION.main.nf.test.config
+++ b/tests/PromethION.main.nf.test.config
@@ -7,5 +7,3 @@ params {
     genome = 'EB1'
     skip_tools = 'bwamem2_index,bwamem2_mem'
 }
-
-

From d2ad680b11bc00f4932af3c032a381f263f60525 Mon Sep 17 00:00:00 2001
From: FranBonath <franziska.bonath@scilifelab.se>
Date: Fri, 7 Nov 2025 10:12:08 +0100
Subject: [PATCH 322/530] adding tubemaps V1

---
 docs/images/seqinspector_tubemap_V1.0.png |  Bin 0 -> 103756 bytes
 docs/images/seqinspector_tubemap_V1.0.svg | 1640 +++++++++++++++++++++
 2 files changed, 1640 insertions(+)
 create mode 100644 docs/images/seqinspector_tubemap_V1.0.png
 create mode 100644 docs/images/seqinspector_tubemap_V1.0.svg

diff --git a/docs/images/seqinspector_tubemap_V1.0.png b/docs/images/seqinspector_tubemap_V1.0.png
new file mode 100644
index 0000000000000000000000000000000000000000..0bb3dfca89fae5e98f39d70dab3a6b193521ad04
GIT binary patch
literal 103756
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From 996087a255fbe36b248a76ea35f8b44818ed5ef1 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 7 Nov 2025 10:28:21 +0100
Subject: [PATCH 323/530] nf-core lint

---
 .nf-core.yml                                  |   4 +
 ro-crate-metadata.json                        |  76 ++-
 tests/MiSeq.main.nf.test                      |   2 -
 tests/MiSeq.main.nf.test.snap                 |   3 +-
 tests/MiSeq_PairedEnd.main.nf.test            |   2 -
 tests/MiSeq_PairedEnd.main.nf.test.snap       |   3 +-
 tests/NovaSeq6000.main.nf.test                |   2 -
 tests/NovaSeq6000.main.nf.test.snap           |   3 +-
 tests/NovaSeq6000.main_subsample.nf.test      |  45 +-
 tests/NovaSeq6000.main_subsample.nf.test.snap | 585 +++++++++++++++++-
 tests/PromethION.main.nf.test                 |   2 -
 tests/PromethION.main.nf.test.snap            |   3 +-
 12 files changed, 646 insertions(+), 84 deletions(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index 69c01ff0..1bb2f77b 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,4 +1,8 @@
 lint:
+  files_exist:
+    - tests/default.nf.test
+  files_unchanged:
+    - .github/CONTRIBUTING.md
   nextflow_config:
     - config_defaults:
         - params.fastq_screen_references
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index fff8a7c6..a6d9804f 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,8 +22,8 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2025-10-16T13:38:57+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by Adrien Coulier.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "datePublished": "2025-11-07T09:27:51+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->\n\n1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))\n2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n3. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
                     "@id": "main.nf"
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#cc905640-68e5-4225-9aba-bfd290c08fdf"
+                    "@id": "#fbe02af1-e9dc-458e-a6f1-649522b5321b"
                 }
             ],
             "name": "nf-core/seqinspector"
@@ -121,31 +121,53 @@
         },
         {
             "@id": "main.nf",
-            "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
+            "@type": [
+                "File",
+                "SoftwareSourceCode",
+                "ComputationalWorkflow"
+            ],
             "creator": [
+                {
+                    "@id": "https://orcid.org/0000-0003-1675-0677"
+                },
                 {
                     "@id": "https://orcid.org/0000-0003-2702-1103"
+                },
+                {
+                    "@id": "#89784800+kedhammar@users.noreply.github.com"
+                },
+                {
+                    "@id": "https://orcid.org/0009-0004-5536-7210"
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2025-10-16T13:38:57Z",
+            "dateModified": "2025-11-07T10:27:51Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
-            "keywords": ["nf-core", "nextflow", "genomics", "quality-control"],
-            "license": ["MIT"],
-            "maintainer": [
-                {
-                    "@id": "https://orcid.org/0000-0003-2702-1103"
-                }
+            "keywords": [
+                "nf-core",
+                "nextflow",
+                "genomics",
+                "quality-control"
+            ],
+            "license": [
+                "MIT"
+            ],
+            "name": [
+                "nf-core/seqinspector"
             ],
-            "name": ["nf-core/seqinspector"],
             "programmingLanguage": {
                 "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow"
             },
             "sdPublisher": {
                 "@id": "https://nf-co.re/"
             },
-            "url": ["https://github.com/nf-core/seqinspector", "https://nf-co.re/seqinspector/dev/"],
-            "version": ["1.0dev"]
+            "url": [
+                "https://github.com/nf-core/seqinspector",
+                "https://nf-co.re/seqinspector/dev/"
+            ],
+            "version": [
+                "1.0dev"
+            ]
         },
         {
             "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow",
@@ -160,11 +182,11 @@
             "version": "!>=25.04.0"
         },
         {
-            "@id": "#cc905640-68e5-4225-9aba-bfd290c08fdf",
+            "@id": "#fbe02af1-e9dc-458e-a6f1-649522b5321b",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#2cb8f151-0728-49b6-969d-b792c1b849b0"
+                    "@id": "#56ac1623-4e68-4598-9703-f769123f08c5"
                 }
             ],
             "mainEntity": {
@@ -173,7 +195,7 @@
             "name": "Test suite for nf-core/seqinspector"
         },
         {
-            "@id": "#2cb8f151-0728-49b6-969d-b792c1b849b0",
+            "@id": "#56ac1623-4e68-4598-9703-f769123f08c5",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/seqinspector",
             "resource": "repos/nf-core/seqinspector/actions/workflows/nf-test.yml",
@@ -301,11 +323,29 @@
             "name": "nf-core",
             "url": "https://nf-co.re/"
         },
+        {
+            "@id": "https://orcid.org/0000-0003-1675-0677",
+            "@type": "Person",
+            "email": "mahesh.binzer-panchal@nbis.se",
+            "name": "Mahesh Binzer-Panchal"
+        },
         {
             "@id": "https://orcid.org/0000-0003-2702-1103",
             "@type": "Person",
             "email": "adrien.coulier@medsci.uu.se",
             "name": "Adrien Coulier"
+        },
+        {
+            "@id": "#89784800+kedhammar@users.noreply.github.com",
+            "@type": "Person",
+            "email": "89784800+kedhammar@users.noreply.github.com",
+            "name": "Alfred Kedhammar"
+        },
+        {
+            "@id": "https://orcid.org/0009-0004-5536-7210",
+            "@type": "Person",
+            "email": "agrimabhatt@n141-p117.eduroam.kth.se",
+            "name": "Agrima Bhatt"
         }
     ]
-}
+}
\ No newline at end of file
diff --git a/tests/MiSeq.main.nf.test b/tests/MiSeq.main.nf.test
index 4cf42243..dd57e94a 100644
--- a/tests/MiSeq.main.nf.test
+++ b/tests/MiSeq.main.nf.test
@@ -28,8 +28,6 @@ nextflow_pipeline {
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
-                    // Number of successful tasks
-                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
                     // All stable path names, with a relative path
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index f73d6a6d..b1174d1b 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -34,7 +34,6 @@
     },
     "MiSeq data test (single end reads)": {
         "content": [
-            6,
             {
                 "BWAMEM2_INDEX": {
                     "bwamem2": "2.2.1"
@@ -179,7 +178,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-06T17:09:30.687814423"
+        "timestamp": "2025-11-07T10:23:17.145777453"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
diff --git a/tests/MiSeq_PairedEnd.main.nf.test b/tests/MiSeq_PairedEnd.main.nf.test
index 92807e95..04655713 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test
+++ b/tests/MiSeq_PairedEnd.main.nf.test
@@ -28,8 +28,6 @@ nextflow_pipeline {
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
-                    // Number of successful tasks
-                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
                     // All stable path names, with a relative path
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index c526e237..10a9b11a 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -1,7 +1,6 @@
 {
     "MiSeq data test (paired end reads)": {
         "content": [
-            11,
             {
                 "BWAMEM2_INDEX": {
                     "bwamem2": "2.2.1"
@@ -248,6 +247,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-06T17:11:17.153150613"
+        "timestamp": "2025-11-07T10:24:43.782493978"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test b/tests/NovaSeq6000.main.nf.test
index 8eea81f7..63dcc300 100644
--- a/tests/NovaSeq6000.main.nf.test
+++ b/tests/NovaSeq6000.main.nf.test
@@ -28,8 +28,6 @@ nextflow_pipeline {
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
-                    // Number of successful tasks
-                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
                     // All stable path names, with a relative path
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index c09e0987..f2985aa3 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -1,7 +1,6 @@
 {
     "NovaSeq6000 data test": {
         "content": [
-            26,
             {
                 "BWAMEM2_INDEX": {
                     "bwamem2": "2.2.1"
@@ -552,6 +551,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-06T17:12:19.300655258"
+        "timestamp": "2025-11-07T10:25:42.576692828"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main_subsample.nf.test b/tests/NovaSeq6000.main_subsample.nf.test
index d006de37..a62e4411 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test
+++ b/tests/NovaSeq6000.main_subsample.nf.test
@@ -15,35 +15,26 @@ nextflow_pipeline {
         }
 
         then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(
+                params.outdir,
+                relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']
+            )
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(
+                params.outdir,
+                ignoreFile: 'tests/.nftignore'
+            )
             assertAll(
-                { assert workflow.success },
+                { assert workflow.success},
                 { assert snapshot(
-                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt"),
-
-                    path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_fastq_screen.txt"),
-
-                    path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt"),
-
-                    path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_fastq_screen.txt"),
-
-                    path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt"),
-                    ).match()
-                },
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
+                    // All stable path names, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
             )
         }
     }
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index 3ba50465..a539c846 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -1,31 +1,570 @@
 {
     "NovaSeq6000 data test sample size": {
         "content": [
-            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-            "multiqc_fastqc.txt:md5,aba942d1e6996b579f19798e5673f514",
-            "multiqc_general_stats.txt:md5,ad1ec9c64cbdb1131a26aeb6de51e31c",
-            "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
-            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-            "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8",
-            "multiqc_general_stats.txt:md5,c73c8d10568a56f6534d280fff701e60",
-            "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
-            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-            "multiqc_fastqc.txt:md5,ff996e1d3dc4a46e0c9535e54d51ccab",
-            "multiqc_general_stats.txt:md5,834e1868b887171cfda72029bbbe2d3f",
-            "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
-            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-            "multiqc_fastqc.txt:md5,3df36ecfe76b25b0c22dcda84bce2b3b",
-            "multiqc_general_stats.txt:md5,274a001b007521970f14d68bd176e5be",
-            "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
-            "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-            "multiqc_fastqc.txt:md5,ce61b4ce4b1d76ec3f20de3bf0c9ec7f",
-            "multiqc_general_stats.txt:md5,d476ad59458a035a329605d5284b6012",
-            "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5"
+            {
+                "BWAMEM2_INDEX": {
+                    "bwamem2": "2.2.1"
+                },
+                "BWAMEM2_MEM": {
+                    "bwamem2": "2.2.1",
+                    "samtools": 1.21
+                },
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "FASTQSCREEN_FASTQSCREEN": {
+                    "fastqscreen": "0.16.0"
+                },
+                "SEQFU_STATS": {
+                    "seqfu": "1.20.3"
+                },
+                "SEQTK_SAMPLE": {
+                    "seqtk": "1.4-r122"
+                },
+                "Workflow": {
+                    "nf-core/seqinspector": "v1.0dev"
+                }
+            },
+            [
+                "bwamem2_index",
+                "bwamem2_index/bwamem2",
+                "bwamem2_index/bwamem2/genome.fa.0123",
+                "bwamem2_index/bwamem2/genome.fa.amb",
+                "bwamem2_index/bwamem2/genome.fa.ann",
+                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
+                "bwamem2_index/bwamem2/genome.fa.pac",
+                "bwamem2_mem",
+                "bwamem2_mem/Sample1_1.bam",
+                "bwamem2_mem/Sample23_3.bam",
+                "bwamem2_mem/SampleA_2.bam",
+                "bwamem2_mem/Undetermined_5.bam",
+                "bwamem2_mem/sampletest_4.bam",
+                "fastqc",
+                "fastqc/Sample1_1_fastqc.html",
+                "fastqc/Sample1_1_fastqc.zip",
+                "fastqc/Sample23_3_fastqc.html",
+                "fastqc/Sample23_3_fastqc.zip",
+                "fastqc/SampleA_2_fastqc.html",
+                "fastqc/SampleA_2_fastqc.zip",
+                "fastqc/Undetermined_5_fastqc.html",
+                "fastqc/Undetermined_5_fastqc.zip",
+                "fastqc/sampletest_4_fastqc.html",
+                "fastqc/sampletest_4_fastqc.zip",
+                "fastqscreen",
+                "fastqscreen/Sample1_1_screen.html",
+                "fastqscreen/Sample1_1_screen.png",
+                "fastqscreen/Sample1_1_screen.txt",
+                "fastqscreen/Sample23_3_screen.html",
+                "fastqscreen/Sample23_3_screen.png",
+                "fastqscreen/Sample23_3_screen.txt",
+                "fastqscreen/SampleA_2_screen.html",
+                "fastqscreen/SampleA_2_screen.png",
+                "fastqscreen/SampleA_2_screen.txt",
+                "fastqscreen/Undetermined_5_screen.html",
+                "fastqscreen/Undetermined_5_screen.png",
+                "fastqscreen/Undetermined_5_screen.txt",
+                "fastqscreen/sampletest_4_screen.html",
+                "fastqscreen/sampletest_4_screen.png",
+                "fastqscreen/sampletest_4_screen.txt",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/global_report/multiqc_data/llms-full.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc.parquet",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_plots",
+                "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu.png",
+                "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
+                "multiqc/global_report/multiqc_report.html",
+                "multiqc/group_reports",
+                "multiqc/group_reports/group1",
+                "multiqc/group_reports/group1/multiqc_data",
+                "multiqc/group_reports/group1/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/group_reports/group1/multiqc_data/llms-full.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc.log",
+                "multiqc/group_reports/group1/multiqc_data/multiqc.parquet",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_citations.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_data.json",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/group1/multiqc_plots",
+                "multiqc/group_reports/group1/multiqc_plots/pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/seqfu.png",
+                "multiqc/group_reports/group1/multiqc_plots/svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/seqfu.svg",
+                "multiqc/group_reports/group1/multiqc_report.html",
+                "multiqc/group_reports/group2",
+                "multiqc/group_reports/group2/multiqc_data",
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+                "sampletest_4_screen.png:md5,1fb60070e8f4b70de0c1b3786b54f27e",
+                "sampletest_4_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "fastq_screen_plot.txt:md5,562b783630f698c3220c951b73b87027",
+                "fastqc-status-check-heatmap.txt:md5,84794d045dc6d91b00e59985bae9d18a",
+                "fastqc_overrepresented_sequences_plot.txt:md5,8a49ca637e473578baa80c57486f6873",
+                "fastqc_per_base_n_content_plot.txt:md5,234d2d338b88166d1432f0fd3887ed90",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,c812a38f8bbea81175c40956f1e9ab99",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,1881dab3459ddec9b2ab33211440289c",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,c34018be31633edf7d82d746d3e2f649",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,e65af797abbcf320c7b91e8ba0a03fe9",
+                "fastqc_sequence_counts_plot.txt:md5,478329307763d250c206e44f0961ab94",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,5c4b313cef9eae4900d6ca22b561c838",
+                "fastqc_sequence_length_distribution_plot.txt:md5,d423f73abb6f1c4e7ebfff407886f5a7",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
+                "multiqc_fastqc.txt:md5,aba942d1e6996b579f19798e5673f514",
+                "multiqc_seqfu.txt:md5,5b54a49079169985795537d83d58bdd9",
+                "fastq_screen_plot.txt:md5,c25d34568f10f131156294d31fbfa994",
+                "fastqc-status-check-heatmap.txt:md5,7ee494f345c09706513e65907788de02",
+                "fastqc_overrepresented_sequences_plot.txt:md5,ca9fa146e7b8a7f562fd79b521ba0f60",
+                "fastqc_per_base_n_content_plot.txt:md5,d0948f903d5cb77880ff7b1b4e0a4f23",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,12040cb996a4f30dbd6e5c313ee8e407",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,c6d912b805a018cc564e7f5b1967f1d8",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,0f71b9cb3d8e09558752a5f9f45cdf2c",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,f50ed03bbcb136505c3724d1ca2a5bea",
+                "fastqc_sequence_counts_plot.txt:md5,bf1fde5dc15633a58f074ddd3eb891a5",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,e37e8e4584f0157a5fa0d53b4834e836",
+                "fastqc_sequence_length_distribution_plot.txt:md5,e102bf11f348e8c24e1d15b336e2f595",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
+                "multiqc_fastqc.txt:md5,ff996e1d3dc4a46e0c9535e54d51ccab",
+                "multiqc_seqfu.txt:md5,5579172a6f8ac09a5ffcb3ce6a99590e",
+                "fastq_screen_plot.txt:md5,44fca6453b0a3d0590271bd7a31cc740",
+                "fastqc-status-check-heatmap.txt:md5,b6872d9dbaa3cce396d48dc137076e53",
+                "fastqc_overrepresented_sequences_plot.txt:md5,19babef6996c0bfdf28e5df89368cbb1",
+                "fastqc_per_base_n_content_plot.txt:md5,25367b78b3d6a063d33814c663fea91e",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,2b4fa8cd21e4e6cb093abbfc221a7095",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,204e907429377d2d568e65d80edad2d2",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,525162fb43c9906641e953aafc59f8bf",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,3a16c4f83d13b5b61999491b0ca9d36c",
+                "fastqc_sequence_counts_plot.txt:md5,cf8c6868dc440beb30414259703a1551",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,1e595565e848ab3f13cfa8479214d3e0",
+                "fastqc_sequence_length_distribution_plot.txt:md5,24ef8f47147dabd210b03c497d340d77",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
+                "multiqc_fastqc.txt:md5,3df36ecfe76b25b0c22dcda84bce2b3b",
+                "multiqc_seqfu.txt:md5,b5434520fa5be5c98be5ed164a464d23",
+                "fastq_screen_plot.txt:md5,5f748d33a7a396547fe8c260b728aa06",
+                "fastqc-status-check-heatmap.txt:md5,bab59a0bd1d676d90cdd986fbba36b26",
+                "fastqc_overrepresented_sequences_plot.txt:md5,79cb259874c52b44f8c69b2075ee498e",
+                "fastqc_per_base_n_content_plot.txt:md5,6ef3683b1b7db0b6db6948185f96959d",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,e7255081223d89b4f3611a57d13974d8",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,dc0ced33f21421d4cba72b4c6e6bf19b",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,7a6b00f36bb522d044c3fa3192e2adf8",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,ed58f918f7d979999e28137ba30f12e3",
+                "fastqc_sequence_counts_plot.txt:md5,29dc291cce9708c51dbe2b58a32cc713",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,77e0c9a542a3d59b173633764a11b404",
+                "fastqc_sequence_length_distribution_plot.txt:md5,c4f58d755233776c341da8dc357f8527",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
+                "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8",
+                "multiqc_seqfu.txt:md5,e2e092852c011abe5ad75cdcd68b9383",
+                "fastq_screen_plot.txt:md5,8622e1dbd0fe62520af6096207b9775d",
+                "fastqc-status-check-heatmap.txt:md5,2a66f5d61b9eb579555905cd5954b04c",
+                "fastqc_overrepresented_sequences_plot.txt:md5,5cdefa954db6e46c286e2984a883eb18",
+                "fastqc_per_base_n_content_plot.txt:md5,92c23e189d98430517e4030e7c9ae038",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,a02cd4679a5991b73d2df6583a2cf01b",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,6152ec5e4f4fd331b89107e024b009ac",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,ea90172d9f32b43fe8f6b91fb54f26c2",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,5ba7c7ccdcd54daf44d996e697cbeadf",
+                "fastqc_sequence_counts_plot.txt:md5,88a5e67b5ce395a7ed3324b176c15cf7",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,041857b1e41e0b47bfc62000cb9f323d",
+                "fastqc_sequence_length_distribution_plot.txt:md5,c2ee6b7c9fc91de049d183422e0a71fc",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5",
+                "multiqc_fastqc.txt:md5,ce61b4ce4b1d76ec3f20de3bf0c9ec7f",
+                "multiqc_seqfu.txt:md5,a1a0b9a0dde0c1c4fe184d44c675dcde",
+                "Sample1_1_seqfu.tsv:md5,269fabf8435defcd327aa69a050b7869",
+                "Sample1_1_seqfu_mqc.txt:md5,a354b0ed16b9cf84aa88f501d7740fd6",
+                "Sample23_3_seqfu.tsv:md5,6fdadbeeefccbf957f880d6852bf9676",
+                "Sample23_3_seqfu_mqc.txt:md5,e94269e3efc8b8192d7ac9c15ea2aa99",
+                "SampleA_2_seqfu.tsv:md5,b980ed694a05825fcf7c8b5b73888eb3",
+                "SampleA_2_seqfu_mqc.txt:md5,1d4b0e918644cf553108b7ccf77b4a01",
+                "Undetermined_5_seqfu.tsv:md5,b4458d41df4dee9321da03f4d4672aae",
+                "Undetermined_5_seqfu_mqc.txt:md5,0c869488cb61d2f87758c621bded212b",
+                "sampletest_4_seqfu.tsv:md5,db3179b0c41a09e6317a5a5c0852f476",
+                "sampletest_4_seqfu_mqc.txt:md5,590b97cc48268629204f59007bae7ad7",
+                "Sample1_1_Sample1_S1_L001_R1_001.fastq.gz:md5,3ccd132ff32399706842b0f1d00f477e",
+                "Sample23_3_Sample23_S3_L001_R1_001.fastq.gz:md5,3802f03450693b42531fdf5b0b542c2f",
+                "SampleA_2_SampleA_S2_L001_R1_001.fastq.gz:md5,f99d5407aac64cb36451c6f0a1db5ade",
+                "Undetermined_5_Undetermined_S0_L001_R1_001.fastq.gz:md5,104dbbef386db0eef3e02c586feb01a1",
+                "sampletest_4_sampletest_S4_L001_R1_001.fastq.gz:md5,30aa24a51e27e24390ac8b90158df8f2"
+            ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.2"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-12-05T15:17:50.525033752"
+        "timestamp": "2025-11-07T10:26:40.559862265"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test b/tests/PromethION.main.nf.test
index 5cb291ef..f4a46aac 100644
--- a/tests/PromethION.main.nf.test
+++ b/tests/PromethION.main.nf.test
@@ -28,8 +28,6 @@ nextflow_pipeline {
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
-                    // Number of successful tasks
-                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
                     // All stable path names, with a relative path
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index 442f70de..0467b847 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -1,7 +1,6 @@
 {
     "PromethION data test": {
         "content": [
-            4,
             {
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -134,6 +133,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-06T17:13:57.307157715"
+        "timestamp": "2025-11-07T10:27:14.736749139"
     }
 }
\ No newline at end of file

From ef54e8ba5e8e7d91050af90638df08df9b6e2eb1 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 7 Nov 2025 10:34:47 +0100
Subject: [PATCH 324/530] Update nextflow_schema.json

---
 nextflow_schema.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 53946a6a..02bdecea 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -94,7 +94,7 @@
                 },
                 "fastq_screen_references": {
                     "type": "string",
-                    "default": "/Users/agrimabhatt/seqinspector/assets/example_fastq_screen_references.csv",
+                    "default": "${projectDir}/assets/example_fastq_screen_references.csv",
                     "fa_icon": "fas fa-search",
                     "description": "A .csv of reference genomes to be mapped against by FastQ Screen"
                 }

From b33eef829135425374a3d9ba90173d8367a4f94b Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 7 Nov 2025 10:40:30 +0100
Subject: [PATCH 325/530] Apply suggestions from code review

---
 .github/workflows/release-announcements.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index 24444c09..039f5e85 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -15,9 +15,9 @@ jobs:
           echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT
 
       - name: get description
-        id: get_topics
+        id: get_description
         run: |
-          echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT
+          echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description')" >> $GITHUB_OUTPUT
 
       - uses: rzr/fediverse-action@master
         with:

From 6d2c04752cad824f5ab929288ab4e17d8ef00b3b Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 7 Nov 2025 10:44:49 +0100
Subject: [PATCH 326/530] Apply suggestions from code review

---
 nextflow.config | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index d9a10865..b49ba16f 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -184,8 +184,7 @@ includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !pa
 
 
 // Load nf-core/seqinspector custom profiles from different institutions.
-// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
-// includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/seqinspector.config" : "/dev/null"
+includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/seqinspector.config" : "/dev/null"
 
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
 // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled

From b2b74a90084bd9d2def861f8f4707720287b72f3 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 7 Nov 2025 10:49:40 +0100
Subject: [PATCH 327/530] remove last trace succeeded size

---
 tests/MiSeq.main.nf.test      | 4 ----
 tests/MiSeq.main.nf.test.snap | 6 ++----
 2 files changed, 2 insertions(+), 8 deletions(-)

diff --git a/tests/MiSeq.main.nf.test b/tests/MiSeq.main.nf.test
index dd57e94a..43ba4c75 100644
--- a/tests/MiSeq.main.nf.test
+++ b/tests/MiSeq.main.nf.test
@@ -62,8 +62,6 @@ nextflow_pipeline {
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
-                    // Number of successful tasks
-                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
                     // All stable path names, with a relative path
@@ -98,8 +96,6 @@ nextflow_pipeline {
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
-                    // Number of successful tasks
-                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
                     // All stable path names, with a relative path
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index b1174d1b..885a1e7a 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -1,7 +1,6 @@
 {
     "Miseq data test (skip all tools)": {
         "content": [
-            1,
             {
                 "Workflow": {
                     "nf-core/seqinspector": "v1.0dev"
@@ -30,7 +29,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-06T17:00:42.873781281"
+        "timestamp": "2025-11-07T10:48:01.699825922"
     },
     "MiSeq data test (single end reads)": {
         "content": [
@@ -182,7 +181,6 @@
     },
     "Miseq data test (skip fastqc)": {
         "content": [
-            5,
             {
                 "BWAMEM2_INDEX": {
                     "bwamem2": "2.2.1"
@@ -269,6 +267,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-06T17:10:07.50637781"
+        "timestamp": "2025-11-07T10:47:45.83823672"
     }
 }
\ No newline at end of file

From b119692a6fe525299295c87926ddf23cacfde8df Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 7 Nov 2025 11:20:56 +0100
Subject: [PATCH 328/530] fix snapshots

---
 ro-crate-metadata.json                        |  52 +--
 tests/MiSeq.main.nf.test.snap                 |  42 +-
 tests/MiSeq_PairedEnd.main.nf.test.snap       |  82 +++-
 tests/NovaSeq6000.main.nf.test.snap           | 172 +++++++-
 tests/NovaSeq6000.main_subsample.nf.test.snap | 388 +++++++++++++++++-
 5 files changed, 698 insertions(+), 38 deletions(-)

diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 1f0cc28e..56334299 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,8 +22,8 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2025-11-07T09:27:51+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->\n\n1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))\n2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n3. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "datePublished": "2025-11-07T10:20:35+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->\n\n1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))\n2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n3. Align reads to reference with ([`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2))\n4. Index aligned BAM files ([`SAMtools`](http://github.com/samtools))\n5. Create FASTA index ([`SAMtools`](http://github.com/samtools))\n6. Collect multiple QC metrics ([`Picard CollectMultipleMetrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html))\n7. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
                     "@id": "main.nf"
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#fbe02af1-e9dc-458e-a6f1-649522b5321b"
+                    "@id": "#b66d14a8-59db-4642-b2a8-9ae193c96008"
                 }
             ],
             "name": "nf-core/seqinspector"
@@ -127,21 +127,24 @@
                 "ComputationalWorkflow"
             ],
             "creator": [
+                {
+                    "@id": "https://orcid.org/0000-0003-2702-1103"
+                },
                 {
                     "@id": "https://orcid.org/0000-0003-1675-0677"
                 },
                 {
-                    "@id": "https://orcid.org/0000-0003-2702-1103"
+                    "@id": "https://orcid.org/0009-0004-5536-7210"
                 },
                 {
-                    "@id": "#89784800+kedhammar@users.noreply.github.com"
+                    "@id": "#max.u.garcia@gmail.com"
                 },
                 {
-                    "@id": "https://orcid.org/0009-0004-5536-7210"
+                    "@id": "#89784800+kedhammar@users.noreply.github.com"
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2025-11-07T10:27:51Z",
+            "dateModified": "2025-11-07T11:20:35Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -152,11 +155,6 @@
             "license": [
                 "MIT"
             ],
-            "maintainer": [
-                {
-                    "@id": "https://orcid.org/0000-0003-2702-1103"
-                }
-            ],
             "name": [
                 "nf-core/seqinspector"
             ],
@@ -187,11 +185,11 @@
             "version": "!>=25.04.0"
         },
         {
-            "@id": "#fbe02af1-e9dc-458e-a6f1-649522b5321b",
+            "@id": "#b66d14a8-59db-4642-b2a8-9ae193c96008",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#56ac1623-4e68-4598-9703-f769123f08c5"
+                    "@id": "#4a975f08-07ae-4c90-84d2-cefcf6352c88"
                 }
             ],
             "mainEntity": {
@@ -200,7 +198,7 @@
             "name": "Test suite for nf-core/seqinspector"
         },
         {
-            "@id": "#56ac1623-4e68-4598-9703-f769123f08c5",
+            "@id": "#4a975f08-07ae-4c90-84d2-cefcf6352c88",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/seqinspector",
             "resource": "repos/nf-core/seqinspector/actions/workflows/nf-test.yml",
@@ -328,12 +326,6 @@
             "name": "nf-core",
             "url": "https://nf-co.re/"
         },
-        {
-            "@id": "https://orcid.org/0000-0003-1675-0677",
-            "@type": "Person",
-            "email": "mahesh.binzer-panchal@nbis.se",
-            "name": "Mahesh Binzer-Panchal"
-        },
         {
             "@id": "https://orcid.org/0000-0003-2702-1103",
             "@type": "Person",
@@ -341,16 +333,28 @@
             "name": "Adrien Coulier"
         },
         {
-            "@id": "#89784800+kedhammar@users.noreply.github.com",
+            "@id": "https://orcid.org/0000-0003-1675-0677",
             "@type": "Person",
-            "email": "89784800+kedhammar@users.noreply.github.com",
-            "name": "Alfred Kedhammar"
+            "email": "mahesh.binzer-panchal@nbis.se",
+            "name": "Mahesh Binzer-Panchal"
         },
         {
             "@id": "https://orcid.org/0009-0004-5536-7210",
             "@type": "Person",
             "email": "agrimabhatt@n141-p117.eduroam.kth.se",
             "name": "Agrima Bhatt"
+        },
+        {
+            "@id": "#max.u.garcia@gmail.com",
+            "@type": "Person",
+            "email": "max.u.garcia@gmail.com",
+            "name": "Maxime U Garcia"
+        },
+        {
+            "@id": "#89784800+kedhammar@users.noreply.github.com",
+            "@type": "Person",
+            "email": "89784800+kedhammar@users.noreply.github.com",
+            "name": "Alfred Kedhammar"
         }
     ]
 }
\ No newline at end of file
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 6e5ce559..9851e445 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -111,6 +111,7 @@
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
                 "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
                 "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
                 "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
                 "multiqc/global_report/multiqc_data/picard_alignment_summary.txt",
@@ -135,6 +136,16 @@
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -149,6 +160,16 @@
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -163,6 +184,16 @@
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "picard_collectmultiplemetrics",
@@ -213,7 +244,8 @@
                 "multiqc_picard_quality_score_distribution.txt:md5,bad70b98811c4cbe4728f53334993703",
                 "multiqc_seqfu.txt:md5,8e6989a2392f599a09a5c3edf8119702",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
                 "picard_QualityScoreDistribution_histogram.txt:md5,bad70b98811c4cbe4728f53334993703",
                 "picard_alignment_readlength_plot.txt:md5,0fe7e17f1c58b7a6291bc1ff80fdfaa0",
                 "picard_alignment_summary.txt:md5,c770d3ee98dadaee77ef43967a974627",
@@ -235,7 +267,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T10:23:17.145777453"
+        "timestamp": "2025-11-07T11:14:40.189991111"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
@@ -299,6 +331,7 @@
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
                 "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
                 "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
                 "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
                 "multiqc/global_report/multiqc_data/picard_alignment_summary.txt",
@@ -391,7 +424,8 @@
                 "multiqc_picard_quality_score_distribution.txt:md5,bad70b98811c4cbe4728f53334993703",
                 "multiqc_seqfu.txt:md5,8e6989a2392f599a09a5c3edf8119702",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
                 "picard_QualityScoreDistribution_histogram.txt:md5,bad70b98811c4cbe4728f53334993703",
                 "picard_alignment_readlength_plot.txt:md5,0fe7e17f1c58b7a6291bc1ff80fdfaa0",
                 "picard_alignment_summary.txt:md5,c770d3ee98dadaee77ef43967a974627",
@@ -413,6 +447,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T10:47:45.83823672"
+        "timestamp": "2025-11-07T11:15:17.347135189"
     }
 }
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index 28d94c0f..728ed4d5 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -94,6 +94,7 @@
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
                 "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
                 "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
                 "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
                 "multiqc/global_report/multiqc_data/picard_alignment_summary_Aligned_Bases.txt",
@@ -118,6 +119,18 @@
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -131,6 +144,18 @@
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -144,6 +169,18 @@
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "multiqc/group_reports",
@@ -176,6 +213,7 @@
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/picard_alignment_readlength_plot.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/picard_alignment_summary_Aligned_Bases.txt",
@@ -200,6 +238,18 @@
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-cnt.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-pct.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-cnt.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-pct.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -213,6 +263,18 @@
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-cnt.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-pct.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-cnt.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-pct.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -226,6 +288,18 @@
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-cnt.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-pct.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-cnt.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-pct.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_report.html",
                 "picard_collectmultiplemetrics",
@@ -294,7 +368,8 @@
                 "multiqc_picard_quality_score_distribution.txt:md5,99be409e325619171b820d762dd023c0",
                 "multiqc_seqfu.txt:md5,1f1e063e4a509a26cee167c3b20389c0",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,f6514f14befb874ded5aed79caba3e7b",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,f6514f14befb874ded5aed79caba3e7b",
                 "picard_QualityScoreDistribution_histogram.txt:md5,99be409e325619171b820d762dd023c0",
                 "picard_alignment_readlength_plot.txt:md5,4172702f791d043135f21e3a227fe712",
                 "picard_alignment_summary_Aligned_Bases.txt:md5,a166c14210e17d3541482b500443f792",
@@ -325,7 +400,8 @@
                 "multiqc_picard_quality_score_distribution.txt:md5,99be409e325619171b820d762dd023c0",
                 "multiqc_seqfu.txt:md5,1f1e063e4a509a26cee167c3b20389c0",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,f6514f14befb874ded5aed79caba3e7b",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,f6514f14befb874ded5aed79caba3e7b",
                 "picard_QualityScoreDistribution_histogram.txt:md5,99be409e325619171b820d762dd023c0",
                 "picard_alignment_readlength_plot.txt:md5,4172702f791d043135f21e3a227fe712",
                 "picard_alignment_summary_Aligned_Bases.txt:md5,a166c14210e17d3541482b500443f792",
@@ -351,6 +427,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T10:24:43.782493978"
+        "timestamp": "2025-11-07T11:16:28.36937489"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index 64107c73..50a55e53 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -104,6 +104,7 @@
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
                 "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
                 "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
                 "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
                 "multiqc/global_report/multiqc_data/picard_alignment_summary.txt",
@@ -129,6 +130,16 @@
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -144,6 +155,16 @@
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -159,6 +180,16 @@
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "multiqc/group_reports",
@@ -193,6 +224,7 @@
                 "multiqc/group_reports/group1/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/group1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
                 "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
                 "multiqc/group_reports/group1/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
                 "multiqc/group_reports/group1/multiqc_data/picard_alignment_readlength_plot.txt",
                 "multiqc/group_reports/group1/multiqc_data/picard_alignment_summary.txt",
@@ -218,6 +250,16 @@
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -233,6 +275,16 @@
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/group1/multiqc_plots/svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -248,6 +300,16 @@
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/group1/multiqc_report.html",
                 "multiqc/group_reports/group2",
@@ -281,6 +343,7 @@
                 "multiqc/group_reports/group2/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/group2/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
                 "multiqc/group_reports/group2/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
                 "multiqc/group_reports/group2/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
                 "multiqc/group_reports/group2/multiqc_data/picard_alignment_readlength_plot.txt",
                 "multiqc/group_reports/group2/multiqc_data/picard_alignment_summary.txt",
@@ -306,6 +369,16 @@
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -321,6 +394,16 @@
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/group2/multiqc_plots/svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -336,6 +419,16 @@
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/group2/multiqc_report.html",
                 "multiqc/group_reports/lane1",
@@ -369,6 +462,7 @@
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/lane1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
                 "multiqc/group_reports/lane1/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
                 "multiqc/group_reports/lane1/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
                 "multiqc/group_reports/lane1/multiqc_data/picard_alignment_readlength_plot.txt",
                 "multiqc/group_reports/lane1/multiqc_data/picard_alignment_summary.txt",
@@ -394,6 +488,16 @@
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -409,6 +513,16 @@
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/lane1/multiqc_plots/svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -424,6 +538,16 @@
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/lane1/multiqc_report.html",
                 "multiqc/group_reports/test",
@@ -457,6 +581,7 @@
                 "multiqc/group_reports/test/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/test/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
                 "multiqc/group_reports/test/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
                 "multiqc/group_reports/test/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
                 "multiqc/group_reports/test/multiqc_data/picard_alignment_readlength_plot.txt",
                 "multiqc/group_reports/test/multiqc_data/picard_alignment_summary.txt",
@@ -482,6 +607,16 @@
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/test/multiqc_plots/png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -497,6 +632,16 @@
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/test/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/test/multiqc_plots/svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -512,6 +657,16 @@
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/test/multiqc_report.html",
                 "picard_collectmultiplemetrics",
@@ -619,7 +774,8 @@
                 "multiqc_picard_quality_score_distribution.txt:md5,182098ce1ff0a664d873c329d54189df",
                 "multiqc_seqfu.txt:md5,5b54a49079169985795537d83d58bdd9",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,ebf56fd9b3b127ff41211e3f79f18b42",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,ebf56fd9b3b127ff41211e3f79f18b42",
                 "picard_QualityScoreDistribution_histogram.txt:md5,182098ce1ff0a664d873c329d54189df",
                 "picard_alignment_readlength_plot.txt:md5,92ab5c6fbe67484da62626736b1b21d4",
                 "picard_alignment_summary.txt:md5,f54187e8515f9b7c32eabaf1f8702224",
@@ -650,7 +806,8 @@
                 "multiqc_picard_quality_score_distribution.txt:md5,59b955203209cfab3d2d21bdfe20997e",
                 "multiqc_seqfu.txt:md5,5579172a6f8ac09a5ffcb3ce6a99590e",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,c3f14084aedc511b9f0aa8410e7cb3b5",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,c3f14084aedc511b9f0aa8410e7cb3b5",
                 "picard_QualityScoreDistribution_histogram.txt:md5,59b955203209cfab3d2d21bdfe20997e",
                 "picard_alignment_readlength_plot.txt:md5,1f8b2f4df8bd5cf879b96cfb2be6d81c",
                 "picard_alignment_summary.txt:md5,0cfafd1ed1920270bb1a5d13bed51480",
@@ -681,7 +838,8 @@
                 "multiqc_picard_quality_score_distribution.txt:md5,140279eb5abac364c4d4c417105da620",
                 "multiqc_seqfu.txt:md5,b5434520fa5be5c98be5ed164a464d23",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,750eadc27875fc8141b64a90789c369f",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,750eadc27875fc8141b64a90789c369f",
                 "picard_QualityScoreDistribution_histogram.txt:md5,140279eb5abac364c4d4c417105da620",
                 "picard_alignment_readlength_plot.txt:md5,a39f6a39dad13dacc2134508dbbf172d",
                 "picard_alignment_summary.txt:md5,fec83821c097bc1850257ce36aa73e5f",
@@ -712,7 +870,8 @@
                 "multiqc_picard_quality_score_distribution.txt:md5,879a4470d08fe6d9b1796f46020fb5f5",
                 "multiqc_seqfu.txt:md5,e2e092852c011abe5ad75cdcd68b9383",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,96652e2e2d693488df9104e5ae8cb4a7",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,96652e2e2d693488df9104e5ae8cb4a7",
                 "picard_QualityScoreDistribution_histogram.txt:md5,879a4470d08fe6d9b1796f46020fb5f5",
                 "picard_alignment_readlength_plot.txt:md5,9b323aa8cd934d084e9c83cfa1da306b",
                 "picard_alignment_summary.txt:md5,4e8970d31940f5e9020851d62e63b2e2",
@@ -743,7 +902,8 @@
                 "multiqc_picard_quality_score_distribution.txt:md5,e9c3ade201964470d2d22569a400fa49",
                 "multiqc_seqfu.txt:md5,a1a0b9a0dde0c1c4fe184d44c675dcde",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,9e05b241aabe39232b5182cb59d8edd5",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,9e05b241aabe39232b5182cb59d8edd5",
                 "picard_QualityScoreDistribution_histogram.txt:md5,e9c3ade201964470d2d22569a400fa49",
                 "picard_alignment_readlength_plot.txt:md5,c2692fde9d899ad61297ad7043fd26b9",
                 "picard_alignment_summary.txt:md5,5996d5b4c94f16c0efd42e2df47e021e",
@@ -777,6 +937,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T10:25:42.576692828"
+        "timestamp": "2025-11-07T11:17:47.210647423"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index a539c846..cb936201 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -15,6 +15,15 @@
                 "FASTQSCREEN_FASTQSCREEN": {
                     "fastqscreen": "0.16.0"
                 },
+                "PICARD_COLLECTMULTIPLEMETRICS": {
+                    "picard": "3.4.0"
+                },
+                "SAMTOOLS_FAIDX": {
+                    "samtools": "1.22.1"
+                },
+                "SAMTOOLS_INDEX": {
+                    "samtools": "1.22.1"
+                },
                 "SEQFU_STATS": {
                     "seqfu": "1.20.3"
                 },
@@ -89,9 +98,26 @@
                 "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -107,6 +133,16 @@
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -122,6 +158,16 @@
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -137,6 +183,16 @@
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "multiqc/group_reports",
@@ -162,9 +218,26 @@
                 "multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group1/multiqc_plots",
                 "multiqc/group_reports/group1/multiqc_plots/pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -180,6 +253,16 @@
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -195,6 +278,16 @@
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/group1/multiqc_plots/svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -210,6 +303,16 @@
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/group1/multiqc_report.html",
                 "multiqc/group_reports/group2",
@@ -234,9 +337,26 @@
                 "multiqc/group_reports/group2/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group2/multiqc_plots",
                 "multiqc/group_reports/group2/multiqc_plots/pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -252,6 +372,16 @@
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -267,6 +397,16 @@
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/group2/multiqc_plots/svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -282,6 +422,16 @@
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/group2/multiqc_report.html",
                 "multiqc/group_reports/lane1",
@@ -306,9 +456,26 @@
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/lane1/multiqc_plots",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -324,6 +491,16 @@
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -339,6 +516,16 @@
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/lane1/multiqc_plots/svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -354,6 +541,16 @@
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/lane1/multiqc_report.html",
                 "multiqc/group_reports/test",
@@ -378,9 +575,26 @@
                 "multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/test/multiqc_plots",
                 "multiqc/group_reports/test/multiqc_plots/pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -396,6 +610,16 @@
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/test/multiqc_plots/png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -411,6 +635,16 @@
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/test/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/test/multiqc_plots/svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -426,10 +660,70 @@
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/test/multiqc_report.html",
+                "picard_collectmultiplemetrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "samtools_faidx",
+                "samtools_faidx/genome.fa.fai",
+                "samtools_faidx/genome.fa.sizes",
+                "samtools_index",
+                "samtools_index/Sample1_1.bam.bai",
+                "samtools_index/Sample23_3.bam.bai",
+                "samtools_index/SampleA_2.bam.bai",
+                "samtools_index/Undetermined_5.bam.bai",
+                "samtools_index/sampletest_4.bam.bai",
                 "seqfu_stats",
                 "seqfu_stats/Sample1_1_seqfu.tsv",
                 "seqfu_stats/Sample1_1_seqfu_mqc.txt",
@@ -483,7 +777,24 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
                 "multiqc_fastqc.txt:md5,aba942d1e6996b579f19798e5673f514",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,ae3f9e644215ac39d2eae114bd52a517",
+                "multiqc_picard_baseContent.txt:md5,8b2efc3fa06d2013348b35f9607292aa",
+                "multiqc_picard_quality_by_cycle.txt:md5,c2774038d1a0142746426e46f9f954dd",
+                "multiqc_picard_quality_score_distribution.txt:md5,792755ee794d375b85a57f58d879f0c6",
                 "multiqc_seqfu.txt:md5,5b54a49079169985795537d83d58bdd9",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,c2774038d1a0142746426e46f9f954dd",
+                "picard_QualityScoreDistribution_histogram.txt:md5,792755ee794d375b85a57f58d879f0c6",
+                "picard_alignment_readlength_plot.txt:md5,ebd1ff06394bd202b8190c46d560bc95",
+                "picard_alignment_summary.txt:md5,e507eccfa0a05b20705f99a3619dde29",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,597d0fd368eab8a21cd7f4a92965ecf6",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,ade1d92e5e6d3bfefd3695f103079b6c",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,af525e84f95ceb4b8496f734db2420fb",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,8b5ada27023f2545792fabbb69a07067",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,a472bba4490d7189df23f6b38a554448",
+                "picard_quality_by_cycle.txt:md5,83d68b4049173f8c9a37f58f1276adc1",
+                "picard_quality_score_distribution.txt:md5,42c08c8a51230d9ecccdad416c06f59c",
                 "fastq_screen_plot.txt:md5,c25d34568f10f131156294d31fbfa994",
                 "fastqc-status-check-heatmap.txt:md5,7ee494f345c09706513e65907788de02",
                 "fastqc_overrepresented_sequences_plot.txt:md5,ca9fa146e7b8a7f562fd79b521ba0f60",
@@ -498,7 +809,24 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
                 "multiqc_fastqc.txt:md5,ff996e1d3dc4a46e0c9535e54d51ccab",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,7bc3f6ef8f47e6f1e060f957025c98aa",
+                "multiqc_picard_baseContent.txt:md5,1426865fe8ee1a36f67636c28500a91c",
+                "multiqc_picard_quality_by_cycle.txt:md5,79bf9f861077de70ec28c9af01783876",
+                "multiqc_picard_quality_score_distribution.txt:md5,a3f8d1937e1f118800aa3d86c1b498c4",
                 "multiqc_seqfu.txt:md5,5579172a6f8ac09a5ffcb3ce6a99590e",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,79bf9f861077de70ec28c9af01783876",
+                "picard_QualityScoreDistribution_histogram.txt:md5,a3f8d1937e1f118800aa3d86c1b498c4",
+                "picard_alignment_readlength_plot.txt:md5,5aed5e7c1395a537bdce7163c93781bd",
+                "picard_alignment_summary.txt:md5,9d0d003456e08f78701e876d0238b5a6",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,73e910febe1ea4d08a9f4e49d6c10615",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,092e732bb44842f2da5416de158c1cc5",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,e81495fde738e2954483195fd0ccfb04",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,ed9ad958081a904a5584757f87b29eb2",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,2b4526a0b0977ebd7fbe326c6d51cf19",
+                "picard_quality_by_cycle.txt:md5,d53617c495e81e011996cd4e9f755e0a",
+                "picard_quality_score_distribution.txt:md5,05f9e89733e43b81acf593efc1a56180",
                 "fastq_screen_plot.txt:md5,44fca6453b0a3d0590271bd7a31cc740",
                 "fastqc-status-check-heatmap.txt:md5,b6872d9dbaa3cce396d48dc137076e53",
                 "fastqc_overrepresented_sequences_plot.txt:md5,19babef6996c0bfdf28e5df89368cbb1",
@@ -513,7 +841,24 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
                 "multiqc_fastqc.txt:md5,3df36ecfe76b25b0c22dcda84bce2b3b",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,4dc89e1a04843d44695ecc8d1f047ee8",
+                "multiqc_picard_baseContent.txt:md5,0a5f9d32dd3061ce4349518c47d69838",
+                "multiqc_picard_quality_by_cycle.txt:md5,ec59b472afc1242ff299011ba456e792",
+                "multiqc_picard_quality_score_distribution.txt:md5,1b8be76b60ee71aa36a98d34e433b9bf",
                 "multiqc_seqfu.txt:md5,b5434520fa5be5c98be5ed164a464d23",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,ec59b472afc1242ff299011ba456e792",
+                "picard_QualityScoreDistribution_histogram.txt:md5,1b8be76b60ee71aa36a98d34e433b9bf",
+                "picard_alignment_readlength_plot.txt:md5,72e0094fcd2546bee02a7ac65a3ea218",
+                "picard_alignment_summary.txt:md5,19586495e6d7904a2a4a7eb9ba17a412",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,a825de2b668791e58f6a4078e0b31483",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,59633faead8aa9027883481b0c7e22af",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,f02153a346f7e24f200bf06af2293352",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,0725af81caa647ec22050c573dfe8cb0",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,3536e6dcc7c7ed972b02d2945da75cb7",
+                "picard_quality_by_cycle.txt:md5,be127a96dd68c14077548d36c0507dc3",
+                "picard_quality_score_distribution.txt:md5,9e27b097f10cb9a9a95a3445b220d104",
                 "fastq_screen_plot.txt:md5,5f748d33a7a396547fe8c260b728aa06",
                 "fastqc-status-check-heatmap.txt:md5,bab59a0bd1d676d90cdd986fbba36b26",
                 "fastqc_overrepresented_sequences_plot.txt:md5,79cb259874c52b44f8c69b2075ee498e",
@@ -528,7 +873,24 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
                 "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,fa26e8b96faa1926d8f41fc3fe959ff7",
+                "multiqc_picard_baseContent.txt:md5,b9d72d8173cdc7649b44b80aa485477c",
+                "multiqc_picard_quality_by_cycle.txt:md5,062547fb888ed508dd1d5733d7bed22e",
+                "multiqc_picard_quality_score_distribution.txt:md5,dd5abab3a7141654fffa3946c50a039b",
                 "multiqc_seqfu.txt:md5,e2e092852c011abe5ad75cdcd68b9383",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,062547fb888ed508dd1d5733d7bed22e",
+                "picard_QualityScoreDistribution_histogram.txt:md5,dd5abab3a7141654fffa3946c50a039b",
+                "picard_alignment_readlength_plot.txt:md5,e5d397c216a0911a73dff5550fa7b1d7",
+                "picard_alignment_summary.txt:md5,ef16e8dbab178f44deebe0f4d321097b",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,8ada743b028ec78996f9dc40f1922941",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,c97859ee1641de9bff58dbd1e82fff20",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,ea86115ef2ca4ff4922486ceb6c6e1e8",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,07a3f1e6b1ed2bc55128fc2a0f46eb92",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,67ee93606c468a7eea7818b2f4b3389f",
+                "picard_quality_by_cycle.txt:md5,974b3baed160e9643f493df1d0ad5000",
+                "picard_quality_score_distribution.txt:md5,869d69ae4e243f0669f63b489563e4f1",
                 "fastq_screen_plot.txt:md5,8622e1dbd0fe62520af6096207b9775d",
                 "fastqc-status-check-heatmap.txt:md5,2a66f5d61b9eb579555905cd5954b04c",
                 "fastqc_overrepresented_sequences_plot.txt:md5,5cdefa954db6e46c286e2984a883eb18",
@@ -543,7 +905,31 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5",
                 "multiqc_fastqc.txt:md5,ce61b4ce4b1d76ec3f20de3bf0c9ec7f",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,55627d8016b72c37c104e03cc156862c",
+                "multiqc_picard_baseContent.txt:md5,974d83faa49711ab4ea1248c59e69393",
+                "multiqc_picard_quality_by_cycle.txt:md5,248ecaf269d8fef1e84ea06f98b6f6ba",
+                "multiqc_picard_quality_score_distribution.txt:md5,5e7e80654e12c500b15f8564ffb12b27",
                 "multiqc_seqfu.txt:md5,a1a0b9a0dde0c1c4fe184d44c675dcde",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,248ecaf269d8fef1e84ea06f98b6f6ba",
+                "picard_QualityScoreDistribution_histogram.txt:md5,5e7e80654e12c500b15f8564ffb12b27",
+                "picard_alignment_readlength_plot.txt:md5,23ff551a5a8eded1857356f38b19039c",
+                "picard_alignment_summary.txt:md5,c741b69e17ed84370732b567ae11c69c",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,fc37dd1ac805881a467b264a7dd76677",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,7993fd56aa542b71bc984cd36c489fd1",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,1bca639db2a2624727f7b6dd2aa1442e",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,a5f0903d77b6060676f7dda249b99738",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,102e653a543ac908ac9ec9b86412d73b",
+                "picard_quality_by_cycle.txt:md5,3d43fd5387c0dc728833c681ea4f73cc",
+                "picard_quality_score_distribution.txt:md5,9d9f1bb12316175cdb88d3ff70305428",
+                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
+                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
+                "Sample1_1.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
+                "Sample23_3.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
+                "SampleA_2.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
+                "Undetermined_5.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
+                "sampletest_4.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
                 "Sample1_1_seqfu.tsv:md5,269fabf8435defcd327aa69a050b7869",
                 "Sample1_1_seqfu_mqc.txt:md5,a354b0ed16b9cf84aa88f501d7740fd6",
                 "Sample23_3_seqfu.tsv:md5,6fdadbeeefccbf957f880d6852bf9676",
@@ -565,6 +951,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T10:26:40.559862265"
+        "timestamp": "2025-11-07T11:18:58.975063972"
     }
 }
\ No newline at end of file

From d45e427ca15b2291c91763696780f2d4652158bb Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 7 Nov 2025 11:37:26 +0100
Subject: [PATCH 329/530] fix snapshots

---
 ro-crate-metadata.json                        |  28 +-
 tests/MiSeq.main.nf.test.snap                 |  42 +-
 tests/MiSeq_PairedEnd.main.nf.test.snap       |  82 +++-
 tests/NovaSeq6000.main.nf.test.snap           | 172 +++++++-
 tests/NovaSeq6000.main_subsample.nf.test.snap | 398 +++++++++++++++++-
 5 files changed, 689 insertions(+), 33 deletions(-)

diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index a6d9804f..f70317aa 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,7 +22,7 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2025-11-07T09:27:51+00:00",
+            "datePublished": "2025-11-07T10:22:25+00:00",
             "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->\n\n1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))\n2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n3. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#fbe02af1-e9dc-458e-a6f1-649522b5321b"
+                    "@id": "#d89695e2-cd58-42f0-a4a4-947519967875"
                 }
             ],
             "name": "nf-core/seqinspector"
@@ -131,17 +131,17 @@
                     "@id": "https://orcid.org/0000-0003-1675-0677"
                 },
                 {
-                    "@id": "https://orcid.org/0000-0003-2702-1103"
+                    "@id": "https://orcid.org/0009-0004-5536-7210"
                 },
                 {
                     "@id": "#89784800+kedhammar@users.noreply.github.com"
                 },
                 {
-                    "@id": "https://orcid.org/0009-0004-5536-7210"
+                    "@id": "https://orcid.org/0000-0003-2702-1103"
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2025-11-07T10:27:51Z",
+            "dateModified": "2025-11-07T11:22:25Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -182,11 +182,11 @@
             "version": "!>=25.04.0"
         },
         {
-            "@id": "#fbe02af1-e9dc-458e-a6f1-649522b5321b",
+            "@id": "#d89695e2-cd58-42f0-a4a4-947519967875",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#56ac1623-4e68-4598-9703-f769123f08c5"
+                    "@id": "#716e19c0-1d90-4d48-a94b-aa1d6a590205"
                 }
             ],
             "mainEntity": {
@@ -195,7 +195,7 @@
             "name": "Test suite for nf-core/seqinspector"
         },
         {
-            "@id": "#56ac1623-4e68-4598-9703-f769123f08c5",
+            "@id": "#716e19c0-1d90-4d48-a94b-aa1d6a590205",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/seqinspector",
             "resource": "repos/nf-core/seqinspector/actions/workflows/nf-test.yml",
@@ -330,10 +330,10 @@
             "name": "Mahesh Binzer-Panchal"
         },
         {
-            "@id": "https://orcid.org/0000-0003-2702-1103",
+            "@id": "https://orcid.org/0009-0004-5536-7210",
             "@type": "Person",
-            "email": "adrien.coulier@medsci.uu.se",
-            "name": "Adrien Coulier"
+            "email": "agrimabhatt@Mac.home",
+            "name": "Agrima Bhatt"
         },
         {
             "@id": "#89784800+kedhammar@users.noreply.github.com",
@@ -342,10 +342,10 @@
             "name": "Alfred Kedhammar"
         },
         {
-            "@id": "https://orcid.org/0009-0004-5536-7210",
+            "@id": "https://orcid.org/0000-0003-2702-1103",
             "@type": "Person",
-            "email": "agrimabhatt@n141-p117.eduroam.kth.se",
-            "name": "Agrima Bhatt"
+            "email": "adrien.coulier@medsci.uu.se",
+            "name": "Adrien Coulier"
         }
     ]
 }
\ No newline at end of file
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index fcfdc5fe..61b512cf 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -111,6 +111,7 @@
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
                 "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
                 "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
                 "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
                 "multiqc/global_report/multiqc_data/picard_alignment_summary.txt",
@@ -135,6 +136,16 @@
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -149,6 +160,16 @@
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -163,6 +184,16 @@
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "picard_collectmultiplemetrics",
@@ -213,7 +244,8 @@
                 "multiqc_picard_quality_score_distribution.txt:md5,bad70b98811c4cbe4728f53334993703",
                 "multiqc_seqfu.txt:md5,8e6989a2392f599a09a5c3edf8119702",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
                 "picard_QualityScoreDistribution_histogram.txt:md5,bad70b98811c4cbe4728f53334993703",
                 "picard_alignment_readlength_plot.txt:md5,0fe7e17f1c58b7a6291bc1ff80fdfaa0",
                 "picard_alignment_summary.txt:md5,c770d3ee98dadaee77ef43967a974627",
@@ -235,7 +267,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T10:23:17.145777453"
+        "timestamp": "2025-11-07T11:23:15.112360835"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
@@ -299,6 +331,7 @@
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
                 "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
                 "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
                 "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
                 "multiqc/global_report/multiqc_data/picard_alignment_summary.txt",
@@ -391,7 +424,8 @@
                 "multiqc_picard_quality_score_distribution.txt:md5,bad70b98811c4cbe4728f53334993703",
                 "multiqc_seqfu.txt:md5,8e6989a2392f599a09a5c3edf8119702",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
                 "picard_QualityScoreDistribution_histogram.txt:md5,bad70b98811c4cbe4728f53334993703",
                 "picard_alignment_readlength_plot.txt:md5,0fe7e17f1c58b7a6291bc1ff80fdfaa0",
                 "picard_alignment_summary.txt:md5,c770d3ee98dadaee77ef43967a974627",
@@ -413,6 +447,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T10:47:45.83823672"
+        "timestamp": "2025-11-07T11:23:52.513224822"
     }
 }
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index fa227fe9..304abcc8 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -94,6 +94,7 @@
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
                 "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
                 "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
                 "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
                 "multiqc/global_report/multiqc_data/picard_alignment_summary_Aligned_Bases.txt",
@@ -118,6 +119,18 @@
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -131,6 +144,18 @@
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -144,6 +169,18 @@
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "multiqc/group_reports",
@@ -176,6 +213,7 @@
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/picard_alignment_readlength_plot.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/picard_alignment_summary_Aligned_Bases.txt",
@@ -200,6 +238,18 @@
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-cnt.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-pct.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-cnt.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-pct.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -213,6 +263,18 @@
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-cnt.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-pct.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-cnt.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-pct.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -226,6 +288,18 @@
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-cnt.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-pct.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-cnt.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-pct.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_report.html",
                 "picard_collectmultiplemetrics",
@@ -294,7 +368,8 @@
                 "multiqc_picard_quality_score_distribution.txt:md5,99be409e325619171b820d762dd023c0",
                 "multiqc_seqfu.txt:md5,1f1e063e4a509a26cee167c3b20389c0",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,f6514f14befb874ded5aed79caba3e7b",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,f6514f14befb874ded5aed79caba3e7b",
                 "picard_QualityScoreDistribution_histogram.txt:md5,99be409e325619171b820d762dd023c0",
                 "picard_alignment_readlength_plot.txt:md5,4172702f791d043135f21e3a227fe712",
                 "picard_alignment_summary_Aligned_Bases.txt:md5,a166c14210e17d3541482b500443f792",
@@ -325,7 +400,8 @@
                 "multiqc_picard_quality_score_distribution.txt:md5,99be409e325619171b820d762dd023c0",
                 "multiqc_seqfu.txt:md5,1f1e063e4a509a26cee167c3b20389c0",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,f6514f14befb874ded5aed79caba3e7b",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,f6514f14befb874ded5aed79caba3e7b",
                 "picard_QualityScoreDistribution_histogram.txt:md5,99be409e325619171b820d762dd023c0",
                 "picard_alignment_readlength_plot.txt:md5,4172702f791d043135f21e3a227fe712",
                 "picard_alignment_summary_Aligned_Bases.txt:md5,a166c14210e17d3541482b500443f792",
@@ -351,6 +427,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T10:24:43.782493978"
+        "timestamp": "2025-11-07T11:25:02.819346496"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index 240ba5f3..cefffe40 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -104,6 +104,7 @@
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
                 "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
                 "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
                 "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
                 "multiqc/global_report/multiqc_data/picard_alignment_summary.txt",
@@ -129,6 +130,16 @@
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -144,6 +155,16 @@
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -159,6 +180,16 @@
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "multiqc/group_reports",
@@ -193,6 +224,7 @@
                 "multiqc/group_reports/group1/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/group1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
                 "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
                 "multiqc/group_reports/group1/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
                 "multiqc/group_reports/group1/multiqc_data/picard_alignment_readlength_plot.txt",
                 "multiqc/group_reports/group1/multiqc_data/picard_alignment_summary.txt",
@@ -218,6 +250,16 @@
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -233,6 +275,16 @@
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/group1/multiqc_plots/svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -248,6 +300,16 @@
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/group1/multiqc_report.html",
                 "multiqc/group_reports/group2",
@@ -281,6 +343,7 @@
                 "multiqc/group_reports/group2/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/group2/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
                 "multiqc/group_reports/group2/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
                 "multiqc/group_reports/group2/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
                 "multiqc/group_reports/group2/multiqc_data/picard_alignment_readlength_plot.txt",
                 "multiqc/group_reports/group2/multiqc_data/picard_alignment_summary.txt",
@@ -306,6 +369,16 @@
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -321,6 +394,16 @@
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/group2/multiqc_plots/svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -336,6 +419,16 @@
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/group2/multiqc_report.html",
                 "multiqc/group_reports/lane1",
@@ -369,6 +462,7 @@
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/lane1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
                 "multiqc/group_reports/lane1/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
                 "multiqc/group_reports/lane1/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
                 "multiqc/group_reports/lane1/multiqc_data/picard_alignment_readlength_plot.txt",
                 "multiqc/group_reports/lane1/multiqc_data/picard_alignment_summary.txt",
@@ -394,6 +488,16 @@
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -409,6 +513,16 @@
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/lane1/multiqc_plots/svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -424,6 +538,16 @@
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/lane1/multiqc_report.html",
                 "multiqc/group_reports/test",
@@ -457,6 +581,7 @@
                 "multiqc/group_reports/test/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/test/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
                 "multiqc/group_reports/test/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
                 "multiqc/group_reports/test/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
                 "multiqc/group_reports/test/multiqc_data/picard_alignment_readlength_plot.txt",
                 "multiqc/group_reports/test/multiqc_data/picard_alignment_summary.txt",
@@ -482,6 +607,16 @@
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/test/multiqc_plots/png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -497,6 +632,16 @@
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/test/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/test/multiqc_plots/svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -512,6 +657,16 @@
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/test/multiqc_report.html",
                 "picard_collectmultiplemetrics",
@@ -619,7 +774,8 @@
                 "multiqc_picard_quality_score_distribution.txt:md5,182098ce1ff0a664d873c329d54189df",
                 "multiqc_seqfu.txt:md5,5b54a49079169985795537d83d58bdd9",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,ebf56fd9b3b127ff41211e3f79f18b42",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,ebf56fd9b3b127ff41211e3f79f18b42",
                 "picard_QualityScoreDistribution_histogram.txt:md5,182098ce1ff0a664d873c329d54189df",
                 "picard_alignment_readlength_plot.txt:md5,92ab5c6fbe67484da62626736b1b21d4",
                 "picard_alignment_summary.txt:md5,f54187e8515f9b7c32eabaf1f8702224",
@@ -650,7 +806,8 @@
                 "multiqc_picard_quality_score_distribution.txt:md5,59b955203209cfab3d2d21bdfe20997e",
                 "multiqc_seqfu.txt:md5,5579172a6f8ac09a5ffcb3ce6a99590e",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,c3f14084aedc511b9f0aa8410e7cb3b5",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,c3f14084aedc511b9f0aa8410e7cb3b5",
                 "picard_QualityScoreDistribution_histogram.txt:md5,59b955203209cfab3d2d21bdfe20997e",
                 "picard_alignment_readlength_plot.txt:md5,1f8b2f4df8bd5cf879b96cfb2be6d81c",
                 "picard_alignment_summary.txt:md5,0cfafd1ed1920270bb1a5d13bed51480",
@@ -681,7 +838,8 @@
                 "multiqc_picard_quality_score_distribution.txt:md5,140279eb5abac364c4d4c417105da620",
                 "multiqc_seqfu.txt:md5,b5434520fa5be5c98be5ed164a464d23",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,750eadc27875fc8141b64a90789c369f",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,750eadc27875fc8141b64a90789c369f",
                 "picard_QualityScoreDistribution_histogram.txt:md5,140279eb5abac364c4d4c417105da620",
                 "picard_alignment_readlength_plot.txt:md5,a39f6a39dad13dacc2134508dbbf172d",
                 "picard_alignment_summary.txt:md5,fec83821c097bc1850257ce36aa73e5f",
@@ -712,7 +870,8 @@
                 "multiqc_picard_quality_score_distribution.txt:md5,879a4470d08fe6d9b1796f46020fb5f5",
                 "multiqc_seqfu.txt:md5,e2e092852c011abe5ad75cdcd68b9383",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,96652e2e2d693488df9104e5ae8cb4a7",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,96652e2e2d693488df9104e5ae8cb4a7",
                 "picard_QualityScoreDistribution_histogram.txt:md5,879a4470d08fe6d9b1796f46020fb5f5",
                 "picard_alignment_readlength_plot.txt:md5,9b323aa8cd934d084e9c83cfa1da306b",
                 "picard_alignment_summary.txt:md5,4e8970d31940f5e9020851d62e63b2e2",
@@ -743,7 +902,8 @@
                 "multiqc_picard_quality_score_distribution.txt:md5,e9c3ade201964470d2d22569a400fa49",
                 "multiqc_seqfu.txt:md5,a1a0b9a0dde0c1c4fe184d44c675dcde",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,9e05b241aabe39232b5182cb59d8edd5",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,9e05b241aabe39232b5182cb59d8edd5",
                 "picard_QualityScoreDistribution_histogram.txt:md5,e9c3ade201964470d2d22569a400fa49",
                 "picard_alignment_readlength_plot.txt:md5,c2692fde9d899ad61297ad7043fd26b9",
                 "picard_alignment_summary.txt:md5,5996d5b4c94f16c0efd42e2df47e021e",
@@ -777,6 +937,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T10:25:42.576692828"
+        "timestamp": "2025-11-07T11:26:26.837592919"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index a539c846..bdd07de6 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -15,6 +15,15 @@
                 "FASTQSCREEN_FASTQSCREEN": {
                     "fastqscreen": "0.16.0"
                 },
+                "PICARD_COLLECTMULTIPLEMETRICS": {
+                    "picard": "3.4.0"
+                },
+                "SAMTOOLS_FAIDX": {
+                    "samtools": "1.22.1"
+                },
+                "SAMTOOLS_INDEX": {
+                    "samtools": "1.22.1"
+                },
                 "SEQFU_STATS": {
                     "seqfu": "1.20.3"
                 },
@@ -89,9 +98,26 @@
                 "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -107,6 +133,16 @@
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -122,6 +158,16 @@
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -137,6 +183,16 @@
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "multiqc/group_reports",
@@ -162,9 +218,26 @@
                 "multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group1/multiqc_plots",
                 "multiqc/group_reports/group1/multiqc_plots/pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -180,6 +253,16 @@
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -195,6 +278,16 @@
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/group1/multiqc_plots/svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -210,6 +303,16 @@
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/group1/multiqc_report.html",
                 "multiqc/group_reports/group2",
@@ -234,9 +337,26 @@
                 "multiqc/group_reports/group2/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group2/multiqc_plots",
                 "multiqc/group_reports/group2/multiqc_plots/pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -252,6 +372,16 @@
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -267,6 +397,16 @@
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/group2/multiqc_plots/svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -282,6 +422,16 @@
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/group2/multiqc_report.html",
                 "multiqc/group_reports/lane1",
@@ -306,9 +456,26 @@
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/lane1/multiqc_plots",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -324,6 +491,16 @@
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -339,6 +516,16 @@
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/lane1/multiqc_plots/svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -354,6 +541,16 @@
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/lane1/multiqc_report.html",
                 "multiqc/group_reports/test",
@@ -378,9 +575,26 @@
                 "multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/test/multiqc_plots",
                 "multiqc/group_reports/test/multiqc_plots/pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -396,6 +610,16 @@
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/test/multiqc_plots/png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -411,6 +635,16 @@
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/test/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/test/multiqc_plots/svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -426,10 +660,70 @@
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/test/multiqc_report.html",
+                "picard_collectmultiplemetrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "samtools_faidx",
+                "samtools_faidx/genome.fa.fai",
+                "samtools_faidx/genome.fa.sizes",
+                "samtools_index",
+                "samtools_index/Sample1_1.bam.bai",
+                "samtools_index/Sample23_3.bam.bai",
+                "samtools_index/SampleA_2.bam.bai",
+                "samtools_index/Undetermined_5.bam.bai",
+                "samtools_index/sampletest_4.bam.bai",
                 "seqfu_stats",
                 "seqfu_stats/Sample1_1_seqfu.tsv",
                 "seqfu_stats/Sample1_1_seqfu_mqc.txt",
@@ -454,11 +748,11 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "Sample1_1.bam:md5,a948b66ba258785fe12aea5d64136b05",
-                "Sample23_3.bam:md5,61e745916240193c0ecced45e6a0b054",
-                "SampleA_2.bam:md5,82a083dcf79d10110a39c736dde463de",
-                "Undetermined_5.bam:md5,6eb240ce5a28b26c48b72e7d84e976f8",
-                "sampletest_4.bam:md5,08e4ce7950bb8b0ae9e83b497991b9c9",
+                "Sample1_1.bam:md5,78344f8d3deffb9abb799382769e70eb",
+                "Sample23_3.bam:md5,74149a4daaf4ee5dfa2e93a3cc5b5009",
+                "SampleA_2.bam:md5,73d7fd05b1741af9871d2418f9f3732b",
+                "Undetermined_5.bam:md5,a3c99695f73e2024c13691b8f1f8905e",
+                "sampletest_4.bam:md5,c0790dc0f7e85a8cd2fb57cf9c9d29fb",
                 "Sample1_1_screen.png:md5,562256290643b51e4374c2225a15f463",
                 "Sample1_1_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
                 "Sample23_3_screen.png:md5,6bb2caf67b9b2ed25d3d5f32c343e9ab",
@@ -483,7 +777,24 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
                 "multiqc_fastqc.txt:md5,aba942d1e6996b579f19798e5673f514",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,ae3f9e644215ac39d2eae114bd52a517",
+                "multiqc_picard_baseContent.txt:md5,8b2efc3fa06d2013348b35f9607292aa",
+                "multiqc_picard_quality_by_cycle.txt:md5,c2774038d1a0142746426e46f9f954dd",
+                "multiqc_picard_quality_score_distribution.txt:md5,792755ee794d375b85a57f58d879f0c6",
                 "multiqc_seqfu.txt:md5,5b54a49079169985795537d83d58bdd9",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,c2774038d1a0142746426e46f9f954dd",
+                "picard_QualityScoreDistribution_histogram.txt:md5,792755ee794d375b85a57f58d879f0c6",
+                "picard_alignment_readlength_plot.txt:md5,ebd1ff06394bd202b8190c46d560bc95",
+                "picard_alignment_summary.txt:md5,e507eccfa0a05b20705f99a3619dde29",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,597d0fd368eab8a21cd7f4a92965ecf6",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,ade1d92e5e6d3bfefd3695f103079b6c",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,af525e84f95ceb4b8496f734db2420fb",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,8b5ada27023f2545792fabbb69a07067",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,a472bba4490d7189df23f6b38a554448",
+                "picard_quality_by_cycle.txt:md5,83d68b4049173f8c9a37f58f1276adc1",
+                "picard_quality_score_distribution.txt:md5,42c08c8a51230d9ecccdad416c06f59c",
                 "fastq_screen_plot.txt:md5,c25d34568f10f131156294d31fbfa994",
                 "fastqc-status-check-heatmap.txt:md5,7ee494f345c09706513e65907788de02",
                 "fastqc_overrepresented_sequences_plot.txt:md5,ca9fa146e7b8a7f562fd79b521ba0f60",
@@ -498,7 +809,24 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
                 "multiqc_fastqc.txt:md5,ff996e1d3dc4a46e0c9535e54d51ccab",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,7bc3f6ef8f47e6f1e060f957025c98aa",
+                "multiqc_picard_baseContent.txt:md5,1426865fe8ee1a36f67636c28500a91c",
+                "multiqc_picard_quality_by_cycle.txt:md5,79bf9f861077de70ec28c9af01783876",
+                "multiqc_picard_quality_score_distribution.txt:md5,a3f8d1937e1f118800aa3d86c1b498c4",
                 "multiqc_seqfu.txt:md5,5579172a6f8ac09a5ffcb3ce6a99590e",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,79bf9f861077de70ec28c9af01783876",
+                "picard_QualityScoreDistribution_histogram.txt:md5,a3f8d1937e1f118800aa3d86c1b498c4",
+                "picard_alignment_readlength_plot.txt:md5,5aed5e7c1395a537bdce7163c93781bd",
+                "picard_alignment_summary.txt:md5,9d0d003456e08f78701e876d0238b5a6",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,73e910febe1ea4d08a9f4e49d6c10615",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,092e732bb44842f2da5416de158c1cc5",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,e81495fde738e2954483195fd0ccfb04",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,ed9ad958081a904a5584757f87b29eb2",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,2b4526a0b0977ebd7fbe326c6d51cf19",
+                "picard_quality_by_cycle.txt:md5,d53617c495e81e011996cd4e9f755e0a",
+                "picard_quality_score_distribution.txt:md5,05f9e89733e43b81acf593efc1a56180",
                 "fastq_screen_plot.txt:md5,44fca6453b0a3d0590271bd7a31cc740",
                 "fastqc-status-check-heatmap.txt:md5,b6872d9dbaa3cce396d48dc137076e53",
                 "fastqc_overrepresented_sequences_plot.txt:md5,19babef6996c0bfdf28e5df89368cbb1",
@@ -513,7 +841,24 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
                 "multiqc_fastqc.txt:md5,3df36ecfe76b25b0c22dcda84bce2b3b",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,4dc89e1a04843d44695ecc8d1f047ee8",
+                "multiqc_picard_baseContent.txt:md5,0a5f9d32dd3061ce4349518c47d69838",
+                "multiqc_picard_quality_by_cycle.txt:md5,ec59b472afc1242ff299011ba456e792",
+                "multiqc_picard_quality_score_distribution.txt:md5,1b8be76b60ee71aa36a98d34e433b9bf",
                 "multiqc_seqfu.txt:md5,b5434520fa5be5c98be5ed164a464d23",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,ec59b472afc1242ff299011ba456e792",
+                "picard_QualityScoreDistribution_histogram.txt:md5,1b8be76b60ee71aa36a98d34e433b9bf",
+                "picard_alignment_readlength_plot.txt:md5,72e0094fcd2546bee02a7ac65a3ea218",
+                "picard_alignment_summary.txt:md5,19586495e6d7904a2a4a7eb9ba17a412",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,a825de2b668791e58f6a4078e0b31483",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,59633faead8aa9027883481b0c7e22af",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,f02153a346f7e24f200bf06af2293352",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,0725af81caa647ec22050c573dfe8cb0",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,3536e6dcc7c7ed972b02d2945da75cb7",
+                "picard_quality_by_cycle.txt:md5,be127a96dd68c14077548d36c0507dc3",
+                "picard_quality_score_distribution.txt:md5,9e27b097f10cb9a9a95a3445b220d104",
                 "fastq_screen_plot.txt:md5,5f748d33a7a396547fe8c260b728aa06",
                 "fastqc-status-check-heatmap.txt:md5,bab59a0bd1d676d90cdd986fbba36b26",
                 "fastqc_overrepresented_sequences_plot.txt:md5,79cb259874c52b44f8c69b2075ee498e",
@@ -528,7 +873,24 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
                 "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,fa26e8b96faa1926d8f41fc3fe959ff7",
+                "multiqc_picard_baseContent.txt:md5,b9d72d8173cdc7649b44b80aa485477c",
+                "multiqc_picard_quality_by_cycle.txt:md5,062547fb888ed508dd1d5733d7bed22e",
+                "multiqc_picard_quality_score_distribution.txt:md5,dd5abab3a7141654fffa3946c50a039b",
                 "multiqc_seqfu.txt:md5,e2e092852c011abe5ad75cdcd68b9383",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,062547fb888ed508dd1d5733d7bed22e",
+                "picard_QualityScoreDistribution_histogram.txt:md5,dd5abab3a7141654fffa3946c50a039b",
+                "picard_alignment_readlength_plot.txt:md5,e5d397c216a0911a73dff5550fa7b1d7",
+                "picard_alignment_summary.txt:md5,ef16e8dbab178f44deebe0f4d321097b",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,8ada743b028ec78996f9dc40f1922941",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,c97859ee1641de9bff58dbd1e82fff20",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,ea86115ef2ca4ff4922486ceb6c6e1e8",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,07a3f1e6b1ed2bc55128fc2a0f46eb92",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,67ee93606c468a7eea7818b2f4b3389f",
+                "picard_quality_by_cycle.txt:md5,974b3baed160e9643f493df1d0ad5000",
+                "picard_quality_score_distribution.txt:md5,869d69ae4e243f0669f63b489563e4f1",
                 "fastq_screen_plot.txt:md5,8622e1dbd0fe62520af6096207b9775d",
                 "fastqc-status-check-heatmap.txt:md5,2a66f5d61b9eb579555905cd5954b04c",
                 "fastqc_overrepresented_sequences_plot.txt:md5,5cdefa954db6e46c286e2984a883eb18",
@@ -543,7 +905,31 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5",
                 "multiqc_fastqc.txt:md5,ce61b4ce4b1d76ec3f20de3bf0c9ec7f",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,55627d8016b72c37c104e03cc156862c",
+                "multiqc_picard_baseContent.txt:md5,974d83faa49711ab4ea1248c59e69393",
+                "multiqc_picard_quality_by_cycle.txt:md5,248ecaf269d8fef1e84ea06f98b6f6ba",
+                "multiqc_picard_quality_score_distribution.txt:md5,5e7e80654e12c500b15f8564ffb12b27",
                 "multiqc_seqfu.txt:md5,a1a0b9a0dde0c1c4fe184d44c675dcde",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,248ecaf269d8fef1e84ea06f98b6f6ba",
+                "picard_QualityScoreDistribution_histogram.txt:md5,5e7e80654e12c500b15f8564ffb12b27",
+                "picard_alignment_readlength_plot.txt:md5,23ff551a5a8eded1857356f38b19039c",
+                "picard_alignment_summary.txt:md5,c741b69e17ed84370732b567ae11c69c",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,fc37dd1ac805881a467b264a7dd76677",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,7993fd56aa542b71bc984cd36c489fd1",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,1bca639db2a2624727f7b6dd2aa1442e",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,a5f0903d77b6060676f7dda249b99738",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,102e653a543ac908ac9ec9b86412d73b",
+                "picard_quality_by_cycle.txt:md5,3d43fd5387c0dc728833c681ea4f73cc",
+                "picard_quality_score_distribution.txt:md5,9d9f1bb12316175cdb88d3ff70305428",
+                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
+                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
+                "Sample1_1.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
+                "Sample23_3.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
+                "SampleA_2.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
+                "Undetermined_5.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
+                "sampletest_4.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
                 "Sample1_1_seqfu.tsv:md5,269fabf8435defcd327aa69a050b7869",
                 "Sample1_1_seqfu_mqc.txt:md5,a354b0ed16b9cf84aa88f501d7740fd6",
                 "Sample23_3_seqfu.tsv:md5,6fdadbeeefccbf957f880d6852bf9676",
@@ -565,6 +951,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T10:26:40.559862265"
+        "timestamp": "2025-11-07T11:27:47.629823181"
     }
 }
\ No newline at end of file

From 17bbc7418440cdfd2b9bf992d21f3ea96ef77bdd Mon Sep 17 00:00:00 2001
From: agrima2010 <163723002+agrima2010@users.noreply.github.com>
Date: Tue, 18 Nov 2025 12:37:02 +0000
Subject: [PATCH 330/530] .bai files in the same folder as bam files

---
 conf/modules.config |  2 +-
 modules.json        | 15 ---------------
 2 files changed, 1 insertion(+), 16 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 7477a104..ed977394 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -67,7 +67,7 @@ process {
 
     withName: 'SAMTOOLS_INDEX' {
         publishDir = [
-            path: { "${params.outdir}/samtools_index" },
+            path: { "${params.outdir}/bwamem2_mem" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
diff --git a/modules.json b/modules.json
index 9e18ccf2..97910dd0 100644
--- a/modules.json
+++ b/modules.json
@@ -57,21 +57,6 @@
                         "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
                         "installed_by": ["modules"]
                     },
-                    "picard/collectmultiplemetrics": {
-                        "branch": "master",
-                        "git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255",
-                        "installed_by": ["modules"]
-                    },
-                    "samtools/faidx": {
-                        "branch": "master",
-                        "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
-                        "installed_by": ["modules"]
-                    },
-                    "samtools/index": {
-                        "branch": "master",
-                        "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
-                        "installed_by": ["modules"]
-                    },
                     "seqfu/stats": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",

From ce94600b2c87e01b9db12dec64d0a264611e4273 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 19 Nov 2025 12:07:41 +0100
Subject: [PATCH 331/530] update snapshots

---
 tests/MiSeq.main.nf.test.snap                 | 14 +++++------
 tests/MiSeq_PairedEnd.main.nf.test.snap       | 11 ++++-----
 tests/NovaSeq6000.main.nf.test.snap           | 23 +++++++++----------
 tests/NovaSeq6000.main_subsample.nf.test.snap | 23 +++++++++----------
 4 files changed, 33 insertions(+), 38 deletions(-)

diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 61b512cf..c6bb7d56 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -73,6 +73,7 @@
                 "bwamem2_index/bwamem2/genome.fa.pac",
                 "bwamem2_mem",
                 "bwamem2_mem/SAMPLE_SINGLE_END_1.bam",
+                "bwamem2_mem/SAMPLE_SINGLE_END_1.bam.bai",
                 "fastqc",
                 "fastqc/SAMPLE_SINGLE_END_1_fastqc.html",
                 "fastqc/SAMPLE_SINGLE_END_1_fastqc.zip",
@@ -210,8 +211,6 @@
                 "samtools_faidx",
                 "samtools_faidx/genome.fa.fai",
                 "samtools_faidx/genome.fa.sizes",
-                "samtools_index",
-                "samtools_index/SAMPLE_SINGLE_END_1.bam.bai",
                 "seqfu_stats",
                 "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu.tsv",
                 "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu_mqc.txt"
@@ -223,6 +222,7 @@
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
                 "SAMPLE_SINGLE_END_1.bam:md5,ed3f6acd94560448218a288623c810e6",
+                "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
                 "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
                 "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
                 "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
@@ -258,7 +258,6 @@
                 "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
-                "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
                 "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,f65c868e562291647d539090698ba5eb",
                 "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
             ]
@@ -267,7 +266,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T11:23:15.112360835"
+        "timestamp": "2025-11-19T11:58:59.644568276"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
@@ -308,6 +307,7 @@
                 "bwamem2_index/bwamem2/genome.fa.pac",
                 "bwamem2_mem",
                 "bwamem2_mem/SAMPLE_SINGLE_END_1.bam",
+                "bwamem2_mem/SAMPLE_SINGLE_END_1.bam.bai",
                 "fastqscreen",
                 "fastqscreen/SAMPLE_SINGLE_END_1_screen.html",
                 "fastqscreen/SAMPLE_SINGLE_END_1_screen.png",
@@ -400,8 +400,6 @@
                 "samtools_faidx",
                 "samtools_faidx/genome.fa.fai",
                 "samtools_faidx/genome.fa.sizes",
-                "samtools_index",
-                "samtools_index/SAMPLE_SINGLE_END_1.bam.bai",
                 "seqfu_stats",
                 "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu.tsv",
                 "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu_mqc.txt"
@@ -413,6 +411,7 @@
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
                 "SAMPLE_SINGLE_END_1.bam:md5,ed3f6acd94560448218a288623c810e6",
+                "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
                 "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
                 "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
                 "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
@@ -438,7 +437,6 @@
                 "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
-                "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
                 "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,f65c868e562291647d539090698ba5eb",
                 "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
             ]
@@ -447,6 +445,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T11:23:52.513224822"
+        "timestamp": "2025-11-19T11:48:51.553934925"
     }
 }
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index 304abcc8..448d2107 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -41,7 +41,9 @@
                 "bwamem2_index/bwamem2/genome.fa.pac",
                 "bwamem2_mem",
                 "bwamem2_mem/SAMPLE_PAIRED_END_1_1.bam",
+                "bwamem2_mem/SAMPLE_PAIRED_END_1_1.bam.bai",
                 "bwamem2_mem/SAMPLE_PAIRED_END_2_2.bam",
+                "bwamem2_mem/SAMPLE_PAIRED_END_2_2.bam.bai",
                 "fastqc",
                 "fastqc/SAMPLE_PAIRED_END_1_1_1_fastqc.html",
                 "fastqc/SAMPLE_PAIRED_END_1_1_1_fastqc.zip",
@@ -324,9 +326,6 @@
                 "samtools_faidx",
                 "samtools_faidx/genome.fa.fai",
                 "samtools_faidx/genome.fa.sizes",
-                "samtools_index",
-                "samtools_index/SAMPLE_PAIRED_END_1_1.bam.bai",
-                "samtools_index/SAMPLE_PAIRED_END_2_2.bam.bai",
                 "seqfu_stats",
                 "seqfu_stats/SAMPLE_PAIRED_END_1_1_seqfu.tsv",
                 "seqfu_stats/SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt",
@@ -340,7 +339,9 @@
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
                 "SAMPLE_PAIRED_END_1_1.bam:md5,fc37892fea524a3c1799f51605c3cc5f",
+                "SAMPLE_PAIRED_END_1_1.bam.bai:md5,82724835c47f8e1d1a86e13ef469b464",
                 "SAMPLE_PAIRED_END_2_2.bam:md5,d68128596af24e2349004a082d507cea",
+                "SAMPLE_PAIRED_END_2_2.bam.bai:md5,3c4bdff0f906f2234fdeee8eea719210",
                 "SAMPLE_PAIRED_END_1_1_1_screen.png:md5,f52ddd0e65f23f68dd8d58d5453417db",
                 "SAMPLE_PAIRED_END_1_1_1_screen.txt:md5,921b08eeb461a2aa1bd42bba53900f70",
                 "SAMPLE_PAIRED_END_1_1_2_screen.png:md5,908f4fceea8aa546106efdaa7ca78f7d",
@@ -415,8 +416,6 @@
                 "picard_quality_score_distribution.txt:md5,ecde9f0e859a6eecc5cea75a156c632d",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
-                "SAMPLE_PAIRED_END_1_1.bam.bai:md5,82724835c47f8e1d1a86e13ef469b464",
-                "SAMPLE_PAIRED_END_2_2.bam.bai:md5,3c4bdff0f906f2234fdeee8eea719210",
                 "SAMPLE_PAIRED_END_1_1_seqfu.tsv:md5,bbd911ff3fa43212dfd4c5a5872dbdb6",
                 "SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt:md5,cd60f746b6749cc66213d031af1b931c",
                 "SAMPLE_PAIRED_END_2_2_seqfu.tsv:md5,152566a128dd657da33465b4966b5799",
@@ -427,6 +426,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T11:25:02.819346496"
+        "timestamp": "2025-11-19T11:50:04.344118749"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index cefffe40..5a98f0b3 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -41,10 +41,15 @@
                 "bwamem2_index/bwamem2/genome.fa.pac",
                 "bwamem2_mem",
                 "bwamem2_mem/Sample1_1.bam",
+                "bwamem2_mem/Sample1_1.bam.bai",
                 "bwamem2_mem/Sample23_3.bam",
+                "bwamem2_mem/Sample23_3.bam.bai",
                 "bwamem2_mem/SampleA_2.bam",
+                "bwamem2_mem/SampleA_2.bam.bai",
                 "bwamem2_mem/Undetermined_5.bam",
+                "bwamem2_mem/Undetermined_5.bam.bai",
                 "bwamem2_mem/sampletest_4.bam",
+                "bwamem2_mem/sampletest_4.bam.bai",
                 "fastqc",
                 "fastqc/Sample1_1_fastqc.html",
                 "fastqc/Sample1_1_fastqc.zip",
@@ -715,12 +720,6 @@
                 "samtools_faidx",
                 "samtools_faidx/genome.fa.fai",
                 "samtools_faidx/genome.fa.sizes",
-                "samtools_index",
-                "samtools_index/Sample1_1.bam.bai",
-                "samtools_index/Sample23_3.bam.bai",
-                "samtools_index/SampleA_2.bam.bai",
-                "samtools_index/Undetermined_5.bam.bai",
-                "samtools_index/sampletest_4.bam.bai",
                 "seqfu_stats",
                 "seqfu_stats/Sample1_1_seqfu.tsv",
                 "seqfu_stats/Sample1_1_seqfu_mqc.txt",
@@ -740,10 +739,15 @@
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
                 "Sample1_1.bam:md5,39c3c91eedd90307315acec7aa0b9a35",
+                "Sample1_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
                 "Sample23_3.bam:md5,3d536a6680470138eb361eed198a8efd",
+                "Sample23_3.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
                 "SampleA_2.bam:md5,ad691a2590eed5bbc56a56dd24493e4e",
+                "SampleA_2.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
                 "Undetermined_5.bam:md5,06077f7de3641b4b86e08f6a9cdb5a97",
+                "Undetermined_5.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
                 "sampletest_4.bam:md5,7dcb21eb9fec77b862af33e692678dbd",
+                "sampletest_4.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
                 "Sample1_1_screen.png:md5,562256290643b51e4374c2225a15f463",
                 "Sample1_1_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
                 "Sample23_3_screen.png:md5,6bb2caf67b9b2ed25d3d5f32c343e9ab",
@@ -916,11 +920,6 @@
                 "picard_quality_score_distribution.txt:md5,1c17c01ef54a6062a8f1ca8408d32958",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
-                "Sample1_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
-                "Sample23_3.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
-                "SampleA_2.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
-                "Undetermined_5.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
-                "sampletest_4.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
                 "Sample1_1_seqfu.tsv:md5,269fabf8435defcd327aa69a050b7869",
                 "Sample1_1_seqfu_mqc.txt:md5,a354b0ed16b9cf84aa88f501d7740fd6",
                 "Sample23_3_seqfu.tsv:md5,6fdadbeeefccbf957f880d6852bf9676",
@@ -937,6 +936,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T11:26:26.837592919"
+        "timestamp": "2025-11-19T11:51:22.144399289"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index bdd07de6..e946b153 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -44,10 +44,15 @@
                 "bwamem2_index/bwamem2/genome.fa.pac",
                 "bwamem2_mem",
                 "bwamem2_mem/Sample1_1.bam",
+                "bwamem2_mem/Sample1_1.bam.bai",
                 "bwamem2_mem/Sample23_3.bam",
+                "bwamem2_mem/Sample23_3.bam.bai",
                 "bwamem2_mem/SampleA_2.bam",
+                "bwamem2_mem/SampleA_2.bam.bai",
                 "bwamem2_mem/Undetermined_5.bam",
+                "bwamem2_mem/Undetermined_5.bam.bai",
                 "bwamem2_mem/sampletest_4.bam",
+                "bwamem2_mem/sampletest_4.bam.bai",
                 "fastqc",
                 "fastqc/Sample1_1_fastqc.html",
                 "fastqc/Sample1_1_fastqc.zip",
@@ -718,12 +723,6 @@
                 "samtools_faidx",
                 "samtools_faidx/genome.fa.fai",
                 "samtools_faidx/genome.fa.sizes",
-                "samtools_index",
-                "samtools_index/Sample1_1.bam.bai",
-                "samtools_index/Sample23_3.bam.bai",
-                "samtools_index/SampleA_2.bam.bai",
-                "samtools_index/Undetermined_5.bam.bai",
-                "samtools_index/sampletest_4.bam.bai",
                 "seqfu_stats",
                 "seqfu_stats/Sample1_1_seqfu.tsv",
                 "seqfu_stats/Sample1_1_seqfu_mqc.txt",
@@ -749,10 +748,15 @@
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
                 "Sample1_1.bam:md5,78344f8d3deffb9abb799382769e70eb",
+                "Sample1_1.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
                 "Sample23_3.bam:md5,74149a4daaf4ee5dfa2e93a3cc5b5009",
+                "Sample23_3.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
                 "SampleA_2.bam:md5,73d7fd05b1741af9871d2418f9f3732b",
+                "SampleA_2.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
                 "Undetermined_5.bam:md5,a3c99695f73e2024c13691b8f1f8905e",
+                "Undetermined_5.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
                 "sampletest_4.bam:md5,c0790dc0f7e85a8cd2fb57cf9c9d29fb",
+                "sampletest_4.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
                 "Sample1_1_screen.png:md5,562256290643b51e4374c2225a15f463",
                 "Sample1_1_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
                 "Sample23_3_screen.png:md5,6bb2caf67b9b2ed25d3d5f32c343e9ab",
@@ -925,11 +929,6 @@
                 "picard_quality_score_distribution.txt:md5,9d9f1bb12316175cdb88d3ff70305428",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
-                "Sample1_1.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
-                "Sample23_3.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
-                "SampleA_2.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
-                "Undetermined_5.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
-                "sampletest_4.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
                 "Sample1_1_seqfu.tsv:md5,269fabf8435defcd327aa69a050b7869",
                 "Sample1_1_seqfu_mqc.txt:md5,a354b0ed16b9cf84aa88f501d7740fd6",
                 "Sample23_3_seqfu.tsv:md5,6fdadbeeefccbf957f880d6852bf9676",
@@ -951,6 +950,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T11:27:47.629823181"
+        "timestamp": "2025-11-19T11:52:38.751102766"
     }
 }
\ No newline at end of file

From b9c09ed11ebb1a70da45e3053e4173032a70eebe Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 19 Nov 2025 12:15:03 +0100
Subject: [PATCH 332/530] update modules

---
 modules.json                                  |  14 +-
 modules/nf-core/bowtie2/build/environment.yml |  10 +-
 modules/nf-core/bowtie2/build/main.nf         |   4 +-
 .../nf-core/bowtie2/build/tests/main.nf.test  |   4 +-
 .../bowtie2/build/tests/main.nf.test.snap     |   8 +-
 modules/nf-core/bowtie2/build/tests/tags.yml  |   2 -
 modules/nf-core/bwamem2/mem/bwamem2-mem.diff  |  18 ++
 modules/nf-core/bwamem2/mem/environment.yml   |   6 +-
 modules/nf-core/bwamem2/mem/main.nf           |   4 +-
 .../bwamem2/mem/tests/main.nf.test.snap       |  40 ++---
 .../buildfromindex/environment.yml            |   2 +-
 .../fastqscreen/buildfromindex/meta.yml       |   3 +-
 .../buildfromindex/tests/main.nf.test.snap    |  46 +++--
 .../fastqscreen/buildfromindex/tests/tags.yml |   2 -
 modules/nf-core/multiqc/main.nf               |   1 +
 modules/nf-core/multiqc/meta.yml              |   4 +-
 modules/nf-core/samtools/faidx/meta.yml       |   3 +-
 .../nf-core/samtools/faidx/tests/main.nf.test |   2 +-
 modules/nf-core/seqfu/stats/environment.yml   |   2 +-
 modules/nf-core/seqfu/stats/main.nf           |  15 +-
 .../nf-core/seqfu/stats/tests/main.nf.test    |  49 +++--
 .../seqfu/stats/tests/main.nf.test.snap       | 170 ++++++++++++++----
 modules/nf-core/seqfu/stats/tests/tags.yml    |   2 -
 modules/nf-core/seqtk/sample/environment.yml  |   2 +
 modules/nf-core/seqtk/sample/main.nf          |   2 +-
 modules/nf-core/seqtk/sample/meta.yml         |   8 +-
 .../nf-core/seqtk/sample/tests/main.nf.test   |  22 +++
 .../seqtk/sample/tests/main.nf.test.snap      |  31 ++++
 .../seqtk/sample/tests/standard.config        |   2 +-
 modules/nf-core/seqtk/sample/tests/tags.yml   |   2 -
 30 files changed, 347 insertions(+), 133 deletions(-)
 delete mode 100644 modules/nf-core/bowtie2/build/tests/tags.yml
 create mode 100644 modules/nf-core/bwamem2/mem/bwamem2-mem.diff
 delete mode 100644 modules/nf-core/fastqscreen/buildfromindex/tests/tags.yml
 delete mode 100644 modules/nf-core/seqfu/stats/tests/tags.yml
 delete mode 100644 modules/nf-core/seqtk/sample/tests/tags.yml

diff --git a/modules.json b/modules.json
index 97910dd0..c6c029f3 100644
--- a/modules.json
+++ b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "bowtie2/build": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["modules"]
                     },
                     "bwamem2/index": {
@@ -17,7 +17,7 @@
                     },
                     "bwamem2/mem": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "d86336f3e7ae0d5f76c67b0859409769cfeb2af2",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/bwamem2/mem/bwamem2-mem.diff"
                     },
@@ -28,7 +28,7 @@
                     },
                     "fastqscreen/buildfromindex": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["modules"]
                     },
                     "fastqscreen/fastqscreen": {
@@ -39,7 +39,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "af27af1be706e6a2bb8fe454175b0cdf77f47b49",
+                        "git_sha": "82a79183037a403ad1b6714e5dbcff25500efaf6",
                         "installed_by": ["modules"]
                     },
                     "picard/collectmultiplemetrics": {
@@ -49,7 +49,7 @@
                     },
                     "samtools/faidx": {
                         "branch": "master",
-                        "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
                         "installed_by": ["modules"]
                     },
                     "samtools/index": {
@@ -59,12 +59,12 @@
                     },
                     "seqfu/stats": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
                         "installed_by": ["modules"]
                     },
                     "seqtk/sample": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
                         "installed_by": ["modules"]
                     }
                 }
diff --git a/modules/nf-core/bowtie2/build/environment.yml b/modules/nf-core/bowtie2/build/environment.yml
index e590f7ce..066ff52e 100644
--- a/modules/nf-core/bowtie2/build/environment.yml
+++ b/modules/nf-core/bowtie2/build/environment.yml
@@ -1,5 +1,13 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bowtie2=2.5.2
+  # renovate: datasource=conda depName=bioconda/bowtie2
+  - bioconda::bowtie2=2.5.4
+  # renovate: datasource=conda depName=bioconda/htslib
+  - bioconda::htslib=1.21
+  # renovate: datasource=conda depName=bioconda/samtools
+  - bioconda::samtools=1.21
+  - conda-forge::pigz=2.8
diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf
index 9e2e0e5e..fb7effec 100644
--- a/modules/nf-core/bowtie2/build/main.nf
+++ b/modules/nf-core/bowtie2/build/main.nf
@@ -4,8 +4,8 @@ process BOWTIE2_BUILD {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bowtie2:2.5.2--py39h6fed5c7_0' :
-        'biocontainers/bowtie2:2.5.2--py39h6fed5c7_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b41b403e81883126c3227fc45840015538e8e2212f13abc9ae84e4b98891d51c/data' :
+        'community.wave.seqera.io/library/bowtie2_htslib_samtools_pigz:edeb13799090a2a6' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/nf-core/bowtie2/build/tests/main.nf.test b/modules/nf-core/bowtie2/build/tests/main.nf.test
index 16376025..ee94c19c 100644
--- a/modules/nf-core/bowtie2/build/tests/main.nf.test
+++ b/modules/nf-core/bowtie2/build/tests/main.nf.test
@@ -1,7 +1,7 @@
 nextflow_process {
 
     name "Test Process BOWTIE2_BUILD"
-    script "modules/nf-core/bowtie2/build/main.nf"
+    script "../main.nf"
     process "BOWTIE2_BUILD"
     tag "modules"
     tag "modules_nfcore"
@@ -15,7 +15,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ],
-                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
                 """
             }
diff --git a/modules/nf-core/bowtie2/build/tests/main.nf.test.snap b/modules/nf-core/bowtie2/build/tests/main.nf.test.snap
index 6875e021..ea5711e4 100644
--- a/modules/nf-core/bowtie2/build/tests/main.nf.test.snap
+++ b/modules/nf-core/bowtie2/build/tests/main.nf.test.snap
@@ -18,7 +18,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,1df11e9b82891527271c889c880d3974"
+                    "versions.yml:md5,d136fb9c16f0a9fb2ae804b2a5fbc09c"
                 ],
                 "index": [
                     [
@@ -36,10 +36,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,1df11e9b82891527271c889c880d3974"
+                    "versions.yml:md5,d136fb9c16f0a9fb2ae804b2a5fbc09c"
                 ]
             }
         ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.02.1"
+        },
         "timestamp": "2023-11-23T11:51:01.107681997"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bowtie2/build/tests/tags.yml b/modules/nf-core/bowtie2/build/tests/tags.yml
deleted file mode 100644
index 81aa61da..00000000
--- a/modules/nf-core/bowtie2/build/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-bowtie2/build:
-  - modules/nf-core/bowtie2/build/**
diff --git a/modules/nf-core/bwamem2/mem/bwamem2-mem.diff b/modules/nf-core/bwamem2/mem/bwamem2-mem.diff
new file mode 100644
index 00000000..be5074e8
--- /dev/null
+++ b/modules/nf-core/bwamem2/mem/bwamem2-mem.diff
@@ -0,0 +1,18 @@
+Changes in component 'nf-core/bwamem2/mem'
+'modules/nf-core/bwamem2/mem/meta.yml' is unchanged
+'modules/nf-core/bwamem2/mem/environment.yml' is unchanged
+Changes in 'bwamem2/mem/main.nf':
+--- modules/nf-core/bwamem2/mem/main.nf
++++ modules/nf-core/bwamem2/mem/main.nf
+@@ -1,6 +1,6 @@
+ process BWAMEM2_MEM {
+     tag "$meta.id"
+-    label 'process_high'
++    label 'process_low'
+ 
+     conda "${moduleDir}/environment.yml"
+     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+
+'modules/nf-core/bwamem2/mem/tests/main.nf.test' is unchanged
+'modules/nf-core/bwamem2/mem/tests/main.nf.test.snap' is unchanged
+************************************************************
diff --git a/modules/nf-core/bwamem2/mem/environment.yml b/modules/nf-core/bwamem2/mem/environment.yml
index c069e281..f3637444 100644
--- a/modules/nf-core/bwamem2/mem/environment.yml
+++ b/modules/nf-core/bwamem2/mem/environment.yml
@@ -6,8 +6,8 @@ channels:
 
 dependencies:
   # renovate: datasource=conda depName=bioconda/bwa-mem2
-  - bwa-mem2=2.2.1
+  - bwa-mem2=2.3
   # renovate: datasource=conda depName=bioconda/htslib
-  - htslib=1.21
+  - htslib=1.22.1
   # renovate: datasource=conda depName=bioconda/samtools
-  - samtools=1.21
+  - samtools=1.22.1
diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf
index ad510447..e12a68b0 100644
--- a/modules/nf-core/bwamem2/mem/main.nf
+++ b/modules/nf-core/bwamem2/mem/main.nf
@@ -4,8 +4,8 @@ process BWAMEM2_MEM {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9ac054213e67b3c9308e409b459080bbe438f8fd6c646c351bc42887f35a42e7/data' :
-        'community.wave.seqera.io/library/bwa-mem2_htslib_samtools:e1f420694f8e42bd' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e0/e05ce34b46ad42810eb29f74e4e304c0cb592b2ca15572929ed8bbaee58faf01/data' :
+        'community.wave.seqera.io/library/bwa-mem2_htslib_samtools:db98f81f55b64113' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap b/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap
index ec90701f..b7d40a68 100644
--- a/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap
+++ b/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap
@@ -1,17 +1,17 @@
 {
     "sarscov2 - [fastq1, fastq2], index, fasta, false": {
         "content": [
-            "9505760d66e1d5a5d34ab79a98228c6",
+            "e414c2d48e2e44c2c52c20ecd88e8bd8",
             "57aeef88ed701a8ebc8e2f0a381b2a6",
             [
-                "versions.yml:md5,ca1b1dcf82b92fb0751816fca16a477a"
+                "versions.yml:md5,3574188ab1f33fd99cff9f5562dfb885"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-03-27T10:57:52.782442426"
+        "timestamp": "2025-09-23T11:44:52.73673293"
     },
     "sarscov2 - [fastq1, fastq2], index, fasta, true - stub": {
         "content": [
@@ -44,7 +44,7 @@
                     ]
                 ],
                 "5": [
-                    "versions.yml:md5,ca1b1dcf82b92fb0751816fca16a477a"
+                    "versions.yml:md5,3574188ab1f33fd99cff9f5562dfb885"
                 ],
                 "bam": [
                     [
@@ -74,56 +74,56 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,ca1b1dcf82b92fb0751816fca16a477a"
+                    "versions.yml:md5,3574188ab1f33fd99cff9f5562dfb885"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-03-27T10:58:37.140104324"
+        "timestamp": "2025-09-23T11:45:14.834888709"
     },
     "sarscov2 - [fastq1, fastq2], index, fasta, true": {
         "content": [
-            "e0c38d5772ca5f4d5d9999f4477e933c",
+            "716ed1ef39deaad346ca7cf86e08f959",
             "af8628d9df18b2d3d4f6fd47ef2bb872",
             [
-                "versions.yml:md5,ca1b1dcf82b92fb0751816fca16a477a"
+                "versions.yml:md5,3574188ab1f33fd99cff9f5562dfb885"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-03-27T10:58:19.047052261"
+        "timestamp": "2025-09-23T11:45:04.750057645"
     },
     "sarscov2 - fastq, index, fasta, false": {
         "content": [
-            "58d05395bbb819e929885bde415947ae",
+            "283a83f604f3f5338acedfee349dccf4",
             "798439cbd7fd81cbcc5078022dc5479d",
             [
-                "versions.yml:md5,ca1b1dcf82b92fb0751816fca16a477a"
+                "versions.yml:md5,3574188ab1f33fd99cff9f5562dfb885"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-03-27T10:56:53.456559296"
+        "timestamp": "2025-09-23T11:44:28.57550711"
     },
     "sarscov2 - fastq, index, fasta, true": {
         "content": [
-            "276189f6f003f99a87664e74fad2893d",
+            "ed99048bb552cac58e39923b550b6d5b",
             "94fcf617f5b994584c4e8d4044e16b4f",
             [
-                "versions.yml:md5,ca1b1dcf82b92fb0751816fca16a477a"
+                "versions.yml:md5,3574188ab1f33fd99cff9f5562dfb885"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-03-27T10:57:21.949711746"
+        "timestamp": "2025-09-23T11:44:40.437183765"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/fastqscreen/buildfromindex/environment.yml b/modules/nf-core/fastqscreen/buildfromindex/environment.yml
index 85764e0d..3b3ba521 100644
--- a/modules/nf-core/fastqscreen/buildfromindex/environment.yml
+++ b/modules/nf-core/fastqscreen/buildfromindex/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::fastq-screen=0.15.3"
+  - bioconda::fastq-screen=0.15.3
diff --git a/modules/nf-core/fastqscreen/buildfromindex/meta.yml b/modules/nf-core/fastqscreen/buildfromindex/meta.yml
index c986c255..0291620b 100644
--- a/modules/nf-core/fastqscreen/buildfromindex/meta.yml
+++ b/modules/nf-core/fastqscreen/buildfromindex/meta.yml
@@ -27,8 +27,7 @@ output:
   database:
     - FastQ_Screen_Genomes:
         type: directory
-        description: fastq screen database folder containing config file and index
-          folders
+        description: fastq screen database folder containing config file and index folders
         pattern: "FastQ_Screen_Genomes"
   versions:
     - versions.yml:
diff --git a/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test.snap b/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test.snap
index 0fe7d7d1..a485079b 100644
--- a/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test.snap
+++ b/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "database": {
+    "sarscov2 - human": {
         "content": [
             [
                 [
@@ -21,25 +21,49 @@
                     ],
                     "fastq_screen.conf:md5,ca56e866c7006a46bdfe4e751e787265"
                 ]
+            ],
+            [
+                "versions.yml:md5,c2bcf85b00046c72d5dccd2dba8ac35c"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "25.02.1"
         },
-        "timestamp": "2024-05-01T20:37:34.647221"
+        "timestamp": "2025-03-25T12:58:36.506586801"
     },
-    "versions": {
+    "sarscov2 - human": {
         "content": [
+            [
+                [
+                    [
+                        "genome.1.bt2:md5,cbe3d0bbea55bc57c99b4bfa25b5fbdf",
+                        "genome.2.bt2:md5,47b153cd1319abc88dda532462651fcf",
+                        "genome.3.bt2:md5,4ed93abba181d8dfab2e303e33114777",
+                        "genome.4.bt2:md5,c25be5f8b0378abf7a58c8a880b87626",
+                        "genome.rev.1.bt2:md5,52be6950579598a990570fbcf5372184",
+                        "genome.rev.2.bt2:md5,e3b4ef343dea4dd571642010a7d09597"
+                    ],
+                    [
+                        "genome.1.bt2:md5,2fbc8eeaf480f03b3a2362a782fa5755",
+                        "genome.2.bt2:md5,a5300e3cf590d4cd8bd5521cac6337d6",
+                        "genome.3.bt2:md5,d2a7a0e1c9891e847a15781c0695b84e",
+                        "genome.4.bt2:md5,a55dc4b09e3e00586de6963800c95b9a",
+                        "genome.rev.1.bt2:md5,93c07f7d04e5da6bf1322ad5f46ac806",
+                        "genome.rev.2.bt2:md5,c3fa30132c0c9b9bc7868059e8e23466"
+                    ],
+                    "fastq_screen.conf:md5,ca56e866c7006a46bdfe4e751e787265"
+                ]
+            ],
             [
                 "versions.yml:md5,c2bcf85b00046c72d5dccd2dba8ac35c"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-01T20:37:35.126085"
+        "timestamp": "2025-03-25T08:34:46.992911211"
     },
     "sarscov2 - human - stub": {
         "content": [
@@ -63,9 +87,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-05-01T20:39:14.913696"
+        "timestamp": "2025-03-25T08:35:14.073325807"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/fastqscreen/buildfromindex/tests/tags.yml b/modules/nf-core/fastqscreen/buildfromindex/tests/tags.yml
deleted file mode 100644
index 9c98e870..00000000
--- a/modules/nf-core/fastqscreen/buildfromindex/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-fastqscreen/buildfromindex:
-  - "modules/nf-core/fastqscreen/buildfromindex/**"
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index c1158fb0..5d0780af 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -52,6 +52,7 @@ process MULTIQC {
     stub:
     """
     mkdir multiqc_data
+    touch multiqc_data/.stub
     mkdir multiqc_plots
     touch multiqc_report.html
 
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index e15333f6..ce30eb73 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -1,6 +1,6 @@
 name: multiqc
-description: Aggregate results from bioinformatics analyses across many samples
-  into a single report
+description: Aggregate results from bioinformatics analyses across many samples into
+  a single report
 keywords:
   - QC
   - bioinformatics tools
diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml
index 31a78efe..b7a2e0c1 100644
--- a/modules/nf-core/samtools/faidx/meta.yml
+++ b/modules/nf-core/samtools/faidx/meta.yml
@@ -1,6 +1,5 @@
 name: samtools_faidx
-description: Index FASTA file, and optionally generate a file of chromosome
-  sizes
+description: Index FASTA file, and optionally generate a file of chromosome sizes
 keywords:
   - index
   - fasta
diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test b/modules/nf-core/samtools/faidx/tests/main.nf.test
index 64219b7d..a505abc1 100644
--- a/modules/nf-core/samtools/faidx/tests/main.nf.test
+++ b/modules/nf-core/samtools/faidx/tests/main.nf.test
@@ -216,4 +216,4 @@ nextflow_process {
         }
     }
 
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/seqfu/stats/environment.yml b/modules/nf-core/seqfu/stats/environment.yml
index 8fa07dfc..210e292b 100644
--- a/modules/nf-core/seqfu/stats/environment.yml
+++ b/modules/nf-core/seqfu/stats/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::seqfu=1.20.3"
+  - bioconda::seqfu=1.22.3
diff --git a/modules/nf-core/seqfu/stats/main.nf b/modules/nf-core/seqfu/stats/main.nf
index 0f8bb3e2..ced2451c 100644
--- a/modules/nf-core/seqfu/stats/main.nf
+++ b/modules/nf-core/seqfu/stats/main.nf
@@ -4,18 +4,17 @@ process SEQFU_STATS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqfu:1.20.3--h1eb128b_0':
-        'biocontainers/seqfu:1.20.3--h1eb128b_0' }"
-
+        'https://depot.galaxyproject.org/singularity/seqfu:1.22.3--hfd12232_2':
+        'biocontainers/seqfu:1.22.3--hfd12232_2' }"
 
     input:
     // stats can get one or more fasta or fastq files
     tuple val(meta), path(files)
 
     output:
-    tuple val(meta), path("*.tsv")    ,  emit: stats
+    tuple val(meta), path("*.tsv")    , emit: stats
     tuple val(meta), path("*_mqc.txt"), emit: multiqc
-    path "versions.yml"               ,  emit: versions
+    path "versions.yml"               , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -40,12 +39,14 @@ process SEQFU_STATS {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
+    echo $args
+
+    touch ${prefix}.tsv
     touch ${prefix}_mqc.txt
-    seqfu stats ${prefix}_mqc.txt > ${prefix}.tsv
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        seqfu: \$(samtools --version |& sed '1!d ; s/samtools //')
+        seqfu: \$(seqfu version)
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/seqfu/stats/tests/main.nf.test b/modules/nf-core/seqfu/stats/tests/main.nf.test
index b889b2bb..3d13b05b 100644
--- a/modules/nf-core/seqfu/stats/tests/main.nf.test
+++ b/modules/nf-core/seqfu/stats/tests/main.nf.test
@@ -9,14 +9,13 @@ nextflow_process {
     tag "seqfu"
     tag "seqfu/stats"
 
-    
     test("seqfu stats - faa") {
         // test with 1 FAA file (with  multiple sequences of different length)
         when {
             process {
                 """
                 input[0] = [
-                    [ id:'test' ], 
+                    [ id:'test_faa' ],
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true)
                 ]
                 """
@@ -26,12 +25,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert process.out.stats },
-                { assert process.out.multiqc },
-                { assert process.out.stats.size() == 1 },
-                { assert snapshot(process.out.versions).match("versions-single") },
-                { assert snapshot(process.out.stats).match("stats-single") },
-                { assert path(process.out.stats.get(0).get(1)).md5 == "26141ef87ad8a6f59a6f283cc0a06fda" }
+                { assert snapshot(process.out).match() }
             )
         }
 
@@ -43,7 +37,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-                            [ id:'test' ],
+                            [ id:'test_multiple' ],
                             [
                                 file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true),
                                 file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
@@ -58,15 +52,34 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert process.out.stats },
-                { assert process.out.multiqc },
-                { assert process.out.stats.size() == 1 },
-                { assert path(process.out.versions[0]).readLines()[1].contains('.') },
-                { assert snapshot(process.out.stats).match("stats-multi") },
-                { assert snapshot(process.out.stats).md5().match("multi-lines") },
-                { assert path(process.out.stats[0][1]).readLines()[0] ==  'File\t#Seq\tTotal bp\tAvg\tN50\tN75\tN90\tauN\tMin\tMax' },
-                { assert path(process.out.multiqc[0][1]).readLines().join('\n').contains('genome.fasta') },
-                { assert path(process.out.multiqc[0][1]).readLines().join('\n').contains('proteome.fasta') }              
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("seqfu stats - faa - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_stub' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success},
+                { assert snapshot(
+                    process.out,
+                    process.out.versions.collect{ path(it).yaml }
+                ).match() }
             )
         }
 
diff --git a/modules/nf-core/seqfu/stats/tests/main.nf.test.snap b/modules/nf-core/seqfu/stats/tests/main.nf.test.snap
index 8049c827..30b16993 100644
--- a/modules/nf-core/seqfu/stats/tests/main.nf.test.snap
+++ b/modules/nf-core/seqfu/stats/tests/main.nf.test.snap
@@ -1,56 +1,156 @@
 {
-    "versions-single": {
+    "seqfu stats - faa - stub": {
         "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_stub"
+                        },
+                        "test_stub.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test_stub"
+                        },
+                        "test_stub_mqc.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,7e7581ee4a87fd1f9969628ae050e689"
+                ],
+                "multiqc": [
+                    [
+                        {
+                            "id": "test_stub"
+                        },
+                        "test_stub_mqc.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test_stub"
+                        },
+                        "test_stub.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7e7581ee4a87fd1f9969628ae050e689"
+                ]
+            },
             [
-                "versions.yml:md5,fd11b4665f68f22e7ad4c646ad3c56cd"
+                {
+                    "SEQFU_STATS": {
+                        "seqfu": "1.22.3"
+                    }
+                }
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-19T20:21:50.896221522"
-    },
-    "multi-lines": {
-        "content": "d5ab14ce74939f856edc64c6a8d250d3",
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-03-19T20:22:03.775940585"
+        "timestamp": "2025-09-24T12:51:50.35812127"
     },
-    "stats-single": {
+    "seqfu stats - faa": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.tsv:md5,26141ef87ad8a6f59a6f283cc0a06fda"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_faa"
+                        },
+                        "test_faa.tsv:md5,0d6bf2cc788f7828761440a1689cac04"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test_faa"
+                        },
+                        "test_faa_mqc.txt:md5,8f3c2edaf1ea5be912c9f99b21b2856c"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,7e7581ee4a87fd1f9969628ae050e689"
+                ],
+                "multiqc": [
+                    [
+                        {
+                            "id": "test_faa"
+                        },
+                        "test_faa_mqc.txt:md5,8f3c2edaf1ea5be912c9f99b21b2856c"
+                    ]
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test_faa"
+                        },
+                        "test_faa.tsv:md5,0d6bf2cc788f7828761440a1689cac04"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7e7581ee4a87fd1f9969628ae050e689"
                 ]
-            ]
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-03-19T20:21:50.937732021"
+        "timestamp": "2025-09-24T12:52:03.19664223"
     },
-    "stats-multi": {
+    "seqfu stats - multiple files": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.tsv:md5,98102573ecf7e3b9e53db1c6e0f02b06"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_multiple"
+                        },
+                        "test_multiple.tsv:md5,d016de3d84187a06c8e19b8dabccb3ae"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test_multiple"
+                        },
+                        "test_multiple_mqc.txt:md5,dbc6e762eebbf756cd0687807de60445"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,7e7581ee4a87fd1f9969628ae050e689"
+                ],
+                "multiqc": [
+                    [
+                        {
+                            "id": "test_multiple"
+                        },
+                        "test_multiple_mqc.txt:md5,dbc6e762eebbf756cd0687807de60445"
+                    ]
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test_multiple"
+                        },
+                        "test_multiple.tsv:md5,d016de3d84187a06c8e19b8dabccb3ae"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7e7581ee4a87fd1f9969628ae050e689"
                 ]
-            ]
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-03-19T20:22:03.681146614"
+        "timestamp": "2025-09-24T12:52:11.315174611"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/seqfu/stats/tests/tags.yml b/modules/nf-core/seqfu/stats/tests/tags.yml
deleted file mode 100644
index 2685ed43..00000000
--- a/modules/nf-core/seqfu/stats/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-seqfu/stats:
-  - "modules/nf-core/seqfu/stats/**"
diff --git a/modules/nf-core/seqtk/sample/environment.yml b/modules/nf-core/seqtk/sample/environment.yml
index 693aa5c1..b1d11cbd 100644
--- a/modules/nf-core/seqtk/sample/environment.yml
+++ b/modules/nf-core/seqtk/sample/environment.yml
@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
diff --git a/modules/nf-core/seqtk/sample/main.nf b/modules/nf-core/seqtk/sample/main.nf
index ea9b839e..0c2aaeda 100644
--- a/modules/nf-core/seqtk/sample/main.nf
+++ b/modules/nf-core/seqtk/sample/main.nf
@@ -20,7 +20,7 @@ process SEQTK_SAMPLE {
     script:
     def args   = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    if (!(args ==~ /.*-s[0-9]+.*/)) {
+    if (!(args ==~ /.*\ -s\ ?[0-9]+.*/)) {
         args += " -s100"
     }
     if ( !sample_size ) {
diff --git a/modules/nf-core/seqtk/sample/meta.yml b/modules/nf-core/seqtk/sample/meta.yml
index 29d95f2a..ed1f3325 100644
--- a/modules/nf-core/seqtk/sample/meta.yml
+++ b/modules/nf-core/seqtk/sample/meta.yml
@@ -6,8 +6,8 @@ keywords:
   - reads
 tools:
   - seqtk:
-      description: Seqtk is a fast and lightweight tool for processing sequences
-        in the FASTA or FASTQ format. Seqtk sample command subsamples sequences.
+      description: Seqtk is a fast and lightweight tool for processing sequences in
+        the FASTA or FASTQ format. Seqtk sample command subsamples sequences.
       homepage: https://github.com/lh3/seqtk
       documentation: https://docs.csc.fi/apps/seqtk/
       tool_dev_url: https://github.com/lh3/seqtk
@@ -25,8 +25,8 @@ input:
         pattern: "*.{fastq.gz}"
         ontologies: []
     - sample_size:
-        type: integer
-        description: Number of reads to sample.
+        type: float
+        description: Fraction (<1.0) or number (>=1) of reads to sample.
 output:
   reads:
     - - meta:
diff --git a/modules/nf-core/seqtk/sample/tests/main.nf.test b/modules/nf-core/seqtk/sample/tests/main.nf.test
index c121c9d9..2152ecd4 100644
--- a/modules/nf-core/seqtk/sample/tests/main.nf.test
+++ b/modules/nf-core/seqtk/sample/tests/main.nf.test
@@ -77,4 +77,26 @@ nextflow_process {
         }
     }
 
+    test("sarscov2_sample_singleend_frac") {
+
+        when {
+            process {
+                """
+                input[0] =  [
+                                [ id:'test', single_end:true ],
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                                0.5
+                            ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
 }
diff --git a/modules/nf-core/seqtk/sample/tests/main.nf.test.snap b/modules/nf-core/seqtk/sample/tests/main.nf.test.snap
index a9fec3c4..aa6991e6 100644
--- a/modules/nf-core/seqtk/sample/tests/main.nf.test.snap
+++ b/modules/nf-core/seqtk/sample/tests/main.nf.test.snap
@@ -91,5 +91,36 @@
             }
         ],
         "timestamp": "2024-02-22T15:58:29.474491"
+    },
+    "sarscov2_sample_singleend_frac": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.sampled_test_1.fastq.gz:md5,7552511dcd914f5183d80fae459bf917"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.sampled_test_1.fastq.gz:md5,7552511dcd914f5183d80fae459bf917"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806"
+                ]
+            }
+        ],
+        "timestamp": "2025-07-15T09:48:30.275951"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/seqtk/sample/tests/standard.config b/modules/nf-core/seqtk/sample/tests/standard.config
index b2dd4b9f..8d1db62f 100644
--- a/modules/nf-core/seqtk/sample/tests/standard.config
+++ b/modules/nf-core/seqtk/sample/tests/standard.config
@@ -3,4 +3,4 @@ process {
         ext.args = '-s100'
         ext.prefix = { "${meta.id}.sampled" }
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/seqtk/sample/tests/tags.yml b/modules/nf-core/seqtk/sample/tests/tags.yml
deleted file mode 100644
index e5d113b8..00000000
--- a/modules/nf-core/seqtk/sample/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-seqtk/sample:
-  - "modules/nf-core/seqtk/sample/**"

From 8e76c46f58517b171afbb5c4c996d5bf05a7d1cd Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 19 Nov 2025 12:23:16 +0100
Subject: [PATCH 333/530] update snapshots once again

---
 ro-crate-metadata.json                        | 30 ++++++------
 tests/MiSeq.main.nf.test.snap                 | 28 +++++------
 tests/MiSeq_PairedEnd.main.nf.test.snap       | 22 ++++-----
 tests/NovaSeq6000.main.nf.test.snap           | 46 +++++++++----------
 tests/NovaSeq6000.main_subsample.nf.test.snap | 46 +++++++++----------
 tests/PromethION.main.nf.test.snap            |  6 +--
 6 files changed, 89 insertions(+), 89 deletions(-)

diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index f70317aa..4846575a 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,7 +22,7 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2025-11-07T10:22:25+00:00",
+            "datePublished": "2025-11-19T11:23:02+00:00",
             "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->\n\n1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))\n2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n3. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#d89695e2-cd58-42f0-a4a4-947519967875"
+                    "@id": "#bd95d18d-7f91-4566-b59b-6538c02da3ab"
                 }
             ],
             "name": "nf-core/seqinspector"
@@ -130,18 +130,18 @@
                 {
                     "@id": "https://orcid.org/0000-0003-1675-0677"
                 },
-                {
-                    "@id": "https://orcid.org/0009-0004-5536-7210"
-                },
                 {
                     "@id": "#89784800+kedhammar@users.noreply.github.com"
                 },
                 {
                     "@id": "https://orcid.org/0000-0003-2702-1103"
+                },
+                {
+                    "@id": "https://orcid.org/0009-0004-5536-7210"
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2025-11-07T11:22:25Z",
+            "dateModified": "2025-11-19T12:23:02Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -182,11 +182,11 @@
             "version": "!>=25.04.0"
         },
         {
-            "@id": "#d89695e2-cd58-42f0-a4a4-947519967875",
+            "@id": "#bd95d18d-7f91-4566-b59b-6538c02da3ab",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#716e19c0-1d90-4d48-a94b-aa1d6a590205"
+                    "@id": "#4c91a9a9-4868-4f2d-b90a-660d84bc358f"
                 }
             ],
             "mainEntity": {
@@ -195,7 +195,7 @@
             "name": "Test suite for nf-core/seqinspector"
         },
         {
-            "@id": "#716e19c0-1d90-4d48-a94b-aa1d6a590205",
+            "@id": "#4c91a9a9-4868-4f2d-b90a-660d84bc358f",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/seqinspector",
             "resource": "repos/nf-core/seqinspector/actions/workflows/nf-test.yml",
@@ -329,12 +329,6 @@
             "email": "mahesh.binzer-panchal@nbis.se",
             "name": "Mahesh Binzer-Panchal"
         },
-        {
-            "@id": "https://orcid.org/0009-0004-5536-7210",
-            "@type": "Person",
-            "email": "agrimabhatt@Mac.home",
-            "name": "Agrima Bhatt"
-        },
         {
             "@id": "#89784800+kedhammar@users.noreply.github.com",
             "@type": "Person",
@@ -346,6 +340,12 @@
             "@type": "Person",
             "email": "adrien.coulier@medsci.uu.se",
             "name": "Adrien Coulier"
+        },
+        {
+            "@id": "https://orcid.org/0009-0004-5536-7210",
+            "@type": "Person",
+            "email": "agrimabhatt@Mac.home",
+            "name": "Agrima Bhatt"
         }
     ]
 }
\ No newline at end of file
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index c6bb7d56..927e3419 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -39,7 +39,7 @@
                 },
                 "BWAMEM2_MEM": {
                     "bwamem2": "2.2.1",
-                    "samtools": 1.21
+                    "samtools": "1.22.1"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -57,7 +57,7 @@
                     "samtools": "1.22.1"
                 },
                 "SEQFU_STATS": {
-                    "seqfu": "1.20.3"
+                    "seqfu": "1.22.3"
                 },
                 "Workflow": {
                     "nf-core/seqinspector": "v1.0dev"
@@ -221,7 +221,7 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "SAMPLE_SINGLE_END_1.bam:md5,ed3f6acd94560448218a288623c810e6",
+                "SAMPLE_SINGLE_END_1.bam:md5,ff8893272a6560cac7067fd8a9406f9b",
                 "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
                 "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
                 "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
@@ -242,7 +242,7 @@
                 "multiqc_picard_baseContent.txt:md5,796e8e0803ad3ed4fd1c76f073784942",
                 "multiqc_picard_quality_by_cycle.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
                 "multiqc_picard_quality_score_distribution.txt:md5,bad70b98811c4cbe4728f53334993703",
-                "multiqc_seqfu.txt:md5,8e6989a2392f599a09a5c3edf8119702",
+                "multiqc_seqfu.txt:md5,7ec63bc3465b3fc8e316e2443ec4c848",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram_1.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
@@ -258,15 +258,15 @@
                 "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
-                "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,f65c868e562291647d539090698ba5eb",
-                "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
+                "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,33a9e44386f308d43881a58394b6b17c",
+                "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,e67e819605ab49182aacf1d676dc885d"
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-19T11:58:59.644568276"
+        "timestamp": "2025-11-19T12:16:11.695977259"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
@@ -276,7 +276,7 @@
                 },
                 "BWAMEM2_MEM": {
                     "bwamem2": "2.2.1",
-                    "samtools": 1.21
+                    "samtools": "1.22.1"
                 },
                 "FASTQSCREEN_FASTQSCREEN": {
                     "fastqscreen": "0.16.0"
@@ -291,7 +291,7 @@
                     "samtools": "1.22.1"
                 },
                 "SEQFU_STATS": {
-                    "seqfu": "1.20.3"
+                    "seqfu": "1.22.3"
                 },
                 "Workflow": {
                     "nf-core/seqinspector": "v1.0dev"
@@ -410,7 +410,7 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "SAMPLE_SINGLE_END_1.bam:md5,ed3f6acd94560448218a288623c810e6",
+                "SAMPLE_SINGLE_END_1.bam:md5,ff8893272a6560cac7067fd8a9406f9b",
                 "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
                 "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
                 "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
@@ -421,7 +421,7 @@
                 "multiqc_picard_baseContent.txt:md5,796e8e0803ad3ed4fd1c76f073784942",
                 "multiqc_picard_quality_by_cycle.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
                 "multiqc_picard_quality_score_distribution.txt:md5,bad70b98811c4cbe4728f53334993703",
-                "multiqc_seqfu.txt:md5,8e6989a2392f599a09a5c3edf8119702",
+                "multiqc_seqfu.txt:md5,7ec63bc3465b3fc8e316e2443ec4c848",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram_1.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
@@ -437,14 +437,14 @@
                 "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
-                "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,f65c868e562291647d539090698ba5eb",
-                "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39"
+                "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,33a9e44386f308d43881a58394b6b17c",
+                "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,e67e819605ab49182aacf1d676dc885d"
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-19T11:48:51.553934925"
+        "timestamp": "2025-11-19T12:16:53.917262693"
     }
 }
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index 448d2107..4b17b6aa 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -7,7 +7,7 @@
                 },
                 "BWAMEM2_MEM": {
                     "bwamem2": "2.2.1",
-                    "samtools": 1.21
+                    "samtools": "1.22.1"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -25,7 +25,7 @@
                     "samtools": "1.22.1"
                 },
                 "SEQFU_STATS": {
-                    "seqfu": "1.20.3"
+                    "seqfu": "1.22.3"
                 },
                 "Workflow": {
                     "nf-core/seqinspector": "v1.0dev"
@@ -338,9 +338,9 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "SAMPLE_PAIRED_END_1_1.bam:md5,fc37892fea524a3c1799f51605c3cc5f",
+                "SAMPLE_PAIRED_END_1_1.bam:md5,44c0ef738b73e26f67ded45ca4cb9e5b",
                 "SAMPLE_PAIRED_END_1_1.bam.bai:md5,82724835c47f8e1d1a86e13ef469b464",
-                "SAMPLE_PAIRED_END_2_2.bam:md5,d68128596af24e2349004a082d507cea",
+                "SAMPLE_PAIRED_END_2_2.bam:md5,9e20db3f3088fc478c223839e3a4ed62",
                 "SAMPLE_PAIRED_END_2_2.bam.bai:md5,3c4bdff0f906f2234fdeee8eea719210",
                 "SAMPLE_PAIRED_END_1_1_1_screen.png:md5,f52ddd0e65f23f68dd8d58d5453417db",
                 "SAMPLE_PAIRED_END_1_1_1_screen.txt:md5,921b08eeb461a2aa1bd42bba53900f70",
@@ -367,7 +367,7 @@
                 "multiqc_picard_baseContent.txt:md5,72b0ae83ed58052bfd768021d377c78f",
                 "multiqc_picard_quality_by_cycle.txt:md5,f6514f14befb874ded5aed79caba3e7b",
                 "multiqc_picard_quality_score_distribution.txt:md5,99be409e325619171b820d762dd023c0",
-                "multiqc_seqfu.txt:md5,1f1e063e4a509a26cee167c3b20389c0",
+                "multiqc_seqfu.txt:md5,139354afd154804b4b77f997277f3ee9",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram_1.txt:md5,f6514f14befb874ded5aed79caba3e7b",
@@ -399,7 +399,7 @@
                 "multiqc_picard_baseContent.txt:md5,72b0ae83ed58052bfd768021d377c78f",
                 "multiqc_picard_quality_by_cycle.txt:md5,f6514f14befb874ded5aed79caba3e7b",
                 "multiqc_picard_quality_score_distribution.txt:md5,99be409e325619171b820d762dd023c0",
-                "multiqc_seqfu.txt:md5,1f1e063e4a509a26cee167c3b20389c0",
+                "multiqc_seqfu.txt:md5,139354afd154804b4b77f997277f3ee9",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram_1.txt:md5,f6514f14befb874ded5aed79caba3e7b",
@@ -416,16 +416,16 @@
                 "picard_quality_score_distribution.txt:md5,ecde9f0e859a6eecc5cea75a156c632d",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
-                "SAMPLE_PAIRED_END_1_1_seqfu.tsv:md5,bbd911ff3fa43212dfd4c5a5872dbdb6",
-                "SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt:md5,cd60f746b6749cc66213d031af1b931c",
-                "SAMPLE_PAIRED_END_2_2_seqfu.tsv:md5,152566a128dd657da33465b4966b5799",
-                "SAMPLE_PAIRED_END_2_2_seqfu_mqc.txt:md5,8a3296956e094e3a95e28431e6009c40"
+                "SAMPLE_PAIRED_END_1_1_seqfu.tsv:md5,be29dfe848eab9a10ee0d46691223eae",
+                "SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt:md5,0aca00c7f64454af520c7e08ec595d2b",
+                "SAMPLE_PAIRED_END_2_2_seqfu.tsv:md5,44a5cb826e001d58208a5855938fa82b",
+                "SAMPLE_PAIRED_END_2_2_seqfu_mqc.txt:md5,ac1740de9ef142c99c993fa9824ead63"
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-19T11:50:04.344118749"
+        "timestamp": "2025-11-19T12:18:12.497819256"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index 5a98f0b3..9b96d508 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -7,7 +7,7 @@
                 },
                 "BWAMEM2_MEM": {
                     "bwamem2": "2.2.1",
-                    "samtools": 1.21
+                    "samtools": "1.22.1"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -25,7 +25,7 @@
                     "samtools": "1.22.1"
                 },
                 "SEQFU_STATS": {
-                    "seqfu": "1.20.3"
+                    "seqfu": "1.22.3"
                 },
                 "Workflow": {
                     "nf-core/seqinspector": "v1.0dev"
@@ -738,15 +738,15 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "Sample1_1.bam:md5,39c3c91eedd90307315acec7aa0b9a35",
+                "Sample1_1.bam:md5,93a7383f6e9a975ba87b315d435ecf18",
                 "Sample1_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
-                "Sample23_3.bam:md5,3d536a6680470138eb361eed198a8efd",
+                "Sample23_3.bam:md5,e1003696a9e3501e122ca584e9a3c519",
                 "Sample23_3.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
-                "SampleA_2.bam:md5,ad691a2590eed5bbc56a56dd24493e4e",
+                "SampleA_2.bam:md5,60f5dd83705aba4edbf460225116b824",
                 "SampleA_2.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
-                "Undetermined_5.bam:md5,06077f7de3641b4b86e08f6a9cdb5a97",
+                "Undetermined_5.bam:md5,9f1a50be15a6504a5b03deec4645a419",
                 "Undetermined_5.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
-                "sampletest_4.bam:md5,7dcb21eb9fec77b862af33e692678dbd",
+                "sampletest_4.bam:md5,6907d7e891e650e0e43539811af81f76",
                 "sampletest_4.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
                 "Sample1_1_screen.png:md5,562256290643b51e4374c2225a15f463",
                 "Sample1_1_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
@@ -776,7 +776,7 @@
                 "multiqc_picard_baseContent.txt:md5,409bf8ce546a573ce6678769b84726fd",
                 "multiqc_picard_quality_by_cycle.txt:md5,ebf56fd9b3b127ff41211e3f79f18b42",
                 "multiqc_picard_quality_score_distribution.txt:md5,182098ce1ff0a664d873c329d54189df",
-                "multiqc_seqfu.txt:md5,5b54a49079169985795537d83d58bdd9",
+                "multiqc_seqfu.txt:md5,18dd2407d4a1791646785123028f69b5",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram_1.txt:md5,ebf56fd9b3b127ff41211e3f79f18b42",
@@ -808,7 +808,7 @@
                 "multiqc_picard_baseContent.txt:md5,740592a5858706d2b4b8f585a1d5492b",
                 "multiqc_picard_quality_by_cycle.txt:md5,c3f14084aedc511b9f0aa8410e7cb3b5",
                 "multiqc_picard_quality_score_distribution.txt:md5,59b955203209cfab3d2d21bdfe20997e",
-                "multiqc_seqfu.txt:md5,5579172a6f8ac09a5ffcb3ce6a99590e",
+                "multiqc_seqfu.txt:md5,6cdb863a3686fbb772aae5a66925ff23",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram_1.txt:md5,c3f14084aedc511b9f0aa8410e7cb3b5",
@@ -840,7 +840,7 @@
                 "multiqc_picard_baseContent.txt:md5,0dd5fa539e4034e3539fb1e7068c7ce5",
                 "multiqc_picard_quality_by_cycle.txt:md5,750eadc27875fc8141b64a90789c369f",
                 "multiqc_picard_quality_score_distribution.txt:md5,140279eb5abac364c4d4c417105da620",
-                "multiqc_seqfu.txt:md5,b5434520fa5be5c98be5ed164a464d23",
+                "multiqc_seqfu.txt:md5,f821357507fda2d4cfd9299f52fa7dc1",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram_1.txt:md5,750eadc27875fc8141b64a90789c369f",
@@ -872,7 +872,7 @@
                 "multiqc_picard_baseContent.txt:md5,6886e1e5179031ddba4958f301930d64",
                 "multiqc_picard_quality_by_cycle.txt:md5,96652e2e2d693488df9104e5ae8cb4a7",
                 "multiqc_picard_quality_score_distribution.txt:md5,879a4470d08fe6d9b1796f46020fb5f5",
-                "multiqc_seqfu.txt:md5,e2e092852c011abe5ad75cdcd68b9383",
+                "multiqc_seqfu.txt:md5,8cced36d66ca9d25d60c006e734aa7e9",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram_1.txt:md5,96652e2e2d693488df9104e5ae8cb4a7",
@@ -904,7 +904,7 @@
                 "multiqc_picard_baseContent.txt:md5,9631916c0a9a736811c47ab4c476428f",
                 "multiqc_picard_quality_by_cycle.txt:md5,9e05b241aabe39232b5182cb59d8edd5",
                 "multiqc_picard_quality_score_distribution.txt:md5,e9c3ade201964470d2d22569a400fa49",
-                "multiqc_seqfu.txt:md5,a1a0b9a0dde0c1c4fe184d44c675dcde",
+                "multiqc_seqfu.txt:md5,ff4ce1c88f39ed24a88bae0a861f75c8",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram_1.txt:md5,9e05b241aabe39232b5182cb59d8edd5",
@@ -920,22 +920,22 @@
                 "picard_quality_score_distribution.txt:md5,1c17c01ef54a6062a8f1ca8408d32958",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
-                "Sample1_1_seqfu.tsv:md5,269fabf8435defcd327aa69a050b7869",
-                "Sample1_1_seqfu_mqc.txt:md5,a354b0ed16b9cf84aa88f501d7740fd6",
-                "Sample23_3_seqfu.tsv:md5,6fdadbeeefccbf957f880d6852bf9676",
-                "Sample23_3_seqfu_mqc.txt:md5,e94269e3efc8b8192d7ac9c15ea2aa99",
-                "SampleA_2_seqfu.tsv:md5,b980ed694a05825fcf7c8b5b73888eb3",
-                "SampleA_2_seqfu_mqc.txt:md5,1d4b0e918644cf553108b7ccf77b4a01",
-                "Undetermined_5_seqfu.tsv:md5,b4458d41df4dee9321da03f4d4672aae",
-                "Undetermined_5_seqfu_mqc.txt:md5,0c869488cb61d2f87758c621bded212b",
-                "sampletest_4_seqfu.tsv:md5,db3179b0c41a09e6317a5a5c0852f476",
-                "sampletest_4_seqfu_mqc.txt:md5,590b97cc48268629204f59007bae7ad7"
+                "Sample1_1_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6",
+                "Sample1_1_seqfu_mqc.txt:md5,24d99524ccd0e6c6255a69d68a871c7a",
+                "Sample23_3_seqfu.tsv:md5,6fac5d3dbce3f3bee72341fe99a399dc",
+                "Sample23_3_seqfu_mqc.txt:md5,4d4f280911a08bb6b753142980178027",
+                "SampleA_2_seqfu.tsv:md5,aec811f267bb2a0ef066a7abb59d2775",
+                "SampleA_2_seqfu_mqc.txt:md5,a819409a5cb64e20c3e54ec5ada4aa27",
+                "Undetermined_5_seqfu.tsv:md5,3a42c5c66a0a118f1a6f6f6e560b0e7e",
+                "Undetermined_5_seqfu_mqc.txt:md5,bd8be908362c5cb08a72f8ae7ab41b0d",
+                "sampletest_4_seqfu.tsv:md5,a5bea0b9c6015dd1a201ffd433e9b377",
+                "sampletest_4_seqfu_mqc.txt:md5,2180961655bbc8a12f0152d6a4b803a2"
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-19T11:51:22.144399289"
+        "timestamp": "2025-11-19T12:19:32.836832601"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index e946b153..212f45a9 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -7,7 +7,7 @@
                 },
                 "BWAMEM2_MEM": {
                     "bwamem2": "2.2.1",
-                    "samtools": 1.21
+                    "samtools": "1.22.1"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -25,7 +25,7 @@
                     "samtools": "1.22.1"
                 },
                 "SEQFU_STATS": {
-                    "seqfu": "1.20.3"
+                    "seqfu": "1.22.3"
                 },
                 "SEQTK_SAMPLE": {
                     "seqtk": "1.4-r122"
@@ -747,15 +747,15 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "Sample1_1.bam:md5,78344f8d3deffb9abb799382769e70eb",
+                "Sample1_1.bam:md5,0bd502d4e221008867c85393cce2b89b",
                 "Sample1_1.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
-                "Sample23_3.bam:md5,74149a4daaf4ee5dfa2e93a3cc5b5009",
+                "Sample23_3.bam:md5,26a49672caec3ab985d3f3dd6bdff530",
                 "Sample23_3.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
-                "SampleA_2.bam:md5,73d7fd05b1741af9871d2418f9f3732b",
+                "SampleA_2.bam:md5,240d536aab1aac8fa3bca402703121df",
                 "SampleA_2.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
-                "Undetermined_5.bam:md5,a3c99695f73e2024c13691b8f1f8905e",
+                "Undetermined_5.bam:md5,f30b23c562a1725f3f23236acab1fd9a",
                 "Undetermined_5.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
-                "sampletest_4.bam:md5,c0790dc0f7e85a8cd2fb57cf9c9d29fb",
+                "sampletest_4.bam:md5,2c37f72ed4f25c971199fbde3af370b9",
                 "sampletest_4.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
                 "Sample1_1_screen.png:md5,562256290643b51e4374c2225a15f463",
                 "Sample1_1_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
@@ -785,7 +785,7 @@
                 "multiqc_picard_baseContent.txt:md5,8b2efc3fa06d2013348b35f9607292aa",
                 "multiqc_picard_quality_by_cycle.txt:md5,c2774038d1a0142746426e46f9f954dd",
                 "multiqc_picard_quality_score_distribution.txt:md5,792755ee794d375b85a57f58d879f0c6",
-                "multiqc_seqfu.txt:md5,5b54a49079169985795537d83d58bdd9",
+                "multiqc_seqfu.txt:md5,18dd2407d4a1791646785123028f69b5",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram_1.txt:md5,c2774038d1a0142746426e46f9f954dd",
@@ -817,7 +817,7 @@
                 "multiqc_picard_baseContent.txt:md5,1426865fe8ee1a36f67636c28500a91c",
                 "multiqc_picard_quality_by_cycle.txt:md5,79bf9f861077de70ec28c9af01783876",
                 "multiqc_picard_quality_score_distribution.txt:md5,a3f8d1937e1f118800aa3d86c1b498c4",
-                "multiqc_seqfu.txt:md5,5579172a6f8ac09a5ffcb3ce6a99590e",
+                "multiqc_seqfu.txt:md5,6cdb863a3686fbb772aae5a66925ff23",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram_1.txt:md5,79bf9f861077de70ec28c9af01783876",
@@ -849,7 +849,7 @@
                 "multiqc_picard_baseContent.txt:md5,0a5f9d32dd3061ce4349518c47d69838",
                 "multiqc_picard_quality_by_cycle.txt:md5,ec59b472afc1242ff299011ba456e792",
                 "multiqc_picard_quality_score_distribution.txt:md5,1b8be76b60ee71aa36a98d34e433b9bf",
-                "multiqc_seqfu.txt:md5,b5434520fa5be5c98be5ed164a464d23",
+                "multiqc_seqfu.txt:md5,f821357507fda2d4cfd9299f52fa7dc1",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram_1.txt:md5,ec59b472afc1242ff299011ba456e792",
@@ -881,7 +881,7 @@
                 "multiqc_picard_baseContent.txt:md5,b9d72d8173cdc7649b44b80aa485477c",
                 "multiqc_picard_quality_by_cycle.txt:md5,062547fb888ed508dd1d5733d7bed22e",
                 "multiqc_picard_quality_score_distribution.txt:md5,dd5abab3a7141654fffa3946c50a039b",
-                "multiqc_seqfu.txt:md5,e2e092852c011abe5ad75cdcd68b9383",
+                "multiqc_seqfu.txt:md5,8cced36d66ca9d25d60c006e734aa7e9",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram_1.txt:md5,062547fb888ed508dd1d5733d7bed22e",
@@ -913,7 +913,7 @@
                 "multiqc_picard_baseContent.txt:md5,974d83faa49711ab4ea1248c59e69393",
                 "multiqc_picard_quality_by_cycle.txt:md5,248ecaf269d8fef1e84ea06f98b6f6ba",
                 "multiqc_picard_quality_score_distribution.txt:md5,5e7e80654e12c500b15f8564ffb12b27",
-                "multiqc_seqfu.txt:md5,a1a0b9a0dde0c1c4fe184d44c675dcde",
+                "multiqc_seqfu.txt:md5,ff4ce1c88f39ed24a88bae0a861f75c8",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram_1.txt:md5,248ecaf269d8fef1e84ea06f98b6f6ba",
@@ -929,16 +929,16 @@
                 "picard_quality_score_distribution.txt:md5,9d9f1bb12316175cdb88d3ff70305428",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
-                "Sample1_1_seqfu.tsv:md5,269fabf8435defcd327aa69a050b7869",
-                "Sample1_1_seqfu_mqc.txt:md5,a354b0ed16b9cf84aa88f501d7740fd6",
-                "Sample23_3_seqfu.tsv:md5,6fdadbeeefccbf957f880d6852bf9676",
-                "Sample23_3_seqfu_mqc.txt:md5,e94269e3efc8b8192d7ac9c15ea2aa99",
-                "SampleA_2_seqfu.tsv:md5,b980ed694a05825fcf7c8b5b73888eb3",
-                "SampleA_2_seqfu_mqc.txt:md5,1d4b0e918644cf553108b7ccf77b4a01",
-                "Undetermined_5_seqfu.tsv:md5,b4458d41df4dee9321da03f4d4672aae",
-                "Undetermined_5_seqfu_mqc.txt:md5,0c869488cb61d2f87758c621bded212b",
-                "sampletest_4_seqfu.tsv:md5,db3179b0c41a09e6317a5a5c0852f476",
-                "sampletest_4_seqfu_mqc.txt:md5,590b97cc48268629204f59007bae7ad7",
+                "Sample1_1_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6",
+                "Sample1_1_seqfu_mqc.txt:md5,24d99524ccd0e6c6255a69d68a871c7a",
+                "Sample23_3_seqfu.tsv:md5,6fac5d3dbce3f3bee72341fe99a399dc",
+                "Sample23_3_seqfu_mqc.txt:md5,4d4f280911a08bb6b753142980178027",
+                "SampleA_2_seqfu.tsv:md5,aec811f267bb2a0ef066a7abb59d2775",
+                "SampleA_2_seqfu_mqc.txt:md5,a819409a5cb64e20c3e54ec5ada4aa27",
+                "Undetermined_5_seqfu.tsv:md5,3a42c5c66a0a118f1a6f6f6e560b0e7e",
+                "Undetermined_5_seqfu_mqc.txt:md5,bd8be908362c5cb08a72f8ae7ab41b0d",
+                "sampletest_4_seqfu.tsv:md5,a5bea0b9c6015dd1a201ffd433e9b377",
+                "sampletest_4_seqfu_mqc.txt:md5,2180961655bbc8a12f0152d6a4b803a2",
                 "Sample1_1_Sample1_S1_L001_R1_001.fastq.gz:md5,3ccd132ff32399706842b0f1d00f477e",
                 "Sample23_3_Sample23_S3_L001_R1_001.fastq.gz:md5,3802f03450693b42531fdf5b0b542c2f",
                 "SampleA_2_SampleA_S2_L001_R1_001.fastq.gz:md5,f99d5407aac64cb36451c6f0a1db5ade",
@@ -950,6 +950,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-19T11:52:38.751102766"
+        "timestamp": "2025-11-19T12:20:48.844054564"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index 0467b847..be8a9183 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -9,7 +9,7 @@
                     "fastqscreen": "0.16.0"
                 },
                 "SEQFU_STATS": {
-                    "seqfu": "1.20.3"
+                    "seqfu": "1.22.3"
                 },
                 "Workflow": {
                     "nf-core/seqinspector": "v1.0dev"
@@ -126,13 +126,13 @@
                 "multiqc_fastqc.txt:md5,1a4b472e13cadc770832b0e20d1de7b0",
                 "multiqc_seqfu.txt:md5,9595d608ff5709f2bdec8cb1016416c0",
                 "hg001_1_seqfu.tsv:md5,b133752c897afbb4d8721b911fa117d4",
-                "hg001_1_seqfu_mqc.txt:md5,6285f582c03faa70e8dcb3503e5db728"
+                "hg001_1_seqfu_mqc.txt:md5,42e3506b02ceb72a6f05cb174505e722"
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T10:27:14.736749139"
+        "timestamp": "2025-11-19T12:21:24.011932536"
     }
 }
\ No newline at end of file

From f38e893aede988df9d53748af97eab504bbf73cc Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 19 Nov 2025 12:43:47 +0100
Subject: [PATCH 334/530] patch fastqscreen/fastqscreen

---
 modules.json                                  |  2 +-
 .../fastqscreen/fastqscreen/environment.yml   |  6 --
 .../fastqscreen/fastqscreen-fastqscreen.diff  | 81 +++++++++++--------
 .../nf-core/fastqscreen/fastqscreen/main.nf   | 42 +++++-----
 .../nf-core/fastqscreen/fastqscreen/meta.yml  | 16 ++--
 .../fastqscreen/tests/main.nf.test.snap       |  6 +-
 .../fastqscreen/fastqscreen/tests/tags.yml    |  2 -
 ro-crate-metadata.json                        | 44 +++++-----
 8 files changed, 105 insertions(+), 94 deletions(-)
 delete mode 100644 modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml

diff --git a/modules.json b/modules.json
index c6c029f3..c96335d6 100644
--- a/modules.json
+++ b/modules.json
@@ -33,7 +33,7 @@
                     },
                     "fastqscreen/fastqscreen": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff"
                     },
diff --git a/modules/nf-core/fastqscreen/fastqscreen/environment.yml b/modules/nf-core/fastqscreen/fastqscreen/environment.yml
index 7d4c8922..9ff968c9 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/environment.yml
+++ b/modules/nf-core/fastqscreen/fastqscreen/environment.yml
@@ -6,9 +6,3 @@ channels:
 dependencies:
   - bioconda::fastq-screen=0.16.0
   - bioconda::perl-gdgraph=1.54
-  # - gzip
-  # - SAMtools
-  # - bowtie
-  # - bowtie2
-  # - bwa
-  # - bismark
diff --git a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
index 658d149b..c6fdd2f1 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
+++ b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
@@ -1,73 +1,90 @@
 Changes in component 'nf-core/fastqscreen/fastqscreen'
+'modules/nf-core/fastqscreen/fastqscreen/meta.yml' is unchanged
 Changes in 'fastqscreen/fastqscreen/environment.yml':
 --- modules/nf-core/fastqscreen/fastqscreen/environment.yml
 +++ modules/nf-core/fastqscreen/fastqscreen/environment.yml
-@@ -4,5 +4,11 @@
+@@ -4,5 +4,5 @@
    - conda-forge
    - bioconda
  dependencies:
--  - "bioconda::fastq-screen=0.15.3"
+-  - bioconda::fastq-screen=0.15.3
 +  - bioconda::fastq-screen=0.16.0
    - bioconda::perl-gdgraph=1.54
-+  # - gzip
-+  # - SAMtools
-+  # - bowtie
-+  # - bowtie2
-+  # - bwa
-+  # - bismark
 
 Changes in 'fastqscreen/fastqscreen/main.nf':
 --- modules/nf-core/fastqscreen/fastqscreen/main.nf
 +++ modules/nf-core/fastqscreen/fastqscreen/main.nf
-@@ -4,12 +4,12 @@
+@@ -1,22 +1,22 @@
+ process FASTQSCREEN_FASTQSCREEN {
+-    tag "$meta.id"
++    tag "${meta.id}"
+     label 'process_medium'
  
      conda "${moduleDir}/environment.yml"
-     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
 -        'https://depot.galaxyproject.org/singularity/fastq-screen:0.15.3--pl5321hdfd78af_0':
 -        'biocontainers/fastq-screen:0.15.3--pl5321hdfd78af_0'}"
-+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fc/fc53eee7ca23c32220a9662fbb63c67769756544b6d74a1ee85cf439ea79a7ee/data' :
-+        'community.wave.seqera.io/library/fastq-screen_perl-gdgraph:5c1786a5d5bc1309'}"
++    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
++        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fc/fc53eee7ca23c32220a9662fbb63c67769756544b6d74a1ee85cf439ea79a7ee/data'
++        : 'community.wave.seqera.io/library/fastq-screen_perl-gdgraph:5c1786a5d5bc1309'}"
  
      input:
 -    tuple val(meta), path(reads)  // .fastq files
 -    path database
 +    tuple val(meta), path(reads, arity: '1..2')
-+    tuple val(ref_names), path(ref_dirs, name:"ref*"), val(ref_basenames), val(ref_aligners)
++    tuple val(ref_names), path(ref_dirs, name: "ref*"), val(ref_basenames), val(ref_aligners)
  
      output:
-     tuple val(meta), path("*.txt")     , emit: txt
-@@ -24,31 +24,42 @@
+-    tuple val(meta), path("*.txt")     , emit: txt
+-    tuple val(meta), path("*.png")     , emit: png  , optional: true
+-    tuple val(meta), path("*.html")    , emit: html
++    tuple val(meta), path("*.txt"), emit: txt
++    tuple val(meta), path("*.png"), emit: png, optional: true
++    tuple val(meta), path("*.html"), emit: html
+     tuple val(meta), path("*.fastq.gz"), emit: fastq, optional: true
+-    path "versions.yml"                , emit: versions
++    path "versions.yml", emit: versions
+ 
+     when:
+     task.ext.when == null || task.ext.when
+@@ -24,31 +24,46 @@
      script:
      def prefix = task.ext.prefix ?: "${meta.id}"
      def args = task.ext.args ?: ""
 +    def config_content = ref_names.withIndex().collect { name, i -> "DATABASE ${name} ./${ref_dirs[i]}/${ref_basenames[i]} ${ref_aligners[i]}" }.join('\n')
  
 +    // Build mv commands to rename the output files. Dual reads will be appended with '_1' and '_2'
-+    def num_reads = reads instanceof List  ? reads.size() : 1
++    def num_reads = reads instanceof List ? reads.size() : 1
 +    def file_extensions = ['txt', 'html', 'png']
-+    def mv_cmd = file_extensions.collect { ext ->
-+        reads.withIndex().collect { read, i ->
-+            "mv ${read.simpleName}_screen.${ext} ${prefix}${num_reads > 1 ? "_${i+1}" : ''}_screen.${ext}"
-+        }.join(' && ')
-+    }.join(' && ')
++    def mv_cmd = file_extensions
++        .collect { ext ->
++            reads
++                .withIndex()
++                .collect { read, i ->
++                    "mv ${read.simpleName}_screen.${ext} ${prefix}${num_reads > 1 ? "_${i + 1}" : ''}_screen.${ext}"
++                }
++                .join(' && ')
++        }
++        .join(' && ')
      """
 -    fastq_screen --threads ${task.cpus} \\
 -        --aligner bowtie2 \\
 -        --conf ${database}/fastq_screen.conf \\
-+    echo '${config_content}' > fastq_screen.conf
-+
-+    fastq_screen \\
-+        --conf fastq_screen.conf \\
-+        --threads ${task.cpus} \\
-         $reads \\
+-        $reads \\
 -        $args \\
-+        $args
++    echo '${config_content}' > fastq_screen.conf
  
 -    cat <<-END_VERSIONS > versions.yml
 -    "${task.process}":
 -        fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//')
 -    END_VERSIONS
-+    $mv_cmd
++    fastq_screen \\
++        --conf fastq_screen.conf \\
++        --threads ${task.cpus} \\
++        ${reads} \\
++        ${args}
++
++    ${mv_cmd}
 +
 +    fastq_screen_version=\$(fastq_screen --version 2>&1 | sed 's/^.*FastQ Screen v//; s/ .*\$//')
 +    echo "\\\"${task.process}\\\":" > versions.yml
@@ -92,12 +109,10 @@ Changes in 'fastqscreen/fastqscreen/main.nf':
 +    echo "\\\"${task.process}\\\":" > versions.yml
 +    echo "    fastqscreen: \$fastq_screen_version" >> versions.yml
      """
- 
+-
  }
 
-'modules/nf-core/fastqscreen/fastqscreen/meta.yml' is unchanged
-'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test' is unchanged
 'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap' is unchanged
 'modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config' is unchanged
-'modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test' is unchanged
 ************************************************************
diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index 21012c1f..dc53ae21 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -1,22 +1,22 @@
 process FASTQSCREEN_FASTQSCREEN {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fc/fc53eee7ca23c32220a9662fbb63c67769756544b6d74a1ee85cf439ea79a7ee/data' :
-        'community.wave.seqera.io/library/fastq-screen_perl-gdgraph:5c1786a5d5bc1309'}"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fc/fc53eee7ca23c32220a9662fbb63c67769756544b6d74a1ee85cf439ea79a7ee/data'
+        : 'community.wave.seqera.io/library/fastq-screen_perl-gdgraph:5c1786a5d5bc1309'}"
 
     input:
     tuple val(meta), path(reads, arity: '1..2')
-    tuple val(ref_names), path(ref_dirs, name:"ref*"), val(ref_basenames), val(ref_aligners)
+    tuple val(ref_names), path(ref_dirs, name: "ref*"), val(ref_basenames), val(ref_aligners)
 
     output:
-    tuple val(meta), path("*.txt")     , emit: txt
-    tuple val(meta), path("*.png")     , emit: png  , optional: true
-    tuple val(meta), path("*.html")    , emit: html
+    tuple val(meta), path("*.txt"), emit: txt
+    tuple val(meta), path("*.png"), emit: png, optional: true
+    tuple val(meta), path("*.html"), emit: html
     tuple val(meta), path("*.fastq.gz"), emit: fastq, optional: true
-    path "versions.yml"                , emit: versions
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,23 +27,28 @@ process FASTQSCREEN_FASTQSCREEN {
     def config_content = ref_names.withIndex().collect { name, i -> "DATABASE ${name} ./${ref_dirs[i]}/${ref_basenames[i]} ${ref_aligners[i]}" }.join('\n')
 
     // Build mv commands to rename the output files. Dual reads will be appended with '_1' and '_2'
-    def num_reads = reads instanceof List  ? reads.size() : 1
+    def num_reads = reads instanceof List ? reads.size() : 1
     def file_extensions = ['txt', 'html', 'png']
-    def mv_cmd = file_extensions.collect { ext ->
-        reads.withIndex().collect { read, i ->
-            "mv ${read.simpleName}_screen.${ext} ${prefix}${num_reads > 1 ? "_${i+1}" : ''}_screen.${ext}"
-        }.join(' && ')
-    }.join(' && ')
+    def mv_cmd = file_extensions
+        .collect { ext ->
+            reads
+                .withIndex()
+                .collect { read, i ->
+                    "mv ${read.simpleName}_screen.${ext} ${prefix}${num_reads > 1 ? "_${i + 1}" : ''}_screen.${ext}"
+                }
+                .join(' && ')
+        }
+        .join(' && ')
     """
     echo '${config_content}' > fastq_screen.conf
 
     fastq_screen \\
         --conf fastq_screen.conf \\
         --threads ${task.cpus} \\
-        $reads \\
-        $args
+        ${reads} \\
+        ${args}
 
-    $mv_cmd
+    ${mv_cmd}
 
     fastq_screen_version=\$(fastq_screen --version 2>&1 | sed 's/^.*FastQ Screen v//; s/ .*\$//')
     echo "\\\"${task.process}\\\":" > versions.yml
@@ -61,5 +66,4 @@ process FASTQSCREEN_FASTQSCREEN {
     echo "\\\"${task.process}\\\":" > versions.yml
     echo "    fastqscreen: \$fastq_screen_version" >> versions.yml
     """
-
 }
diff --git a/modules/nf-core/fastqscreen/fastqscreen/meta.yml b/modules/nf-core/fastqscreen/fastqscreen/meta.yml
index 7d96f0b8..81e15b02 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/meta.yml
+++ b/modules/nf-core/fastqscreen/fastqscreen/meta.yml
@@ -30,10 +30,10 @@ input:
           List of input FastQ files of size 1 and 2 for single-end and paired-end data,
           respectively.
         ontologies: []
-  - - ref_names: {}
-    - ref_dirs: {}
-    - ref_basenames: {}
-    - ref_aligners: {}
+  - database:
+      type: directory
+      description: fastq screen database folder containing config file and index folders
+      pattern: "FastQ_Screen_Genomes"
 output:
   txt:
     - - meta:
@@ -59,8 +59,8 @@ output:
           description: Groovy Map containing sample information
       - "*.html":
           type: file
-          description: HTML file containing mapping results as a table and
-            graphical representation
+          description: HTML file containing mapping results as a table and graphical
+            representation
           pattern: "*.html"
           ontologies: []
   fastq:
@@ -69,8 +69,8 @@ output:
           description: Groovy Map containing sample information
       - "*.fastq.gz":
           type: file
-          description: FastQ file containing reads that did not align to any
-            database (optional)
+          description: FastQ file containing reads that did not align to any database
+            (optional)
           pattern: "*.fastq.gz"
           ontologies:
             - edam: http://edamontology.org/format_3989 # GZIP format
diff --git a/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap b/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap
index 2afffdea..042f3bb4 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap
+++ b/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap
@@ -124,9 +124,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2024-08-31T05:45:54.845041829"
+        "timestamp": "2025-03-25T08:38:33.98646086"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml b/modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml
deleted file mode 100644
index b03bfb45..00000000
--- a/modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-fastqscreen/fastqscreen:
-  - "modules/nf-core/fastqscreen/fastqscreen/**"
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 4846575a..e578707d 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,7 +22,7 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2025-11-19T11:23:02+00:00",
+            "datePublished": "2025-11-19T11:42:42+00:00",
             "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->\n\n1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))\n2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n3. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#bd95d18d-7f91-4566-b59b-6538c02da3ab"
+                    "@id": "#71038893-a262-4eae-bd98-7ea776c53d1b"
                 }
             ],
             "name": "nf-core/seqinspector"
@@ -128,20 +128,20 @@
             ],
             "creator": [
                 {
-                    "@id": "https://orcid.org/0000-0003-1675-0677"
+                    "@id": "https://orcid.org/0000-0003-2702-1103"
                 },
                 {
-                    "@id": "#89784800+kedhammar@users.noreply.github.com"
+                    "@id": "https://orcid.org/0000-0003-1675-0677"
                 },
                 {
-                    "@id": "https://orcid.org/0000-0003-2702-1103"
+                    "@id": "https://orcid.org/0009-0004-5536-7210"
                 },
                 {
-                    "@id": "https://orcid.org/0009-0004-5536-7210"
+                    "@id": "#89784800+kedhammar@users.noreply.github.com"
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2025-11-19T12:23:02Z",
+            "dateModified": "2025-11-19T12:42:42Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -182,11 +182,11 @@
             "version": "!>=25.04.0"
         },
         {
-            "@id": "#bd95d18d-7f91-4566-b59b-6538c02da3ab",
+            "@id": "#71038893-a262-4eae-bd98-7ea776c53d1b",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#4c91a9a9-4868-4f2d-b90a-660d84bc358f"
+                    "@id": "#993ccba2-3cbf-4d2d-9b44-21757f3c0ac7"
                 }
             ],
             "mainEntity": {
@@ -195,7 +195,7 @@
             "name": "Test suite for nf-core/seqinspector"
         },
         {
-            "@id": "#4c91a9a9-4868-4f2d-b90a-660d84bc358f",
+            "@id": "#993ccba2-3cbf-4d2d-9b44-21757f3c0ac7",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/seqinspector",
             "resource": "repos/nf-core/seqinspector/actions/workflows/nf-test.yml",
@@ -323,29 +323,29 @@
             "name": "nf-core",
             "url": "https://nf-co.re/"
         },
-        {
-            "@id": "https://orcid.org/0000-0003-1675-0677",
-            "@type": "Person",
-            "email": "mahesh.binzer-panchal@nbis.se",
-            "name": "Mahesh Binzer-Panchal"
-        },
-        {
-            "@id": "#89784800+kedhammar@users.noreply.github.com",
-            "@type": "Person",
-            "email": "89784800+kedhammar@users.noreply.github.com",
-            "name": "Alfred Kedhammar"
-        },
         {
             "@id": "https://orcid.org/0000-0003-2702-1103",
             "@type": "Person",
             "email": "adrien.coulier@medsci.uu.se",
             "name": "Adrien Coulier"
         },
+        {
+            "@id": "https://orcid.org/0000-0003-1675-0677",
+            "@type": "Person",
+            "email": "mahesh.binzer-panchal@nbis.se",
+            "name": "Mahesh Binzer-Panchal"
+        },
         {
             "@id": "https://orcid.org/0009-0004-5536-7210",
             "@type": "Person",
             "email": "agrimabhatt@Mac.home",
             "name": "Agrima Bhatt"
+        },
+        {
+            "@id": "#89784800+kedhammar@users.noreply.github.com",
+            "@type": "Person",
+            "email": "89784800+kedhammar@users.noreply.github.com",
+            "name": "Alfred Kedhammar"
         }
     ]
 }
\ No newline at end of file

From c28635a538a5eef13ad4941821d92668da9d226f Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Wed, 19 Nov 2025 13:27:53 +0100
Subject: [PATCH 335/530] Update CHANGELOG.md

---
 CHANGELOG.md | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b56499bb..aaf4d24a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -23,8 +23,9 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#96](https://github.com/nf-core/seqinspector/pull/96) Added missing citations to citation tool
 - [#103](https://github.com/nf-core/seqinspector/pull/103) Configure full-tests
 - [#110](https://github.com/nf-core/seqinspector/pull/110) Update input schema to accept either tar file or directory as rundir, and fastq messages and patterns.
-- [#127] (https://github.com/nf-core/seqinspector/pull/127) Added alignment tools - bwamem2 - index and mem
-- [#128] (https://github.com/nf-core/seqinspector/pull/128) Added Picard tools - Collect Multiple Mterics to collect QC metrics
+- [#127](https://github.com/nf-core/seqinspector/pull/127) Added alignment tools - bwamem2 - index and mem
+- [#128](https://github.com/nf-core/seqinspector/pull/128) Added Picard tools - Collect Multiple Mterics to collect QC metrics
+- [#132](https://github.com/nf-core/seqinspector/pull/132) Added a bwamem2 index params for faster output
 
 ### `Fixed`
 

From 205c2e33cda5db931add0ef194d433cb139b7713 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 19 Nov 2025 14:25:01 +0100
Subject: [PATCH 336/530] solve merge conflicts

---
 tests/MiSeq.main.nf.test.snap                 |  8 --------
 tests/NovaSeq6000.main_subsample.nf.test.snap | 16 ++++------------
 2 files changed, 4 insertions(+), 20 deletions(-)

diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index eabf7f14..bb666659 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -266,11 +266,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-<<<<<<< HEAD
         "timestamp": "2025-11-07T11:14:40.189991111"
-=======
-        "timestamp": "2025-11-19T12:16:11.695977259"
->>>>>>> dev
     },
     "Miseq data test (skip fastqc)": {
         "content": [
@@ -449,10 +445,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-<<<<<<< HEAD
         "timestamp": "2025-11-07T11:15:17.347135189"
-=======
-        "timestamp": "2025-11-19T12:16:53.917262693"
->>>>>>> dev
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index e36b7e9e..e242b338 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -785,11 +785,7 @@
                 "multiqc_picard_baseContent.txt:md5,8b2efc3fa06d2013348b35f9607292aa",
                 "multiqc_picard_quality_by_cycle.txt:md5,c2774038d1a0142746426e46f9f954dd",
                 "multiqc_picard_quality_score_distribution.txt:md5,792755ee794d375b85a57f58d879f0c6",
-<<<<<<< HEAD
-                "multiqc_seqfu.txt:md5,5b54a49079169985795537d83d58bdd9",
-=======
                 "multiqc_seqfu.txt:md5,18dd2407d4a1791646785123028f69b5",
->>>>>>> dev
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram_1.txt:md5,c2774038d1a0142746426e46f9f954dd",
@@ -821,11 +817,7 @@
                 "multiqc_picard_baseContent.txt:md5,1426865fe8ee1a36f67636c28500a91c",
                 "multiqc_picard_quality_by_cycle.txt:md5,79bf9f861077de70ec28c9af01783876",
                 "multiqc_picard_quality_score_distribution.txt:md5,a3f8d1937e1f118800aa3d86c1b498c4",
-<<<<<<< HEAD
-                "multiqc_seqfu.txt:md5,5579172a6f8ac09a5ffcb3ce6a99590e",
-=======
                 "multiqc_seqfu.txt:md5,6cdb863a3686fbb772aae5a66925ff23",
->>>>>>> dev
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram_1.txt:md5,79bf9f861077de70ec28c9af01783876",
@@ -857,7 +849,7 @@
                 "multiqc_picard_baseContent.txt:md5,0a5f9d32dd3061ce4349518c47d69838",
                 "multiqc_picard_quality_by_cycle.txt:md5,ec59b472afc1242ff299011ba456e792",
                 "multiqc_picard_quality_score_distribution.txt:md5,1b8be76b60ee71aa36a98d34e433b9bf",
-                "multiqc_seqfu.txt:md5,b5434520fa5be5c98be5ed164a464d23",
+                "multiqc_seqfu.txt:md5,f821357507fda2d4cfd9299f52fa7dc1",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram_1.txt:md5,ec59b472afc1242ff299011ba456e792",
@@ -889,7 +881,7 @@
                 "multiqc_picard_baseContent.txt:md5,b9d72d8173cdc7649b44b80aa485477c",
                 "multiqc_picard_quality_by_cycle.txt:md5,062547fb888ed508dd1d5733d7bed22e",
                 "multiqc_picard_quality_score_distribution.txt:md5,dd5abab3a7141654fffa3946c50a039b",
-                "multiqc_seqfu.txt:md5,e2e092852c011abe5ad75cdcd68b9383",
+                "multiqc_seqfu.txt:md5,8cced36d66ca9d25d60c006e734aa7e9",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram_1.txt:md5,062547fb888ed508dd1d5733d7bed22e",
@@ -921,7 +913,7 @@
                 "multiqc_picard_baseContent.txt:md5,974d83faa49711ab4ea1248c59e69393",
                 "multiqc_picard_quality_by_cycle.txt:md5,248ecaf269d8fef1e84ea06f98b6f6ba",
                 "multiqc_picard_quality_score_distribution.txt:md5,5e7e80654e12c500b15f8564ffb12b27",
-                "multiqc_seqfu.txt:md5,a1a0b9a0dde0c1c4fe184d44c675dcde",
+                "multiqc_seqfu.txt:md5,ff4ce1c88f39ed24a88bae0a861f75c8",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram_1.txt:md5,248ecaf269d8fef1e84ea06f98b6f6ba",
@@ -958,6 +950,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T11:18:58.975063972"
+        "timestamp": "2025-11-19T14:24:39.696680631"
     }
 }
\ No newline at end of file

From 9214a5b22be7d6aebe59807beb9c8a3b7f87db34 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Thu, 20 Nov 2025 09:32:31 +0000
Subject: [PATCH 337/530] Template update for nf-core/tools version 3.5.1

---
 .github/workflows/awsfulltest.yml             |  2 +-
 .github/workflows/awstest.yml                 |  2 +-
 .github/workflows/download_pipeline.yml       |  2 +-
 .github/workflows/fix_linting.yml             |  2 +-
 .github/workflows/linting.yml                 |  6 +--
 .github/workflows/nf-test.yml                 |  4 +-
 .github/workflows/release-announcements.yml   |  9 ++---
 .../workflows/template-version-comment.yml    |  2 +-
 .nf-core.yml                                  |  4 +-
 .prettierignore                               |  2 +
 README.md                                     |  4 +-
 modules.json                                  |  4 +-
 modules/nf-core/multiqc/environment.yml       |  2 +-
 modules/nf-core/multiqc/main.nf               |  4 +-
 .../nf-core/multiqc/tests/main.nf.test.snap   | 24 ++++++------
 nextflow.config                               |  2 -
 ro-crate-metadata.json                        | 14 +++----
 .../main.nf                                   |  6 +--
 .../nf-core/utils_nfcore_pipeline/main.nf     |  2 +-
 workflows/seqinspector.nf                     | 38 ++++++++++++++-----
 20 files changed, 75 insertions(+), 60 deletions(-)

diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 301eca73..b1b33ad7 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -40,7 +40,7 @@ jobs:
             }
           profiles: test_full
 
-      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+      - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: Seqera Platform debug log file
           path: |
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index 3fa92b8c..b3346993 100644
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@@ -25,7 +25,7 @@ jobs:
             }
           profiles: test
 
-      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+      - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: Seqera Platform debug log file
           path: |
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 6d94bcbf..45884ff9 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -127,7 +127,7 @@ jobs:
           fi
 
       - name: Upload Nextflow logfile for debugging purposes
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: nextflow_logfile.txt
           path: .nextflow.log*
diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml
index 276dcf34..205093c1 100644
--- a/.github/workflows/fix_linting.yml
+++ b/.github/workflows/fix_linting.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 30e66026..7a527a34 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -11,7 +11,7 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Set up Python 3.14
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
@@ -28,7 +28,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
@@ -71,7 +71,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index e20bf6d0..c98d76ec 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -40,7 +40,7 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
           ls -la ./
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           fetch-depth: 0
 
@@ -85,7 +85,7 @@ jobs:
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
 
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           fetch-depth: 0
 
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index e64cebd6..431d3d44 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -15,10 +15,9 @@ jobs:
           echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT
 
       - name: get description
-        id: get_topics
+        id: get_description
         run: |
-          echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description' >> $GITHUB_OUTPUT
-
+          echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description')" >> $GITHUB_OUTPUT
       - uses: rzr/fediverse-action@master
         with:
           access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
@@ -27,9 +26,7 @@ jobs:
           # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release
           message: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
-
-            ${{ steps.get_topics.outputs.description }}
-
+            ${{ steps.get_description.outputs.description }}
             Please see the changelog: ${{ github.event.release.html_url }}
 
             ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml
index c5988af9..e8560fc7 100644
--- a/.github/workflows/template-version-comment.yml
+++ b/.github/workflows/template-version-comment.yml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           ref: ${{ github.event.pull_request.head.sha }}
 
diff --git a/.nf-core.yml b/.nf-core.yml
index 95804289..ceb658d7 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,12 +1,12 @@
 lint:
   files_exist:
-    - .github/workflows/ci.yml
+    - tests/default.nf.test
   files_unchanged:
     - .github/CONTRIBUTING.md
   nextflow_config:
     - config_defaults:
         - params.fastq_screen_references
-nf_core_version: 3.4.1
+nf_core_version: 3.5.1
 repository_type: pipeline
 template:
   author: Adrien Coulier
diff --git a/.prettierignore b/.prettierignore
index 2255e3e3..dd749d43 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -12,3 +12,5 @@ testing*
 bin/
 .nf-test/
 ro-crate-metadata.json
+modules/nf-core/
+subworkflows/nf-core/
diff --git a/README.md b/README.md
index 7d114ecb..204e181b 100644
--- a/README.md
+++ b/README.md
@@ -5,13 +5,13 @@
   </picture>
 </h1>
 
-[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/seqinspector)
+[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/seqinspector)
 [![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
-[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)
+[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
diff --git a/modules.json b/modules.json
index c716c132..9e94dfd6 100644
--- a/modules.json
+++ b/modules.json
@@ -12,7 +12,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "e10b76ca0c66213581bec2833e30d31f239dec0b",
+                        "git_sha": "af27af1be706e6a2bb8fe454175b0cdf77f47b49",
                         "installed_by": ["modules"]
                     }
                 }
@@ -26,7 +26,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index dd513cbd..d02016a0 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::multiqc=1.31
+  - bioconda::multiqc=1.32
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 5288f5cc..c1158fb0 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,8 +3,8 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ef/eff0eafe78d5f3b65a6639265a16b89fdca88d06d18894f90fcdb50142004329/data' :
-        'community.wave.seqera.io/library/multiqc:1.31--1efbafd542a23882' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8c/8c6c120d559d7ee04c7442b61ad7cf5a9e8970be5feefb37d68eeaa60c1034eb/data' :
+        'community.wave.seqera.io/library/multiqc:1.32--d58f60e4deb769bf' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index 17881d15..a88bafd6 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f"
+                "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-09-08T20:57:36.139055243"
+        "timestamp": "2025-10-27T13:33:24.356715"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f"
+                "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-09-08T20:59:15.142230631"
+        "timestamp": "2025-10-27T13:34:11.103619"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f"
+                "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-09-08T20:58:29.629087066"
+        "timestamp": "2025-10-27T13:34:04.615233"
     }
 }
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index ba1b179c..3e26497f 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -170,8 +170,6 @@ profiles {
     test_full { includeConfig 'conf/test_full.config' }
 }
 
-// Set AWS client to anonymous when using the default igenomes_base
-aws.client.anonymous = !params.igenomes_ignore && params.igenomes_base?.startsWith('s3://ngi-igenomes/igenomes/') ?: false
 // Load nf-core custom profiles from different institutions
 
 // If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included.
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index fff8a7c6..2662b98b 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,8 +22,8 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2025-10-16T13:38:57+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by Adrien Coulier.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "datePublished": "2025-11-20T09:32:26+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by Adrien Coulier.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
                     "@id": "main.nf"
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#cc905640-68e5-4225-9aba-bfd290c08fdf"
+                    "@id": "#ac0a8bf0-7553-40cd-ac01-50ae6184f724"
                 }
             ],
             "name": "nf-core/seqinspector"
@@ -128,7 +128,7 @@
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2025-10-16T13:38:57Z",
+            "dateModified": "2025-11-20T09:32:26Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": ["nf-core", "nextflow", "genomics", "quality-control"],
             "license": ["MIT"],
@@ -160,11 +160,11 @@
             "version": "!>=25.04.0"
         },
         {
-            "@id": "#cc905640-68e5-4225-9aba-bfd290c08fdf",
+            "@id": "#ac0a8bf0-7553-40cd-ac01-50ae6184f724",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#2cb8f151-0728-49b6-969d-b792c1b849b0"
+                    "@id": "#6e9e5864-2ba6-4edc-8e26-0abfa747f70c"
                 }
             ],
             "mainEntity": {
@@ -173,7 +173,7 @@
             "name": "Test suite for nf-core/seqinspector"
         },
         {
-            "@id": "#2cb8f151-0728-49b6-969d-b792c1b849b0",
+            "@id": "#6e9e5864-2ba6-4edc-8e26-0abfa747f70c",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/seqinspector",
             "resource": "repos/nf-core/seqinspector/actions/workflows/nf-test.yml",
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index 314467d9..0e56d79c 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -39,7 +39,7 @@ workflow PIPELINE_INITIALISATION {
 
     main:
 
-    ch_versions = Channel.empty()
+    ch_versions = channel.empty()
 
     //
     // Print version and exit if required and dump pipeline parameters to JSON file
@@ -64,7 +64,7 @@ workflow PIPELINE_INITIALISATION {
 \033[0;35m  nf-core/seqinspector ${workflow.manifest.version}\033[0m
 -\033[2m----------------------------------------------------\033[0m-
 """
-    after_text = """${workflow.manifest.doi ? "\n* The pipeline\n" : ""}${workflow.manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${workflow.manifest.doi ? "\n" : ""}
+    after_text = """${workflow.manifest.doi ? "\n* The pipeline\n" : ""}${workflow.manifest.doi.tokenize(",").collect { doi -> "    https://doi.org/${doi.trim().replace('https://doi.org/','')}"}.join("\n")}${workflow.manifest.doi ? "\n" : ""}
 * The nf-core framework
     https://doi.org/10.1038/s41587-020-0439-x
 
@@ -101,7 +101,7 @@ workflow PIPELINE_INITIALISATION {
     // Create channel from input file provided through params.input
     //
 
-    Channel
+    channel
         .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
         .map {
             meta, fastq_1, fastq_2 ->
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index bfd25876..2f30e9a4 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -98,7 +98,7 @@ def workflowVersionToYAML() {
 // Get channel of software versions used in pipeline in YAML format
 //
 def softwareVersionsToYAML(ch_versions) {
-    return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML()))
+    return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(channel.of(workflowVersionToYAML()))
 }
 
 //
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index a009066f..727a1548 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -22,8 +22,8 @@ workflow SEQINSPECTOR {
     ch_samplesheet // channel: samplesheet read in from --input
     main:
 
-    ch_versions = Channel.empty()
-    ch_multiqc_files = Channel.empty()
+    ch_versions = channel.empty()
+    ch_multiqc_files = channel.empty()
     //
     // MODULE: Run FastQC
     //
@@ -36,7 +36,25 @@ workflow SEQINSPECTOR {
     //
     // Collate and save software versions
     //
-    softwareVersionsToYAML(ch_versions)
+    def topic_versions = Channel.topic("versions")
+        .distinct()
+        .branch { entry ->
+            versions_file: entry instanceof Path
+            versions_tuple: true
+        }
+
+    def topic_versions_string = topic_versions.versions_tuple
+        .map { process, tool, version ->
+            [ process[process.lastIndexOf(':')+1..-1], "  ${tool}: ${version}" ]
+        }
+        .groupTuple(by:0)
+        .map { process, tool_versions ->
+            tool_versions.unique().sort()
+            "${process}:\n${tool_versions.join('\n')}"
+        }
+
+    softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file))
+        .mix(topic_versions_string)
         .collectFile(
             storeDir: "${params.outdir}/pipeline_info",
             name: 'nf_core_'  +  'seqinspector_software_'  + 'mqc_'  + 'versions.yml',
@@ -48,24 +66,24 @@ workflow SEQINSPECTOR {
     //
     // MODULE: MultiQC
     //
-    ch_multiqc_config        = Channel.fromPath(
+    ch_multiqc_config        = channel.fromPath(
         "$projectDir/assets/multiqc_config.yml", checkIfExists: true)
     ch_multiqc_custom_config = params.multiqc_config ?
-        Channel.fromPath(params.multiqc_config, checkIfExists: true) :
-        Channel.empty()
+        channel.fromPath(params.multiqc_config, checkIfExists: true) :
+        channel.empty()
     ch_multiqc_logo          = params.multiqc_logo ?
-        Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
-        Channel.empty()
+        channel.fromPath(params.multiqc_logo, checkIfExists: true) :
+        channel.empty()
 
     summary_params      = paramsSummaryMap(
         workflow, parameters_schema: "nextflow_schema.json")
-    ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
+    ch_workflow_summary = channel.value(paramsSummaryMultiqc(summary_params))
     ch_multiqc_files = ch_multiqc_files.mix(
         ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
     ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
         file(params.multiqc_methods_description, checkIfExists: true) :
         file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
-    ch_methods_description                = Channel.value(
+    ch_methods_description                = channel.value(
         methodsDescriptionText(ch_multiqc_custom_methods_description))
 
     ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)

From f281848d28a7cd204bf73ccc1786a3d60026b541 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <163723002+agrima2010@users.noreply.github.com>
Date: Thu, 20 Nov 2025 10:19:26 +0000
Subject: [PATCH 338/530] removed hasta config and corrected
 nextflow_schema.json

---
 conf/seqinspector_v1.0_stage_resources.config | 72 -------------------
 1 file changed, 72 deletions(-)
 delete mode 100644 conf/seqinspector_v1.0_stage_resources.config

diff --git a/conf/seqinspector_v1.0_stage_resources.config b/conf/seqinspector_v1.0_stage_resources.config
deleted file mode 100644
index c7f4f647..00000000
--- a/conf/seqinspector_v1.0_stage_resources.config
+++ /dev/null
@@ -1,72 +0,0 @@
-process {
-
-
-    // TODO nf-core: Check the defaults for all processes
-    cpus   = { 1      * task.attempt }
-    memory = { 6.GB   * task.attempt }
-    time   = { 4.h    * task.attempt }
-
-    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
-    maxRetries    = 2
-    maxErrors     = '-1'
-
-
-    // Subsampling reads
-    withName: 'SEQTK_SAMPLE' {
-        cpus = 6
-        memory = { 4.GB * task.attempt }
-        time = { 4.h * task.attempt }
-    }
-
-    // Quality control
-    withName: 'FASTQC' {
-        cpus = 2
-        memory = { 36.GB * task.attempt }
-        time = { 8.h * task.attempt }
-    }
-    withName: 'SEQFU_STATS' {
-        cpus = 6
-        memory = { 4.GB * task.attempt }
-        time = { 4.h * task.attempt }
-    }
-    withName: 'FASTQSCREEN_FASTQSCREEN' {
-        cpus = 6
-        memory = { 36.GB * task.attempt }
-        time = { 8.h * task.attempt }
-    }
-
-    // Reference genome processing
-    withName: 'BWAMEM2_INDEX' {
-        cpus = 12
-        memory = { 72.GB * task.attempt }
-        time = { 16.h * task.attempt }
-    }
-    withName: 'BWAMEM2_MEM' {
-        cpus = 6
-        memory = { 35.GB * task.attempt }
-        time = { 16.h * task.attempt }
-    }
-    withName: 'SAMTOOLS_INDEX' {
-        cpus = 6
-        memory = { 4.GB * task.attempt }
-        time = { 4.h * task.attempt }
-    }
-    withName: 'SAMTOOLS_FAIDX' {
-        cpus = 6
-        memory = { 6.GB * task.attempt }
-        time = { 4.h * task.attempt }
-    }
-    // Picard metrics
-    withName: 'PICARD_COLLECTMULTIPLEMETRICS' {
-        cpus = 4
-        memory = { 8.GB * task.attempt }
-        time = { 4.h * task.attempt }
-    }
-
-    // MultiQC aggregation
-    withName: 'MULTIQC_GLOBAL|MULTIQC_PER_TAG' {
-        cpus = 4
-        memory = { 4.GB * task.attempt }
-        time = { 4.h * task.attempt }
-    }
-}

From 6edf19f3b2647df26aba9e36cc99b8f94b5ce200 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <163723002+agrima2010@users.noreply.github.com>
Date: Thu, 20 Nov 2025 11:05:29 +0000
Subject: [PATCH 339/530] nextflow_schema.json

---
 nextflow_schema.json | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 00310552..2b3f78dc 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -97,6 +97,9 @@
                     "default": "${projectDir}/assets/example_fastq_screen_references.csv",
                     "fa_icon": "fas fa-search",
                     "description": "A .csv of reference genomes to be mapped against by FastQ Screen"
+                },
+                "bwa_index": {
+                    "type": "string"
                 }
             }
         },
@@ -283,10 +286,5 @@
         {
             "$ref": "#/$defs/generic_options"
         }
-    ],
-    "properties": {
-        "bwa_index": {
-            "type": "string"
-        }
-    }
+    ]
 }

From aff9444c283468dce330eed813f41bb89ea7b98f Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <163723002+agrima2010@users.noreply.github.com>
Date: Thu, 20 Nov 2025 11:07:22 +0000
Subject: [PATCH 340/530] nextflow.config

---
 nextflow.config | 2 --
 1 file changed, 2 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 2397152c..e92db43a 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -19,8 +19,6 @@ params {
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
     igenomes_ignore            = false
     sort_bam                   = true
-    bwa_index                  = null
-
     // Fastqscreen options
     fastq_screen_references    = "${projectDir}/assets/example_fastq_screen_references.csv"
 

From d9373dddc28bbb33f0c7fb81c92eeff741b67882 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <163723002+agrima2010@users.noreply.github.com>
Date: Thu, 20 Nov 2025 11:10:16 +0000
Subject: [PATCH 341/530] removed channel output of BAM from seqinspector.nf

---
 workflows/seqinspector.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index b7c665b6..9472748a 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -154,7 +154,6 @@ workflow SEQINSPECTOR {
         )
         ch_bwamem2_mem = BWAMEM2_MEM.out.bam
         ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions)
-        ch_bwamem2_mem.view { "BAM: ${it}" }
     }
     // MODULE: Index BAM files with Samtools
     if (!("samtools_index" in skip_tools) && !("bwamem2_mem" in skip_tools)) {

From 2bc95ba0d293001002e710228a5c4af9eb4de88c Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <163723002+agrima2010@users.noreply.github.com>
Date: Thu, 20 Nov 2025 11:40:32 +0000
Subject: [PATCH 342/530] bwa_index added to nextflow.config

---
 nextflow.config | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nextflow.config b/nextflow.config
index e92db43a..6ce84baf 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -19,6 +19,7 @@ params {
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
     igenomes_ignore            = false
     sort_bam                   = true
+    bwa_index                  = null
     // Fastqscreen options
     fastq_screen_references    = "${projectDir}/assets/example_fastq_screen_references.csv"
 

From 1fc87a8adfd2e3f844995eac8951e927d3426c3b Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <163723002+agrima2010@users.noreply.github.com>
Date: Thu, 20 Nov 2025 12:52:51 +0100
Subject: [PATCH 343/530] Update nextflow_schema.json

Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
---
 nextflow_schema.json | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 2b3f78dc..5d663de7 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -99,7 +99,12 @@
                     "description": "A .csv of reference genomes to be mapped against by FastQ Screen"
                 },
                 "bwa_index": {
-                    "type": "string"
+                    "type": "string",
+                    "format": "directory-path",
+                    "exists": true,
+                    "fa_icon": "fas fa-copy",
+                    "description": "Path to BWA mem indices.",
+                    "help_text": "If you wish to recompute indices available on igenomes, set `--bwa false`.\n\n> **NB** If none provided, will be generated automatically from the FASTA reference. Combine with `--save_reference` to save for future runs.\n\nIf you use AWS iGenomes, this has already been set for you appropriately."
                 }
             }
         },

From 3a77ea6432482c76dd6ab01da3a01d58c09a6506 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 20 Nov 2025 13:11:03 +0100
Subject: [PATCH 344/530] fix multiqc modules install

---
 modules.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules.json b/modules.json
index b75426a8..69e8fb48 100644
--- a/modules.json
+++ b/modules.json
@@ -39,7 +39,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "af27af1be706e6a2bb8fe454175b0cdf77f47b49",
+                        "git_sha": "82a79183037a403ad1b6714e5dbcff25500efaf6",
                         "installed_by": ["modules"]
                     },
                     "picard/collectmultiplemetrics": {

From b85608cadecbaee9d857d63d45a8e269e1c1ad2e Mon Sep 17 00:00:00 2001
From: matrulda <matilda.aslin@medsci.uu.se>
Date: Mon, 24 Nov 2025 10:42:06 +0100
Subject: [PATCH 345/530] Update rundirparser test and add nextflow config for
 it

---
 modules/local/rundirparser/tests/main.nf.test | 52 +++++--------------
 .../local/rundirparser/tests/nextflow.config  |  1 +
 2 files changed, 14 insertions(+), 39 deletions(-)
 create mode 100644 modules/local/rundirparser/tests/nextflow.config

diff --git a/modules/local/rundirparser/tests/main.nf.test b/modules/local/rundirparser/tests/main.nf.test
index 0dc321de..eb239b9a 100644
--- a/modules/local/rundirparser/tests/main.nf.test
+++ b/modules/local/rundirparser/tests/main.nf.test
@@ -1,71 +1,45 @@
-// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
-// nf-core modules test rundirparser
 nextflow_process {
 
     name "Test Process RUNDIRPARSER"
     script "../main.nf"
     process "RUNDIRPARSER"
+    config "./nextflow.config"
 
-    tag "modules"
-    tag "modules_"
-    tag "rundirparser"
+    test("Should run without failures") {
 
-    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used
-    test("sarscov2 - bam") {
-
-        // TODO nf-core: If you are created a test for a chained module
-        // (the module requires running more than one process to generate the required output)
-        // add the 'setup' method here.
-        // You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules).
 
         when {
             process {
                 """
-                // TODO nf-core: define inputs of the process here. Example:
-
-                input[0] = [
-                    [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
-                ]
+                input[0] = file("$moduleDir/tests/data/test_rundir")
                 """
             }
         }
 
         then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-                //TODO nf-core: Add all required assertions to verify the test output.
-                // See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples.
-            )
+            assert process.success
+            assert snapshot(process.out.yml).match()
+            assert process.out.versions.size() == 1
         }
 
-    }
 
-    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
-    test("sarscov2 - bam - stub") {
+    }
 
-        options "-stub"
+    test("Should create correct yaml structure") {
 
         when {
             process {
                 """
-                // TODO nf-core: define inputs of the process here. Example:
-
-                input[0] = [
-                    [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
-                ]
+                input[0] = file("$moduleDir/tests/data/test_rundir")
                 """
             }
         }
 
         then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-                //TODO nf-core: Add all required assertions to verify the test output.
-            )
+            def yamlcontent = path(process.out.yml[0]).yaml
+
+            assert yamlcontent.custom_data.my_data_type.data."Instrument type" == "NovaSeqXPlus"
+            assert snapshot(process.out.yml).match()
         }
 
     }
diff --git a/modules/local/rundirparser/tests/nextflow.config b/modules/local/rundirparser/tests/nextflow.config
new file mode 100644
index 00000000..651f0b86
--- /dev/null
+++ b/modules/local/rundirparser/tests/nextflow.config
@@ -0,0 +1 @@
+nextflow.enable.moduleBinaries = true

From 6e961e87ef90379db49fba59b075918687acebb2 Mon Sep 17 00:00:00 2001
From: Karthik Nair <karthik.nair1194@gmail.com>
Date: Mon, 24 Nov 2025 11:12:51 +0100
Subject: [PATCH 346/530] Fix #94. Remove outdated TODOs

---
 conf/test.config | 2 --
 1 file changed, 2 deletions(-)

diff --git a/conf/test.config b/conf/test.config
index 286d1cf8..06607879 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -15,8 +15,6 @@ params {
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Input data
-    // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
-    // TODO nf-core: Give any required params for the test so that command line flags are not needed
     input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
     fastq_screen_references = "${projectDir}/assets/example_fastq_screen_references.csv"
 

From a3ad873e26be0e735d9ed0e02fee0532db6f1983 Mon Sep 17 00:00:00 2001
From: Karthik Nair <karthik.nair1194@gmail.com>
Date: Mon, 24 Nov 2025 11:22:00 +0100
Subject: [PATCH 347/530] Add #94 to Changelog

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index aaf4d24a..1c791381 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -33,7 +33,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#99](https://github.com/nf-core/seqinspector/pull/99) Fix group reports for paired reads
 - [#107](https://github.com/nf-core/seqinspector/pull/107) Put SeqFU-stats section reports together
 - [#112](https://github.com/nf-core/seqinspector/pull/112) Making fastq_screen_references value to use parentDir
-
+- [#94] (https://github.com/nf-core/seqinspector/issues/94) Go through and validate test data
 ### `Dependencies`
 
 - [#116](https://github.com/nf-core/seqinspector/pull/116) Update MultiQC to 1.28

From ab40404b6cb1158c54951b801ff3d532a8df54a8 Mon Sep 17 00:00:00 2001
From: Karthik Nair <karthik.nair1194@gmail.com>
Date: Mon, 24 Nov 2025 11:23:06 +0100
Subject: [PATCH 348/530] Add #94 to Changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1c791381..23462dee 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -34,6 +34,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#107](https://github.com/nf-core/seqinspector/pull/107) Put SeqFU-stats section reports together
 - [#112](https://github.com/nf-core/seqinspector/pull/112) Making fastq_screen_references value to use parentDir
 - [#94] (https://github.com/nf-core/seqinspector/issues/94) Go through and validate test data
+
 ### `Dependencies`
 
 - [#116](https://github.com/nf-core/seqinspector/pull/116) Update MultiQC to 1.28

From abf53dc504019b3ae55f1323a86462c54547129a Mon Sep 17 00:00:00 2001
From: Franziska Bonath <41994400+FranBonath@users.noreply.github.com>
Date: Mon, 24 Nov 2025 11:24:26 +0100
Subject: [PATCH 349/530] Update README.md
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Pontus Höjer <pontus.hojer@scilifelab.se>
---
 README.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 3c4f9a36..55dfc17c 100644
--- a/README.md
+++ b/README.md
@@ -32,9 +32,9 @@
 
 1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))
 2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-3. Sequence statistics ([`SeqFu Stats`](https://github.com/telatin/seqfu2))
-4. Contamination QC ([`FastQ Screen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/))
-5. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+3. Report read counts and lengths statistics ([`SeqFu Stats`](https://github.com/telatin/seqfu2))
+4. Screen reads against references ([`FastQ Screen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/))
+5. Compile QC results into report ([`MultiQC`](http://multiqc.info/))
 
 ## Usage
 

From 8c09da2dc3fd10c456e96d685d95589de37cf349 Mon Sep 17 00:00:00 2001
From: FranBonath <franziska.bonath@scilifelab.se>
Date: Mon, 24 Nov 2025 11:40:06 +0100
Subject: [PATCH 350/530] add tubemap and logo to intro page

---
 README.md        | 4 ++++
 conf/test.config | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 8ad43f23..3d8ffddc 100644
--- a/README.md
+++ b/README.md
@@ -21,6 +21,8 @@
 
 ## Introduction
 
+![nf-core/seqinspector logo](docs/images/nf-core-seqinspector_logo_light.png)
+
 **nf-core/seqinspector** is a bioinformatics pipeline that ...
 
 <!-- TODO nf-core:
@@ -41,6 +43,8 @@
 6. Collect multiple QC metrics ([`Picard CollectMultipleMetrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html))
 7. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
 
+![nf-core/seqinspector metro map](docs/images/seqinspector_tubemap_V1.0.png)
+
 ## Usage
 
 > [!NOTE]
diff --git a/conf/test.config b/conf/test.config
index 286d1cf8..7371a410 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -27,7 +27,7 @@ params {
 process {
     resourceLimits = [
         cpus: 4,
-        memory: '15.GB',
+        memory: '8.GB',
         time: '1.h'
     ]
 

From 317cfd4a307f5d7ce9669502e3eed0d74e2178e8 Mon Sep 17 00:00:00 2001
From: FranBonath <franziska.bonath@scilifelab.se>
Date: Mon, 24 Nov 2025 11:56:30 +0100
Subject: [PATCH 351/530] update tubemap and some updates to README

---
 README.md                                 |   14 +-
 docs/images/seqinspector_tubemap_V1.0.png |  Bin 103756 -> 94473 bytes
 docs/images/seqinspector_tubemap_V1.0.svg | 2831 ++++++++++-----------
 3 files changed, 1295 insertions(+), 1550 deletions(-)

diff --git a/README.md b/README.md
index 4343adfb..428ad644 100644
--- a/README.md
+++ b/README.md
@@ -22,8 +22,9 @@
 ## Introduction
 
 ![nf-core/seqinspector logo](docs/images/nf-core-seqinspector_logo_light.png)
+![nf-core/seqinspector hex logo](docs/images/nfcore-seqinspector-logo-hex-light.png)
 
-**nf-core/seqinspector** is a bioinformatics pipeline that that processes raw sequencedata (FASTQ) to provide comprehensive quality control. It can perform subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants. The pipeline generates detailed MultiQC reports with flexible output options, ranging from individual sample reports to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments.
+**nf-core/seqinspector** is a bioinformatics pipeline that that processes raw sequencedata (FASTQ) to provide comprehensive quality control. It can perform subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants. The pipeline generates detailed MultiQC reports with flexible output options, ranging from individual sample reports to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments. If provided, nf-core/seqinspector can also parse statistics from an Illumina run folder directory into the final MultiQC reports.
 
 <!-- TODO nf-core:
    Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the
@@ -36,11 +37,12 @@
 
 1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))
 2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-3. Align reads to reference with ([`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2))
-4. Index aligned BAM files ([`SAMtools`](http://github.com/samtools))
-5. Create FASTA index ([`SAMtools`](http://github.com/samtools))
-6. Collect multiple QC metrics ([`Picard CollectMultipleMetrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html))
-7. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+3. Basic contamination detection ([`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/))
+4. Align reads to reference with ([`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2))
+5. Index aligned BAM files ([`SAMtools`](http://github.com/samtools))
+6. Create FASTA index ([`SAMtools`](http://github.com/samtools))
+7. Collect multiple QC metrics ([`Picard CollectMultipleMetrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html))
+8. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
 
 ![nf-core/seqinspector metro map](docs/images/seqinspector_tubemap_V1.0.png)
 
diff --git a/docs/images/seqinspector_tubemap_V1.0.png b/docs/images/seqinspector_tubemap_V1.0.png
index 0bb3dfca89fae5e98f39d70dab3a6b193521ad04..2429e6393a108efbf6f7e12b5a4b8cf409cd08ec 100644
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From 7996d9e1ee861f079d63a700758a8aa55e547d71 Mon Sep 17 00:00:00 2001
From: FranBonath <franziska.bonath@scilifelab.se>
Date: Mon, 24 Nov 2025 12:00:56 +0100
Subject: [PATCH 352/530] update tubmap again

---
 docs/images/seqinspector_tubemap_V1.0.png | Bin 94473 -> 85545 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs/images/seqinspector_tubemap_V1.0.png b/docs/images/seqinspector_tubemap_V1.0.png
index 2429e6393a108efbf6f7e12b5a4b8cf409cd08ec..4a505165acb6f7c77ff86879745fd2b21babde84 100644
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U+^dg3LBLB~SVk!IiN=Tj0WS*UqyPW_


From 930f0f2d28fda12016834de568aeb6182de3b626 Mon Sep 17 00:00:00 2001
From: FranBonath <franziska.bonath@scilifelab.se>
Date: Mon, 24 Nov 2025 12:15:18 +0100
Subject: [PATCH 353/530] add SeqFu Stats to README.md

---
 README.md | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index 428ad644..2b9f4b8b 100644
--- a/README.md
+++ b/README.md
@@ -38,11 +38,12 @@
 1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))
 2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
 3. Basic contamination detection ([`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/))
-4. Align reads to reference with ([`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2))
-5. Index aligned BAM files ([`SAMtools`](http://github.com/samtools))
-6. Create FASTA index ([`SAMtools`](http://github.com/samtools))
-7. Collect multiple QC metrics ([`Picard CollectMultipleMetrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html))
-8. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+4. Sequence statistics ([`SeqFu Stats`](https://github.com/telatin/seqfu2))
+5. Align reads to reference with ([`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2))
+6. Index aligned BAM files ([`SAMtools`](http://github.com/samtools))
+7. Create FASTA index ([`SAMtools`](http://github.com/samtools))
+8. Collect multiple QC metrics ([`Picard CollectMultipleMetrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html))
+9. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
 
 ![nf-core/seqinspector metro map](docs/images/seqinspector_tubemap_V1.0.png)
 

From 2aad60bf299f8a23a248b1f9a96074213eeccad6 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Mon, 24 Nov 2025 14:17:31 +0100
Subject: [PATCH 354/530] Install picard_collecthsmetrics.

---
 .../picard/collecthsmetrics/environment.yml   |   8 +
 .../nf-core/picard/collecthsmetrics/main.nf   |  83 +++
 .../nf-core/picard/collecthsmetrics/meta.yml  | 114 ++++
 .../collecthsmetrics/tests/main.nf.test       | 234 +++++++
 .../collecthsmetrics/tests/main.nf.test.snap  | 594 ++++++++++++++++++
 5 files changed, 1033 insertions(+)
 create mode 100644 modules/nf-core/picard/collecthsmetrics/environment.yml
 create mode 100644 modules/nf-core/picard/collecthsmetrics/main.nf
 create mode 100644 modules/nf-core/picard/collecthsmetrics/meta.yml
 create mode 100644 modules/nf-core/picard/collecthsmetrics/tests/main.nf.test
 create mode 100644 modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap

diff --git a/modules/nf-core/picard/collecthsmetrics/environment.yml b/modules/nf-core/picard/collecthsmetrics/environment.yml
new file mode 100644
index 00000000..b4ac4fe0
--- /dev/null
+++ b/modules/nf-core/picard/collecthsmetrics/environment.yml
@@ -0,0 +1,8 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  # renovate: datasource=conda depName=bioconda/picard
+  - bioconda::picard=3.4.0
diff --git a/modules/nf-core/picard/collecthsmetrics/main.nf b/modules/nf-core/picard/collecthsmetrics/main.nf
new file mode 100644
index 00000000..b86053e5
--- /dev/null
+++ b/modules/nf-core/picard/collecthsmetrics/main.nf
@@ -0,0 +1,83 @@
+process PICARD_COLLECTHSMETRICS {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' :
+        'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }"
+
+    input:
+    tuple val(meta), path(bam), path(bai), path(bait_intervals, stageAs: "baits/*"), path(target_intervals, stageAs: 'targets/*')
+    tuple val(meta2), path(ref)
+    tuple val(meta3), path(ref_fai)
+    tuple val(meta4), path(ref_dict)
+    tuple val(meta5), path(ref_gzi) // ref_gzi only required if reference is gzipped
+
+    output:
+    tuple val(meta), path("*_metrics")  , emit: metrics
+    path "versions.yml"                 , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def reference = ref ? "--REFERENCE_SEQUENCE ${ref}" : ""
+
+    def avail_mem = 3072
+    if (!task.memory) {
+        log.info '[Picard CollectHsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = (task.memory.mega*0.8).intValue()
+    }
+
+    def bait_interval_list = bait_intervals
+    def bait_intervallist_cmd = ""
+    if (bait_intervals =~ /.(bed|bed.gz)$/){
+        bait_interval_list = bait_intervals.toString().replaceAll(/.(bed|bed.gz)$/, ".interval_list")
+        bait_intervallist_cmd = "picard -Xmx${avail_mem}M BedToIntervalList --INPUT ${bait_intervals} --OUTPUT ${bait_interval_list} --SEQUENCE_DICTIONARY ${ref_dict} --TMP_DIR ."
+    }
+
+    def target_interval_list = target_intervals
+    def target_intervallist_cmd = ""
+    if (target_intervals =~ /.(bed|bed.gz)$/){
+        target_interval_list = target_intervals.toString().replaceAll(/.(bed|bed.gz)$/, ".interval_list")
+        target_intervallist_cmd = "picard -Xmx${avail_mem}M BedToIntervalList --INPUT ${target_intervals} --OUTPUT ${target_interval_list} --SEQUENCE_DICTIONARY ${ref_dict} --TMP_DIR ."
+    }
+
+
+    """
+
+    $bait_intervallist_cmd
+    $target_intervallist_cmd
+
+    picard \\
+        -Xmx${avail_mem}M \\
+        CollectHsMetrics \\
+        $args \\
+        $reference \\
+        --BAIT_INTERVALS $bait_interval_list \\
+        --TARGET_INTERVALS $target_interval_list \\
+        --INPUT $bam \\
+        --OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics
+
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        picard: \$(echo \$(picard CollectHsMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.CollectHsMetrics.coverage_metrics
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        picard: \$(echo \$(picard CollectHsMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/picard/collecthsmetrics/meta.yml b/modules/nf-core/picard/collecthsmetrics/meta.yml
new file mode 100644
index 00000000..511ae959
--- /dev/null
+++ b/modules/nf-core/picard/collecthsmetrics/meta.yml
@@ -0,0 +1,114 @@
+name: picard_collecthsmetrics
+description: Collects hybrid-selection (HS) metrics for a SAM or BAM file.
+keywords:
+  - alignment
+  - metrics
+  - statistics
+  - insert
+  - hybrid-selection
+  - quality
+  - bam
+tools:
+  - picard:
+      description: |
+        A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)
+        data and formats such as SAM/BAM/CRAM and VCF.
+      homepage: https://broadinstitute.github.io/picard/
+      documentation: https://broadinstitute.github.io/picard/
+      tool_dev_url: https://github.com/broadinstitute/picard/
+      licence: ["MIT"]
+      identifier: biotools:picard_tools
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: An aligned BAM/CRAM/SAM file
+        pattern: "*.{bam,cram,sam}"
+        ontologies: []
+    - bai:
+        type: file
+        description: Optional aligned BAM/CRAM/SAM file index
+        pattern: "*.{bai,crai,sai}"
+        ontologies: []
+    - bait_intervals:
+        type: file
+        description: An interval file that contains the locations of the baits used.
+        pattern: "*.{interval_list,bed,bed.gz}"
+        ontologies: []
+    - target_intervals:
+        type: file
+        description: An interval file that contains the locations of the targets.
+        pattern: "*.{interval_list,bed,bed.gz}"
+        ontologies: []
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'genome' ]
+    - ref:
+        type: file
+        description: |
+          A reference file to calculate dropout metrics measuring reduced representation of reads.
+          Optional input.
+        pattern: "*.{fa,fa.gz,fasta,fasta.gz,fna,fna.gz}"
+        ontologies: []
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'genome' ]
+    - ref_fai:
+        type: file
+        description: Index of reference file. Only needed when reference is supplied.
+        pattern: "*.fai"
+        ontologies: []
+  - - meta4:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'genome' ]
+    - ref_dict:
+        type: file
+        description: Sequence dictionary of FASTA file. Only needed when bed interval
+          lists are supplied.
+        pattern: "*.dict"
+        ontologies: []
+  - - meta5:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'genome' ]
+    - ref_gzi:
+        type: file
+        description: Index of reference file. Only needed when gzipped reference is supplied.
+        pattern: "*.gzi"
+        ontologies: []
+output:
+  metrics:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*_metrics":
+          type: file
+          description: Alignment metrics files generated by picard
+          pattern: "*_{metrics}"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
+authors:
+  - "@projectoriented"
+  - "@matthdsm"
+maintainers:
+  - "@projectoriented"
+  - "@matthdsm"
diff --git a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test
new file mode 100644
index 00000000..fe40e7b0
--- /dev/null
+++ b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test
@@ -0,0 +1,234 @@
+nextflow_process {
+
+    name "Test Process PICARD_COLLECTHSMETRICS"
+    script "../main.nf"
+    process "PICARD_COLLECTHSMETRICS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "picard"
+    tag "picard/collecthsmetrics"
+
+    test("sarscov2 - bam") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true)
+                    ]
+                input[1] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
+                input[2] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]
+                input[3] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)]
+                input[4] = [[:],[]]
+                """
+            }
+        }
+
+        then {
+            def size = path(process.out.metrics[0][1]).size()
+            def lines = path(process.out.metrics[0][1]).readLines()[0..100]
+            lines.remove(3)  // remove timestamp
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.metrics[0][1]).name,
+                    size,
+                    lines,
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam - gzippedfa") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                        [ id:'test', single_end:false ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true)
+                    ]
+                input[1] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)]
+                input[2] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz.fai', checkIfExists: true)]
+                input[3] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)]
+                input[4] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz.gzi', checkIfExists: true)]
+                """
+            }
+        }
+
+        then {
+            def size = path(process.out.metrics[0][1]).size()
+            def lines = path(process.out.metrics[0][1]).readLines()[0..100]
+            lines.remove(3)  // remove timestamp
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.metrics[0][1]).name,
+                    size,
+                    lines,
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true)
+                    ]
+                input[1] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
+                input[2] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]
+                input[3] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)]
+                input[4] = [[:],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam - nofasta") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true)
+                    ]
+                input[1] = [[:],[]]
+                input[2] = [[:],[]]
+                input[3] = [[:],[]]
+                input[4] = [[:],[]]
+                """
+            }
+        }
+
+        then {
+            def size = path(process.out.metrics[0][1]).size()
+            def lines = path(process.out.metrics[0][1]).readLines()[0..100]
+            lines.remove(3)  // remove timestamp
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.metrics[0][1]).name,
+                    size,
+                    lines,
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam - bed") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/baits.bed', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
+                    ]
+
+                input[1] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
+                input[2] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]
+                input[3] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)]
+                input[4] = [[:],[]]
+                """
+            }
+        }
+
+        then {
+            def size = path(process.out.metrics[0][1]).size()
+            def lines = path(process.out.metrics[0][1]).readLines()[0..100]
+            lines.remove(3)  // remove timestamp
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.metrics[0][1]).name,
+                    size,
+                    lines,
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam - samebed") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/baits.bed', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/baits.bed', checkIfExists: true)
+                    ]
+
+                input[1] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
+                input[2] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]
+                input[3] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)]
+                input[4] = [[:],[]]
+                """
+            }
+        }
+
+        then {
+            def size = path(process.out.metrics[0][1]).size()
+            def lines = path(process.out.metrics[0][1]).readLines()[0..100]
+            lines.remove(3)  // remove timestamp
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.metrics[0][1]).name,
+                    size,
+                    lines,
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+
+    }
+}
diff --git a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap
new file mode 100644
index 00000000..11b0f7c5
--- /dev/null
+++ b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap
@@ -0,0 +1,594 @@
+{
+    "sarscov2 - bam - nofasta": {
+        "content": [
+            "test.CollectHsMetrics.coverage_metrics",
+            3548,
+            [
+                "## htsjdk.samtools.metrics.StringHeader",
+                "# CollectHsMetrics --BAIT_INTERVALS baits/baits.interval_list --TARGET_INTERVALS targets/targets.interval_list --INPUT test.paired_end.sorted.bam --OUTPUT test.CollectHsMetrics.coverage_metrics --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false",
+                "## htsjdk.samtools.metrics.StringHeader",
+                "",
+                "## METRICS CLASS\tpicard.analysis.directed.HsMetrics",
+                "BAIT_SET\tBAIT_TERRITORY\tBAIT_DESIGN_EFFICIENCY\tON_BAIT_BASES\tNEAR_BAIT_BASES\tOFF_BAIT_BASES\tPCT_SELECTED_BASES\tPCT_OFF_BAIT\tON_BAIT_VS_SELECTED\tMEAN_BAIT_COVERAGE\tPCT_USABLE_BASES_ON_BAIT\tPCT_USABLE_BASES_ON_TARGET\tFOLD_ENRICHMENT\tHS_LIBRARY_SIZE\tHS_PENALTY_10X\tHS_PENALTY_20X\tHS_PENALTY_30X\tHS_PENALTY_40X\tHS_PENALTY_50X\tHS_PENALTY_100X\tTARGET_TERRITORY\tGENOME_SIZE\tTOTAL_READS\tPF_READS\tPF_BASES\tPF_UNIQUE_READS\tPF_UQ_READS_ALIGNED\tPF_BASES_ALIGNED\tPF_UQ_BASES_ALIGNED\tON_TARGET_BASES\tPCT_PF_READS\tPCT_PF_UQ_READS\tPCT_PF_UQ_READS_ALIGNED\tMEAN_TARGET_COVERAGE\tMEDIAN_TARGET_COVERAGE\tMAX_TARGET_COVERAGE\tMIN_TARGET_COVERAGE\tZERO_CVG_TARGETS_PCT\tPCT_EXC_DUPE\tPCT_EXC_ADAPTER\tPCT_EXC_MAPQ\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_OFF_TARGET\tFOLD_80_BASE_PENALTY\tPCT_TARGET_BASES_1X\tPCT_TARGET_BASES_2X\tPCT_TARGET_BASES_10X\tPCT_TARGET_BASES_20X\tPCT_TARGET_BASES_30X\tPCT_TARGET_BASES_40X\tPCT_TARGET_BASES_50X\tPCT_TARGET_BASES_100X\tPCT_TARGET_BASES_250X\tPCT_TARGET_BASES_500X\tPCT_TARGET_BASES_1000X\tPCT_TARGET_BASES_2500X\tPCT_TARGET_BASES_5000X\tPCT_TARGET_BASES_10000X\tPCT_TARGET_BASES_25000X\tPCT_TARGET_BASES_50000X\tPCT_TARGET_BASES_100000X\tAT_DROPOUT\tGC_DROPOUT\tHET_SNP_SENSITIVITY\tHET_SNP_Q\tSAMPLE\tLIBRARY\tREAD_GROUP",
+                "baits\t158\t0.594937\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.000181\t4.995204\t\t0\t0\t0\t0\t0\t0\t94\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t5\t1\t1\t0.985\t0.053191\t0\t1\t0\t0.75\t0\t0\t0.005438\t0.054487\t0.259516\t0.680377\t?\t0.053191\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.015734\t0\t\t\t",
+                "",
+                "## HISTOGRAM\tjava.lang.Integer",
+                "coverage_or_base_quality\thigh_quality_coverage_count\tunfiltered_baseq_count",
+                "0\t89\t0",
+                "1\t5\t0",
+                "2\t0\t0",
+                "3\t0\t0",
+                "4\t0\t0",
+                "5\t0\t0",
+                "6\t0\t0",
+                "7\t0\t0",
+                "8\t0\t0",
+                "9\t0\t0",
+                "10\t0\t0",
+                "11\t0\t0",
+                "12\t0\t0",
+                "13\t0\t0",
+                "14\t0\t5",
+                "15\t0\t0",
+                "16\t0\t0",
+                "17\t0\t0",
+                "18\t0\t0",
+                "19\t0\t0",
+                "20\t0\t0",
+                "21\t0\t1",
+                "22\t0\t0",
+                "23\t0\t0",
+                "24\t0\t0",
+                "25\t0\t0",
+                "26\t0\t0",
+                "27\t0\t0",
+                "28\t0\t0",
+                "29\t0\t0",
+                "30\t0\t0",
+                "31\t0\t0",
+                "32\t0\t1",
+                "33\t0\t0",
+                "34\t0\t0",
+                "35\t0\t0",
+                "36\t0\t3",
+                "37\t0\t0",
+                "38\t0\t0",
+                "39\t0\t0",
+                "40\t0\t0",
+                "41\t0\t0",
+                "42\t0\t0",
+                "43\t0\t0",
+                "44\t0\t0",
+                "45\t0\t0",
+                "46\t0\t0",
+                "47\t0\t0",
+                "48\t0\t0",
+                "49\t0\t0",
+                "50\t0\t0",
+                "51\t0\t0",
+                "52\t0\t0",
+                "53\t0\t0",
+                "54\t0\t0",
+                "55\t0\t0",
+                "56\t0\t0",
+                "57\t0\t0",
+                "58\t0\t0",
+                "59\t0\t0",
+                "60\t0\t0",
+                "61\t0\t0",
+                "62\t0\t0",
+                "63\t0\t0",
+                "64\t0\t0",
+                "65\t0\t0",
+                "66\t0\t0",
+                "67\t0\t0",
+                "68\t0\t0",
+                "69\t0\t0",
+                "70\t0\t0",
+                "71\t0\t0",
+                "72\t0\t0",
+                "73\t0\t0",
+                "74\t0\t0",
+                "75\t0\t0",
+                "76\t0\t0",
+                "77\t0\t0",
+                "78\t0\t0",
+                "79\t0\t0",
+                "80\t0\t0",
+                "81\t0\t0",
+                "82\t0\t0",
+                "83\t0\t0",
+                "84\t0\t0",
+                "85\t0\t0",
+                "86\t0\t0",
+                "87\t0\t0",
+                "88\t0\t0",
+                "89\t0\t0"
+            ],
+            [
+                "versions.yml:md5,533cf1e35d36fdacbb762f5df2e1b322"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.7"
+        },
+        "timestamp": "2025-09-15T10:37:59.62099935"
+    },
+    "sarscov2 - bam - gzippedfa": {
+        "content": [
+            "test.CollectHsMetrics.coverage_metrics",
+            3601,
+            [
+                "## htsjdk.samtools.metrics.StringHeader",
+                "# CollectHsMetrics --BAIT_INTERVALS baits/baits.interval_list --TARGET_INTERVALS targets/targets.interval_list --INPUT test.paired_end.sorted.bam --OUTPUT test.CollectHsMetrics.coverage_metrics --REFERENCE_SEQUENCE genome.fasta.gz --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false",
+                "## htsjdk.samtools.metrics.StringHeader",
+                "",
+                "## METRICS CLASS\tpicard.analysis.directed.HsMetrics",
+                "BAIT_SET\tBAIT_TERRITORY\tBAIT_DESIGN_EFFICIENCY\tON_BAIT_BASES\tNEAR_BAIT_BASES\tOFF_BAIT_BASES\tPCT_SELECTED_BASES\tPCT_OFF_BAIT\tON_BAIT_VS_SELECTED\tMEAN_BAIT_COVERAGE\tPCT_USABLE_BASES_ON_BAIT\tPCT_USABLE_BASES_ON_TARGET\tFOLD_ENRICHMENT\tHS_LIBRARY_SIZE\tHS_PENALTY_10X\tHS_PENALTY_20X\tHS_PENALTY_30X\tHS_PENALTY_40X\tHS_PENALTY_50X\tHS_PENALTY_100X\tTARGET_TERRITORY\tGENOME_SIZE\tTOTAL_READS\tPF_READS\tPF_BASES\tPF_UNIQUE_READS\tPF_UQ_READS_ALIGNED\tPF_BASES_ALIGNED\tPF_UQ_BASES_ALIGNED\tON_TARGET_BASES\tPCT_PF_READS\tPCT_PF_UQ_READS\tPCT_PF_UQ_READS_ALIGNED\tMEAN_TARGET_COVERAGE\tMEDIAN_TARGET_COVERAGE\tMAX_TARGET_COVERAGE\tMIN_TARGET_COVERAGE\tZERO_CVG_TARGETS_PCT\tPCT_EXC_DUPE\tPCT_EXC_ADAPTER\tPCT_EXC_MAPQ\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_OFF_TARGET\tFOLD_80_BASE_PENALTY\tPCT_TARGET_BASES_1X\tPCT_TARGET_BASES_2X\tPCT_TARGET_BASES_10X\tPCT_TARGET_BASES_20X\tPCT_TARGET_BASES_30X\tPCT_TARGET_BASES_40X\tPCT_TARGET_BASES_50X\tPCT_TARGET_BASES_100X\tPCT_TARGET_BASES_250X\tPCT_TARGET_BASES_500X\tPCT_TARGET_BASES_1000X\tPCT_TARGET_BASES_2500X\tPCT_TARGET_BASES_5000X\tPCT_TARGET_BASES_10000X\tPCT_TARGET_BASES_25000X\tPCT_TARGET_BASES_50000X\tPCT_TARGET_BASES_100000X\tAT_DROPOUT\tGC_DROPOUT\tHET_SNP_SENSITIVITY\tHET_SNP_Q\tSAMPLE\tLIBRARY\tREAD_GROUP",
+                "baits\t158\t0.594937\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.000181\t4.995204\t\t0\t0\t0\t0\t0\t0\t94\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t5\t1\t1\t0.985\t0.053191\t0\t1\t0\t0.75\t0\t0\t0.005438\t0.054487\t0.259516\t0.680377\t?\t0.053191\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t76.595745\t23.404255\t0.015734\t0\t\t\t",
+                "",
+                "## HISTOGRAM\tjava.lang.Integer",
+                "coverage_or_base_quality\thigh_quality_coverage_count\tunfiltered_baseq_count",
+                "0\t89\t0",
+                "1\t5\t0",
+                "2\t0\t0",
+                "3\t0\t0",
+                "4\t0\t0",
+                "5\t0\t0",
+                "6\t0\t0",
+                "7\t0\t0",
+                "8\t0\t0",
+                "9\t0\t0",
+                "10\t0\t0",
+                "11\t0\t0",
+                "12\t0\t0",
+                "13\t0\t0",
+                "14\t0\t5",
+                "15\t0\t0",
+                "16\t0\t0",
+                "17\t0\t0",
+                "18\t0\t0",
+                "19\t0\t0",
+                "20\t0\t0",
+                "21\t0\t1",
+                "22\t0\t0",
+                "23\t0\t0",
+                "24\t0\t0",
+                "25\t0\t0",
+                "26\t0\t0",
+                "27\t0\t0",
+                "28\t0\t0",
+                "29\t0\t0",
+                "30\t0\t0",
+                "31\t0\t0",
+                "32\t0\t1",
+                "33\t0\t0",
+                "34\t0\t0",
+                "35\t0\t0",
+                "36\t0\t3",
+                "37\t0\t0",
+                "38\t0\t0",
+                "39\t0\t0",
+                "40\t0\t0",
+                "41\t0\t0",
+                "42\t0\t0",
+                "43\t0\t0",
+                "44\t0\t0",
+                "45\t0\t0",
+                "46\t0\t0",
+                "47\t0\t0",
+                "48\t0\t0",
+                "49\t0\t0",
+                "50\t0\t0",
+                "51\t0\t0",
+                "52\t0\t0",
+                "53\t0\t0",
+                "54\t0\t0",
+                "55\t0\t0",
+                "56\t0\t0",
+                "57\t0\t0",
+                "58\t0\t0",
+                "59\t0\t0",
+                "60\t0\t0",
+                "61\t0\t0",
+                "62\t0\t0",
+                "63\t0\t0",
+                "64\t0\t0",
+                "65\t0\t0",
+                "66\t0\t0",
+                "67\t0\t0",
+                "68\t0\t0",
+                "69\t0\t0",
+                "70\t0\t0",
+                "71\t0\t0",
+                "72\t0\t0",
+                "73\t0\t0",
+                "74\t0\t0",
+                "75\t0\t0",
+                "76\t0\t0",
+                "77\t0\t0",
+                "78\t0\t0",
+                "79\t0\t0",
+                "80\t0\t0",
+                "81\t0\t0",
+                "82\t0\t0",
+                "83\t0\t0",
+                "84\t0\t0",
+                "85\t0\t0",
+                "86\t0\t0",
+                "87\t0\t0",
+                "88\t0\t0",
+                "89\t0\t0"
+            ],
+            [
+                "versions.yml:md5,533cf1e35d36fdacbb762f5df2e1b322"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.7"
+        },
+        "timestamp": "2025-09-15T10:37:32.831030701"
+    },
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,533cf1e35d36fdacbb762f5df2e1b322"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.7"
+        },
+        "timestamp": "2025-09-15T10:37:42.492104283"
+    },
+    "sarscov2 - bam - samebed": {
+        "content": [
+            "test.CollectHsMetrics.coverage_metrics",
+            3586,
+            [
+                "## htsjdk.samtools.metrics.StringHeader",
+                "# CollectHsMetrics --BAIT_INTERVALS baits/baits.interval_list --TARGET_INTERVALS targets/baits.interval_list --INPUT test.paired_end.sorted.bam --OUTPUT test.CollectHsMetrics.coverage_metrics --REFERENCE_SEQUENCE genome.fasta --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false",
+                "## htsjdk.samtools.metrics.StringHeader",
+                "",
+                "## METRICS CLASS\tpicard.analysis.directed.HsMetrics",
+                "BAIT_SET\tBAIT_TERRITORY\tBAIT_DESIGN_EFFICIENCY\tON_BAIT_BASES\tNEAR_BAIT_BASES\tOFF_BAIT_BASES\tPCT_SELECTED_BASES\tPCT_OFF_BAIT\tON_BAIT_VS_SELECTED\tMEAN_BAIT_COVERAGE\tPCT_USABLE_BASES_ON_BAIT\tPCT_USABLE_BASES_ON_TARGET\tFOLD_ENRICHMENT\tHS_LIBRARY_SIZE\tHS_PENALTY_10X\tHS_PENALTY_20X\tHS_PENALTY_30X\tHS_PENALTY_40X\tHS_PENALTY_50X\tHS_PENALTY_100X\tTARGET_TERRITORY\tGENOME_SIZE\tTOTAL_READS\tPF_READS\tPF_BASES\tPF_UNIQUE_READS\tPF_UQ_READS_ALIGNED\tPF_BASES_ALIGNED\tPF_UQ_BASES_ALIGNED\tON_TARGET_BASES\tPCT_PF_READS\tPCT_PF_UQ_READS\tPCT_PF_UQ_READS_ALIGNED\tMEAN_TARGET_COVERAGE\tMEDIAN_TARGET_COVERAGE\tMAX_TARGET_COVERAGE\tMIN_TARGET_COVERAGE\tZERO_CVG_TARGETS_PCT\tPCT_EXC_DUPE\tPCT_EXC_ADAPTER\tPCT_EXC_MAPQ\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_OFF_TARGET\tFOLD_80_BASE_PENALTY\tPCT_TARGET_BASES_1X\tPCT_TARGET_BASES_2X\tPCT_TARGET_BASES_10X\tPCT_TARGET_BASES_20X\tPCT_TARGET_BASES_30X\tPCT_TARGET_BASES_40X\tPCT_TARGET_BASES_50X\tPCT_TARGET_BASES_100X\tPCT_TARGET_BASES_250X\tPCT_TARGET_BASES_500X\tPCT_TARGET_BASES_1000X\tPCT_TARGET_BASES_2500X\tPCT_TARGET_BASES_5000X\tPCT_TARGET_BASES_10000X\tPCT_TARGET_BASES_25000X\tPCT_TARGET_BASES_50000X\tPCT_TARGET_BASES_100000X\tAT_DROPOUT\tGC_DROPOUT\tHET_SNP_SENSITIVITY\tHET_SNP_Q\tSAMPLE\tLIBRARY\tREAD_GROUP",
+                "baits\t158\t1\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.013782\t4.995204\t\t0\t0\t0\t0\t0\t0\t158\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t381\t1\t1\t0.985\t2.411392\t2\t3\t2\t0\t0\t0\t0.005438\t0.054487\t0.259516\t0.666655\t1.205696\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t7.018506\t0\t0.394337\t2\t\t\t",
+                "",
+                "## HISTOGRAM\tjava.lang.Integer",
+                "coverage_or_base_quality\thigh_quality_coverage_count\tunfiltered_baseq_count",
+                "0\t0\t0",
+                "1\t0\t0",
+                "2\t93\t0",
+                "3\t65\t0",
+                "4\t0\t0",
+                "5\t0\t0",
+                "6\t0\t0",
+                "7\t0\t0",
+                "8\t0\t0",
+                "9\t0\t0",
+                "10\t0\t0",
+                "11\t0\t0",
+                "12\t0\t0",
+                "13\t0\t0",
+                "14\t0\t28",
+                "15\t0\t0",
+                "16\t0\t0",
+                "17\t0\t0",
+                "18\t0\t0",
+                "19\t0\t0",
+                "20\t0\t0",
+                "21\t0\t9",
+                "22\t0\t0",
+                "23\t0\t0",
+                "24\t0\t0",
+                "25\t0\t0",
+                "26\t0\t0",
+                "27\t0\t20",
+                "28\t0\t0",
+                "29\t0\t0",
+                "30\t0\t0",
+                "31\t0\t0",
+                "32\t0\t90",
+                "33\t0\t0",
+                "34\t0\t0",
+                "35\t0\t0",
+                "36\t0\t262",
+                "37\t0\t0",
+                "38\t0\t0",
+                "39\t0\t0",
+                "40\t0\t0",
+                "41\t0\t0",
+                "42\t0\t0",
+                "43\t0\t0",
+                "44\t0\t0",
+                "45\t0\t0",
+                "46\t0\t0",
+                "47\t0\t0",
+                "48\t0\t0",
+                "49\t0\t0",
+                "50\t0\t0",
+                "51\t0\t0",
+                "52\t0\t0",
+                "53\t0\t0",
+                "54\t0\t0",
+                "55\t0\t0",
+                "56\t0\t0",
+                "57\t0\t0",
+                "58\t0\t0",
+                "59\t0\t0",
+                "60\t0\t0",
+                "61\t0\t0",
+                "62\t0\t0",
+                "63\t0\t0",
+                "64\t0\t0",
+                "65\t0\t0",
+                "66\t0\t0",
+                "67\t0\t0",
+                "68\t0\t0",
+                "69\t0\t0",
+                "70\t0\t0",
+                "71\t0\t0",
+                "72\t0\t0",
+                "73\t0\t0",
+                "74\t0\t0",
+                "75\t0\t0",
+                "76\t0\t0",
+                "77\t0\t0",
+                "78\t0\t0",
+                "79\t0\t0",
+                "80\t0\t0",
+                "81\t0\t0",
+                "82\t0\t0",
+                "83\t0\t0",
+                "84\t0\t0",
+                "85\t0\t0",
+                "86\t0\t0",
+                "87\t0\t0",
+                "88\t0\t0",
+                "89\t0\t0"
+            ],
+            [
+                "versions.yml:md5,533cf1e35d36fdacbb762f5df2e1b322"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.7"
+        },
+        "timestamp": "2025-09-15T10:38:39.302597954"
+    },
+    "sarscov2 - bam": {
+        "content": [
+            "test.CollectHsMetrics.coverage_metrics",
+            3598,
+            [
+                "## htsjdk.samtools.metrics.StringHeader",
+                "# CollectHsMetrics --BAIT_INTERVALS baits/baits.interval_list --TARGET_INTERVALS targets/targets.interval_list --INPUT test.paired_end.sorted.bam --OUTPUT test.CollectHsMetrics.coverage_metrics --REFERENCE_SEQUENCE genome.fasta --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false",
+                "## htsjdk.samtools.metrics.StringHeader",
+                "",
+                "## METRICS CLASS\tpicard.analysis.directed.HsMetrics",
+                "BAIT_SET\tBAIT_TERRITORY\tBAIT_DESIGN_EFFICIENCY\tON_BAIT_BASES\tNEAR_BAIT_BASES\tOFF_BAIT_BASES\tPCT_SELECTED_BASES\tPCT_OFF_BAIT\tON_BAIT_VS_SELECTED\tMEAN_BAIT_COVERAGE\tPCT_USABLE_BASES_ON_BAIT\tPCT_USABLE_BASES_ON_TARGET\tFOLD_ENRICHMENT\tHS_LIBRARY_SIZE\tHS_PENALTY_10X\tHS_PENALTY_20X\tHS_PENALTY_30X\tHS_PENALTY_40X\tHS_PENALTY_50X\tHS_PENALTY_100X\tTARGET_TERRITORY\tGENOME_SIZE\tTOTAL_READS\tPF_READS\tPF_BASES\tPF_UNIQUE_READS\tPF_UQ_READS_ALIGNED\tPF_BASES_ALIGNED\tPF_UQ_BASES_ALIGNED\tON_TARGET_BASES\tPCT_PF_READS\tPCT_PF_UQ_READS\tPCT_PF_UQ_READS_ALIGNED\tMEAN_TARGET_COVERAGE\tMEDIAN_TARGET_COVERAGE\tMAX_TARGET_COVERAGE\tMIN_TARGET_COVERAGE\tZERO_CVG_TARGETS_PCT\tPCT_EXC_DUPE\tPCT_EXC_ADAPTER\tPCT_EXC_MAPQ\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_OFF_TARGET\tFOLD_80_BASE_PENALTY\tPCT_TARGET_BASES_1X\tPCT_TARGET_BASES_2X\tPCT_TARGET_BASES_10X\tPCT_TARGET_BASES_20X\tPCT_TARGET_BASES_30X\tPCT_TARGET_BASES_40X\tPCT_TARGET_BASES_50X\tPCT_TARGET_BASES_100X\tPCT_TARGET_BASES_250X\tPCT_TARGET_BASES_500X\tPCT_TARGET_BASES_1000X\tPCT_TARGET_BASES_2500X\tPCT_TARGET_BASES_5000X\tPCT_TARGET_BASES_10000X\tPCT_TARGET_BASES_25000X\tPCT_TARGET_BASES_50000X\tPCT_TARGET_BASES_100000X\tAT_DROPOUT\tGC_DROPOUT\tHET_SNP_SENSITIVITY\tHET_SNP_Q\tSAMPLE\tLIBRARY\tREAD_GROUP",
+                "baits\t158\t0.594937\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.000181\t4.995204\t\t0\t0\t0\t0\t0\t0\t94\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t5\t1\t1\t0.985\t0.053191\t0\t1\t0\t0.75\t0\t0\t0.005438\t0.054487\t0.259516\t0.680377\t?\t0.053191\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t76.595745\t23.404255\t0.015734\t0\t\t\t",
+                "",
+                "## HISTOGRAM\tjava.lang.Integer",
+                "coverage_or_base_quality\thigh_quality_coverage_count\tunfiltered_baseq_count",
+                "0\t89\t0",
+                "1\t5\t0",
+                "2\t0\t0",
+                "3\t0\t0",
+                "4\t0\t0",
+                "5\t0\t0",
+                "6\t0\t0",
+                "7\t0\t0",
+                "8\t0\t0",
+                "9\t0\t0",
+                "10\t0\t0",
+                "11\t0\t0",
+                "12\t0\t0",
+                "13\t0\t0",
+                "14\t0\t5",
+                "15\t0\t0",
+                "16\t0\t0",
+                "17\t0\t0",
+                "18\t0\t0",
+                "19\t0\t0",
+                "20\t0\t0",
+                "21\t0\t1",
+                "22\t0\t0",
+                "23\t0\t0",
+                "24\t0\t0",
+                "25\t0\t0",
+                "26\t0\t0",
+                "27\t0\t0",
+                "28\t0\t0",
+                "29\t0\t0",
+                "30\t0\t0",
+                "31\t0\t0",
+                "32\t0\t1",
+                "33\t0\t0",
+                "34\t0\t0",
+                "35\t0\t0",
+                "36\t0\t3",
+                "37\t0\t0",
+                "38\t0\t0",
+                "39\t0\t0",
+                "40\t0\t0",
+                "41\t0\t0",
+                "42\t0\t0",
+                "43\t0\t0",
+                "44\t0\t0",
+                "45\t0\t0",
+                "46\t0\t0",
+                "47\t0\t0",
+                "48\t0\t0",
+                "49\t0\t0",
+                "50\t0\t0",
+                "51\t0\t0",
+                "52\t0\t0",
+                "53\t0\t0",
+                "54\t0\t0",
+                "55\t0\t0",
+                "56\t0\t0",
+                "57\t0\t0",
+                "58\t0\t0",
+                "59\t0\t0",
+                "60\t0\t0",
+                "61\t0\t0",
+                "62\t0\t0",
+                "63\t0\t0",
+                "64\t0\t0",
+                "65\t0\t0",
+                "66\t0\t0",
+                "67\t0\t0",
+                "68\t0\t0",
+                "69\t0\t0",
+                "70\t0\t0",
+                "71\t0\t0",
+                "72\t0\t0",
+                "73\t0\t0",
+                "74\t0\t0",
+                "75\t0\t0",
+                "76\t0\t0",
+                "77\t0\t0",
+                "78\t0\t0",
+                "79\t0\t0",
+                "80\t0\t0",
+                "81\t0\t0",
+                "82\t0\t0",
+                "83\t0\t0",
+                "84\t0\t0",
+                "85\t0\t0",
+                "86\t0\t0",
+                "87\t0\t0",
+                "88\t0\t0",
+                "89\t0\t0"
+            ],
+            [
+                "versions.yml:md5,533cf1e35d36fdacbb762f5df2e1b322"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.7"
+        },
+        "timestamp": "2025-09-15T10:37:15.861292725"
+    },
+    "sarscov2 - bam - bed": {
+        "content": [
+            "test.CollectHsMetrics.coverage_metrics",
+            3595,
+            [
+                "## htsjdk.samtools.metrics.StringHeader",
+                "# CollectHsMetrics --BAIT_INTERVALS baits/baits.interval_list --TARGET_INTERVALS targets/test.interval_list --INPUT test.paired_end.sorted.bam --OUTPUT test.CollectHsMetrics.coverage_metrics --REFERENCE_SEQUENCE genome.fasta --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false",
+                "## htsjdk.samtools.metrics.StringHeader",
+                "",
+                "## METRICS CLASS\tpicard.analysis.directed.HsMetrics",
+                "BAIT_SET\tBAIT_TERRITORY\tBAIT_DESIGN_EFFICIENCY\tON_BAIT_BASES\tNEAR_BAIT_BASES\tOFF_BAIT_BASES\tPCT_SELECTED_BASES\tPCT_OFF_BAIT\tON_BAIT_VS_SELECTED\tMEAN_BAIT_COVERAGE\tPCT_USABLE_BASES_ON_BAIT\tPCT_USABLE_BASES_ON_TARGET\tFOLD_ENRICHMENT\tHS_LIBRARY_SIZE\tHS_PENALTY_10X\tHS_PENALTY_20X\tHS_PENALTY_30X\tHS_PENALTY_40X\tHS_PENALTY_50X\tHS_PENALTY_100X\tTARGET_TERRITORY\tGENOME_SIZE\tTOTAL_READS\tPF_READS\tPF_BASES\tPF_UNIQUE_READS\tPF_UQ_READS_ALIGNED\tPF_BASES_ALIGNED\tPF_UQ_BASES_ALIGNED\tON_TARGET_BASES\tPCT_PF_READS\tPCT_PF_UQ_READS\tPCT_PF_UQ_READS_ALIGNED\tMEAN_TARGET_COVERAGE\tMEDIAN_TARGET_COVERAGE\tMAX_TARGET_COVERAGE\tMIN_TARGET_COVERAGE\tZERO_CVG_TARGETS_PCT\tPCT_EXC_DUPE\tPCT_EXC_ADAPTER\tPCT_EXC_MAPQ\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_OFF_TARGET\tFOLD_80_BASE_PENALTY\tPCT_TARGET_BASES_1X\tPCT_TARGET_BASES_2X\tPCT_TARGET_BASES_10X\tPCT_TARGET_BASES_20X\tPCT_TARGET_BASES_30X\tPCT_TARGET_BASES_40X\tPCT_TARGET_BASES_50X\tPCT_TARGET_BASES_100X\tPCT_TARGET_BASES_250X\tPCT_TARGET_BASES_500X\tPCT_TARGET_BASES_1000X\tPCT_TARGET_BASES_2500X\tPCT_TARGET_BASES_5000X\tPCT_TARGET_BASES_10000X\tPCT_TARGET_BASES_25000X\tPCT_TARGET_BASES_50000X\tPCT_TARGET_BASES_100000X\tAT_DROPOUT\tGC_DROPOUT\tHET_SNP_SENSITIVITY\tHET_SNP_Q\tSAMPLE\tLIBRARY\tREAD_GROUP",
+                "baits\t158\t0.594937\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.000181\t4.995204\t\t0\t0\t0\t0\t0\t0\t94\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t5\t1\t1\t0.985\t0.053191\t0\t1\t0\t0.75\t0\t0\t0.005438\t0.054487\t0.259516\t0.680377\t?\t0.053191\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t76.595745\t23.404255\t0.015734\t0\t\t\t",
+                "",
+                "## HISTOGRAM\tjava.lang.Integer",
+                "coverage_or_base_quality\thigh_quality_coverage_count\tunfiltered_baseq_count",
+                "0\t89\t0",
+                "1\t5\t0",
+                "2\t0\t0",
+                "3\t0\t0",
+                "4\t0\t0",
+                "5\t0\t0",
+                "6\t0\t0",
+                "7\t0\t0",
+                "8\t0\t0",
+                "9\t0\t0",
+                "10\t0\t0",
+                "11\t0\t0",
+                "12\t0\t0",
+                "13\t0\t0",
+                "14\t0\t5",
+                "15\t0\t0",
+                "16\t0\t0",
+                "17\t0\t0",
+                "18\t0\t0",
+                "19\t0\t0",
+                "20\t0\t0",
+                "21\t0\t1",
+                "22\t0\t0",
+                "23\t0\t0",
+                "24\t0\t0",
+                "25\t0\t0",
+                "26\t0\t0",
+                "27\t0\t0",
+                "28\t0\t0",
+                "29\t0\t0",
+                "30\t0\t0",
+                "31\t0\t0",
+                "32\t0\t1",
+                "33\t0\t0",
+                "34\t0\t0",
+                "35\t0\t0",
+                "36\t0\t3",
+                "37\t0\t0",
+                "38\t0\t0",
+                "39\t0\t0",
+                "40\t0\t0",
+                "41\t0\t0",
+                "42\t0\t0",
+                "43\t0\t0",
+                "44\t0\t0",
+                "45\t0\t0",
+                "46\t0\t0",
+                "47\t0\t0",
+                "48\t0\t0",
+                "49\t0\t0",
+                "50\t0\t0",
+                "51\t0\t0",
+                "52\t0\t0",
+                "53\t0\t0",
+                "54\t0\t0",
+                "55\t0\t0",
+                "56\t0\t0",
+                "57\t0\t0",
+                "58\t0\t0",
+                "59\t0\t0",
+                "60\t0\t0",
+                "61\t0\t0",
+                "62\t0\t0",
+                "63\t0\t0",
+                "64\t0\t0",
+                "65\t0\t0",
+                "66\t0\t0",
+                "67\t0\t0",
+                "68\t0\t0",
+                "69\t0\t0",
+                "70\t0\t0",
+                "71\t0\t0",
+                "72\t0\t0",
+                "73\t0\t0",
+                "74\t0\t0",
+                "75\t0\t0",
+                "76\t0\t0",
+                "77\t0\t0",
+                "78\t0\t0",
+                "79\t0\t0",
+                "80\t0\t0",
+                "81\t0\t0",
+                "82\t0\t0",
+                "83\t0\t0",
+                "84\t0\t0",
+                "85\t0\t0",
+                "86\t0\t0",
+                "87\t0\t0",
+                "88\t0\t0",
+                "89\t0\t0"
+            ],
+            [
+                "versions.yml:md5,533cf1e35d36fdacbb762f5df2e1b322"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.7"
+        },
+        "timestamp": "2025-09-15T10:38:18.912909604"
+    }
+}
\ No newline at end of file

From bbd7eedabdbea19f0fbf865246fdb6f48dc0c3be Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Mon, 24 Nov 2025 14:17:59 +0100
Subject: [PATCH 355/530] Install picard_createsequencedictionary.

---
 .../createsequencedictionary/environment.yml  |  8 +++
 .../picard/createsequencedictionary/main.nf   | 54 ++++++++++++++++
 .../picard/createsequencedictionary/meta.yml  | 53 ++++++++++++++++
 .../tests/main.nf.test                        | 61 +++++++++++++++++++
 .../tests/main.nf.test.snap                   | 48 +++++++++++++++
 5 files changed, 224 insertions(+)
 create mode 100644 modules/nf-core/picard/createsequencedictionary/environment.yml
 create mode 100644 modules/nf-core/picard/createsequencedictionary/main.nf
 create mode 100644 modules/nf-core/picard/createsequencedictionary/meta.yml
 create mode 100644 modules/nf-core/picard/createsequencedictionary/tests/main.nf.test
 create mode 100644 modules/nf-core/picard/createsequencedictionary/tests/main.nf.test.snap

diff --git a/modules/nf-core/picard/createsequencedictionary/environment.yml b/modules/nf-core/picard/createsequencedictionary/environment.yml
new file mode 100644
index 00000000..b4ac4fe0
--- /dev/null
+++ b/modules/nf-core/picard/createsequencedictionary/environment.yml
@@ -0,0 +1,8 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  # renovate: datasource=conda depName=bioconda/picard
+  - bioconda::picard=3.4.0
diff --git a/modules/nf-core/picard/createsequencedictionary/main.nf b/modules/nf-core/picard/createsequencedictionary/main.nf
new file mode 100644
index 00000000..4e241979
--- /dev/null
+++ b/modules/nf-core/picard/createsequencedictionary/main.nf
@@ -0,0 +1,54 @@
+process PICARD_CREATESEQUENCEDICTIONARY {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' :
+        'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*.dict"), emit: reference_dict
+    path "versions.yml"            , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def avail_mem = 3072
+    if (!task.memory) {
+        log.info '[Picard CreateSequenceDictionary] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = (task.memory.mega*0.8).intValue()
+    }
+    """
+    picard \\
+        -Xmx${avail_mem}M \\
+        CreateSequenceDictionary  \\
+        $args \\
+        --REFERENCE $fasta \\
+        --OUTPUT ${prefix}.dict
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        picard: \$(picard CreateSequenceDictionary --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.dict
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        picard: \$(echo \$(picard CreateSequenceDictionary --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
+    END_VERSIONS
+    """
+
+}
diff --git a/modules/nf-core/picard/createsequencedictionary/meta.yml b/modules/nf-core/picard/createsequencedictionary/meta.yml
new file mode 100644
index 00000000..97e0ddea
--- /dev/null
+++ b/modules/nf-core/picard/createsequencedictionary/meta.yml
@@ -0,0 +1,53 @@
+name: picard_createsequencedictionary
+description: Creates a sequence dictionary for a reference sequence.
+keywords:
+  - sequence
+  - dictionary
+  - picard
+tools:
+  - picard:
+      description: |
+        Creates a sequence dictionary file (with ".dict" extension) from a reference sequence provided in FASTA format, which is required by many processing and analysis tools. The output file contains a header but no SAMRecords, and the header contains only sequence records.
+      homepage: https://broadinstitute.github.io/picard/
+      documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360036712531-CreateSequenceDictionary-Picard-
+      tool_dev_url: https://github.com/broadinstitute/picard
+      licence: ["MIT"]
+      identifier: biotools:picard_tools
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - fasta:
+        type: file
+        description: The reference fasta file
+        pattern: "*.fasta"
+        ontologies: []
+output:
+  reference_dict:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.dict":
+          type: file
+          description: picard dictionary file
+          pattern: "*.{dict}"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
+authors:
+  - "@sateeshperi"
+  - "@mjcipriano"
+  - "@hseabolt"
+maintainers:
+  - "@sateeshperi"
+  - "@mjcipriano"
+  - "@hseabolt"
diff --git a/modules/nf-core/picard/createsequencedictionary/tests/main.nf.test b/modules/nf-core/picard/createsequencedictionary/tests/main.nf.test
new file mode 100644
index 00000000..8152be96
--- /dev/null
+++ b/modules/nf-core/picard/createsequencedictionary/tests/main.nf.test
@@ -0,0 +1,61 @@
+nextflow_process {
+
+    name "Test Process PICARD_CREATESEQUENCEDICTIONARY"
+    script "../main.nf"
+    process "PICARD_CREATESEQUENCEDICTIONARY"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "picard"
+    tag "picard/createsequencedictionary"
+
+    test("sarscov2 - fasta") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.reference_dict[0][1]).name,
+                    process.out.versions
+                    ).match()
+                }
+
+            )
+        }
+
+    }
+
+    test("sarscov2 - fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/picard/createsequencedictionary/tests/main.nf.test.snap b/modules/nf-core/picard/createsequencedictionary/tests/main.nf.test.snap
new file mode 100644
index 00000000..9227bcd1
--- /dev/null
+++ b/modules/nf-core/picard/createsequencedictionary/tests/main.nf.test.snap
@@ -0,0 +1,48 @@
+{
+    "sarscov2 - fasta - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.dict:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,7df655404f48c3fd86b49d231fdefddf"
+                ],
+                "reference_dict": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.dict:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7df655404f48c3fd86b49d231fdefddf"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.7"
+        },
+        "timestamp": "2025-09-15T10:47:11.69898685"
+    },
+    "sarscov2 - fasta": {
+        "content": [
+            "test.dict",
+            [
+                "versions.yml:md5,7df655404f48c3fd86b49d231fdefddf"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.7"
+        },
+        "timestamp": "2025-09-15T10:47:02.784849055"
+    }
+}
\ No newline at end of file

From 4acac74dcf5015e7e20e6f85aab5bff273e6f1c9 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Mon, 24 Nov 2025 14:18:27 +0100
Subject: [PATCH 356/530] Add test samplesheet and test config.

---
 assets/cg_test_samplesheet.csv |  2 ++
 conf/cg_test.config            | 30 ++++++++++++++++++++++++++++++
 2 files changed, 32 insertions(+)
 create mode 100644 assets/cg_test_samplesheet.csv
 create mode 100644 conf/cg_test.config

diff --git a/assets/cg_test_samplesheet.csv b/assets/cg_test_samplesheet.csv
new file mode 100644
index 00000000..a1913b20
--- /dev/null
+++ b/assets/cg_test_samplesheet.csv
@@ -0,0 +1,2 @@
+sample,fastq_1,fastq_2,rundir,tags
+raredisease_test_sample,https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz,,test
\ No newline at end of file
diff --git a/conf/cg_test.config b/conf/cg_test.config
new file mode 100644
index 00000000..93477fff
--- /dev/null
+++ b/conf/cg_test.config
@@ -0,0 +1,30 @@
+
+params {
+    input                           = "${projectDir}/assets/cg_test_samplesheet.csv"
+    pipelines_testdata_base_path    = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease'
+    skip_tools                      = null
+    fasta                           = params.pipelines_testdata_base_path + '/reference/reference.fasta'
+    genome                          = 'GRCh37'
+    bait_intervals                  = params.pipelines_testdata_base_path + '/reference/target.bed'
+    target_intervals                = params.bait_intervals
+}
+
+process {
+
+    // Add limits to be able to run on local computer.
+    
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+
+    withName: PICARD_COLLECTHSMETRICS {
+        ext.args = { [
+            "--COVERAGE_CAP 50000",
+            "--METRIC_ACCUMULATION_LEVEL ALL_READS"
+			].join(' ') }
+
+    }
+
+}

From 38b2fae191c559da4cad0795b4f5fb6af129800a Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Mon, 24 Nov 2025 14:19:21 +0100
Subject: [PATCH 357/530] Change modules.json to include installed modules.

---
 modules.json | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/modules.json b/modules.json
index 69e8fb48..3476ca7d 100644
--- a/modules.json
+++ b/modules.json
@@ -42,11 +42,21 @@
                         "git_sha": "82a79183037a403ad1b6714e5dbcff25500efaf6",
                         "installed_by": ["modules"]
                     },
+                    "picard/collecthsmetrics": {
+                        "branch": "master",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
+                        "installed_by": ["modules"]
+                    },
                     "picard/collectmultiplemetrics": {
                         "branch": "master",
                         "git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255",
                         "installed_by": ["modules"]
                     },
+                    "picard/createsequencedictionary": {
+                        "branch": "master",
+                        "git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255",
+                        "installed_by": ["modules"]
+                    },
                     "samtools/faidx": {
                         "branch": "master",
                         "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",

From 71f1fe74db2ad7fee03cbe22bebcc94fe981a9ff Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Mon, 24 Nov 2025 14:19:39 +0100
Subject: [PATCH 358/530] Set up input parameters.

---
 nextflow.config      |  9 ++++++++-
 nextflow_schema.json | 39 +++++++++++++++++++++++++++++++++++++--
 2 files changed, 45 insertions(+), 3 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 6ce84baf..ad7c5ff8 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -13,7 +13,7 @@ params {
     // Input options
     input                      = null
     sample_size                = 0
-    skip_tools                 = ''
+    skip_tools                 = 'picard_collecthsmetrics'
     // References
     genome                     = null
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
@@ -46,6 +46,11 @@ params {
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
     trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 
+    // picard_collecthsmetrics options
+    bait_intervals              = null
+    target_intervals            = null
+    ref_dict                    = null
+
     // Config options
     config_profile_name        = null
     config_profile_description = null
@@ -54,6 +59,7 @@ params {
     custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
     config_profile_contact     = null
     config_profile_url         = null
+    
 
     // Schema validation default options
     validate_params            = true
@@ -174,6 +180,7 @@ profiles {
     }
     test      { includeConfig 'conf/test.config'      }
     test_full { includeConfig 'conf/test_full.config' }
+    test_cg   { includeConfig 'conf/cg_test.config'   }
 }
 
 // Load nf-core custom profiles from different institutions
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 5d663de7..a3794d3c 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -31,7 +31,6 @@
                 },
                 "outdir": {
                     "type": "string",
-                    "default": null,
                     "format": "directory-path",
                     "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
                     "fa_icon": "fas fa-folder-open"
@@ -51,7 +50,8 @@
                 "skip_tools": {
                     "type": "string",
                     "description": "Comma-separated string of tools to skip",
-                    "pattern": "^((fastqc|fastqscreen|seqfu_stats|seqtk_sample|bwamem2_index|bwamem2_mem|picard_collectmultiplemetrics|samtools_faidx|samtools_index)?,?)*(?<!,)$"
+                    "pattern": "^((fastqc|fastqscreen|seqfu_stats|seqtk_sample|bwamem2_index|bwamem2_mem|picard_collectmultiplemetrics|samtools_faidx|samtools_index|picard_collecthsmetrics)?,?)*(?<!,)$",
+                    "default": "picard_collecthsmetrics"
                 }
             }
         },
@@ -276,6 +276,38 @@
                     "description": "Display hidden parameters in the help message (only works when --help or --help_full are provided)."
                 }
             }
+        },
+        "picard_collecthsmetrics_options": {
+            "title": "picard_collecthsmetrics options",
+            "type": "object",
+            "description": "",
+            "default": "",
+            "properties": {
+                "bait_intervals": {
+                    "type": "string",
+                    "description": "Path to bait intervals file.",
+                    "hidden": true,
+                    "pattern": "^\\S+.(bed|bed.gz|interval_list)$",
+                    "format": "file-path",
+                    "exists": true
+                },
+                "target_intervals": {
+                    "type": "string",
+                    "description": "Path to target intervals file.",
+                    "hidden": true,
+                    "pattern": "^\\S+.(bed|bed.gz|interval_list)$",
+                    "format": "file-path",
+                    "exists": true
+                },
+                "ref_dict": {
+                    "type": "string",
+                    "hidden": true,
+                    "description": "Sequence dictionary for the reference fasta file provided.",
+                    "pattern": "^\\S+.dict$",
+                    "format": "file-path",
+                    "exists": true
+                }
+            }
         }
     },
     "allOf": [
@@ -290,6 +322,9 @@
         },
         {
             "$ref": "#/$defs/generic_options"
+        },
+        {
+            "$ref": "#/$defs/picard_collecthsmetrics_options"
         }
     ]
 }

From 62cc3cee0adb2927db85a0c889495b5d3951c0ed Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Mon, 24 Nov 2025 14:20:44 +0100
Subject: [PATCH 359/530] Add picard_collecthsmetrics to workflow.

---
 workflows/seqinspector.nf | 86 ++++++++++++++++++++++++++++++---------
 1 file changed, 66 insertions(+), 20 deletions(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index bcf88f8c..fc2fa4a3 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -1,4 +1,4 @@
-include { samplesheetToList             } from 'plugin/nf-schema'
+include { samplesheetToList } from 'plugin/nf-schema'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -6,23 +6,25 @@ include { samplesheetToList             } from 'plugin/nf-schema'
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { BWAMEM2_INDEX                 } from '../modules/nf-core/bwamem2/index'
-include { BWAMEM2_MEM                   } from '../modules/nf-core/bwamem2/mem'
-include { FASTQC                        } from '../modules/nf-core/fastqc'
-include { FASTQSCREEN_FASTQSCREEN       } from '../modules/nf-core/fastqscreen/fastqscreen'
+include { BWAMEM2_INDEX } from '../modules/nf-core/bwamem2/index'
+include { BWAMEM2_MEM } from '../modules/nf-core/bwamem2/mem'
+include { FASTQC } from '../modules/nf-core/fastqc'
+include { FASTQSCREEN_FASTQSCREEN } from '../modules/nf-core/fastqscreen/fastqscreen'
 include { PICARD_COLLECTMULTIPLEMETRICS } from '../modules/nf-core/picard/collectmultiplemetrics'
-include { SAMTOOLS_FAIDX                } from '../modules/nf-core/samtools/faidx'
-include { SAMTOOLS_INDEX                } from '../modules/nf-core/samtools/index'
-include { SEQFU_STATS                   } from '../modules/nf-core/seqfu/stats'
-include { SEQTK_SAMPLE                  } from '../modules/nf-core/seqtk/sample'
+include { SAMTOOLS_FAIDX } from '../modules/nf-core/samtools/faidx'
+include { SAMTOOLS_INDEX } from '../modules/nf-core/samtools/index'
+include { SEQFU_STATS } from '../modules/nf-core/seqfu/stats'
+include { SEQTK_SAMPLE } from '../modules/nf-core/seqtk/sample'
+include { PICARD_COLLECTHSMETRICS } from '../modules/nf-core/picard/collecthsmetrics/main'
+include { PICARD_CREATESEQUENCEDICTIONARY } from '../modules/nf-core/picard/createsequencedictionary/main'
 
-include { MULTIQC as MULTIQC_GLOBAL     } from '../modules/nf-core/multiqc'
-include { MULTIQC as MULTIQC_PER_TAG    } from '../modules/nf-core/multiqc'
+include { MULTIQC as MULTIQC_GLOBAL } from '../modules/nf-core/multiqc'
+include { MULTIQC as MULTIQC_PER_TAG } from '../modules/nf-core/multiqc'
 
-include { paramsSummaryMap              } from 'plugin/nf-schema'
-include { paramsSummaryMultiqc          } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-include { softwareVersionsToYAML        } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-include { methodsDescriptionText        } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline'
+include { paramsSummaryMap } from 'plugin/nf-schema'
+include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -48,6 +50,7 @@ workflow SEQINSPECTOR {
     ch_samtools_index = channel.empty()
     ch_reference_fasta_fai = channel.empty()
     ch_reference_fasta = channel.empty()
+    ch_ref_dict = channel.empty()
 
     //
     // MODULE: Run Seqtk sample to perform subsampling
@@ -201,9 +204,52 @@ workflow SEQINSPECTOR {
         ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
     }
 
+    if (!("picard_collecthsmetrics" in skip_tools) && !("bwamem2_mem" in skip_tools)) {
+
+        if (("picard_collectmultiplemetrics" in skip_tools)){
+            ch_bam_bai = ch_bwamem2_mem.join(ch_samtools_index, failOnDuplicate: true, failOnMismatch: true)
+        }
+
+        ch_bait_intervals = channel
+            .fromPath(params.bait_intervals)
+            .collect()
+
+        ch_target_intervals = channel
+            .fromPath(params.target_intervals)
+            .collect()
+
+
+        ch_hsmetrics_in = ch_bam_bai
+            .combine(ch_bait_intervals)
+            .combine(ch_target_intervals)
+
+
+        if (!params.ref_dict) {
+            PICARD_CREATESEQUENCEDICTIONARY(
+                ch_reference_fasta
+            )
+            ch_ref_dict = PICARD_CREATESEQUENCEDICTIONARY.out.reference_dict
+        }
+        else {
+            ch_ref_dict = channel.fromPath(params.ref_dict).map { [[id: it.simpleName], it] }
+        }
+
+        PICARD_COLLECTHSMETRICS(
+            ch_hsmetrics_in,
+            ch_reference_fasta,
+            [[], []],
+            ch_ref_dict,
+            [[], []],
+        )
+        ch_multiqc_files = ch_multiqc_files.mix(PICARD_COLLECTHSMETRICS.out.metrics)
+        ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
+    }
+
+
     // Collate and save software versions
     //
-    def topic_versions = Channel.topic("versions")
+    def topic_versions = Channel
+        .topic("versions")
         .distinct()
         .branch { entry ->
             versions_file: entry instanceof Path
@@ -212,9 +258,9 @@ workflow SEQINSPECTOR {
 
     def topic_versions_string = topic_versions.versions_tuple
         .map { process, tool, version ->
-            [ process[process.lastIndexOf(':')+1..-1], "  ${tool}: ${version}" ]
+            [process[process.lastIndexOf(':') + 1..-1], "  ${tool}: ${version}"]
         }
-        .groupTuple(by:0)
+        .groupTuple(by: 0)
         .map { process, tool_versions ->
             tool_versions.unique().sort()
             "${process}:\n${tool_versions.join('\n')}"
@@ -318,7 +364,7 @@ workflow SEQINSPECTOR {
     )
 
     emit:
-    global_report   = MULTIQC_GLOBAL.out.report.toList() // channel: [ /path/to/multiqc_report.html ]
+    global_report = MULTIQC_GLOBAL.out.report.toList() // channel: [ /path/to/multiqc_report.html ]
     grouped_reports = MULTIQC_PER_TAG.out.report.toList() // channel: [ /path/to/multiqc_report.html ]
-    versions        = ch_versions // channel: [ path(versions.yml) ]
+    versions = ch_versions // channel: [ path(versions.yml) ]
 }

From df6ebc115256159793a35b27de8923eb10c55879 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Mon, 24 Nov 2025 14:33:45 +0100
Subject: [PATCH 360/530] Make SAMTOOLS_INDEX required if bwamem2_mem is run.

---
 nextflow_schema.json      | 2 +-
 workflows/seqinspector.nf | 4 +---
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index a3794d3c..17365de6 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -50,7 +50,7 @@
                 "skip_tools": {
                     "type": "string",
                     "description": "Comma-separated string of tools to skip",
-                    "pattern": "^((fastqc|fastqscreen|seqfu_stats|seqtk_sample|bwamem2_index|bwamem2_mem|picard_collectmultiplemetrics|samtools_faidx|samtools_index|picard_collecthsmetrics)?,?)*(?<!,)$",
+                    "pattern": "^((fastqc|fastqscreen|seqfu_stats|seqtk_sample|bwamem2_index|bwamem2_mem|picard_collectmultiplemetrics|samtools_faidx|picard_collecthsmetrics)?,?)*(?<!,)$",
                     "default": "picard_collecthsmetrics"
                 }
             }
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index fc2fa4a3..99301292 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -157,9 +157,7 @@ workflow SEQINSPECTOR {
         )
         ch_bwamem2_mem = BWAMEM2_MEM.out.bam
         ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions)
-    }
-    // MODULE: Index BAM files with Samtools
-    if (!("samtools_index" in skip_tools) && !("bwamem2_mem" in skip_tools)) {
+
         SAMTOOLS_INDEX(
             ch_bwamem2_mem
         )

From 72291c378ffc1f53e16a8728895701718cf34b96 Mon Sep 17 00:00:00 2001
From: matrulda <matilda.aslin@medsci.uu.se>
Date: Mon, 24 Nov 2025 14:54:50 +0100
Subject: [PATCH 361/530] Rundirparser: Add tar support, remove dummy script,
 update format of illumina mqc file

---
 modules/local/rundirparser/main.nf            | 27 ++++++-
 .../resources/usr/bin/parse_illumina.py       | 31 ++++----
 .../resources/usr/bin/rundirparser.py         | 72 -------------------
 workflows/seqinspector.nf                     |  1 -
 4 files changed, 39 insertions(+), 92 deletions(-)
 delete mode 100755 modules/local/rundirparser/resources/usr/bin/rundirparser.py

diff --git a/modules/local/rundirparser/main.nf b/modules/local/rundirparser/main.nf
index c702e57b..66c7aafc 100644
--- a/modules/local/rundirparser/main.nf
+++ b/modules/local/rundirparser/main.nf
@@ -18,10 +18,33 @@ process RUNDIRPARSER {
     task.ext.when == null || task.ext.when
 
     script:
+    def input_tar = rundir.toString().endsWith(".tar.gz") ? true : false
+    def input_dir = input_tar ? rundir.toString() - '.tar.gz' : rundir
     """
+
+    if [ ! -d ${input_dir} ]; then
+        mkdir -p ${input_dir}
+    fi
+
+    if ${input_tar}; then
+        ## Ensures --strip-components only applied when top level of tar contents is a directory
+        ## If just files or multiple directories, place all in $input_dir
+
+        if [[ \$(tar -taf ${rundir} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then
+            tar \\
+                -C $input_dir --strip-components 1 \\
+                -xavf \\
+                $rundir
+        else
+            tar \\
+                -C $input_dir \\
+                -xavf \\
+                $rundir
+        fi
+    fi
+
     # TODO: check what kind of seq platfrom to decide which script to use
-    rundirparser.py ${rundir}
-    parse_illumina.py ${rundir}
+    parse_illumina.py ${input_dir}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/rundirparser/resources/usr/bin/parse_illumina.py b/modules/local/rundirparser/resources/usr/bin/parse_illumina.py
index 5d210aba..7c70a6da 100755
--- a/modules/local/rundirparser/resources/usr/bin/parse_illumina.py
+++ b/modules/local/rundirparser/resources/usr/bin/parse_illumina.py
@@ -18,7 +18,8 @@ def read_run_parameters(directory):
         with open(alt_2) as f:
             return xmltodict.parse(f.read())
     else:
-        raise Exception("[Rr]unParameters.xml not found!")
+        raise Exception("Could not find Illumina [Rr]unParameters.xml. "
+                        "Please provide RunParameters.xml or skip module.")
 
 
 def find(d, tag):
@@ -53,7 +54,7 @@ def construct_data(run_parameters):
         for key, value in run_parameters_tags.items():
             info = list(find(run_parameters, key))
             if info:
-                data[value] = info[0]
+                data[value] = {"Value": info[0]}
         return data
 
 
@@ -64,22 +65,18 @@ def construct_multiqc_yaml(directory):
 
     data = construct_data(run_parameters)
 
-    #TODO: MultiQC currently ignores the data in this yaml RUDE
     metadata = {
-        "custom_data": {
-            "my_data_type": {
-                "id": "mqc_seq_metadata",
-                "section_name": "Sequencing instrument metadata",
-                "description": directory_name,
-                "plot_type": "table",
-                "pconfig": {
-                    "id": 'custom_table',
-                    "title": 'Custom Table',
-                    "no_headers": "true",
-                    },
-                "data": data,
-            }
-        }
+        "id": "mqc_seq_metadata",
+        "section_name": "Sequencing instrument metadata",
+        "description": "Sequencing metadata gathered from the run directory",
+        "plot_type": "table",
+        "pconfig": {
+            "id": 'mqc_seq_metadata',
+            "title": 'Run directory Metadata',
+            "col1_header": "Metadata",
+            },
+        "data": data,
+
     }
 
     return metadata
diff --git a/modules/local/rundirparser/resources/usr/bin/rundirparser.py b/modules/local/rundirparser/resources/usr/bin/rundirparser.py
deleted file mode 100755
index b8db68df..00000000
--- a/modules/local/rundirparser/resources/usr/bin/rundirparser.py
+++ /dev/null
@@ -1,72 +0,0 @@
-#!/usr/bin/env python
-import sys
-import yaml
-
-
-def parse_rundir(rundir):
-    # Dummy implementation, replace with actual logic
-
-    sequencing_platform = None
-
-    yml_contents = """# plot_type: 'table'
-# section_name: 'rundir stats'
-# description: 'dummy rundir stats'
-# pconfig:
-#     namespace: 'Cust Data'
-# headers:
-#     col1:
-#         title: '#Seqs'
-#         description: 'Number of sequences'
-#         format: '{:,.0f}'
-#     col2:
-#         title: 'Total bp'
-#         description: 'Total size of the dataset'
-#     col3:
-#         title: 'Avg'
-#         description: 'Average sequence length'
-#     col4:
-#         title: 'N50'
-#         description: '50% of the sequences are longer than this size'
-#     col5:
-#         title: 'N75'
-#         description: '75% of the sequences are longer than this size'
-#     col6:
-#         title: 'N90'
-#         description: '90% of the sequences are longer than this size'
-#     col7:
-#         title: 'Min'
-#         description: 'Length of the shortest sequence'
-#     col8:
-#         title: 'Max'
-#         description: 'Length of the longest sequence'
-#     col9:
-#         title: 'auN'
-#         description: 'Area under the Nx curve'
-#     col10:
-#         title: 'GC'
-#         description: 'Relative GC content (excluding Ns)'
-"""
-    tsv_contents = f"""Sample	col1	col2	col3	col4	col5	col6	col7	col8	col9	col10
-{rundir}	10	147806	14780.6000000	22507	16573	15322	22801.9181765	344	33340	NaN
-"""
-
-    contents = yml_contents + tsv_contents
-
-    """
-    File names should be unique between sequencing platforms, but otherwise identical
-    so multiple rundirs of the same platform will be written to the same table
-    in the MultiQC report.
-    """
-    outname = f"{sequencing_platform or 'rundirparser'}_mqc.txt"
-
-    with open(outname, "w") as f:
-        f.write(contents)
-
-
-def main():
-    rundir = sys.argv[1]
-    parse_rundir(rundir)
-
-
-if __name__ == "__main__":
-    main()
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 5d23a17f..ea61b383 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -14,7 +14,6 @@ include { PICARD_COLLECTMULTIPLEMETRICS } from '../modules/nf-core/picard/collec
 include { SAMTOOLS_FAIDX                } from '../modules/nf-core/samtools/faidx'
 include { SAMTOOLS_INDEX                } from '../modules/nf-core/samtools/index'
 include { SEQFU_STATS                   } from '../modules/nf-core/seqfu/stats'
-include { FASTQSCREEN_FASTQSCREEN       } from '../modules/nf-core/fastqscreen/fastqscreen/main'
 include { RUNDIRPARSER                  } from '../modules/local/rundirparser/main'
 include { SEQTK_SAMPLE                  } from '../modules/nf-core/seqtk/sample'
 

From f422cd8102c6863149f503dc33a3668745a63446 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Mon, 24 Nov 2025 15:06:32 +0100
Subject: [PATCH 362/530] Remove skip condition for samtools_index when calling
 picard_collectmultiplemetrics.

---
 workflows/seqinspector.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 99301292..0dc21fe1 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -180,7 +180,7 @@ workflow SEQINSPECTOR {
 
     // MODULE: Prepare BAM/BAI tuples for Picard
     // Combine BAM and BAI outputs for Picard
-    if (!("picard_collectmultiplemetrics" in skip_tools) && !("bwamem2_mem" in skip_tools) && !("samtools_index" in skip_tools) && !("samtools_faidx" in skip_tools)) {
+    if (!("picard_collectmultiplemetrics" in skip_tools) && !("bwamem2_mem" in skip_tools) && !("samtools_faidx" in skip_tools)) {
 
         // Prepare BAM/BAI tuples for Picard
         ch_bam_bai = ch_bwamem2_mem.join(ch_samtools_index, failOnDuplicate: true, failOnMismatch: true)

From f91167b2be210ca151def8052ece15ec3a304c6a Mon Sep 17 00:00:00 2001
From: FranBonath <franziska.bonath@scilifelab.se>
Date: Mon, 24 Nov 2025 15:29:56 +0100
Subject: [PATCH 363/530] Have tools list in README in Table

---
 README.md | 30 ++++++++++++------------------
 1 file changed, 12 insertions(+), 18 deletions(-)

diff --git a/README.md b/README.md
index 2b9f4b8b..5af57238 100644
--- a/README.md
+++ b/README.md
@@ -26,24 +26,18 @@
 
 **nf-core/seqinspector** is a bioinformatics pipeline that that processes raw sequencedata (FASTQ) to provide comprehensive quality control. It can perform subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants. The pipeline generates detailed MultiQC reports with flexible output options, ranging from individual sample reports to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments. If provided, nf-core/seqinspector can also parse statistics from an Illumina run folder directory into the final MultiQC reports.
 
-<!-- TODO nf-core:
-   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the
-   major pipeline sections and the types of output it produces. You're giving an overview to someone new
-   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction
--->
-
-<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
-     workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->
-
-1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))
-2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-3. Basic contamination detection ([`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/))
-4. Sequence statistics ([`SeqFu Stats`](https://github.com/telatin/seqfu2))
-5. Align reads to reference with ([`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2))
-6. Index aligned BAM files ([`SAMtools`](http://github.com/samtools))
-7. Create FASTA index ([`SAMtools`](http://github.com/samtools))
-8. Collect multiple QC metrics ([`Picard CollectMultipleMetrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html))
-9. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+<!-- TODO: add a search tool that accepts a tree for `Compatibility with Data`. -->
+
+| Tool Type           | Tool Name                                                                          | Tool Description                            | Compatibility with Data | Dependencies        |
+| ------------------- | ---------------------------------------------------------------------------------- | ------------------------------------------- | ----------------------- | ------------------- |
+| `Subsampling`       | [`Seqtk`](https://github.com/lh3/seqtk)                                            | Global subsampling of reads                 | [RNA, DNA, synthetic]   | [N/A]               |
+| `QC`                | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)             | Read QC                                     | [RNA, DNA]              | [N/A]               |
+| `QC`                | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)  | Basic contamination detection               | [RNA, DNA]              | [N/A]               |
+| `QC`                | [`SeqFu Stats`](https://github.com/telatin/seqfu2)                                 | Sequence statistics                         | [RNA, DNA]              | [N/A]               |
+| `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2)                                  | Align reads to reference                    | [RNA, DNA]              | [N/A]               |
+| `Indexing`          | [`SAMtools`](http://github.com/samtools)                                           | Index aligned BAM files, create FASTA index | [DNA]                   | [N/A]               |
+| `QC`                | [`Picard`](https://broadinstitute.github.io/picard/picard-metric-definitions.html) | Collect multiple QC metrics                 | [RNA, DNA]              | [Bwamem2, SAMtools] |
+| `Reporting`         | [`MultiQC`](http://multiqc.info/)                                                  | Present QC for raw reads                    | [RNA, DNA, synthetic]   | [N/A]               |
 
 ![nf-core/seqinspector metro map](docs/images/seqinspector_tubemap_V1.0.png)
 

From 0894a2b61ca1f3fa44cbe93eae459e644b4845a1 Mon Sep 17 00:00:00 2001
From: ramprasadn <20065894+ramprasadn@users.noreply.github.com>
Date: Mon, 24 Nov 2025 15:41:29 +0100
Subject: [PATCH 364/530] lint errors

---
 .nf-core.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.nf-core.yml b/.nf-core.yml
index ceb658d7..385527a3 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -3,6 +3,9 @@ lint:
     - tests/default.nf.test
   files_unchanged:
     - .github/CONTRIBUTING.md
+    - docs/images/nf-core-seqinspector_logo_dark.png
+    - docs/images/nf-core-seqinspector_logo_light.png
+    - assets/nf-core-seqinspector_logo_light.png
   nextflow_config:
     - config_defaults:
         - params.fastq_screen_references

From 4c4214b0f1d10a704f0aff5e612e520f46643c38 Mon Sep 17 00:00:00 2001
From: FranBonath <franziska.bonath@scilifelab.se>
Date: Mon, 24 Nov 2025 15:50:52 +0100
Subject: [PATCH 365/530] add darkmode options in README, add darkmode tubemap

---
 README.md                                     |   19 +-
 .../images/seqinspector_tubemap_V1.0_dark.png |  Bin 0 -> 71596 bytes
 .../images/seqinspector_tubemap_V1.0_dark.svg | 2801 +++++++++++++++++
 3 files changed, 2817 insertions(+), 3 deletions(-)
 create mode 100644 docs/images/seqinspector_tubemap_V1.0_dark.png
 create mode 100644 docs/images/seqinspector_tubemap_V1.0_dark.svg

diff --git a/README.md b/README.md
index 5af57238..fea648b4 100644
--- a/README.md
+++ b/README.md
@@ -21,8 +21,17 @@
 
 ## Introduction
 
-![nf-core/seqinspector logo](docs/images/nf-core-seqinspector_logo_light.png)
-![nf-core/seqinspector hex logo](docs/images/nfcore-seqinspector-logo-hex-light.png)
+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-seqinspector_logo_dark.png">
+  <source media="(prefers-color-scheme: light)" srcset="docs/images/nf-core-seqinspector_logo_light.png">
+  <img alt="Fallback image description" src="docs/images/nf-core-seqinspector_logo_light.png">
+</picture>
+
+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="docs/images/nfcore-seqinspector-logo-hex-dark.png">
+  <source media="(prefers-color-scheme: light)" srcset="docs/images/nfcore-seqinspector-logo-hex-light.png">
+  <img alt="Fallback image description" src="docs/images/nfcore-seqinspector-logo-hex-light.png">
+</picture>
 
 **nf-core/seqinspector** is a bioinformatics pipeline that that processes raw sequencedata (FASTQ) to provide comprehensive quality control. It can perform subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants. The pipeline generates detailed MultiQC reports with flexible output options, ranging from individual sample reports to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments. If provided, nf-core/seqinspector can also parse statistics from an Illumina run folder directory into the final MultiQC reports.
 
@@ -39,7 +48,11 @@
 | `QC`                | [`Picard`](https://broadinstitute.github.io/picard/picard-metric-definitions.html) | Collect multiple QC metrics                 | [RNA, DNA]              | [Bwamem2, SAMtools] |
 | `Reporting`         | [`MultiQC`](http://multiqc.info/)                                                  | Present QC for raw reads                    | [RNA, DNA, synthetic]   | [N/A]               |
 
-![nf-core/seqinspector metro map](docs/images/seqinspector_tubemap_V1.0.png)
+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="docs/images/seqinspector_tubemap_V1.0_dark.png">
+  <source media="(prefers-color-scheme: light)" srcset="docs/images/seqinspector_tubemap_V1.0.png">
+  <img alt="Fallback image description" src="docs/images/seqinspector_tubemap_V1.0.png">
+</picture>
 
 ## Usage
 
diff --git a/docs/images/seqinspector_tubemap_V1.0_dark.png b/docs/images/seqinspector_tubemap_V1.0_dark.png
new file mode 100644
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From 06e66acc3d30e5c1e0cf15c327741a3d16100ac0 Mon Sep 17 00:00:00 2001
From: ramprasadn <20065894+ramprasadn@users.noreply.github.com>
Date: Mon, 24 Nov 2025 15:57:48 +0100
Subject: [PATCH 366/530] lint warnings

---
 assets/methods_description_template.yml          |  2 --
 nextflow.config                                  |  1 -
 ro-crate-metadata.json                           | 16 ++++++++--------
 .../utils_nfcore_seqinspector_pipeline/main.nf   |  1 -
 4 files changed, 8 insertions(+), 12 deletions(-)

diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml
index 3eadd2bd..a5e583a4 100644
--- a/assets/methods_description_template.yml
+++ b/assets/methods_description_template.yml
@@ -3,8 +3,6 @@ description: "Suggested text and references to use when describing pipeline usag
 section_name: "nf-core/seqinspector Methods Description"
 section_href: "https://github.com/nf-core/seqinspector"
 plot_type: "html"
-## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
-## You inject any metadata in the Nextflow '${workflow}' object
 data: |
   <h4>Methods</h4>
   <p>Data was processed using nf-core/seqinspector v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
diff --git a/nextflow.config b/nextflow.config
index 6ce84baf..b2c43bec 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -9,7 +9,6 @@
 // Global default params, used in configs
 params {
 
-    // TODO nf-core: Specify your pipeline's command line flags
     // Input options
     input                      = null
     sample_size                = 0
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 401821d3..787b2cb5 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,8 +22,8 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2025-11-20T09:32:26+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by Adrien Coulier.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "datePublished": "2025-11-24T14:37:12+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->\n\n1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))\n2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n3. Align reads to reference with ([`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2))\n4. Index aligned BAM files ([`SAMtools`](http://github.com/samtools))\n5. Create FASTA index ([`SAMtools`](http://github.com/samtools))\n6. Collect multiple QC metrics ([`Picard CollectMultipleMetrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html))\n7. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
                     "@id": "main.nf"
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#ac0a8bf0-7553-40cd-ac01-50ae6184f724"
+                    "@id": "#485f7eea-d7ee-4fc7-b525-b19d8b1785d9"
                 }
             ],
             "name": "nf-core/seqinspector"
@@ -144,7 +144,7 @@
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2025-11-20T09:32:26Z",
+            "dateModified": "2025-11-24T15:37:12Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -185,11 +185,11 @@
             "version": "!>=25.04.0"
         },
         {
-            "@id": "#ac0a8bf0-7553-40cd-ac01-50ae6184f724",
+            "@id": "#485f7eea-d7ee-4fc7-b525-b19d8b1785d9",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#6e9e5864-2ba6-4edc-8e26-0abfa747f70c"
+                    "@id": "#5046cfd6-7adc-440b-8923-715e3d592be8"
                 }
             ],
             "mainEntity": {
@@ -198,7 +198,7 @@
             "name": "Test suite for nf-core/seqinspector"
         },
         {
-            "@id": "#6e9e5864-2ba6-4edc-8e26-0abfa747f70c",
+            "@id": "#5046cfd6-7adc-440b-8923-715e3d592be8",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/seqinspector",
             "resource": "repos/nf-core/seqinspector/actions/workflows/nf-test.yml",
@@ -353,7 +353,7 @@
         {
             "@id": "https://orcid.org/0009-0004-5536-7210",
             "@type": "Person",
-            "email": "agrimabhatt@n141-p117.eduroam.kth.se",
+            "email": "163723002+agrima2010@users.noreply.github.com",
             "name": "Agrima Bhatt"
         }
     ]
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index 81c645a0..009b7947 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -212,7 +212,6 @@ workflow PIPELINE_COMPLETION {
 def validateInputParameters() {
     // genomeExistsError()
 
-    // TODO: Add code to further validate pipeline parameters here
 }
 
 //

From 226c89f5c4505f60ffaf422af1cf9e8ac416088e Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Mon, 24 Nov 2025 15:59:44 +0100
Subject: [PATCH 367/530] Add qc_bam subworkflow to run
 picard_collecthsmetrics.

---
 subworkflows/local/qc_bam.nf | 60 ++++++++++++++++++++++++++++++++++++
 workflows/seqinspector.nf    | 48 +++++------------------------
 2 files changed, 68 insertions(+), 40 deletions(-)
 create mode 100644 subworkflows/local/qc_bam.nf

diff --git a/subworkflows/local/qc_bam.nf b/subworkflows/local/qc_bam.nf
new file mode 100644
index 00000000..b24c664c
--- /dev/null
+++ b/subworkflows/local/qc_bam.nf
@@ -0,0 +1,60 @@
+//
+// A quality check subworkflow for processed bam files.
+//
+
+include { PICARD_COLLECTHSMETRICS } from '../../modules/nf-core/picard/collecthsmetrics/main'
+include { PICARD_CREATESEQUENCEDICTIONARY } from '../../modules/nf-core/picard/createsequencedictionary/main'
+
+workflow QC_BAM {
+    take:
+
+        ch_bam_bai
+        ch_reference_fasta
+        ch_reference_fasta_fai
+
+    main:
+
+        ch_versions = channel.empty()
+
+
+        ch_bait_intervals = channel
+            .fromPath(params.bait_intervals)
+            .collect()
+
+        ch_target_intervals = channel
+            .fromPath(params.target_intervals)
+            .collect()
+
+
+        ch_hsmetrics_in = ch_bam_bai
+            .combine(ch_bait_intervals)
+            .combine(ch_target_intervals)
+
+
+        if (!params.ref_dict) {
+            PICARD_CREATESEQUENCEDICTIONARY(
+                ch_reference_fasta
+            )
+            ch_ref_dict = PICARD_CREATESEQUENCEDICTIONARY.out.reference_dict
+            ch_versions = ch_versions.mix(PICARD_CREATESEQUENCEDICTIONARY.out.versions.first())
+        }
+        else {
+            ch_ref_dict = channel.fromPath(params.ref_dict).map { [[id: it.simpleName], it] }
+        }
+
+        PICARD_COLLECTHSMETRICS(
+            ch_hsmetrics_in,
+            ch_reference_fasta,
+            ch_reference_fasta_fai,
+            ch_ref_dict,
+            [[], []],
+        )
+        ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
+
+
+    emit:
+
+        hs_metrics = PICARD_COLLECTHSMETRICS.out.metrics
+        versions = ch_versions
+
+}
\ No newline at end of file
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 0dc21fe1..534f6269 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -15,8 +15,7 @@ include { SAMTOOLS_FAIDX } from '../modules/nf-core/samtools/faidx'
 include { SAMTOOLS_INDEX } from '../modules/nf-core/samtools/index'
 include { SEQFU_STATS } from '../modules/nf-core/seqfu/stats'
 include { SEQTK_SAMPLE } from '../modules/nf-core/seqtk/sample'
-include { PICARD_COLLECTHSMETRICS } from '../modules/nf-core/picard/collecthsmetrics/main'
-include { PICARD_CREATESEQUENCEDICTIONARY } from '../modules/nf-core/picard/createsequencedictionary/main'
+include { QC_BAM } from '../subworkflows/local/qc_bam'
 
 include { MULTIQC as MULTIQC_GLOBAL } from '../modules/nf-core/multiqc'
 include { MULTIQC as MULTIQC_PER_TAG } from '../modules/nf-core/multiqc'
@@ -202,46 +201,15 @@ workflow SEQINSPECTOR {
         ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
     }
 
-    if (!("picard_collecthsmetrics" in skip_tools) && !("bwamem2_mem" in skip_tools)) {
-
-        if (("picard_collectmultiplemetrics" in skip_tools)){
-            ch_bam_bai = ch_bwamem2_mem.join(ch_samtools_index, failOnDuplicate: true, failOnMismatch: true)
-        }
-
-        ch_bait_intervals = channel
-            .fromPath(params.bait_intervals)
-            .collect()
-
-        ch_target_intervals = channel
-            .fromPath(params.target_intervals)
-            .collect()
-
-
-        ch_hsmetrics_in = ch_bam_bai
-            .combine(ch_bait_intervals)
-            .combine(ch_target_intervals)
-
-
-        if (!params.ref_dict) {
-            PICARD_CREATESEQUENCEDICTIONARY(
-                ch_reference_fasta
-            )
-            ch_ref_dict = PICARD_CREATESEQUENCEDICTIONARY.out.reference_dict
-        }
-        else {
-            ch_ref_dict = channel.fromPath(params.ref_dict).map { [[id: it.simpleName], it] }
-        }
-
-        PICARD_COLLECTHSMETRICS(
-            ch_hsmetrics_in,
+    if (!("picard_collecthsmetrics" in skip_tools) && !("picard_collectmultiplemetrics" in skip_tools)) {
+        QC_BAM(
+            ch_bam_bai,
             ch_reference_fasta,
-            [[], []],
-            ch_ref_dict,
-            [[], []],
-        )
-        ch_multiqc_files = ch_multiqc_files.mix(PICARD_COLLECTHSMETRICS.out.metrics)
-        ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
+            ch_reference_fasta_fai,
+            )
     }
+    ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.hs_metrics)
+    ch_versions = ch_versions.mix(QC_BAM.out.versions)
 
 
     // Collate and save software versions

From 069ee40cc0fbaffe2bcee74bee166f4e8b04def8 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Mon, 24 Nov 2025 16:55:05 +0100
Subject: [PATCH 368/530] Add subworkflow qc_bam.

---
 subworkflows/local/qc_bam.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/qc_bam.nf b/subworkflows/local/qc_bam.nf
index b24c664c..f6d53107 100644
--- a/subworkflows/local/qc_bam.nf
+++ b/subworkflows/local/qc_bam.nf
@@ -36,7 +36,7 @@ workflow QC_BAM {
                 ch_reference_fasta
             )
             ch_ref_dict = PICARD_CREATESEQUENCEDICTIONARY.out.reference_dict
-            ch_versions = ch_versions.mix(PICARD_CREATESEQUENCEDICTIONARY.out.versions.first())
+            ch_versions = ch_versions.mix(PICARD_CREATESEQUENCEDICTIONARY.out.versions)
         }
         else {
             ch_ref_dict = channel.fromPath(params.ref_dict).map { [[id: it.simpleName], it] }

From 98ab4a3a01a63780f50b1f3ecb6adbfe91134caa Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Mon, 24 Nov 2025 17:05:18 +0100
Subject: [PATCH 369/530] Add subworkflow QC_BAM.

---
 subworkflows/local/qc_bam/main.nf | 60 +++++++++++++++++++++++++++++++
 1 file changed, 60 insertions(+)
 create mode 100644 subworkflows/local/qc_bam/main.nf

diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf
new file mode 100644
index 00000000..13a35b0a
--- /dev/null
+++ b/subworkflows/local/qc_bam/main.nf
@@ -0,0 +1,60 @@
+//
+// A quality check subworkflow for processed bam files.
+//
+
+include { PICARD_COLLECTHSMETRICS } from '../../../modules/nf-core/picard/collecthsmetrics/main'
+include { PICARD_CREATESEQUENCEDICTIONARY } from '../../../modules/nf-core/picard/createsequencedictionary/main'
+
+workflow QC_BAM {
+    take:
+
+        ch_bam_bai
+        ch_reference_fasta
+        ch_reference_fasta_fai
+
+    main:
+
+        ch_versions = channel.empty()
+
+
+        ch_bait_intervals = channel
+            .fromPath(params.bait_intervals)
+            .collect()
+
+        ch_target_intervals = channel
+            .fromPath(params.target_intervals)
+            .collect()
+
+
+        ch_hsmetrics_in = ch_bam_bai
+            .combine(ch_bait_intervals)
+            .combine(ch_target_intervals)
+
+
+        if (!params.ref_dict) {
+            PICARD_CREATESEQUENCEDICTIONARY(
+                ch_reference_fasta
+            )
+            ch_ref_dict = PICARD_CREATESEQUENCEDICTIONARY.out.reference_dict
+            ch_versions = ch_versions.mix(PICARD_CREATESEQUENCEDICTIONARY.out.versions)
+        }
+        else {
+            ch_ref_dict = channel.fromPath(params.ref_dict).map { [[id: it.simpleName], it] }
+        }
+
+        PICARD_COLLECTHSMETRICS(
+            ch_hsmetrics_in,
+            ch_reference_fasta,
+            ch_reference_fasta_fai,
+            ch_ref_dict,
+            [[], []],
+        )
+        ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
+
+
+    emit:
+
+        hs_metrics = PICARD_COLLECTHSMETRICS.out.metrics
+        versions = ch_versions
+
+}
\ No newline at end of file

From 2083cfc8f601c24eabb1be0f8e361bc759c9fb70 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Mon, 24 Nov 2025 17:06:16 +0100
Subject: [PATCH 370/530] Add logic to skip collecthsmetrics by default through
 addin "run_picard_collecthsmetrics" flag.

---
 conf/cg_test.config       | 2 +-
 nextflow.config           | 3 ++-
 nextflow_schema.json      | 8 ++++++--
 workflows/seqinspector.nf | 4 ++--
 4 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/conf/cg_test.config b/conf/cg_test.config
index 93477fff..97255d78 100644
--- a/conf/cg_test.config
+++ b/conf/cg_test.config
@@ -2,7 +2,7 @@
 params {
     input                           = "${projectDir}/assets/cg_test_samplesheet.csv"
     pipelines_testdata_base_path    = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease'
-    skip_tools                      = null
+    run_picard_collecthsmetrics     = true
     fasta                           = params.pipelines_testdata_base_path + '/reference/reference.fasta'
     genome                          = 'GRCh37'
     bait_intervals                  = params.pipelines_testdata_base_path + '/reference/target.bed'
diff --git a/nextflow.config b/nextflow.config
index ad7c5ff8..f126d6d6 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -13,7 +13,7 @@ params {
     // Input options
     input                      = null
     sample_size                = 0
-    skip_tools                 = 'picard_collecthsmetrics'
+    skip_tools                 = ''
     // References
     genome                     = null
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
@@ -47,6 +47,7 @@ params {
     trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 
     // picard_collecthsmetrics options
+    run_picard_collecthsmetrics = false
     bait_intervals              = null
     target_intervals            = null
     ref_dict                    = null
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 17365de6..0e429729 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -50,8 +50,7 @@
                 "skip_tools": {
                     "type": "string",
                     "description": "Comma-separated string of tools to skip",
-                    "pattern": "^((fastqc|fastqscreen|seqfu_stats|seqtk_sample|bwamem2_index|bwamem2_mem|picard_collectmultiplemetrics|samtools_faidx|picard_collecthsmetrics)?,?)*(?<!,)$",
-                    "default": "picard_collecthsmetrics"
+                    "pattern": "^((fastqc|fastqscreen|seqfu_stats|seqtk_sample|bwamem2_index|bwamem2_mem|picard_collectmultiplemetrics|samtools_faidx|picard_collecthsmetrics)?,?)*(?<!,)$"
                 }
             }
         },
@@ -283,6 +282,11 @@
             "description": "",
             "default": "",
             "properties": {
+                "run_picard_collecthsmetrics": {
+                    "type": "boolean",
+                    "hidden": true,
+                    "description": "Run picard_colecthsmetrics for QC of bam files."
+                },
                 "bait_intervals": {
                     "type": "string",
                     "description": "Path to bait intervals file.",
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 534f6269..1be68dd1 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -201,12 +201,12 @@ workflow SEQINSPECTOR {
         ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
     }
 
-    if (!("picard_collecthsmetrics" in skip_tools) && !("picard_collectmultiplemetrics" in skip_tools)) {
+    if (params.run_picard_collecthsmetrics && !("picard_collectmultiplemetrics" in skip_tools)) {
         QC_BAM(
             ch_bam_bai,
             ch_reference_fasta,
             ch_reference_fasta_fai,
-            )
+        )
     }
     ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.hs_metrics)
     ch_versions = ch_versions.mix(QC_BAM.out.versions)

From 66f0c38bafd9ad88a8a5b160f41005bcd49101dd Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrima2010@users.noreply.github.com>
Date: Mon, 24 Nov 2025 18:11:41 +0100
Subject: [PATCH 371/530] Modified seqinspector.nf and added subworkflow

---
 subworkflows/local/prepare_genome/main.nf | 63 +++++++++++++++++++++++
 workflows/seqinspector.nf                 | 60 +++++----------------
 2 files changed, 75 insertions(+), 48 deletions(-)
 create mode 100644 subworkflows/local/prepare_genome/main.nf

diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf
new file mode 100644
index 00000000..3cfe3679
--- /dev/null
+++ b/subworkflows/local/prepare_genome/main.nf
@@ -0,0 +1,63 @@
+//
+// Prepare reference genome files
+
+include { BWAMEM2_INDEX                 } from '../modules/nf-core/bwamem2/index'
+include { SAMTOOLS_FAIDX                } from '../modules/nf-core/samtools/faidx'
+
+workflow PREPARE_GENOME {
+    take:
+    fasta_fai                
+    fasta_file               
+    bwa_index
+
+    main:
+    // Initialize all channels that might be used later
+    ch_bwamem2_index = channel.empty()
+    ch_reference_fasta_fai = channel.empty()
+    ch_reference_fasta = channel.empty()
+    ch_versions      = channel.empty()
+
+    if (!("bwamem2_index" in skip_tools)) {
+        ch_reference_fasta = channel.fromPath(fasta_file, checkIfExists: true).map { file -> tuple([id: file.name], file) }.collect()
+
+        if (bwa_index) {
+            // Use pre-built index when --bwa_index parameter is provided
+            ch_bwamem2_index = channel.fromPath(bwa_index, checkIfExists: true)
+                .map { index_dir -> tuple([id: index_dir.name], index_dir) }
+                .collect()
+
+        }
+        else {
+            // Build index from reference FASTA when no pre-built index is provided
+            BWAMEM2_INDEX(
+                ch_reference_fasta
+            )
+            ch_bwamem2_index = BWAMEM2_INDEX.out.index
+            ch_versions = ch_versions.mix(BWAMEM2_INDEX.out.versions)
+
+        }
+    }
+
+    if (!("samtools_faidx" in skip_tools)) {
+
+        // Assume ch_fasta emits tuple(meta, fasta)
+        SAMTOOLS_FAIDX(
+            ch_reference_fasta,
+            [[:], []],
+            true,
+        )
+        ch_reference_fasta_fai = SAMTOOLS_FAIDX.out.fai
+        ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions)
+    }
+
+ // Gather versions
+    ch_versions = ch_versions.mix(BWAMEM2_INDEX.out.versions)
+    ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions)
+
+
+    emit:
+        BWAMEM2_INDEX.out.index       = ch_bwamem2_index
+        SAMTOOLS_FAIDX.out.fai        = ch_reference_fasta_fai
+        versions                      = ch_versions
+
+}       
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index bcf88f8c..61433463 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -6,7 +6,7 @@ include { samplesheetToList             } from 'plugin/nf-schema'
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { BWAMEM2_INDEX                 } from '../modules/nf-core/bwamem2/index'
+// nf-core
 include { BWAMEM2_MEM                   } from '../modules/nf-core/bwamem2/mem'
 include { FASTQC                        } from '../modules/nf-core/fastqc'
 include { FASTQSCREEN_FASTQSCREEN       } from '../modules/nf-core/fastqscreen/fastqscreen'
@@ -24,6 +24,9 @@ include { paramsSummaryMultiqc          } from '../subworkflows/nf-core/utils_nf
 include { softwareVersionsToYAML        } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { methodsDescriptionText        } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline'
 
+// local
+include { PREPARE_GENOME                } from '../subworkflows/local/prepare_genome'
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     RUN MAIN WORKFLOW
@@ -43,11 +46,15 @@ workflow SEQINSPECTOR {
     ch_multiqc_extra_files = channel.empty()
 
     // Initialize all channels that might be used later
-    ch_bwamem2_index = channel.empty()
     ch_bwamem2_mem = channel.empty()
     ch_samtools_index = channel.empty()
-    ch_reference_fasta_fai = channel.empty()
-    ch_reference_fasta = channel.empty()
+
+    PREPARE_GENOME (
+            ch_bwamem2_index,
+            ch_reference_fasta_fai,
+            ch_reference_fasta,
+        )
+
 
     //
     // MODULE: Run Seqtk sample to perform subsampling
@@ -117,33 +124,7 @@ workflow SEQINSPECTOR {
         ch_multiqc_files = ch_multiqc_files.mix(FASTQSCREEN_FASTQSCREEN.out.txt)
         ch_versions = ch_versions.mix(FASTQSCREEN_FASTQSCREEN.out.versions.first())
     }
-    // MODULE: Create BWA-MEM2 index of the reference genome OR use pre-built index
-    if (!("bwamem2_index" in skip_tools)) {
-        // Always create the reference FASTA channel since it's needed by BWAMEM2_MEM
-        ch_reference_fasta = channel.fromPath(fasta_file, checkIfExists: true).map { file -> tuple([id: file.name], file) }.collect()
-
-        if (params.bwa_index) {
-            // Use pre-built index when --bwa_index parameter is provided
-            ch_bwamem2_index = channel.fromPath(params.bwa_index, checkIfExists: true)
-                .map { index_dir -> tuple([id: index_dir.name], index_dir) }
-                .collect()
-
-            // Add debug output to verify the pre-built index is being used
-            ch_bwamem2_index.view { "Using pre-built BWA-MEM2 index: ${it}" }
-        }
-        else {
-            // Build index from reference FASTA when no pre-built index is provided
-            BWAMEM2_INDEX(
-                ch_reference_fasta
-            )
-            ch_bwamem2_index = BWAMEM2_INDEX.out.index
-            ch_versions = ch_versions.mix(BWAMEM2_INDEX.out.versions)
-
-            // Add debug output to verify the index was built
-            ch_bwamem2_index.view { "Built BWA-MEM2 index: ${it}" }
-        }
-    }
-
+    
     // MODULE: Align reads with BWA-MEM2
     if (!("bwamem2_mem" in skip_tools)) {
         BWAMEM2_MEM(
@@ -164,19 +145,6 @@ workflow SEQINSPECTOR {
         ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions)
     }
 
-    // MODULE: Index reference FASTA with Samtools faidx
-    if (!("samtools_faidx" in skip_tools)) {
-
-        // Assume ch_fasta emits tuple(meta, fasta)
-        SAMTOOLS_FAIDX(
-            ch_reference_fasta,
-            [[:], []],
-            true,
-        )
-        ch_reference_fasta_fai = SAMTOOLS_FAIDX.out.fai
-        ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions)
-    }
-
     // MODULE: Prepare BAM/BAI tuples for Picard
     // Combine BAM and BAI outputs for Picard
     if (!("picard_collectmultiplemetrics" in skip_tools) && !("bwamem2_mem" in skip_tools) && !("samtools_index" in skip_tools) && !("samtools_faidx" in skip_tools)) {
@@ -184,13 +152,9 @@ workflow SEQINSPECTOR {
         // Prepare BAM/BAI tuples for Picard
         ch_bam_bai = ch_bwamem2_mem.join(ch_samtools_index, failOnDuplicate: true, failOnMismatch: true)
 
-        ch_bam_bai.view { "Combined BAM/BAI for Picard: ${it}" }
         ch_fasta = ch_reference_fasta
         ch_fai = ch_reference_fasta_fai
 
-        ch_fasta.view { "FASTA for Picard: ${it}" }
-        ch_fai.view { "FAI for Picard: ${it}" }
-
         PICARD_COLLECTMULTIPLEMETRICS(
             ch_bam_bai,
             ch_fasta,

From 8a68c93683843b41df3597eb007824b0acbd8515 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 25 Nov 2025 09:37:42 +0100
Subject: [PATCH 372/530] Add TMP_DIR argument to picard_collecthsmetrics.

---
 conf/cg_test.config | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/conf/cg_test.config b/conf/cg_test.config
index 97255d78..37d13ded 100644
--- a/conf/cg_test.config
+++ b/conf/cg_test.config
@@ -22,7 +22,8 @@ process {
     withName: PICARD_COLLECTHSMETRICS {
         ext.args = { [
             "--COVERAGE_CAP 50000",
-            "--METRIC_ACCUMULATION_LEVEL ALL_READS"
+            "--METRIC_ACCUMULATION_LEVEL ALL_READS",
+            "--TMP_DIR ."
 			].join(' ') }
 
     }

From 3693ca5b2b8fd8fb7f8521f391fdd9c08f21ec86 Mon Sep 17 00:00:00 2001
From: FranBonath <franziska.bonath@scilifelab.se>
Date: Tue, 25 Nov 2025 09:41:57 +0100
Subject: [PATCH 373/530] update README and usage.md

---
 README.md     | 25 +++++++++++--------------
 docs/usage.md | 20 +++++++++++++-------
 2 files changed, 24 insertions(+), 21 deletions(-)

diff --git a/README.md b/README.md
index fea648b4..3f6a3866 100644
--- a/README.md
+++ b/README.md
@@ -37,16 +37,16 @@
 
 <!-- TODO: add a search tool that accepts a tree for `Compatibility with Data`. -->
 
-| Tool Type           | Tool Name                                                                          | Tool Description                            | Compatibility with Data | Dependencies        |
-| ------------------- | ---------------------------------------------------------------------------------- | ------------------------------------------- | ----------------------- | ------------------- |
-| `Subsampling`       | [`Seqtk`](https://github.com/lh3/seqtk)                                            | Global subsampling of reads                 | [RNA, DNA, synthetic]   | [N/A]               |
-| `QC`                | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)             | Read QC                                     | [RNA, DNA]              | [N/A]               |
-| `QC`                | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)  | Basic contamination detection               | [RNA, DNA]              | [N/A]               |
-| `QC`                | [`SeqFu Stats`](https://github.com/telatin/seqfu2)                                 | Sequence statistics                         | [RNA, DNA]              | [N/A]               |
-| `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2)                                  | Align reads to reference                    | [RNA, DNA]              | [N/A]               |
-| `Indexing`          | [`SAMtools`](http://github.com/samtools)                                           | Index aligned BAM files, create FASTA index | [DNA]                   | [N/A]               |
-| `QC`                | [`Picard`](https://broadinstitute.github.io/picard/picard-metric-definitions.html) | Collect multiple QC metrics                 | [RNA, DNA]              | [Bwamem2, SAMtools] |
-| `Reporting`         | [`MultiQC`](http://multiqc.info/)                                                  | Present QC for raw reads                    | [RNA, DNA, synthetic]   | [N/A]               |
+| Tool Type           | Tool Name                                                                          | Tool Description                            | Compatibility with Data | Dependencies                    | Default tool |
+| ------------------- | ---------------------------------------------------------------------------------- | ------------------------------------------- | ----------------------- | ------------------------------- | ------------ |
+| `Subsampling`       | [`Seqtk`](https://github.com/lh3/seqtk)                                            | Global subsampling of reads                 | [RNA, DNA, synthetic]   | [N/A]                           | no           |
+| `QC`                | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)             | Read QC                                     | [RNA, DNA]              | [N/A]                           | yes          |
+| `QC`                | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)  | Basic contamination detection               | [RNA, DNA]              | [N/A]                           | yes          |
+| `QC`                | [`SeqFu Stats`](https://github.com/telatin/seqfu2)                                 | Sequence statistics                         | [RNA, DNA]              | [N/A]                           | yes          |
+| `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2)                                  | Align reads to reference                    | [RNA, DNA]              | [N/A]                           | yes          |
+| `Indexing`          | [`SAMtools`](http://github.com/samtools)                                           | Index aligned BAM files, create FASTA index | [DNA]                   | [N/A]                           | yes          |
+| `QC`                | [`Picard`](https://broadinstitute.github.io/picard/picard-metric-definitions.html) | Collect multiple QC metrics                 | [RNA, DNA]              | [Bwamem2, SAMtools, `--genome`] | yes          |
+| `Reporting`         | [`MultiQC`](http://multiqc.info/)                                                  | Present QC for raw reads                    | [RNA, DNA, synthetic]   | [N/A]                           | yes          |
 
 <picture>
   <source media="(prefers-color-scheme: dark)" srcset="docs/images/seqinspector_tubemap_V1.0_dark.png">
@@ -92,7 +92,7 @@ For more details about the output files and reports, please refer to the
 
 ## Credits
 
-nf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/).
+nf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/) and [Clinical Genomics Stockholm](https://clinical.scilifelab.se/).
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 
@@ -106,9 +106,6 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 ## Citations
 
-<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
-<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
-
 <!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
diff --git a/docs/usage.md b/docs/usage.md
index e31a7862..a077e648 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -2,15 +2,21 @@
 
 ## :warning: Please read this documentation on the nf-core website: [https://nf-co.re/seqinspector/usage](https://nf-co.re/seqinspector/usage)
 
-> _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._
-
 ## Introduction
 
-<!-- TODO nf-core: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website. -->
+### General points
+
+The nf-core/seqinspector pipeline is a general QC pipeline for sequencing data. The current version only supports data in fastq format.
+The pipeline is meant to include a large amount of possible QC tools to chose from, but not all of them may be relevant to your data. As such we highly recommend to familiarize yourself with the different QC tools available and to remove any QC tool you would like to exclude with the `--skip-tools` command line parameter. For repeated use we suggest to create a params file containing the `--skip-tools` parameters (for details see the "Running the pipeline" section).
+Be aware that some tools are skipped by default and will need to be included in the list of skipped tools when curating your own list. To identify defaults included or excluded please check out the overview table in the Introduction.
+
+### What nf-core/seqinspector is not for
+
+The results of the nf-core/seqinspector pipeline are not meant to be used for any downstream analysis, but are exclusively for QC purposes. Even tools that may be used in other pipelines as a starting point for analysis are run in a QC perspective, most likely with a downsampled input.
 
 ## Samplesheet input
 
-You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location.
+You will need to create a samplesheet with information about the samples/fastq files you would like to analyse before running the pipeline. Use this parameter to specify its location.
 
 ```bash
 --input '[path to samplesheet file]'
@@ -51,7 +57,7 @@ Another [example samplesheet](../assets/samplesheet.csv) has been provided with
 
 ## Running the pipeline
 
-The typical command for running the pipeline is as follows:
+A typical command for running the pipeline is as follows:
 
 ```bash
 nextflow run nf-core/seqinspector --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker
@@ -100,7 +106,7 @@ nextflow run nf-core/seqinspector --input ./samplesheet.csv --outdir ./results -
 
 ### Skipping tools
 
-Some tools might not be compatible with your data. In this case it might be desired to skip some of them. This can be done easily by providing a comma-separated list of tools to be skipped with the `--skip_tools` parameter.
+Some tools might not be compatible with your data. In this case you can skip them by providing a comma-separated list of tools to be skipped with the `--skip_tools` parameter.
 
 In case you want to make this more permanent, it is recommended to specify this in a params file, or even in your own nextflow configuration file. The nextflow configuration file can also be use to customise tool arguments. See official [nexflow](https://www.nextflow.io/docs/latest/config.html) and [nf-core](https://nf-co.re/docs/usage/configuration#customising-tool-arguments) documentation for further details.
 
@@ -123,7 +129,7 @@ This version number will be logged in reports when you run the pipeline, so that
 To further assist in reproducibility, you can use share and reuse [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
 
 > [!TIP]
-> If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
+> If you wish to share such profiles (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
 
 ## Core Nextflow arguments
 

From 48eec4e0dd63b4dfc474b278bfd4baa268cead9f Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 25 Nov 2025 10:18:01 +0100
Subject: [PATCH 374/530] Create subworkflow directory. Change channels created
 from params to seqcinspector.nf instead of subworkflow.

---
 subworkflows/local/qc_bam/main.nf | 23 +++--------------------
 workflows/seqinspector.nf         | 19 ++++++++++++++++++-
 2 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf
index 13a35b0a..59105ff3 100644
--- a/subworkflows/local/qc_bam/main.nf
+++ b/subworkflows/local/qc_bam/main.nf
@@ -8,39 +8,22 @@ include { PICARD_CREATESEQUENCEDICTIONARY } from '../../../modules/nf-core/picar
 workflow QC_BAM {
     take:
 
-        ch_bam_bai
+        ch_hsmetrics_in
         ch_reference_fasta
         ch_reference_fasta_fai
+        ch_ref_dict
 
     main:
 
         ch_versions = channel.empty()
 
-
-        ch_bait_intervals = channel
-            .fromPath(params.bait_intervals)
-            .collect()
-
-        ch_target_intervals = channel
-            .fromPath(params.target_intervals)
-            .collect()
-
-
-        ch_hsmetrics_in = ch_bam_bai
-            .combine(ch_bait_intervals)
-            .combine(ch_target_intervals)
-
-
-        if (!params.ref_dict) {
+        if (!ch_ref_dict) {
             PICARD_CREATESEQUENCEDICTIONARY(
                 ch_reference_fasta
             )
             ch_ref_dict = PICARD_CREATESEQUENCEDICTIONARY.out.reference_dict
             ch_versions = ch_versions.mix(PICARD_CREATESEQUENCEDICTIONARY.out.versions)
         }
-        else {
-            ch_ref_dict = channel.fromPath(params.ref_dict).map { [[id: it.simpleName], it] }
-        }
 
         PICARD_COLLECTHSMETRICS(
             ch_hsmetrics_in,
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 1be68dd1..d971966b 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -202,10 +202,27 @@ workflow SEQINSPECTOR {
     }
 
     if (params.run_picard_collecthsmetrics && !("picard_collectmultiplemetrics" in skip_tools)) {
+
+        ch_bait_intervals = channel
+            .fromPath(params.bait_intervals)
+            .collect()
+
+        ch_target_intervals = channel
+            .fromPath(params.target_intervals)
+            .collect()
+
+
+        ch_hsmetrics_in = ch_bam_bai
+            .combine(ch_bait_intervals)
+            .combine(ch_target_intervals)
+
+        ch_ref_dict = channel.fromPath(params.ref_dict).map { [[id: it.simpleName], it]
+
         QC_BAM(
-            ch_bam_bai,
+            ch_hsmetrics_in,
             ch_reference_fasta,
             ch_reference_fasta_fai,
+            ch_ref_dict,
         )
     }
     ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.hs_metrics)

From 75b2f5efacf46e7b0f3655dd07c0ac6cd855a4dd Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 25 Nov 2025 10:20:10 +0100
Subject: [PATCH 375/530] Add curly braket.

---
 workflows/seqinspector.nf | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index d971966b..f662aaf5 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -203,12 +203,10 @@ workflow SEQINSPECTOR {
 
     if (params.run_picard_collecthsmetrics && !("picard_collectmultiplemetrics" in skip_tools)) {
 
-        ch_bait_intervals = channel
-            .fromPath(params.bait_intervals)
+        ch_bait_intervals = channel.fromPath(params.bait_intervals)
             .collect()
 
-        ch_target_intervals = channel
-            .fromPath(params.target_intervals)
+        ch_target_intervals = channel.fromPath(params.target_intervals)
             .collect()
 
 
@@ -216,7 +214,7 @@ workflow SEQINSPECTOR {
             .combine(ch_bait_intervals)
             .combine(ch_target_intervals)
 
-        ch_ref_dict = channel.fromPath(params.ref_dict).map { [[id: it.simpleName], it]
+        ch_ref_dict = channel.fromPath(params.ref_dict).map { [[id: it.simpleName], it] }
 
         QC_BAM(
             ch_hsmetrics_in,

From f014036b36d5c9d1f237bf41b862a5ee65f0554e Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 25 Nov 2025 10:23:52 +0100
Subject: [PATCH 376/530] Add second sample to samplesheet.

---
 assets/cg_test_samplesheet.csv | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/assets/cg_test_samplesheet.csv b/assets/cg_test_samplesheet.csv
index a1913b20..d9875790 100644
--- a/assets/cg_test_samplesheet.csv
+++ b/assets/cg_test_samplesheet.csv
@@ -1,2 +1,3 @@
 sample,fastq_1,fastq_2,rundir,tags
-raredisease_test_sample,https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz,,test
\ No newline at end of file
+raredisease_test_sample,https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz,,test
+raredisease_test_sample_2,https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz,,test_2
\ No newline at end of file

From bc3320f262520586ffd247a243ec5c302d5cc2a1 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 25 Nov 2025 10:35:09 +0100
Subject: [PATCH 377/530] Fix ch_ref_dict.

---
 subworkflows/local/qc_bam/main.nf | 9 +++++++--
 workflows/seqinspector.nf         | 3 +--
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf
index 59105ff3..e7329fa0 100644
--- a/subworkflows/local/qc_bam/main.nf
+++ b/subworkflows/local/qc_bam/main.nf
@@ -11,19 +11,24 @@ workflow QC_BAM {
         ch_hsmetrics_in
         ch_reference_fasta
         ch_reference_fasta_fai
-        ch_ref_dict
+        ref_dict
 
     main:
 
         ch_versions = channel.empty()
 
-        if (!ch_ref_dict) {
+        if (!ref_dict) {
             PICARD_CREATESEQUENCEDICTIONARY(
                 ch_reference_fasta
             )
             ch_ref_dict = PICARD_CREATESEQUENCEDICTIONARY.out.reference_dict
             ch_versions = ch_versions.mix(PICARD_CREATESEQUENCEDICTIONARY.out.versions)
         }
+        else{
+            ch_ref_dict = channel.fromPath(ref_dict, checkIfExists: true).map{ [[id: it.simpleName], it]}
+        }
+
+        ch_ref_dict
 
         PICARD_COLLECTHSMETRICS(
             ch_hsmetrics_in,
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index f662aaf5..efd3074d 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -214,13 +214,12 @@ workflow SEQINSPECTOR {
             .combine(ch_bait_intervals)
             .combine(ch_target_intervals)
 
-        ch_ref_dict = channel.fromPath(params.ref_dict).map { [[id: it.simpleName], it] }
 
         QC_BAM(
             ch_hsmetrics_in,
             ch_reference_fasta,
             ch_reference_fasta_fai,
-            ch_ref_dict,
+            params.ref_dict,
         )
     }
     ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.hs_metrics)

From 5381e4e0679871e096b7bc2e4910b7f5cfe0e01d Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 25 Nov 2025 10:45:44 +0100
Subject: [PATCH 378/530] Remove outdated qc_bam.nf.

---
 subworkflows/local/qc_bam.nf | 60 ------------------------------------
 1 file changed, 60 deletions(-)
 delete mode 100644 subworkflows/local/qc_bam.nf

diff --git a/subworkflows/local/qc_bam.nf b/subworkflows/local/qc_bam.nf
deleted file mode 100644
index f6d53107..00000000
--- a/subworkflows/local/qc_bam.nf
+++ /dev/null
@@ -1,60 +0,0 @@
-//
-// A quality check subworkflow for processed bam files.
-//
-
-include { PICARD_COLLECTHSMETRICS } from '../../modules/nf-core/picard/collecthsmetrics/main'
-include { PICARD_CREATESEQUENCEDICTIONARY } from '../../modules/nf-core/picard/createsequencedictionary/main'
-
-workflow QC_BAM {
-    take:
-
-        ch_bam_bai
-        ch_reference_fasta
-        ch_reference_fasta_fai
-
-    main:
-
-        ch_versions = channel.empty()
-
-
-        ch_bait_intervals = channel
-            .fromPath(params.bait_intervals)
-            .collect()
-
-        ch_target_intervals = channel
-            .fromPath(params.target_intervals)
-            .collect()
-
-
-        ch_hsmetrics_in = ch_bam_bai
-            .combine(ch_bait_intervals)
-            .combine(ch_target_intervals)
-
-
-        if (!params.ref_dict) {
-            PICARD_CREATESEQUENCEDICTIONARY(
-                ch_reference_fasta
-            )
-            ch_ref_dict = PICARD_CREATESEQUENCEDICTIONARY.out.reference_dict
-            ch_versions = ch_versions.mix(PICARD_CREATESEQUENCEDICTIONARY.out.versions)
-        }
-        else {
-            ch_ref_dict = channel.fromPath(params.ref_dict).map { [[id: it.simpleName], it] }
-        }
-
-        PICARD_COLLECTHSMETRICS(
-            ch_hsmetrics_in,
-            ch_reference_fasta,
-            ch_reference_fasta_fai,
-            ch_ref_dict,
-            [[], []],
-        )
-        ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
-
-
-    emit:
-
-        hs_metrics = PICARD_COLLECTHSMETRICS.out.metrics
-        versions = ch_versions
-
-}
\ No newline at end of file

From 74732972163c0e594e437a81f19c52b37df100e1 Mon Sep 17 00:00:00 2001
From: Franziska Bonath <41994400+FranBonath@users.noreply.github.com>
Date: Tue, 25 Nov 2025 10:51:26 +0100
Subject: [PATCH 379/530] Update README.md

Co-authored-by: Matthias Zepper <6963520+MatthiasZepper@users.noreply.github.com>
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index fea648b4..b9978f5d 100644
--- a/README.md
+++ b/README.md
@@ -33,7 +33,7 @@
   <img alt="Fallback image description" src="docs/images/nfcore-seqinspector-logo-hex-light.png">
 </picture>
 
-**nf-core/seqinspector** is a bioinformatics pipeline that that processes raw sequencedata (FASTQ) to provide comprehensive quality control. It can perform subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants. The pipeline generates detailed MultiQC reports with flexible output options, ranging from individual sample reports to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments. If provided, nf-core/seqinspector can also parse statistics from an Illumina run folder directory into the final MultiQC reports.
+**nf-core/seqinspector** is a bioinformatics pipeline that that processes raw sequence data (FASTQ) to provide comprehensive quality control. It can perform subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants. The pipeline generates detailed MultiQC reports with flexible output options, ranging from individual sample reports to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments. If provided, nf-core/seqinspector can also parse statistics from an Illumina run folder directory into the final MultiQC reports.
 
 <!-- TODO: add a search tool that accepts a tree for `Compatibility with Data`. -->
 

From b478b368e8a34310b83944cab311bafea6c51829 Mon Sep 17 00:00:00 2001
From: Franziska Bonath <41994400+FranBonath@users.noreply.github.com>
Date: Tue, 25 Nov 2025 10:51:39 +0100
Subject: [PATCH 380/530] Update README.md

Co-authored-by: Matthias Zepper <6963520+MatthiasZepper@users.noreply.github.com>
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index b9978f5d..c4dd802b 100644
--- a/README.md
+++ b/README.md
@@ -46,7 +46,7 @@
 | `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2)                                  | Align reads to reference                    | [RNA, DNA]              | [N/A]               |
 | `Indexing`          | [`SAMtools`](http://github.com/samtools)                                           | Index aligned BAM files, create FASTA index | [DNA]                   | [N/A]               |
 | `QC`                | [`Picard`](https://broadinstitute.github.io/picard/picard-metric-definitions.html) | Collect multiple QC metrics                 | [RNA, DNA]              | [Bwamem2, SAMtools] |
-| `Reporting`         | [`MultiQC`](http://multiqc.info/)                                                  | Present QC for raw reads                    | [RNA, DNA, synthetic]   | [N/A]               |
+| `Reporting`         | [`MultiQC`](http://multiqc.info/)                                                  | Aggregate and visualise results                    | [RNA, DNA, synthetic]   | [N/A]               |
 
 <picture>
   <source media="(prefers-color-scheme: dark)" srcset="docs/images/seqinspector_tubemap_V1.0_dark.png">

From 95582a09b6740504a6727734e817b49107def826 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Tue, 25 Nov 2025 09:53:38 +0000
Subject: [PATCH 381/530] [automated] Fix code linting

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index c4dd802b..a4d0e51f 100644
--- a/README.md
+++ b/README.md
@@ -46,7 +46,7 @@
 | `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2)                                  | Align reads to reference                    | [RNA, DNA]              | [N/A]               |
 | `Indexing`          | [`SAMtools`](http://github.com/samtools)                                           | Index aligned BAM files, create FASTA index | [DNA]                   | [N/A]               |
 | `QC`                | [`Picard`](https://broadinstitute.github.io/picard/picard-metric-definitions.html) | Collect multiple QC metrics                 | [RNA, DNA]              | [Bwamem2, SAMtools] |
-| `Reporting`         | [`MultiQC`](http://multiqc.info/)                                                  | Aggregate and visualise results                    | [RNA, DNA, synthetic]   | [N/A]               |
+| `Reporting`         | [`MultiQC`](http://multiqc.info/)                                                  | Aggregate and visualise results             | [RNA, DNA, synthetic]   | [N/A]               |
 
 <picture>
   <source media="(prefers-color-scheme: dark)" srcset="docs/images/seqinspector_tubemap_V1.0_dark.png">

From 34baa10c1e34cfa42509b43ebc781591509e6695 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 25 Nov 2025 10:57:52 +0100
Subject: [PATCH 382/530] Change if order in qc_bam.

---
 subworkflows/local/qc_bam/main.nf | 46 ++++++++++++++-----------------
 1 file changed, 20 insertions(+), 26 deletions(-)

diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf
index e7329fa0..c4f77a1c 100644
--- a/subworkflows/local/qc_bam/main.nf
+++ b/subworkflows/local/qc_bam/main.nf
@@ -7,7 +7,6 @@ include { PICARD_CREATESEQUENCEDICTIONARY } from '../../../modules/nf-core/picar
 
 workflow QC_BAM {
     take:
-
         ch_hsmetrics_in
         ch_reference_fasta
         ch_reference_fasta_fai
@@ -15,34 +14,29 @@ workflow QC_BAM {
 
     main:
 
-        ch_versions = channel.empty()
-
-        if (!ref_dict) {
-            PICARD_CREATESEQUENCEDICTIONARY(
-                ch_reference_fasta
-            )
-            ch_ref_dict = PICARD_CREATESEQUENCEDICTIONARY.out.reference_dict
-            ch_versions = ch_versions.mix(PICARD_CREATESEQUENCEDICTIONARY.out.versions)
-        }
-        else{
-            ch_ref_dict = channel.fromPath(ref_dict, checkIfExists: true).map{ [[id: it.simpleName], it]}
-        }
-
-        ch_ref_dict
+    ch_versions = channel.empty()
 
-        PICARD_COLLECTHSMETRICS(
-            ch_hsmetrics_in,
-            ch_reference_fasta,
-            ch_reference_fasta_fai,
-            ch_ref_dict,
-            [[], []],
+    if (ref_dict) {
+        ch_ref_dict = channel.fromPath(ref_dict, checkIfExists: true).map { [[id: it.simpleName], it] }
+    }
+    else {
+        PICARD_CREATESEQUENCEDICTIONARY(
+            ch_reference_fasta
         )
-        ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
-
+        ch_ref_dict = PICARD_CREATESEQUENCEDICTIONARY.out.reference_dict
+        ch_versions = ch_versions.mix(PICARD_CREATESEQUENCEDICTIONARY.out.versions)
+    }
+
+    PICARD_COLLECTHSMETRICS(
+        ch_hsmetrics_in,
+        ch_reference_fasta,
+        ch_reference_fasta_fai,
+        ch_ref_dict,
+        [[], []],
+    )
+    ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
 
     emit:
-
         hs_metrics = PICARD_COLLECTHSMETRICS.out.metrics
         versions = ch_versions
-
-}
\ No newline at end of file
+}

From 9f1305e81a5cdd0f516b51462e3616d76913ee9e Mon Sep 17 00:00:00 2001
From: FranBonath <franziska.bonath@scilifelab.se>
Date: Tue, 25 Nov 2025 11:13:03 +0100
Subject: [PATCH 383/530] update output.md

---
 docs/output.md | 68 ++++++++++++++++++++++++++++++++++++++++++++------
 1 file changed, 60 insertions(+), 8 deletions(-)

diff --git a/docs/output.md b/docs/output.md
index 3d3c3497..7daa6e6d 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -8,12 +8,16 @@ The directories listed below will be created in the results directory after the
 
 ## Pipeline overview
 
-The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
+The pipeline is built using [Nextflow](https://www.nextflow.io/) and can generate output files from the following steps:
 
 - [Seqtk](#seqtk) - Subsample a specific number of reads per sample
 - [FastQC](#fastqc) - Raw read QC
 - [SeqFu Stats](#seqfu_stats) - Statistics for FASTA or FASTQ files
 - [FastQ Screen](#fastqscreen) - Mapping against a set of references for basic contamination QC
+- [BWA-MEM2_INDEX](#bwamem2_index) - Create BWA-MEM2 index of a chosen reference genome OR use pre-built index
+- [BWA-MEM2_MEM](#bwamem2_mem) - Mapping reads against a chosen reference genome
+- [Samtools index](#samtools-index) - Index BAM files with Samtools
+- [Picard collect multiple metrics](#picard-collect-multiple-metrics) - Combine BAM and BAI outputs for Picard
 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
@@ -42,6 +46,19 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
 
+### SeqFu Stats
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `seqfu_stats/`
+  - `*.tsv`: Tab-separated file containing quality metrics.
+  - `*_mqc.txt`: File containing the same quality metrics as the TSV file, ready to be read by MultiQC.
+
+</details>
+
+[SeqFu](https://telatin.github.io/seqfu2/) is general-purpose program to manipulate and parse information from FASTA/FASTQ files, supporting gzipped input files. Includes functions to interleave and de-interleave FASTQ files, to rename sequences and to count and print statistics on sequence lengths. In this pipeline, the `seqfu stats` module is used to produce general quality metrics statistics.
+
 ### FastQ Screen
 
 <details markdown="1">
@@ -49,7 +66,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 - `fastqscreen/`
   - `*_screen.html`: Interactive graphical report.
-  - `*_screen.pdf`: Static graphical report.
+  - `*_screen.png`: Static graphical report.
   - `*_screen.txt` : Text-based report.
 
 </details>
@@ -67,18 +84,53 @@ See `assets/example_fastq_screen_references.csv` for example.
 
 The `.csv` is provided as a pipeline parameter `fastq_screen_references` and is used to construct a `FastQ Screen` configuration file within the context of the process work directory in order to properly mount the references.
 
-### SeqFu Stats
+### BWAMEM2_INDEX
 
 <details markdown="1">
 <summary>Output files</summary>
 
-- `seqfu/`
-  - `*.tsv`: Tab-separated file containing quality metrics.
-  - `*_mqc.txt`: File containing the same quality metrics as the TSV file, ready to be read by MultiQC.
+Generates the full set of bwamem2 indexes:
 
-</details>
+- `bwamem2_index/`
+  - `*.fa`
+  - `*.fa.amb`
+  - `*.fa.ann`
+  - `*.fa.bwt`
+  - `*.fa.pac`
 
-[SeqFu](https://telatin.github.io/seqfu2/) is general-purpose program to manipulate and parse information from FASTA/FASTQ files, supporting gzipped input files. Includes functions to interleave and de-interleave FASTQ files, to rename sequences and to count and print statistics on sequence lengths. In this pipeline, the `seqfu stats` module is used to produce general quality metrics statistics.
+### BWAMEM2_MEM
+
+[BWA-mem2](https://github.com/bwa-mem2/bwa-mem2) is a tool next version of bwa-mem for mapping sequencies with low divergence against a reference genome with increased processing speed (~1.3-3.1x). Aligned reads are then potentially filtered and coordinate-sorted using [samtools](#samtools-index).
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `bwamem2/`
+  - `*.bam`: The original BAM file containing read alignments to the reference genome.
+  - `*.bam.bai`: BAM index files
+
+### Samtools index
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `samtools_faidex`
+  - `*.fa.fai`
+  - `*.fa.fai`
+
+### Picard collect multiple metrics
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `picard_collectmultiplemetrics`
+  - `*.CollectMultipleMetrics.alignment_summary_metrics`
+  - `*.CollectMultipleMetrics.base_distribution_by_cycle_metrics`
+  - `*.CollectMultipleMetrics.base_distribution_by_cycle.pdf`
+  - `*.CollectMultipleMetrics.quality_by_cycle_metrics`
+  - `*.CollectMultipleMetrics.quality_by_cycle.pdf`
+  - `*.CollectMultipleMetrics.quality_distribution.pdf`
+  - `*.CollectMultipleMetrics.read_length_histogram.pdf`
 
 ### MultiQC
 

From 0743b5801507dd9187b6c40845ccea911f2a59be Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrima2010@users.noreply.github.com>
Date: Tue, 25 Nov 2025 11:17:02 +0100
Subject: [PATCH 384/530] Added subworkflow prepare_genome

---
 subworkflows/local/prepare_genome/main.nf | 15 ++++++++-------
 workflows/seqinspector.nf                 | 18 +++++++++---------
 2 files changed, 17 insertions(+), 16 deletions(-)

diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf
index 3cfe3679..fa1c9a2d 100644
--- a/subworkflows/local/prepare_genome/main.nf
+++ b/subworkflows/local/prepare_genome/main.nf
@@ -1,14 +1,15 @@
 //
 // Prepare reference genome files
 
-include { BWAMEM2_INDEX                 } from '../modules/nf-core/bwamem2/index'
-include { SAMTOOLS_FAIDX                } from '../modules/nf-core/samtools/faidx'
+include { BWAMEM2_INDEX                 } from '../../../modules/nf-core/bwamem2/index'
+include { SAMTOOLS_FAIDX                } from '../../../modules/nf-core/samtools/faidx'
 
 workflow PREPARE_GENOME {
+
     take:
-    fasta_fai                
-    fasta_file               
+    fasta_file
     bwa_index
+    skip_tools
 
     main:
     // Initialize all channels that might be used later
@@ -56,8 +57,8 @@ workflow PREPARE_GENOME {
 
 
     emit:
-        BWAMEM2_INDEX.out.index       = ch_bwamem2_index
-        SAMTOOLS_FAIDX.out.fai        = ch_reference_fasta_fai
-        versions                      = ch_versions
+    bwamem2_index = BWAMEM2_INDEX.out.index
+    reference_fasta_fai =     SAMTOOLS_FAIDX.out.fai
+    versions            = ch_versions
 
 }       
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 61433463..7468bb69 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -44,16 +44,15 @@ workflow SEQINSPECTOR {
     ch_versions = channel.empty()
     ch_multiqc_files = channel.empty()
     ch_multiqc_extra_files = channel.empty()
-
-    // Initialize all channels that might be used later
     ch_bwamem2_mem = channel.empty()
     ch_samtools_index = channel.empty()
 
-    PREPARE_GENOME (
-            ch_bwamem2_index,
-            ch_reference_fasta_fai,
-            ch_reference_fasta,
-        )
+
+PREPARE_GENOME (
+        fasta_file,
+        params.bwa_index,
+        skip_tools,
+)
 
 
     //
@@ -127,9 +126,10 @@ workflow SEQINSPECTOR {
     
     // MODULE: Align reads with BWA-MEM2
     if (!("bwamem2_mem" in skip_tools)) {
+                ch_reference_fasta = channel.fromPath(fasta_file, checkIfExists: true).map { file -> tuple([id: file.name], file) }.collect()
         BWAMEM2_MEM(
             ch_sample_sized,
-            ch_bwamem2_index,
+            PREPARE_GENOME.out.bwamem2_index,
             ch_reference_fasta,
             params.sort_bam ?: true,
         )
@@ -153,7 +153,7 @@ workflow SEQINSPECTOR {
         ch_bam_bai = ch_bwamem2_mem.join(ch_samtools_index, failOnDuplicate: true, failOnMismatch: true)
 
         ch_fasta = ch_reference_fasta
-        ch_fai = ch_reference_fasta_fai
+        ch_fai = PREPARE_GENOME.out.reference_fasta_fai
 
         PICARD_COLLECTMULTIPLEMETRICS(
             ch_bam_bai,

From edf90765437c306f9c94eafbdc10bedd69dbafba Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 25 Nov 2025 11:18:05 +0100
Subject: [PATCH 385/530] Move creation of ch_hsmetrics_in to qc_bam.

---
 subworkflows/local/qc_bam/main.nf | 8 +++++++-
 workflows/seqinspector.nf         | 9 +++------
 2 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf
index c4f77a1c..2528da06 100644
--- a/subworkflows/local/qc_bam/main.nf
+++ b/subworkflows/local/qc_bam/main.nf
@@ -7,7 +7,9 @@ include { PICARD_CREATESEQUENCEDICTIONARY } from '../../../modules/nf-core/picar
 
 workflow QC_BAM {
     take:
-        ch_hsmetrics_in
+        ch_bam_bai
+        ch_bait_intervals
+        ch_target_intervals
         ch_reference_fasta
         ch_reference_fasta_fai
         ref_dict
@@ -16,6 +18,10 @@ workflow QC_BAM {
 
     ch_versions = channel.empty()
 
+    ch_hsmetrics_in = ch_bam_bai
+            .combine(ch_bait_intervals)
+            .combine(ch_target_intervals)
+
     if (ref_dict) {
         ch_ref_dict = channel.fromPath(ref_dict, checkIfExists: true).map { [[id: it.simpleName], it] }
     }
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index efd3074d..9137a86f 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -210,13 +210,10 @@ workflow SEQINSPECTOR {
             .collect()
 
 
-        ch_hsmetrics_in = ch_bam_bai
-            .combine(ch_bait_intervals)
-            .combine(ch_target_intervals)
-
-
         QC_BAM(
-            ch_hsmetrics_in,
+            ch_bam_bai,
+            ch_bait_intervals,
+            ch_target_intervals,
             ch_reference_fasta,
             ch_reference_fasta_fai,
             params.ref_dict,

From bf11922cf427afee9e896efdcbc6ea178a7aa769 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 25 Nov 2025 11:25:53 +0100
Subject: [PATCH 386/530] Add qc_bam test!

---
 subworkflows/local/qc_bam/tests/main.nf.test  | 44 ++++++++++++++
 .../local/qc_bam/tests/main.nf.test.snap      | 57 +++++++++++++++++++
 .../local/qc_bam/tests/nextflow.config        | 12 ++++
 3 files changed, 113 insertions(+)
 create mode 100644 subworkflows/local/qc_bam/tests/main.nf.test
 create mode 100644 subworkflows/local/qc_bam/tests/main.nf.test.snap
 create mode 100644 subworkflows/local/qc_bam/tests/nextflow.config

diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test
new file mode 100644
index 00000000..4fc86de5
--- /dev/null
+++ b/subworkflows/local/qc_bam/tests/main.nf.test
@@ -0,0 +1,44 @@
+nextflow_workflow {
+
+    name "Test Workflow QC_BAM"
+    script "subworkflows/local/qc_bam/main.nf"
+    workflow "QC_BAM"
+    tag 'subworkflows'
+    tag 'qc_bam'
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                pipelines_testdata_base_path    = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease'
+                run_picard_collecthsmetrics     = true
+                config "./nextflow.config"
+                outdir = "$outputDir"
+
+            }
+            workflow {
+                """
+                input[0] = channel.of(
+                    [
+                        [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'],
+                        [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)],
+                        [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)]
+                    ]
+                )
+                input[1] = channel.fromPath(params.pipelines_testdata_base_path + '/reference/target.bed', checkIfExists: true).collect()
+                input[2] = channel.fromPath(params.pipelines_testdata_base_path + '/reference/target.bed', checkIfExists: true).collect()
+                input[3]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta', checkIfExists: true)).collect()
+                input[4]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta.fai', checkIfExists: true)).collect()
+                input[5]  = null
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert snapshot(workflow.out).match()
+        }
+
+    }
+
+}
diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap
new file mode 100644
index 00000000..2c9323c1
--- /dev/null
+++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap
@@ -0,0 +1,57 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "earlycasualcaiman",
+                            "sample": "earlycasualcaiman",
+                            "single_end": false,
+                            "num_lanes": 1,
+                            "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'",
+                            "lane": 1,
+                            "sex": 1,
+                            "phenotype": 1,
+                            "paternal": 0,
+                            "maternal": 0,
+                            "case_id": "justhusky"
+                        },
+                        "earlycasualcaiman.CollectHsMetrics.coverage_metrics:md5,038240391cd0e8c529282d48f8fc6ced"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,40396221974da20b7f066d5fab9ffb3a",
+                    "versions.yml:md5,8508bd28eaf1fffcdc4d78e4d9f95393"
+                ],
+                "hs_metrics": [
+                    [
+                        {
+                            "id": "earlycasualcaiman",
+                            "sample": "earlycasualcaiman",
+                            "single_end": false,
+                            "num_lanes": 1,
+                            "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'",
+                            "lane": 1,
+                            "sex": 1,
+                            "phenotype": 1,
+                            "paternal": 0,
+                            "maternal": 0,
+                            "case_id": "justhusky"
+                        },
+                        "earlycasualcaiman.CollectHsMetrics.coverage_metrics:md5,038240391cd0e8c529282d48f8fc6ced"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,40396221974da20b7f066d5fab9ffb3a",
+                    "versions.yml:md5,8508bd28eaf1fffcdc4d78e4d9f95393"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-11-25T11:24:54.058046"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/local/qc_bam/tests/nextflow.config b/subworkflows/local/qc_bam/tests/nextflow.config
new file mode 100644
index 00000000..345dcdab
--- /dev/null
+++ b/subworkflows/local/qc_bam/tests/nextflow.config
@@ -0,0 +1,12 @@
+process {
+    
+    withName: PICARD_COLLECTHSMETRICS {
+        ext.args = { [
+            "--COVERAGE_CAP 50000",
+            "--METRIC_ACCUMULATION_LEVEL ALL_READS",
+            "--TMP_DIR ."
+			].join(' ') }
+
+    }
+
+}

From f8158fdf21ed41e1a0594c0702068ec68c8e0ec9 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 25 Nov 2025 11:26:18 +0100
Subject: [PATCH 387/530] Remove test config and samplesheet.

---
 assets/cg_test_samplesheet.csv |  3 ---
 conf/cg_test.config            | 31 -------------------------------
 2 files changed, 34 deletions(-)
 delete mode 100644 assets/cg_test_samplesheet.csv
 delete mode 100644 conf/cg_test.config

diff --git a/assets/cg_test_samplesheet.csv b/assets/cg_test_samplesheet.csv
deleted file mode 100644
index d9875790..00000000
--- a/assets/cg_test_samplesheet.csv
+++ /dev/null
@@ -1,3 +0,0 @@
-sample,fastq_1,fastq_2,rundir,tags
-raredisease_test_sample,https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz,,test
-raredisease_test_sample_2,https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz,,test_2
\ No newline at end of file
diff --git a/conf/cg_test.config b/conf/cg_test.config
deleted file mode 100644
index 37d13ded..00000000
--- a/conf/cg_test.config
+++ /dev/null
@@ -1,31 +0,0 @@
-
-params {
-    input                           = "${projectDir}/assets/cg_test_samplesheet.csv"
-    pipelines_testdata_base_path    = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease'
-    run_picard_collecthsmetrics     = true
-    fasta                           = params.pipelines_testdata_base_path + '/reference/reference.fasta'
-    genome                          = 'GRCh37'
-    bait_intervals                  = params.pipelines_testdata_base_path + '/reference/target.bed'
-    target_intervals                = params.bait_intervals
-}
-
-process {
-
-    // Add limits to be able to run on local computer.
-    
-    resourceLimits = [
-        cpus: 4,
-        memory: '15.GB',
-        time: '1.h'
-    ]
-
-    withName: PICARD_COLLECTHSMETRICS {
-        ext.args = { [
-            "--COVERAGE_CAP 50000",
-            "--METRIC_ACCUMULATION_LEVEL ALL_READS",
-            "--TMP_DIR ."
-			].join(' ') }
-
-    }
-
-}

From 73efbf712d4625e51168c1fb207ea58ae7a2836e Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrima2010@users.noreply.github.com>
Date: Tue, 25 Nov 2025 11:28:08 +0100
Subject: [PATCH 388/530] Minor changes

---
 workflows/seqinspector.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 7468bb69..c900f7c6 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -127,6 +127,7 @@ PREPARE_GENOME (
     // MODULE: Align reads with BWA-MEM2
     if (!("bwamem2_mem" in skip_tools)) {
                 ch_reference_fasta = channel.fromPath(fasta_file, checkIfExists: true).map { file -> tuple([id: file.name], file) }.collect()
+        
         BWAMEM2_MEM(
             ch_sample_sized,
             PREPARE_GENOME.out.bwamem2_index,

From 0e3f63f438b5a0805b20ffebc20047680b7bb311 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <agrima2010@users.noreply.github.com>
Date: Tue, 25 Nov 2025 11:31:09 +0100
Subject: [PATCH 389/530] Snapshots

---
 assets/nf-core-seqinspector_logo_light.png    | Bin 112501 -> 110870 bytes
 .../images/nf-core-seqinspector_logo_dark.png | Bin 29094 -> 28728 bytes
 .../nf-core-seqinspector_logo_light.png       | Bin 24719 -> 24391 bytes
 ro-crate-metadata.json                        |   2 +-
 tests/MiSeq.main.nf.test.snap                 | 222 +-----------------
 5 files changed, 4 insertions(+), 220 deletions(-)

diff --git a/assets/nf-core-seqinspector_logo_light.png b/assets/nf-core-seqinspector_logo_light.png
index 647c46d40c36d92bfb701a6a98b1a9b30b73a825..b03851ab318eb0271d4da135561e1f7a2f901827 100644
GIT binary patch
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diff --git a/docs/images/nf-core-seqinspector_logo_dark.png b/docs/images/nf-core-seqinspector_logo_dark.png
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diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 401821d3..5e4e372a 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -23,7 +23,7 @@
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
             "datePublished": "2025-11-20T09:32:26+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by Adrien Coulier.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that that processes raw sequencedata (FASTQ) to provide comprehensive quality control. It can perform subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants. The pipeline generates detailed MultiQC reports with flexible output options, ranging from individual sample reports to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments.\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n\n1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))\n2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n3. Align reads to reference with ([`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2))\n4. Index aligned BAM files ([`SAMtools`](http://github.com/samtools))\n5. Create FASTA index ([`SAMtools`](http://github.com/samtools))\n6. Collect multiple QC metrics ([`Picard CollectMultipleMetrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html))\n7. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
                     "@id": "main.nf"
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index bb666659..8703fee3 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -34,239 +34,23 @@
     "MiSeq data test (single end reads)": {
         "content": [
             {
-                "BWAMEM2_INDEX": {
-                    "bwamem2": "2.2.1"
-                },
-                "BWAMEM2_MEM": {
-                    "bwamem2": "2.2.1",
-                    "samtools": "1.22.1"
-                },
-                "FASTQC": {
-                    "fastqc": "0.12.1"
-                },
-                "FASTQSCREEN_FASTQSCREEN": {
-                    "fastqscreen": "0.16.0"
-                },
-                "PICARD_COLLECTMULTIPLEMETRICS": {
-                    "picard": "3.4.0"
-                },
-                "SAMTOOLS_FAIDX": {
-                    "samtools": "1.22.1"
-                },
-                "SAMTOOLS_INDEX": {
-                    "samtools": "1.22.1"
-                },
-                "SEQFU_STATS": {
-                    "seqfu": "1.22.3"
-                },
                 "Workflow": {
                     "nf-core/seqinspector": "v1.0dev"
                 }
             },
             [
-                "bwamem2_index",
-                "bwamem2_index/bwamem2",
-                "bwamem2_index/bwamem2/genome.fa.0123",
-                "bwamem2_index/bwamem2/genome.fa.amb",
-                "bwamem2_index/bwamem2/genome.fa.ann",
-                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
-                "bwamem2_index/bwamem2/genome.fa.pac",
-                "bwamem2_mem",
-                "bwamem2_mem/SAMPLE_SINGLE_END_1.bam",
-                "bwamem2_mem/SAMPLE_SINGLE_END_1.bam.bai",
-                "fastqc",
-                "fastqc/SAMPLE_SINGLE_END_1_fastqc.html",
-                "fastqc/SAMPLE_SINGLE_END_1_fastqc.zip",
-                "fastqscreen",
-                "fastqscreen/SAMPLE_SINGLE_END_1_screen.html",
-                "fastqscreen/SAMPLE_SINGLE_END_1_screen.png",
-                "fastqscreen/SAMPLE_SINGLE_END_1_screen.txt",
-                "multiqc",
-                "multiqc/global_report",
-                "multiqc/global_report/multiqc_data",
-                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
-                "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
-                "multiqc/global_report/multiqc_data/llms-full.txt",
-                "multiqc/global_report/multiqc_data/multiqc.log",
-                "multiqc/global_report/multiqc_data/multiqc.parquet",
-                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
-                "multiqc/global_report/multiqc_data/multiqc_data.json",
-                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
-                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
-                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
-                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
-                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
-                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
-                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
-                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
-                "multiqc/global_report/multiqc_data/picard_alignment_summary.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
-                "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt",
-                "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
-                "multiqc/global_report/multiqc_plots",
-                "multiqc/global_report/multiqc_plots/pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
-                "multiqc/global_report/multiqc_plots/png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
-                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
-                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu.png",
-                "multiqc/global_report/multiqc_plots/svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
-                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
-                "multiqc/global_report/multiqc_report.html",
-                "picard_collectmultiplemetrics",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
-                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
-                "samtools_faidx",
-                "samtools_faidx/genome.fa.fai",
-                "samtools_faidx/genome.fa.sizes",
-                "seqfu_stats",
-                "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu.tsv",
-                "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu_mqc.txt"
+                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"
             ],
             [
-                "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
-                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
-                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
-                "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
-                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "SAMPLE_SINGLE_END_1.bam:md5,ff8893272a6560cac7067fd8a9406f9b",
-                "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
-                "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
-                "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
-                "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
-                "fastqc-status-check-heatmap.txt:md5,8f98652c377741c974e485652a19f37f",
-                "fastqc_overrepresented_sequences_plot.txt:md5,cdc7479933cae03e0043ae794f81c304",
-                "fastqc_per_base_n_content_plot.txt:md5,dd8d6976dc5ea8cf67d9fa2c3be9e24b",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,5f9a98d3068aab17f26731ae0615f41a",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,1de1333bb959189dcf8230706f60dbfc",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,62f140bfa52d462c9c499dfdabc35476",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,5fda43eb9b7c60cf6b4348f734a94b26",
-                "fastqc_sequence_counts_plot.txt:md5,00cd6842465f7aa9ae75434e175946a6",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,c3befe0812d2f1c23d5e75e6fccf0622",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607",
-                "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,fe082d3b5dcc3d338e25bc027e17dc99",
-                "multiqc_picard_baseContent.txt:md5,796e8e0803ad3ed4fd1c76f073784942",
-                "multiqc_picard_quality_by_cycle.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
-                "multiqc_picard_quality_score_distribution.txt:md5,bad70b98811c4cbe4728f53334993703",
-                "multiqc_seqfu.txt:md5,7ec63bc3465b3fc8e316e2443ec4c848",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
-                "picard_QualityScoreDistribution_histogram.txt:md5,bad70b98811c4cbe4728f53334993703",
-                "picard_alignment_readlength_plot.txt:md5,0fe7e17f1c58b7a6291bc1ff80fdfaa0",
-                "picard_alignment_summary.txt:md5,c770d3ee98dadaee77ef43967a974627",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,65d43b083e90830aa9451bde65a261b8",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,31dc4f314d8e3f8e086e7ae761638023",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,d92fac15687942c0f9c436ba0cf55fc9",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,00b76f45bbfc9acd2774f90612e53333",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,5451af67007a16e7645d0393011414af",
-                "picard_quality_by_cycle.txt:md5,46fbe44a9788f2e9184e2c1d689c2876",
-                "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77",
-                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
-                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
-                "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,33a9e44386f308d43881a58394b6b17c",
-                "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,e67e819605ab49182aacf1d676dc885d"
+                
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T11:14:40.189991111"
+        "timestamp": "2025-11-25T11:30:37.224306"
     },
     "Miseq data test (skip fastqc)": {
         "content": [

From f876645bcbd13746a454ecea22b9cf5c14547ca4 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 25 Nov 2025 11:33:04 +0100
Subject: [PATCH 390/530] Add defaults for collecthsmetrics in modules.config.

---
 conf/modules.config | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/conf/modules.config b/conf/modules.config
index f33f71aa..5c3ec743 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -59,6 +59,15 @@ process {
         ]
     }
 
+    withName: 'PICARD_COLLECTHSMETRICS' {
+        publishDir = [
+            path: { "${params.outdir}/picard_collecthsmetrics" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+        ext.args = {"--TMP_DIR ."}
+    }
+
     withName: 'SAMTOOLS_FAIDX' {
         publishDir = [
             path: { "${params.outdir}/samtools_faidx" },

From 15142b8aac0cf33a3bb9e48e7d5b89a7d82c3924 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 25 Nov 2025 11:48:34 +0100
Subject: [PATCH 391/530] Fix so output files are only accessed if QC_BAM is
 run.

---
 workflows/seqinspector.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 9137a86f..b1815cf8 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -218,9 +218,10 @@ workflow SEQINSPECTOR {
             ch_reference_fasta_fai,
             params.ref_dict,
         )
-    }
+
     ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.hs_metrics)
     ch_versions = ch_versions.mix(QC_BAM.out.versions)
+    }
 
 
     // Collate and save software versions

From 49e10958eea3201660a6d0d1d8806bf05f22c689 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <163723002+agrima2010@users.noreply.github.com>
Date: Tue, 25 Nov 2025 10:57:39 +0000
Subject: [PATCH 392/530] ss

---
 subworkflows/local/prepare_genome/main.nf     |   9 +-
 tests/MiSeq.main.nf.test.snap                 | 226 +++++++++++++++++-
 tests/MiSeq_PairedEnd.main.nf.test.snap       |   8 +-
 tests/NovaSeq6000.main.nf.test.snap           |   8 +-
 tests/NovaSeq6000.main_subsample.nf.test.snap |   8 +-
 tests/PromethION.main.nf.test.snap            |   2 +-
 6 files changed, 221 insertions(+), 40 deletions(-)

diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf
index fa1c9a2d..958d42b1 100644
--- a/subworkflows/local/prepare_genome/main.nf
+++ b/subworkflows/local/prepare_genome/main.nf
@@ -51,14 +51,9 @@ workflow PREPARE_GENOME {
         ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions)
     }
 
- // Gather versions
-    ch_versions = ch_versions.mix(BWAMEM2_INDEX.out.versions)
-    ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions)
-
-
     emit:
-    bwamem2_index = BWAMEM2_INDEX.out.index
-    reference_fasta_fai =     SAMTOOLS_FAIDX.out.fai
+    bwamem2_index = ch_bwamem2_index
+    reference_fasta_fai =     ch_reference_fasta_fai
     versions            = ch_versions
 
 }       
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 8703fee3..2413892e 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -29,35 +29,242 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T10:48:01.699825922"
+        "timestamp": "2025-11-25T10:51:19.181078123"
     },
     "MiSeq data test (single end reads)": {
         "content": [
             {
+                "BWAMEM2_MEM": {
+                    "bwamem2": "2.2.1",
+                    "samtools": "1.22.1"
+                },
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "FASTQSCREEN_FASTQSCREEN": {
+                    "fastqscreen": "0.16.0"
+                },
+                "PICARD_COLLECTMULTIPLEMETRICS": {
+                    "picard": "3.4.0"
+                },
+                "SAMTOOLS_INDEX": {
+                    "samtools": "1.22.1"
+                },
+                "SEQFU_STATS": {
+                    "seqfu": "1.22.3"
+                },
                 "Workflow": {
                     "nf-core/seqinspector": "v1.0dev"
                 }
             },
             [
+                "bwamem2_index",
+                "bwamem2_index/bwamem2",
+                "bwamem2_index/bwamem2/genome.fa.0123",
+                "bwamem2_index/bwamem2/genome.fa.amb",
+                "bwamem2_index/bwamem2/genome.fa.ann",
+                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
+                "bwamem2_index/bwamem2/genome.fa.pac",
+                "bwamem2_mem",
+                "bwamem2_mem/SAMPLE_SINGLE_END_1.bam",
+                "bwamem2_mem/SAMPLE_SINGLE_END_1.bam.bai",
+                "fastqc",
+                "fastqc/SAMPLE_SINGLE_END_1_fastqc.html",
+                "fastqc/SAMPLE_SINGLE_END_1_fastqc.zip",
+                "fastqscreen",
+                "fastqscreen/SAMPLE_SINGLE_END_1_screen.html",
+                "fastqscreen/SAMPLE_SINGLE_END_1_screen.png",
+                "fastqscreen/SAMPLE_SINGLE_END_1_screen.txt",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/global_report/multiqc_data/llms-full.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc.parquet",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
+                "multiqc/global_report/multiqc_plots",
+                "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu.png",
+                "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
+                "multiqc/global_report/multiqc_report.html",
+                "picard_collectmultiplemetrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
-                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"
+                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "samtools_faidx",
+                "samtools_faidx/genome.fa.fai",
+                "samtools_faidx/genome.fa.sizes",
+                "seqfu_stats",
+                "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu.tsv",
+                "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu_mqc.txt"
             ],
             [
-                
+                "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
+                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
+                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
+                "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
+                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
+                "SAMPLE_SINGLE_END_1.bam:md5,ff8893272a6560cac7067fd8a9406f9b",
+                "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
+                "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
+                "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
+                "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
+                "fastqc-status-check-heatmap.txt:md5,8f98652c377741c974e485652a19f37f",
+                "fastqc_overrepresented_sequences_plot.txt:md5,cdc7479933cae03e0043ae794f81c304",
+                "fastqc_per_base_n_content_plot.txt:md5,dd8d6976dc5ea8cf67d9fa2c3be9e24b",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,5f9a98d3068aab17f26731ae0615f41a",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,1de1333bb959189dcf8230706f60dbfc",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,62f140bfa52d462c9c499dfdabc35476",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,5fda43eb9b7c60cf6b4348f734a94b26",
+                "fastqc_sequence_counts_plot.txt:md5,00cd6842465f7aa9ae75434e175946a6",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,c3befe0812d2f1c23d5e75e6fccf0622",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607",
+                "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,fe082d3b5dcc3d338e25bc027e17dc99",
+                "multiqc_picard_baseContent.txt:md5,796e8e0803ad3ed4fd1c76f073784942",
+                "multiqc_picard_quality_by_cycle.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
+                "multiqc_picard_quality_score_distribution.txt:md5,bad70b98811c4cbe4728f53334993703",
+                "multiqc_seqfu.txt:md5,7ec63bc3465b3fc8e316e2443ec4c848",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
+                "picard_QualityScoreDistribution_histogram.txt:md5,bad70b98811c4cbe4728f53334993703",
+                "picard_alignment_readlength_plot.txt:md5,0fe7e17f1c58b7a6291bc1ff80fdfaa0",
+                "picard_alignment_summary.txt:md5,c770d3ee98dadaee77ef43967a974627",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,65d43b083e90830aa9451bde65a261b8",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,31dc4f314d8e3f8e086e7ae761638023",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,d92fac15687942c0f9c436ba0cf55fc9",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,00b76f45bbfc9acd2774f90612e53333",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,5451af67007a16e7645d0393011414af",
+                "picard_quality_by_cycle.txt:md5,46fbe44a9788f2e9184e2c1d689c2876",
+                "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77",
+                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
+                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
+                "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,33a9e44386f308d43881a58394b6b17c",
+                "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,e67e819605ab49182aacf1d676dc885d"
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-25T11:30:37.224306"
+        "timestamp": "2025-11-25T10:37:31.301182496"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
             {
-                "BWAMEM2_INDEX": {
-                    "bwamem2": "2.2.1"
-                },
                 "BWAMEM2_MEM": {
                     "bwamem2": "2.2.1",
                     "samtools": "1.22.1"
@@ -68,9 +275,6 @@
                 "PICARD_COLLECTMULTIPLEMETRICS": {
                     "picard": "3.4.0"
                 },
-                "SAMTOOLS_FAIDX": {
-                    "samtools": "1.22.1"
-                },
                 "SAMTOOLS_INDEX": {
                     "samtools": "1.22.1"
                 },
@@ -229,6 +433,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T11:15:17.347135189"
+        "timestamp": "2025-11-25T10:38:32.729517527"
     }
 }
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index 3e0a637a..b8d1f6d1 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -2,9 +2,6 @@
     "MiSeq data test (paired end reads)": {
         "content": [
             {
-                "BWAMEM2_INDEX": {
-                    "bwamem2": "2.2.1"
-                },
                 "BWAMEM2_MEM": {
                     "bwamem2": "2.2.1",
                     "samtools": "1.22.1"
@@ -18,9 +15,6 @@
                 "PICARD_COLLECTMULTIPLEMETRICS": {
                     "picard": "3.4.0"
                 },
-                "SAMTOOLS_FAIDX": {
-                    "samtools": "1.22.1"
-                },
                 "SAMTOOLS_INDEX": {
                     "samtools": "1.22.1"
                 },
@@ -426,6 +420,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T11:16:28.36937489"
+        "timestamp": "2025-11-25T10:40:16.383291844"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index d5d362f2..527e1be2 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -2,9 +2,6 @@
     "NovaSeq6000 data test": {
         "content": [
             {
-                "BWAMEM2_INDEX": {
-                    "bwamem2": "2.2.1"
-                },
                 "BWAMEM2_MEM": {
                     "bwamem2": "2.2.1",
                     "samtools": "1.22.1"
@@ -18,9 +15,6 @@
                 "PICARD_COLLECTMULTIPLEMETRICS": {
                     "picard": "3.4.0"
                 },
-                "SAMTOOLS_FAIDX": {
-                    "samtools": "1.22.1"
-                },
                 "SAMTOOLS_INDEX": {
                     "samtools": "1.22.1"
                 },
@@ -936,6 +930,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T11:17:47.210647423"
+        "timestamp": "2025-11-25T10:42:40.72799341"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index e242b338..7360c6c8 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -2,9 +2,6 @@
     "NovaSeq6000 data test sample size": {
         "content": [
             {
-                "BWAMEM2_INDEX": {
-                    "bwamem2": "2.2.1"
-                },
                 "BWAMEM2_MEM": {
                     "bwamem2": "2.2.1",
                     "samtools": "1.22.1"
@@ -18,9 +15,6 @@
                 "PICARD_COLLECTMULTIPLEMETRICS": {
                     "picard": "3.4.0"
                 },
-                "SAMTOOLS_FAIDX": {
-                    "samtools": "1.22.1"
-                },
                 "SAMTOOLS_INDEX": {
                     "samtools": "1.22.1"
                 },
@@ -950,6 +944,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-19T14:24:39.696680631"
+        "timestamp": "2025-11-25T10:44:53.483227254"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index 46aefe80..a7d07255 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -133,6 +133,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T10:27:14.736749139"
+        "timestamp": "2025-11-25T10:57:28.062541336"
     }
 }
\ No newline at end of file

From 452ca7b7d26f3ac66a12a2a205b2c02b58a58863 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <163723002+agrima2010@users.noreply.github.com>
Date: Tue, 25 Nov 2025 11:07:01 +0000
Subject: [PATCH 393/530] fix precommit

---
 subworkflows/local/prepare_genome/main.nf | 2 +-
 workflows/seqinspector.nf                 | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf
index 958d42b1..602472cc 100644
--- a/subworkflows/local/prepare_genome/main.nf
+++ b/subworkflows/local/prepare_genome/main.nf
@@ -56,4 +56,4 @@ workflow PREPARE_GENOME {
     reference_fasta_fai =     ch_reference_fasta_fai
     versions            = ch_versions
 
-}       
+}
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index c900f7c6..08bba00c 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -123,11 +123,11 @@ PREPARE_GENOME (
         ch_multiqc_files = ch_multiqc_files.mix(FASTQSCREEN_FASTQSCREEN.out.txt)
         ch_versions = ch_versions.mix(FASTQSCREEN_FASTQSCREEN.out.versions.first())
     }
-    
+
     // MODULE: Align reads with BWA-MEM2
     if (!("bwamem2_mem" in skip_tools)) {
                 ch_reference_fasta = channel.fromPath(fasta_file, checkIfExists: true).map { file -> tuple([id: file.name], file) }.collect()
-        
+
         BWAMEM2_MEM(
             ch_sample_sized,
             PREPARE_GENOME.out.bwamem2_index,

From 14f626cde0538ec8e0113109a4044a020fa1a7df Mon Sep 17 00:00:00 2001
From: matrulda <matilda.aslin@medsci.uu.se>
Date: Tue, 25 Nov 2025 13:31:45 +0100
Subject: [PATCH 394/530] Add rundirparser as skip option

---
 nextflow_schema.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 5d663de7..a99601c8 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -51,7 +51,7 @@
                 "skip_tools": {
                     "type": "string",
                     "description": "Comma-separated string of tools to skip",
-                    "pattern": "^((fastqc|fastqscreen|seqfu_stats|seqtk_sample|bwamem2_index|bwamem2_mem|picard_collectmultiplemetrics|samtools_faidx|samtools_index)?,?)*(?<!,)$"
+                    "pattern": "^((fastqc|fastqscreen|seqfu_stats|seqtk_sample|bwamem2_index|bwamem2_mem|picard_collectmultiplemetrics|samtools_faidx|samtools_index|rundirparser)?,?)*(?<!,)$"
                 }
             }
         },

From c7444af4568030dd41e891b49ae4c6843a071d26 Mon Sep 17 00:00:00 2001
From: matrulda <matilda.aslin@medsci.uu.se>
Date: Tue, 25 Nov 2025 13:33:14 +0100
Subject: [PATCH 395/530] Adapt tests for rundirparser (only NovaSeq6000 test
 data have the required file for the test)

---
 tests/MiSeq.main.nf.test                      |  5 +--
 tests/MiSeq_PairedEnd.main.nf.test            |  1 +
 tests/NovaSeq6000.main.nf.test.config         |  5 +++
 tests/NovaSeq6000.main.nf.test.snap           | 36 +++++++++++++++++--
 tests/NovaSeq6000.main_subsample.nf.test.snap | 36 +++++++++++++++++--
 tests/PromethION.main.nf.test                 |  1 +
 6 files changed, 78 insertions(+), 6 deletions(-)

diff --git a/tests/MiSeq.main.nf.test b/tests/MiSeq.main.nf.test
index 43ba4c75..f8f325b9 100644
--- a/tests/MiSeq.main.nf.test
+++ b/tests/MiSeq.main.nf.test
@@ -11,6 +11,7 @@ nextflow_pipeline {
             config "./MiSeq.main.nf.test.config"
             params {
                 outdir = "$outputDir"
+                skip_tools = "rundirparser"
             }
         }
 
@@ -44,7 +45,7 @@ nextflow_pipeline {
             config "./MiSeq.main.nf.test.config"
             params {
                 outdir = "$outputDir"
-                skip_tools = "fastqc"
+                skip_tools = "fastqc,rundirparser"
             }
         }
 
@@ -78,7 +79,7 @@ nextflow_pipeline {
             config "./MiSeq.main.nf.test.config"
             params {
                 outdir = "$outputDir"
-                skip_tools = "fastqc,fastqscreen,seqfu_stats,seqtk_sample,bwamem2_index,bwamem2_mem"
+                skip_tools = "fastqc,fastqscreen,seqfu_stats,seqtk_sample,bwamem2_index,bwamem2_mem,rundirparser"
             }
         }
 
diff --git a/tests/MiSeq_PairedEnd.main.nf.test b/tests/MiSeq_PairedEnd.main.nf.test
index 04655713..2a69711a 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test
+++ b/tests/MiSeq_PairedEnd.main.nf.test
@@ -11,6 +11,7 @@ nextflow_pipeline {
             config "./MiSeq_PairedEnd.main.nf.test.config"
             params {
                 outdir = "$outputDir"
+                skip_tools = "rundirparser"
             }
         }
 
diff --git a/tests/NovaSeq6000.main.nf.test.config b/tests/NovaSeq6000.main.nf.test.config
index cad5edd9..dbdd5409 100644
--- a/tests/NovaSeq6000.main.nf.test.config
+++ b/tests/NovaSeq6000.main.nf.test.config
@@ -4,4 +4,9 @@ includeConfig 'nextflow.config'
 // Load the correct samplesheet for that test
 params {
     input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
+    fastq_screen_references = "${projectDir}/assets/example_fastq_screen_references.csv"
+
+    // Genome references
+    genome = 'R64-1-1'
+
 }
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index d5d362f2..5b3c29f7 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -18,6 +18,10 @@
                 "PICARD_COLLECTMULTIPLEMETRICS": {
                     "picard": "3.4.0"
                 },
+                "RUNDIRPARSER": {
+                    "PyYAML": "6.0.2",
+                    "Python": "3.13.2"
+                },
                 "SAMTOOLS_FAIDX": {
                     "samtools": "1.22.1"
                 },
@@ -100,6 +104,7 @@
                 "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_mqc_seq_metadata.txt",
                 "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
                 "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
                 "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
@@ -135,6 +140,7 @@
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/mqc_seq_metadata.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
@@ -160,6 +166,7 @@
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/mqc_seq_metadata.png",
                 "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
                 "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
@@ -185,6 +192,7 @@
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/mqc_seq_metadata.svg",
                 "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
@@ -220,6 +228,7 @@
                 "multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_mqc_seq_metadata.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_picard_baseContent.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
@@ -255,6 +264,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/mqc_seq_metadata.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
@@ -280,6 +290,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/mqc_seq_metadata.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_readlength_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-cnt.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-pct.png",
@@ -305,6 +316,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/mqc_seq_metadata.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-pct.svg",
@@ -339,6 +351,7 @@
                 "multiqc/group_reports/group2/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_mqc_seq_metadata.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_picard_baseContent.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_by_cycle.txt",
@@ -374,6 +387,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/mqc_seq_metadata.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
@@ -399,6 +413,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/mqc_seq_metadata.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_readlength_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-cnt.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-pct.png",
@@ -424,6 +439,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/mqc_seq_metadata.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-pct.svg",
@@ -458,6 +474,7 @@
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_mqc_seq_metadata.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_baseContent.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
@@ -493,6 +510,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/mqc_seq_metadata.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
@@ -518,6 +536,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/mqc_seq_metadata.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_readlength_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-cnt.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-pct.png",
@@ -543,6 +562,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/mqc_seq_metadata.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-pct.svg",
@@ -577,6 +597,7 @@
                 "multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_mqc_seq_metadata.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_picard_baseContent.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_by_cycle.txt",
@@ -612,6 +633,7 @@
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/mqc_seq_metadata.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
@@ -637,6 +659,7 @@
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/test/multiqc_plots/png/mqc_seq_metadata.png",
                 "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_readlength_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-cnt.png",
                 "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-pct.png",
@@ -662,6 +685,7 @@
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/mqc_seq_metadata.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-pct.svg",
@@ -717,6 +741,8 @@
                 "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "rundirparser",
+                "rundirparser/200624_A00834_0183_BHMTFYDRXX_illumina_mqc.yml",
                 "samtools_faidx",
                 "samtools_faidx/genome.fa.fai",
                 "samtools_faidx/genome.fa.sizes",
@@ -772,6 +798,7 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
                 "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
                 "multiqc_picard_AlignmentSummaryMetrics.txt:md5,5bdb2f162266ab68005cbfc0a45e311e",
                 "multiqc_picard_baseContent.txt:md5,409bf8ce546a573ce6678769b84726fd",
                 "multiqc_picard_quality_by_cycle.txt:md5,ebf56fd9b3b127ff41211e3f79f18b42",
@@ -804,6 +831,7 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
                 "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
                 "multiqc_picard_AlignmentSummaryMetrics.txt:md5,e4cb1b13e6a7298d172ed112a0479b5a",
                 "multiqc_picard_baseContent.txt:md5,740592a5858706d2b4b8f585a1d5492b",
                 "multiqc_picard_quality_by_cycle.txt:md5,c3f14084aedc511b9f0aa8410e7cb3b5",
@@ -836,6 +864,7 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
                 "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
                 "multiqc_picard_AlignmentSummaryMetrics.txt:md5,d4e63eed820edcc71b3e37d793983bd7",
                 "multiqc_picard_baseContent.txt:md5,0dd5fa539e4034e3539fb1e7068c7ce5",
                 "multiqc_picard_quality_by_cycle.txt:md5,750eadc27875fc8141b64a90789c369f",
@@ -868,6 +897,7 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
                 "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
                 "multiqc_picard_AlignmentSummaryMetrics.txt:md5,22093b80f335c4c53633b01a930157f4",
                 "multiqc_picard_baseContent.txt:md5,6886e1e5179031ddba4958f301930d64",
                 "multiqc_picard_quality_by_cycle.txt:md5,96652e2e2d693488df9104e5ae8cb4a7",
@@ -900,6 +930,7 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5",
                 "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
                 "multiqc_picard_AlignmentSummaryMetrics.txt:md5,edf7faad1da9922fdc692e9cba5cc0c4",
                 "multiqc_picard_baseContent.txt:md5,9631916c0a9a736811c47ab4c476428f",
                 "multiqc_picard_quality_by_cycle.txt:md5,9e05b241aabe39232b5182cb59d8edd5",
@@ -918,6 +949,7 @@
                 "picard_base_distribution_by_cycle__Undetermined.txt:md5,1380831484d1b069a2fd4a20437118bf",
                 "picard_quality_by_cycle.txt:md5,b6fc46e18ac875ba02775e7cbf1b8e8b",
                 "picard_quality_score_distribution.txt:md5,1c17c01ef54a6062a8f1ca8408d32958",
+                "200624_A00834_0183_BHMTFYDRXX_illumina_mqc.yml:md5,29e05fed18bca0e9a857c992b6d59a40",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "Sample1_1_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6",
@@ -933,9 +965,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.3",
+            "nf-test": "0.9.2",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-07T11:17:47.210647423"
+        "timestamp": "2025-11-25T10:22:20.735912684"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index e242b338..61a1eb6d 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -18,6 +18,10 @@
                 "PICARD_COLLECTMULTIPLEMETRICS": {
                     "picard": "3.4.0"
                 },
+                "RUNDIRPARSER": {
+                    "PyYAML": "6.0.2",
+                    "Python": "3.13.2"
+                },
                 "SAMTOOLS_FAIDX": {
                     "samtools": "1.22.1"
                 },
@@ -103,6 +107,7 @@
                 "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_mqc_seq_metadata.txt",
                 "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
                 "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
                 "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
@@ -138,6 +143,7 @@
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/mqc_seq_metadata.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
@@ -163,6 +169,7 @@
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/mqc_seq_metadata.png",
                 "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
                 "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
@@ -188,6 +195,7 @@
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/mqc_seq_metadata.svg",
                 "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
@@ -223,6 +231,7 @@
                 "multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_mqc_seq_metadata.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_picard_baseContent.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
@@ -258,6 +267,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/mqc_seq_metadata.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
@@ -283,6 +293,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/mqc_seq_metadata.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_readlength_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-cnt.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-pct.png",
@@ -308,6 +319,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/mqc_seq_metadata.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-pct.svg",
@@ -342,6 +354,7 @@
                 "multiqc/group_reports/group2/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_mqc_seq_metadata.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_picard_baseContent.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_by_cycle.txt",
@@ -377,6 +390,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/mqc_seq_metadata.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
@@ -402,6 +416,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/mqc_seq_metadata.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_readlength_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-cnt.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-pct.png",
@@ -427,6 +442,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/mqc_seq_metadata.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-pct.svg",
@@ -461,6 +477,7 @@
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_mqc_seq_metadata.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_baseContent.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
@@ -496,6 +513,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/mqc_seq_metadata.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
@@ -521,6 +539,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/mqc_seq_metadata.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_readlength_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-cnt.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-pct.png",
@@ -546,6 +565,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/mqc_seq_metadata.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-pct.svg",
@@ -580,6 +600,7 @@
                 "multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_mqc_seq_metadata.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_picard_baseContent.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_by_cycle.txt",
@@ -615,6 +636,7 @@
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/mqc_seq_metadata.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
@@ -640,6 +662,7 @@
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/test/multiqc_plots/png/mqc_seq_metadata.png",
                 "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_readlength_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-cnt.png",
                 "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-pct.png",
@@ -665,6 +688,7 @@
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/mqc_seq_metadata.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-pct.svg",
@@ -720,6 +744,8 @@
                 "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "rundirparser",
+                "rundirparser/200624_A00834_0183_BHMTFYDRXX_illumina_mqc.yml",
                 "samtools_faidx",
                 "samtools_faidx/genome.fa.fai",
                 "samtools_faidx/genome.fa.sizes",
@@ -781,6 +807,7 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
                 "multiqc_fastqc.txt:md5,aba942d1e6996b579f19798e5673f514",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
                 "multiqc_picard_AlignmentSummaryMetrics.txt:md5,ae3f9e644215ac39d2eae114bd52a517",
                 "multiqc_picard_baseContent.txt:md5,8b2efc3fa06d2013348b35f9607292aa",
                 "multiqc_picard_quality_by_cycle.txt:md5,c2774038d1a0142746426e46f9f954dd",
@@ -813,6 +840,7 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
                 "multiqc_fastqc.txt:md5,ff996e1d3dc4a46e0c9535e54d51ccab",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
                 "multiqc_picard_AlignmentSummaryMetrics.txt:md5,7bc3f6ef8f47e6f1e060f957025c98aa",
                 "multiqc_picard_baseContent.txt:md5,1426865fe8ee1a36f67636c28500a91c",
                 "multiqc_picard_quality_by_cycle.txt:md5,79bf9f861077de70ec28c9af01783876",
@@ -845,6 +873,7 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
                 "multiqc_fastqc.txt:md5,3df36ecfe76b25b0c22dcda84bce2b3b",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
                 "multiqc_picard_AlignmentSummaryMetrics.txt:md5,4dc89e1a04843d44695ecc8d1f047ee8",
                 "multiqc_picard_baseContent.txt:md5,0a5f9d32dd3061ce4349518c47d69838",
                 "multiqc_picard_quality_by_cycle.txt:md5,ec59b472afc1242ff299011ba456e792",
@@ -877,6 +906,7 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
                 "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
                 "multiqc_picard_AlignmentSummaryMetrics.txt:md5,fa26e8b96faa1926d8f41fc3fe959ff7",
                 "multiqc_picard_baseContent.txt:md5,b9d72d8173cdc7649b44b80aa485477c",
                 "multiqc_picard_quality_by_cycle.txt:md5,062547fb888ed508dd1d5733d7bed22e",
@@ -909,6 +939,7 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5",
                 "multiqc_fastqc.txt:md5,ce61b4ce4b1d76ec3f20de3bf0c9ec7f",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
                 "multiqc_picard_AlignmentSummaryMetrics.txt:md5,55627d8016b72c37c104e03cc156862c",
                 "multiqc_picard_baseContent.txt:md5,974d83faa49711ab4ea1248c59e69393",
                 "multiqc_picard_quality_by_cycle.txt:md5,248ecaf269d8fef1e84ea06f98b6f6ba",
@@ -927,6 +958,7 @@
                 "picard_base_distribution_by_cycle__Undetermined.txt:md5,102e653a543ac908ac9ec9b86412d73b",
                 "picard_quality_by_cycle.txt:md5,3d43fd5387c0dc728833c681ea4f73cc",
                 "picard_quality_score_distribution.txt:md5,9d9f1bb12316175cdb88d3ff70305428",
+                "200624_A00834_0183_BHMTFYDRXX_illumina_mqc.yml:md5,29e05fed18bca0e9a857c992b6d59a40",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "Sample1_1_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6",
@@ -947,9 +979,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.3",
+            "nf-test": "0.9.2",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-19T14:24:39.696680631"
+        "timestamp": "2025-11-25T10:31:07.07892869"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test b/tests/PromethION.main.nf.test
index f4a46aac..e33288d6 100644
--- a/tests/PromethION.main.nf.test
+++ b/tests/PromethION.main.nf.test
@@ -11,6 +11,7 @@ nextflow_pipeline {
             config "./PromethION.main.nf.test.config"
             params {
                 outdir = "$outputDir"
+                skip_tools = "rundirparser"
             }
         }
 

From 0009fb6cf0193bb8ee1d59b00a16a90c2c56678f Mon Sep 17 00:00:00 2001
From: eliott <eliottob6@gmail.com>
Date: Tue, 25 Nov 2025 13:33:28 +0100
Subject: [PATCH 396/530] Add information about run_picard_collecthsmetrics
 flag to usage.md

---
 docs/usage.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/docs/usage.md b/docs/usage.md
index e31a7862..f3694d02 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -98,6 +98,8 @@ Optionally, the `sample_size` parameter allows you to subset a random number of
 nextflow run nf-core/seqinspector --input ./samplesheet.csv --outdir ./results --sample_size 1000000 -profile docker
 ```
 
+The pipeline support hybrid-selection data, use the flag `--run_picard_collecthsmetrics` if you want to run the QC tool [picard CollectHSmetrics](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard). This tool is not run by default.
+
 ### Skipping tools
 
 Some tools might not be compatible with your data. In this case it might be desired to skip some of them. This can be done easily by providing a comma-separated list of tools to be skipped with the `--skip_tools` parameter.

From 3e62620ba22beaaef877c13f7c721c9b4ee7b1b5 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <163723002+agrima2010@users.noreply.github.com>
Date: Tue, 25 Nov 2025 12:34:52 +0000
Subject: [PATCH 397/530] Changed parameter bwa_index to bwamem2 and changed
 channel names

---
 nextflow.config                           | 2 +-
 nextflow_schema.json                      | 2 +-
 subworkflows/local/prepare_genome/main.nf | 8 ++++----
 workflows/seqinspector.nf                 | 2 +-
 4 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 6ce84baf..c87c9a52 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -19,7 +19,7 @@ params {
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
     igenomes_ignore            = false
     sort_bam                   = true
-    bwa_index                  = null
+    bwamem2                    = null
     // Fastqscreen options
     fastq_screen_references    = "${projectDir}/assets/example_fastq_screen_references.csv"
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 5d663de7..2b926578 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -98,7 +98,7 @@
                     "fa_icon": "fas fa-search",
                     "description": "A .csv of reference genomes to be mapped against by FastQ Screen"
                 },
-                "bwa_index": {
+                "bwamem2": {
                     "type": "string",
                     "format": "directory-path",
                     "exists": true,
diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf
index 602472cc..ad5b372e 100644
--- a/subworkflows/local/prepare_genome/main.nf
+++ b/subworkflows/local/prepare_genome/main.nf
@@ -8,7 +8,7 @@ workflow PREPARE_GENOME {
 
     take:
     fasta_file
-    bwa_index
+    bwamem2
     skip_tools
 
     main:
@@ -21,9 +21,9 @@ workflow PREPARE_GENOME {
     if (!("bwamem2_index" in skip_tools)) {
         ch_reference_fasta = channel.fromPath(fasta_file, checkIfExists: true).map { file -> tuple([id: file.name], file) }.collect()
 
-        if (bwa_index) {
+        if (bwamem2) {
             // Use pre-built index when --bwa_index parameter is provided
-            ch_bwamem2_index = channel.fromPath(bwa_index, checkIfExists: true)
+            ch_bwamem2_index = channel.fromPath(bwamem2, checkIfExists: true)
                 .map { index_dir -> tuple([id: index_dir.name], index_dir) }
                 .collect()
 
@@ -53,7 +53,7 @@ workflow PREPARE_GENOME {
 
     emit:
     bwamem2_index = ch_bwamem2_index
-    reference_fasta_fai =     ch_reference_fasta_fai
+    reference_fai =     ch_reference_fasta_fai
     versions            = ch_versions
 
 }
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 08bba00c..b15f2742 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -154,7 +154,7 @@ PREPARE_GENOME (
         ch_bam_bai = ch_bwamem2_mem.join(ch_samtools_index, failOnDuplicate: true, failOnMismatch: true)
 
         ch_fasta = ch_reference_fasta
-        ch_fai = PREPARE_GENOME.out.reference_fasta_fai
+        ch_fai = PREPARE_GENOME.out.reference_fai
 
         PICARD_COLLECTMULTIPLEMETRICS(
             ch_bam_bai,

From b4ef71c0c084e4c739d3d3c3f40c2e2b82889fd3 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 25 Nov 2025 13:34:56 +0100
Subject: [PATCH 398/530] Update README.md

---
 README.md | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index a4d0e51f..901555ae 100644
--- a/README.md
+++ b/README.md
@@ -37,15 +37,16 @@
 
 <!-- TODO: add a search tool that accepts a tree for `Compatibility with Data`. -->
 
-| Tool Type           | Tool Name                                                                          | Tool Description                            | Compatibility with Data | Dependencies        |
-| ------------------- | ---------------------------------------------------------------------------------- | ------------------------------------------- | ----------------------- | ------------------- |
+| Tool Type           | Tool Name                                                                          | Tool Description                            | Compatibility with Data | Dependencies        | Default |
+| ------------------- | ---------------------------------------------------------------------------------- | ------------------------------------------- | ----------------------- | ------------------- | - |
 | `Subsampling`       | [`Seqtk`](https://github.com/lh3/seqtk)                                            | Global subsampling of reads                 | [RNA, DNA, synthetic]   | [N/A]               |
 | `QC`                | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)             | Read QC                                     | [RNA, DNA]              | [N/A]               |
 | `QC`                | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)  | Basic contamination detection               | [RNA, DNA]              | [N/A]               |
 | `QC`                | [`SeqFu Stats`](https://github.com/telatin/seqfu2)                                 | Sequence statistics                         | [RNA, DNA]              | [N/A]               |
 | `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2)                                  | Align reads to reference                    | [RNA, DNA]              | [N/A]               |
 | `Indexing`          | [`SAMtools`](http://github.com/samtools)                                           | Index aligned BAM files, create FASTA index | [DNA]                   | [N/A]               |
-| `QC`                | [`Picard`](https://broadinstitute.github.io/picard/picard-metric-definitions.html) | Collect multiple QC metrics                 | [RNA, DNA]              | [Bwamem2, SAMtools] |
+| `QC`                | [`Picard_collectmultiplemetrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html) | Collect multiple QC metrics                 | [RNA, DNA]              | [Bwamem2, SAMtools] |
+ `QC`                | [`Picard_collecthsmetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard) | Collect alignment QC metrics of hybrid-selection data. | [RNA, DNA]              | [Bwamem2, SAMtools, `--fasta`, `--run_picard_collecths_metrics`, `--bait_intervals`, `--target_intervals` (`--ref_dict`)] | No
 | `Reporting`         | [`MultiQC`](http://multiqc.info/)                                                  | Aggregate and visualise results             | [RNA, DNA, synthetic]   | [N/A]               |
 
 <picture>

From dfbc994ff246a4b86ea221c309c3c8002029d5f3 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 25 Nov 2025 13:38:31 +0100
Subject: [PATCH 399/530] Update CITATIONS.md.

---
 CITATIONS.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CITATIONS.md b/CITATIONS.md
index 36704d9e..e03247d4 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -38,6 +38,8 @@
 
 - [Picard Tools](https://broadinstitute.github.io/picard/)
 
+> Broad Institute, “Picard Toolkit.” 2019. GitHub Repository. https://broadinstitute.github.io/picard/
+
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)

From 40cd40ac06a6f87299a1d21d5f043a215980b7b1 Mon Sep 17 00:00:00 2001
From: eliott <eliottob6@gmail.com>
Date: Tue, 25 Nov 2025 13:38:42 +0100
Subject: [PATCH 400/530] Add PR link to CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 73aba95b..040f7eba 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -29,6 +29,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#127](https://github.com/nf-core/seqinspector/pull/127) Added alignment tools - bwamem2 - index and mem
 - [#128](https://github.com/nf-core/seqinspector/pull/128) Added Picard tools - Collect Multiple Mterics to collect QC metrics
 - [#132](https://github.com/nf-core/seqinspector/pull/132) Added a bwamem2 index params for faster output
+- [#154](https://github.com/nf-core/seqinspector/pull/154) Added a subworkflow QC_BAM including picard_collecthsmetrics for alignment QC of hybrid-selection data
 
 ### `Fixed`
 

From f413842c34264a8b69eae1568cae41640070cf85 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 25 Nov 2025 13:46:40 +0100
Subject: [PATCH 401/530] Update output.md.

---
 docs/output.md | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/docs/output.md b/docs/output.md
index 3d3c3497..3d845aba 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -14,6 +14,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - [FastQC](#fastqc) - Raw read QC
 - [SeqFu Stats](#seqfu_stats) - Statistics for FASTA or FASTQ files
 - [FastQ Screen](#fastqscreen) - Mapping against a set of references for basic contamination QC
+- [Picard collecthsmetrics](#picard-collecthsmetrics) - Collect alignment QC metrics of hybrid-selection data
 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
@@ -80,6 +81,18 @@ The `.csv` is provided as a pipeline parameter `fastq_screen_references` and is
 
 [SeqFu](https://telatin.github.io/seqfu2/) is general-purpose program to manipulate and parse information from FASTA/FASTQ files, supporting gzipped input files. Includes functions to interleave and de-interleave FASTQ files, to rename sequences and to count and print statistics on sequence lengths. In this pipeline, the `seqfu stats` module is used to produce general quality metrics statistics.
 
+### Picard collecthsmetrics
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `seqfu/`
+  - `*<file>`: <File description.>
+ 
+</details>
+
+[Picard_collecthsmetrics](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard) is a tool to collect metrics on the aligment SAM/BAM files that are specific for sequence datasets generated through hybrid-selection (mostly used to capture exon-specific sequences for targeted sequencing).
+
 ### MultiQC
 
 nf-core/seqinspector will generate the following MultiQC reports:

From 14ed1343b210551ca5d19b2a0161f65658e7d3e1 Mon Sep 17 00:00:00 2001
From: matrulda <matilda.aslin@medsci.uu.se>
Date: Tue, 25 Nov 2025 13:50:49 +0100
Subject: [PATCH 402/530] WIP: Updating module test for rundirparser

---
 modules/local/rundirparser/tests/main.nf.test | 11 +++++--
 .../rundirparser/tests/main.nf.test.snap      | 10 +++++++
 .../local/rundirparser/tests/nextflow.config  | 29 +++++++++++++++++++
 3 files changed, 48 insertions(+), 2 deletions(-)
 create mode 100644 modules/local/rundirparser/tests/main.nf.test.snap

diff --git a/modules/local/rundirparser/tests/main.nf.test b/modules/local/rundirparser/tests/main.nf.test
index eb239b9a..b1899c72 100644
--- a/modules/local/rundirparser/tests/main.nf.test
+++ b/modules/local/rundirparser/tests/main.nf.test
@@ -11,9 +11,12 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = file("$moduleDir/tests/data/test_rundir")
+                input[0] = [[], file("$moduleDir/tests/data/test_rundir")]
                 """
             }
+            params {
+                outdir = "results"
+            }
         }
 
         then {
@@ -30,9 +33,13 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = file("$moduleDir/tests/data/test_rundir")
+                input[0] = [[], file("$moduleDir/tests/data/test_rundir")]
                 """
             }
+            params {
+                outdir = "results"
+            }
+
         }
 
         then {
diff --git a/modules/local/rundirparser/tests/main.nf.test.snap b/modules/local/rundirparser/tests/main.nf.test.snap
new file mode 100644
index 00000000..81e38dca
--- /dev/null
+++ b/modules/local/rundirparser/tests/main.nf.test.snap
@@ -0,0 +1,10 @@
+{
+    "Should run without failures": {
+        "content": null,
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-11-25T13:44:30.894411279"
+    }
+}
\ No newline at end of file
diff --git a/modules/local/rundirparser/tests/nextflow.config b/modules/local/rundirparser/tests/nextflow.config
index 651f0b86..ff74e779 100644
--- a/modules/local/rundirparser/tests/nextflow.config
+++ b/modules/local/rundirparser/tests/nextflow.config
@@ -1 +1,30 @@
 nextflow.enable.moduleBinaries = true
+
+process {
+    withName: 'RUNDIRPARSER' {
+        publishDir = [
+            path: "$PWD",
+            //path: { "${params.outdir}/rundirparser" },
+            mode: "copy",
+            // The process _mqc.txt outputs should have identical names for the same sequencing platforms
+            // in order to be grouped together in the MultiQC report, but here we need to enforce uniqueness
+            // to avoid overwriting results in the publishDir.
+            saveAs: { filename -> filename.equals('versions.yml') ? null : "${dir_meta.dirname}_$filename" }
+        ]
+
+    }
+}
+
+
+timeline {
+    overwrite = true
+}
+report {
+    overwrite = true
+}
+trace {
+    overwrite = true
+}
+dag {
+    overwrite = true
+}

From cc77efabc7192d6fd67ea607ee14ce571c33c241 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 25 Nov 2025 13:51:55 +0100
Subject: [PATCH 403/530] Remove cg_test profile.

---
 nextflow.config | 1 -
 1 file changed, 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index f126d6d6..6764d168 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -181,7 +181,6 @@ profiles {
     }
     test      { includeConfig 'conf/test.config'      }
     test_full { includeConfig 'conf/test_full.config' }
-    test_cg   { includeConfig 'conf/cg_test.config'   }
 }
 
 // Load nf-core custom profiles from different institutions

From d0a960aea081f7d0b2bc3f6708bcb3488d0d17c8 Mon Sep 17 00:00:00 2001
From: eliott <eliottob6@gmail.com>
Date: Tue, 25 Nov 2025 13:55:54 +0100
Subject: [PATCH 404/530] Add output file description for CollectHsMetrics in
 output.md

---
 docs/output.md | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/docs/output.md b/docs/output.md
index 3d3c3497..6bed6376 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -80,6 +80,19 @@ The `.csv` is provided as a pipeline parameter `fastq_screen_references` and is
 
 [SeqFu](https://telatin.github.io/seqfu2/) is general-purpose program to manipulate and parse information from FASTA/FASTQ files, supporting gzipped input files. Includes functions to interleave and de-interleave FASTQ files, to rename sequences and to count and print statistics on sequence lengths. In this pipeline, the `seqfu stats` module is used to produce general quality metrics statistics.
 
+
+### Picard_CollectHSmetrics
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `picard_collecthsmetrics/``
+   - `*.coverage_metrics`: Tab-separated file containing quality metrics for hybrid-selection data.
+
+</details>
+
+[CollectHsMetrics (Picard)](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard) is a tool that collects metrics from a SAM/BAM file of targeted sequencing data (hybrid-selection) like whole exome sequencing or panel sequencing.
+
 ### MultiQC
 
 nf-core/seqinspector will generate the following MultiQC reports:

From ae00279ab83d2d9383adb88bc6e1928caada29d4 Mon Sep 17 00:00:00 2001
From: FranBonath <franziska.bonath@scilifelab.se>
Date: Tue, 25 Nov 2025 14:02:24 +0100
Subject: [PATCH 405/530] update tools table in README

---
 README.md | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/README.md b/README.md
index 3f6a3866..8f75df37 100644
--- a/README.md
+++ b/README.md
@@ -37,16 +37,16 @@
 
 <!-- TODO: add a search tool that accepts a tree for `Compatibility with Data`. -->
 
-| Tool Type           | Tool Name                                                                          | Tool Description                            | Compatibility with Data | Dependencies                    | Default tool |
-| ------------------- | ---------------------------------------------------------------------------------- | ------------------------------------------- | ----------------------- | ------------------------------- | ------------ |
-| `Subsampling`       | [`Seqtk`](https://github.com/lh3/seqtk)                                            | Global subsampling of reads                 | [RNA, DNA, synthetic]   | [N/A]                           | no           |
-| `QC`                | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)             | Read QC                                     | [RNA, DNA]              | [N/A]                           | yes          |
-| `QC`                | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)  | Basic contamination detection               | [RNA, DNA]              | [N/A]                           | yes          |
-| `QC`                | [`SeqFu Stats`](https://github.com/telatin/seqfu2)                                 | Sequence statistics                         | [RNA, DNA]              | [N/A]                           | yes          |
-| `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2)                                  | Align reads to reference                    | [RNA, DNA]              | [N/A]                           | yes          |
-| `Indexing`          | [`SAMtools`](http://github.com/samtools)                                           | Index aligned BAM files, create FASTA index | [DNA]                   | [N/A]                           | yes          |
-| `QC`                | [`Picard`](https://broadinstitute.github.io/picard/picard-metric-definitions.html) | Collect multiple QC metrics                 | [RNA, DNA]              | [Bwamem2, SAMtools, `--genome`] | yes          |
-| `Reporting`         | [`MultiQC`](http://multiqc.info/)                                                  | Present QC for raw reads                    | [RNA, DNA, synthetic]   | [N/A]                           | yes          |
+| Tool Type           | Tool Name                                                                                                   | Tool Description                                                                              | Compatibility with Data | Dependencies                    | Default tool |
+| ------------------- | ----------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------- | ----------------------- | ------------------------------- | ------------ |
+| `Subsampling`       | [`Seqtk`](https://github.com/lh3/seqtk)                                                                     | Global subsampling of reads. Only performs subsampling if `--sample_size` parameter is given. | [RNA, DNA, synthetic]   | [N/A]                           | yes          |
+| `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2)                                                           | Align reads to reference                                                                      | [RNA, DNA]              | [N/A]                           | yes          |
+| `Indexing`          | [`SAMtools`](http://github.com/samtools)                                                                    | Index aligned BAM files, create FASTA index                                                   | [DNA]                   | [N/A]                           | yes          |
+| `QC`                | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)                                      | Read QC                                                                                       | [RNA, DNA]              | [N/A]                           | yes          |
+| `QC`                | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)                           | Basic contamination detection                                                                 | [RNA, DNA]              | [N/A]                           | yes          |
+| `QC`                | [`SeqFu Stats`](https://github.com/telatin/seqfu2)                                                          | Sequence statistics                                                                           | [RNA, DNA]              | [N/A]                           | yes          |
+| `QC`                | [`Picard collect multiple metrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html) | Collect multiple QC metrics                                                                   | [RNA, DNA]              | [Bwamem2, SAMtools, `--genome`] | yes          |
+| `Reporting`         | [`MultiQC`](http://multiqc.info/)                                                                           | Present QC for raw reads                                                                      | [RNA, DNA, synthetic]   | [N/A]                           | yes          |
 
 <picture>
   <source media="(prefers-color-scheme: dark)" srcset="docs/images/seqinspector_tubemap_V1.0_dark.png">

From c35a1d9cafae2eb36921934cd416f8cd3357d38e Mon Sep 17 00:00:00 2001
From: eliott <eliottob6@gmail.com>
Date: Tue, 25 Nov 2025 14:13:22 +0100
Subject: [PATCH 406/530] Add File description for collecthsmetrics in
 output.md

---
 docs/output.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/output.md b/docs/output.md
index 3d845aba..2185319c 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -86,8 +86,8 @@ The `.csv` is provided as a pipeline parameter `fastq_screen_references` and is
 <details markdown="1">
 <summary>Output files</summary>
 
-- `seqfu/`
-  - `*<file>`: <File description.>
+- `picard_collecthsmetrics/`
+  - `*.coverage_metrics`: Tab-separated file containing quality metrics for hybrid-selection data.
  
 </details>
 

From 0b3af151ee9252df5d75d8095074ceb558a78bc1 Mon Sep 17 00:00:00 2001
From: Franziska Bonath <41994400+FranBonath@users.noreply.github.com>
Date: Tue, 25 Nov 2025 14:20:08 +0100
Subject: [PATCH 407/530] Update README.md

Co-authored-by: Karthik Nair <35717861+KarNair@users.noreply.github.com>
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 95df0759..2f1283d4 100644
--- a/README.md
+++ b/README.md
@@ -39,7 +39,7 @@
 
 | Tool Type           | Tool Name                                                                                                   | Tool Description                                                                              | Compatibility with Data | Dependencies                    | Default tool |
 | ------------------- | ----------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------- | ----------------------- | ------------------------------- | ------------ |
-| `Subsampling`       | [`Seqtk`](https://github.com/lh3/seqtk)                                                                     | Global subsampling of reads. Only performs subsampling if `--sample_size` parameter is given. | [RNA, DNA, synthetic]   | [N/A]                           | yes          |
+| `Subsampling`       | [`Seqtk`](https://github.com/lh3/seqtk)                                                                     | Global subsampling of reads. Only performs subsampling if `--sample_size` parameter is given. | [RNA, DNA, synthetic]   | [N/A]                           | no          |
 | `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2)                                                           | Align reads to reference                                                                      | [RNA, DNA]              | [N/A]                           | yes          |
 | `Indexing`          | [`SAMtools`](http://github.com/samtools)                                                                    | Index aligned BAM files, create FASTA index                                                   | [DNA]                   | [N/A]                           | yes          |
 | `QC`                | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)                                      | Read QC                                                                                       | [RNA, DNA]              | [N/A]                           | yes          |

From 76038b5279359fd6b43ce3b0b8834192aadf671f Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Tue, 25 Nov 2025 13:21:32 +0000
Subject: [PATCH 408/530] [automated] Fix code linting

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 2f1283d4..e67fe62a 100644
--- a/README.md
+++ b/README.md
@@ -39,7 +39,7 @@
 
 | Tool Type           | Tool Name                                                                                                   | Tool Description                                                                              | Compatibility with Data | Dependencies                    | Default tool |
 | ------------------- | ----------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------- | ----------------------- | ------------------------------- | ------------ |
-| `Subsampling`       | [`Seqtk`](https://github.com/lh3/seqtk)                                                                     | Global subsampling of reads. Only performs subsampling if `--sample_size` parameter is given. | [RNA, DNA, synthetic]   | [N/A]                           | no          |
+| `Subsampling`       | [`Seqtk`](https://github.com/lh3/seqtk)                                                                     | Global subsampling of reads. Only performs subsampling if `--sample_size` parameter is given. | [RNA, DNA, synthetic]   | [N/A]                           | no           |
 | `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2)                                                           | Align reads to reference                                                                      | [RNA, DNA]              | [N/A]                           | yes          |
 | `Indexing`          | [`SAMtools`](http://github.com/samtools)                                                                    | Index aligned BAM files, create FASTA index                                                   | [DNA]                   | [N/A]                           | yes          |
 | `QC`                | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)                                      | Read QC                                                                                       | [RNA, DNA]              | [N/A]                           | yes          |

From 985ddcb43858c625df2f9b543df62f3b97b5cf22 Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <163723002+agrima2010@users.noreply.github.com>
Date: Tue, 25 Nov 2025 13:21:43 +0000
Subject: [PATCH 409/530] Added params in root main.nf and snapshots

---
 main.nf                                       |   4 +
 subworkflows/local/prepare_genome/main.nf     |  20 +-
 tests/MiSeq.main.nf.test.snap                 | 216 +--------
 tests/MiSeq_PairedEnd.main.nf.test.snap       | 199 +--------
 tests/NovaSeq6000.main.nf.test.snap           | 411 +-----------------
 tests/NovaSeq6000.main_subsample.nf.test.snap | 411 +-----------------
 tests/PromethION.main.nf.test.snap            |   2 +-
 workflows/seqinspector.nf                     |  29 +-
 8 files changed, 34 insertions(+), 1258 deletions(-)

diff --git a/main.nf b/main.nf
index 56bbfec3..3de00b77 100644
--- a/main.nf
+++ b/main.nf
@@ -16,6 +16,7 @@
 
 params.fasta = getGenomeAttribute('fasta')
 
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
@@ -44,10 +45,13 @@ workflow NFCORE_SEQINSPECTOR {
     //
     // WORKFLOW: Run pipeline
     //
+    skip_tools = params.skip_tools ? params.skip_tools.split(',') : []
 
     SEQINSPECTOR(
         samplesheet,
         params.fasta,
+        skip_tools,
+        params.bwamem2
     )
 
     emit:
diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf
index ad5b372e..013d4db2 100644
--- a/subworkflows/local/prepare_genome/main.nf
+++ b/subworkflows/local/prepare_genome/main.nf
@@ -7,22 +7,20 @@ include { SAMTOOLS_FAIDX                } from '../../../modules/nf-core/samtool
 workflow PREPARE_GENOME {
 
     take:
-    fasta_file
+    ch_reference_fasta
     bwamem2
     skip_tools
 
     main:
     // Initialize all channels that might be used later
-    ch_bwamem2_index = channel.empty()
-    ch_reference_fasta_fai = channel.empty()
-    ch_reference_fasta = channel.empty()
-    ch_versions      = channel.empty()
+    ch_bwamem2_index      = channel.empty()
+    ch_reference_fai      = channel.empty()
+    ch_reference_fasta    = channel.empty()
+    ch_versions           = channel.empty()
 
     if (!("bwamem2_index" in skip_tools)) {
-        ch_reference_fasta = channel.fromPath(fasta_file, checkIfExists: true).map { file -> tuple([id: file.name], file) }.collect()
-
         if (bwamem2) {
-            // Use pre-built index when --bwa_index parameter is provided
+            // Use pre-built index when --bwamem2 parameter is provided
             ch_bwamem2_index = channel.fromPath(bwamem2, checkIfExists: true)
                 .map { index_dir -> tuple([id: index_dir.name], index_dir) }
                 .collect()
@@ -47,13 +45,13 @@ workflow PREPARE_GENOME {
             [[:], []],
             true,
         )
-        ch_reference_fasta_fai = SAMTOOLS_FAIDX.out.fai
+        ch_reference_fai = SAMTOOLS_FAIDX.out.fai
         ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions)
     }
 
     emit:
     bwamem2_index = ch_bwamem2_index
-    reference_fai =     ch_reference_fasta_fai
-    versions            = ch_versions
+    reference_fai = ch_reference_fai
+    versions      = ch_versions
 
 }
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 2413892e..ff3e6b3a 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -29,27 +29,17 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-25T10:51:19.181078123"
+        "timestamp": "2025-11-25T13:17:00.197170378"
     },
     "MiSeq data test (single end reads)": {
         "content": [
             {
-                "BWAMEM2_MEM": {
-                    "bwamem2": "2.2.1",
-                    "samtools": "1.22.1"
-                },
                 "FASTQC": {
                     "fastqc": "0.12.1"
                 },
                 "FASTQSCREEN_FASTQSCREEN": {
                     "fastqscreen": "0.16.0"
                 },
-                "PICARD_COLLECTMULTIPLEMETRICS": {
-                    "picard": "3.4.0"
-                },
-                "SAMTOOLS_INDEX": {
-                    "samtools": "1.22.1"
-                },
                 "SEQFU_STATS": {
                     "seqfu": "1.22.3"
                 },
@@ -58,16 +48,6 @@
                 }
             },
             [
-                "bwamem2_index",
-                "bwamem2_index/bwamem2",
-                "bwamem2_index/bwamem2/genome.fa.0123",
-                "bwamem2_index/bwamem2/genome.fa.amb",
-                "bwamem2_index/bwamem2/genome.fa.ann",
-                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
-                "bwamem2_index/bwamem2/genome.fa.pac",
-                "bwamem2_mem",
-                "bwamem2_mem/SAMPLE_SINGLE_END_1.bam",
-                "bwamem2_mem/SAMPLE_SINGLE_END_1.bam.bai",
                 "fastqc",
                 "fastqc/SAMPLE_SINGLE_END_1_fastqc.html",
                 "fastqc/SAMPLE_SINGLE_END_1_fastqc.zip",
@@ -97,26 +77,9 @@
                 "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
-                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
-                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
-                "multiqc/global_report/multiqc_data/picard_alignment_summary.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
-                "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt",
-                "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -131,16 +94,6 @@
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -155,16 +108,6 @@
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
-                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
-                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -179,44 +122,15 @@
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
-                "picard_collectmultiplemetrics",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
-                "samtools_faidx",
-                "samtools_faidx/genome.fa.fai",
-                "samtools_faidx/genome.fa.sizes",
                 "seqfu_stats",
                 "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu.tsv",
                 "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu_mqc.txt"
             ],
             [
-                "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
-                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
-                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
-                "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
-                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "SAMPLE_SINGLE_END_1.bam:md5,ff8893272a6560cac7067fd8a9406f9b",
-                "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
                 "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
                 "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
                 "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
@@ -232,26 +146,7 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607",
                 "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,fe082d3b5dcc3d338e25bc027e17dc99",
-                "multiqc_picard_baseContent.txt:md5,796e8e0803ad3ed4fd1c76f073784942",
-                "multiqc_picard_quality_by_cycle.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
-                "multiqc_picard_quality_score_distribution.txt:md5,bad70b98811c4cbe4728f53334993703",
                 "multiqc_seqfu.txt:md5,7ec63bc3465b3fc8e316e2443ec4c848",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
-                "picard_QualityScoreDistribution_histogram.txt:md5,bad70b98811c4cbe4728f53334993703",
-                "picard_alignment_readlength_plot.txt:md5,0fe7e17f1c58b7a6291bc1ff80fdfaa0",
-                "picard_alignment_summary.txt:md5,c770d3ee98dadaee77ef43967a974627",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,65d43b083e90830aa9451bde65a261b8",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,31dc4f314d8e3f8e086e7ae761638023",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,d92fac15687942c0f9c436ba0cf55fc9",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,00b76f45bbfc9acd2774f90612e53333",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,5451af67007a16e7645d0393011414af",
-                "picard_quality_by_cycle.txt:md5,46fbe44a9788f2e9184e2c1d689c2876",
-                "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77",
-                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
-                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,33a9e44386f308d43881a58394b6b17c",
                 "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,e67e819605ab49182aacf1d676dc885d"
             ]
@@ -260,24 +155,14 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-25T10:37:31.301182496"
+        "timestamp": "2025-11-25T13:16:09.970027338"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
             {
-                "BWAMEM2_MEM": {
-                    "bwamem2": "2.2.1",
-                    "samtools": "1.22.1"
-                },
                 "FASTQSCREEN_FASTQSCREEN": {
                     "fastqscreen": "0.16.0"
                 },
-                "PICARD_COLLECTMULTIPLEMETRICS": {
-                    "picard": "3.4.0"
-                },
-                "SAMTOOLS_INDEX": {
-                    "samtools": "1.22.1"
-                },
                 "SEQFU_STATS": {
                     "seqfu": "1.22.3"
                 },
@@ -286,16 +171,6 @@
                 }
             },
             [
-                "bwamem2_index",
-                "bwamem2_index/bwamem2",
-                "bwamem2_index/bwamem2/genome.fa.0123",
-                "bwamem2_index/bwamem2/genome.fa.amb",
-                "bwamem2_index/bwamem2/genome.fa.ann",
-                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
-                "bwamem2_index/bwamem2/genome.fa.pac",
-                "bwamem2_mem",
-                "bwamem2_mem/SAMPLE_SINGLE_END_1.bam",
-                "bwamem2_mem/SAMPLE_SINGLE_END_1.bam.bai",
                 "fastqscreen",
                 "fastqscreen/SAMPLE_SINGLE_END_1_screen.html",
                 "fastqscreen/SAMPLE_SINGLE_END_1_screen.png",
@@ -310,121 +185,36 @@
                 "multiqc/global_report/multiqc_data/multiqc_citations.txt",
                 "multiqc/global_report/multiqc_data/multiqc_data.json",
                 "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
-                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
-                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
-                "multiqc/global_report/multiqc_data/picard_alignment_summary.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
-                "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt",
-                "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
-                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
-                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
-                "picard_collectmultiplemetrics",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
-                "samtools_faidx",
-                "samtools_faidx/genome.fa.fai",
-                "samtools_faidx/genome.fa.sizes",
                 "seqfu_stats",
                 "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu.tsv",
                 "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu_mqc.txt"
             ],
             [
-                "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
-                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
-                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
-                "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
-                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "SAMPLE_SINGLE_END_1.bam:md5,ff8893272a6560cac7067fd8a9406f9b",
-                "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
                 "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
                 "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
                 "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,fe082d3b5dcc3d338e25bc027e17dc99",
-                "multiqc_picard_baseContent.txt:md5,796e8e0803ad3ed4fd1c76f073784942",
-                "multiqc_picard_quality_by_cycle.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
-                "multiqc_picard_quality_score_distribution.txt:md5,bad70b98811c4cbe4728f53334993703",
                 "multiqc_seqfu.txt:md5,7ec63bc3465b3fc8e316e2443ec4c848",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
-                "picard_QualityScoreDistribution_histogram.txt:md5,bad70b98811c4cbe4728f53334993703",
-                "picard_alignment_readlength_plot.txt:md5,0fe7e17f1c58b7a6291bc1ff80fdfaa0",
-                "picard_alignment_summary.txt:md5,c770d3ee98dadaee77ef43967a974627",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,65d43b083e90830aa9451bde65a261b8",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,31dc4f314d8e3f8e086e7ae761638023",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,d92fac15687942c0f9c436ba0cf55fc9",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,00b76f45bbfc9acd2774f90612e53333",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,5451af67007a16e7645d0393011414af",
-                "picard_quality_by_cycle.txt:md5,46fbe44a9788f2e9184e2c1d689c2876",
-                "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77",
-                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
-                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,33a9e44386f308d43881a58394b6b17c",
                 "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,e67e819605ab49182aacf1d676dc885d"
             ]
@@ -433,6 +223,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-25T10:38:32.729517527"
+        "timestamp": "2025-11-25T13:16:42.837673249"
     }
 }
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index b8d1f6d1..f359d589 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -2,22 +2,12 @@
     "MiSeq data test (paired end reads)": {
         "content": [
             {
-                "BWAMEM2_MEM": {
-                    "bwamem2": "2.2.1",
-                    "samtools": "1.22.1"
-                },
                 "FASTQC": {
                     "fastqc": "0.12.1"
                 },
                 "FASTQSCREEN_FASTQSCREEN": {
                     "fastqscreen": "0.16.0"
                 },
-                "PICARD_COLLECTMULTIPLEMETRICS": {
-                    "picard": "3.4.0"
-                },
-                "SAMTOOLS_INDEX": {
-                    "samtools": "1.22.1"
-                },
                 "SEQFU_STATS": {
                     "seqfu": "1.22.3"
                 },
@@ -26,18 +16,6 @@
                 }
             },
             [
-                "bwamem2_index",
-                "bwamem2_index/bwamem2",
-                "bwamem2_index/bwamem2/genome.fa.0123",
-                "bwamem2_index/bwamem2/genome.fa.amb",
-                "bwamem2_index/bwamem2/genome.fa.ann",
-                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
-                "bwamem2_index/bwamem2/genome.fa.pac",
-                "bwamem2_mem",
-                "bwamem2_mem/SAMPLE_PAIRED_END_1_1.bam",
-                "bwamem2_mem/SAMPLE_PAIRED_END_1_1.bam.bai",
-                "bwamem2_mem/SAMPLE_PAIRED_END_2_2.bam",
-                "bwamem2_mem/SAMPLE_PAIRED_END_2_2.bam.bai",
                 "fastqc",
                 "fastqc/SAMPLE_PAIRED_END_1_1_1_fastqc.html",
                 "fastqc/SAMPLE_PAIRED_END_1_1_1_fastqc.zip",
@@ -81,27 +59,9 @@
                 "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
-                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
-                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
-                "multiqc/global_report/multiqc_data/picard_alignment_summary_Aligned_Bases.txt",
-                "multiqc/global_report/multiqc_data/picard_alignment_summary_Aligned_Reads.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
-                "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt",
-                "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -115,18 +75,6 @@
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -140,18 +88,6 @@
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-pct.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-pct.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
-                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
-                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -165,18 +101,6 @@
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "multiqc/group_reports",
@@ -200,27 +124,9 @@
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_baseContent.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_quality_by_cycle.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_sources.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/picard_alignment_readlength_plot.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/picard_alignment_summary_Aligned_Bases.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/picard_alignment_summary_Aligned_Reads.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/picard_quality_by_cycle.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_plots",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -234,18 +140,6 @@
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-cnt.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-pct.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-cnt.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-pct.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -259,18 +153,6 @@
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_readlength_plot.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-cnt.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-pct.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-cnt.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-pct.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_quality_by_cycle.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -284,42 +166,10 @@
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-cnt.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-pct.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-cnt.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-pct.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_quality_by_cycle.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_report.html",
-                "picard_collectmultiplemetrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.alignment_summary_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.read_length_histogram.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.alignment_summary_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
-                "samtools_faidx",
-                "samtools_faidx/genome.fa.fai",
-                "samtools_faidx/genome.fa.sizes",
                 "seqfu_stats",
                 "seqfu_stats/SAMPLE_PAIRED_END_1_1_seqfu.tsv",
                 "seqfu_stats/SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt",
@@ -327,15 +177,6 @@
                 "seqfu_stats/SAMPLE_PAIRED_END_2_2_seqfu_mqc.txt"
             ],
             [
-                "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
-                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
-                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
-                "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
-                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "SAMPLE_PAIRED_END_1_1.bam:md5,44c0ef738b73e26f67ded45ca4cb9e5b",
-                "SAMPLE_PAIRED_END_1_1.bam.bai:md5,82724835c47f8e1d1a86e13ef469b464",
-                "SAMPLE_PAIRED_END_2_2.bam:md5,9e20db3f3088fc478c223839e3a4ed62",
-                "SAMPLE_PAIRED_END_2_2.bam.bai:md5,3c4bdff0f906f2234fdeee8eea719210",
                 "SAMPLE_PAIRED_END_1_1_1_screen.png:md5,f52ddd0e65f23f68dd8d58d5453417db",
                 "SAMPLE_PAIRED_END_1_1_1_screen.txt:md5,921b08eeb461a2aa1bd42bba53900f70",
                 "SAMPLE_PAIRED_END_1_1_2_screen.png:md5,908f4fceea8aa546106efdaa7ca78f7d",
@@ -357,25 +198,7 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,5ef00028497d3271c9f0ea9a961db1e5",
                 "multiqc_fastqc.txt:md5,bc499ad273fd1c887056c31b82544984",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,35d289ee535a0442db72a65391f375eb",
-                "multiqc_picard_baseContent.txt:md5,72b0ae83ed58052bfd768021d377c78f",
-                "multiqc_picard_quality_by_cycle.txt:md5,f6514f14befb874ded5aed79caba3e7b",
-                "multiqc_picard_quality_score_distribution.txt:md5,99be409e325619171b820d762dd023c0",
                 "multiqc_seqfu.txt:md5,139354afd154804b4b77f997277f3ee9",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,f6514f14befb874ded5aed79caba3e7b",
-                "picard_QualityScoreDistribution_histogram.txt:md5,99be409e325619171b820d762dd023c0",
-                "picard_alignment_readlength_plot.txt:md5,4172702f791d043135f21e3a227fe712",
-                "picard_alignment_summary_Aligned_Bases.txt:md5,a166c14210e17d3541482b500443f792",
-                "picard_alignment_summary_Aligned_Reads.txt:md5,c5e5228e85ffb2182274d641ffa6743f",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,3fe18f1144eb85f9206d1bee4eb11bb3",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,2e1383b692e76f4b915ccbe9bb9b9170",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,2a595bc9ac547f3b5224a57a6b0a127d",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,157ea873dd2faff46efdd62f7f6aa84c",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,98f4e5ed094b41eb131d493b4f06bcd6",
-                "picard_quality_by_cycle.txt:md5,2634f306a33f648bac74bc7cd3253f9e",
-                "picard_quality_score_distribution.txt:md5,ecde9f0e859a6eecc5cea75a156c632d",
                 "fastq_screen_plot.txt:md5,642264b93871c724aaa5d38b91c752dd",
                 "fastqc-status-check-heatmap.txt:md5,8e29ad6b23e03267c33bd9ed3385a44b",
                 "fastqc_adapter_content_plot.txt:md5,46fbd727a4996a3f0310d0423c628445",
@@ -389,27 +212,7 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,5ef00028497d3271c9f0ea9a961db1e5",
                 "multiqc_fastqc.txt:md5,bc499ad273fd1c887056c31b82544984",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,35d289ee535a0442db72a65391f375eb",
-                "multiqc_picard_baseContent.txt:md5,72b0ae83ed58052bfd768021d377c78f",
-                "multiqc_picard_quality_by_cycle.txt:md5,f6514f14befb874ded5aed79caba3e7b",
-                "multiqc_picard_quality_score_distribution.txt:md5,99be409e325619171b820d762dd023c0",
                 "multiqc_seqfu.txt:md5,139354afd154804b4b77f997277f3ee9",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,f6514f14befb874ded5aed79caba3e7b",
-                "picard_QualityScoreDistribution_histogram.txt:md5,99be409e325619171b820d762dd023c0",
-                "picard_alignment_readlength_plot.txt:md5,4172702f791d043135f21e3a227fe712",
-                "picard_alignment_summary_Aligned_Bases.txt:md5,a166c14210e17d3541482b500443f792",
-                "picard_alignment_summary_Aligned_Reads.txt:md5,c5e5228e85ffb2182274d641ffa6743f",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,3fe18f1144eb85f9206d1bee4eb11bb3",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,2e1383b692e76f4b915ccbe9bb9b9170",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,2a595bc9ac547f3b5224a57a6b0a127d",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,157ea873dd2faff46efdd62f7f6aa84c",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,98f4e5ed094b41eb131d493b4f06bcd6",
-                "picard_quality_by_cycle.txt:md5,2634f306a33f648bac74bc7cd3253f9e",
-                "picard_quality_score_distribution.txt:md5,ecde9f0e859a6eecc5cea75a156c632d",
-                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
-                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "SAMPLE_PAIRED_END_1_1_seqfu.tsv:md5,be29dfe848eab9a10ee0d46691223eae",
                 "SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt:md5,0aca00c7f64454af520c7e08ec595d2b",
                 "SAMPLE_PAIRED_END_2_2_seqfu.tsv:md5,44a5cb826e001d58208a5855938fa82b",
@@ -420,6 +223,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-25T10:40:16.383291844"
+        "timestamp": "2025-11-25T13:17:39.398776674"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index 527e1be2..5ecffa85 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -2,22 +2,12 @@
     "NovaSeq6000 data test": {
         "content": [
             {
-                "BWAMEM2_MEM": {
-                    "bwamem2": "2.2.1",
-                    "samtools": "1.22.1"
-                },
                 "FASTQC": {
                     "fastqc": "0.12.1"
                 },
                 "FASTQSCREEN_FASTQSCREEN": {
                     "fastqscreen": "0.16.0"
                 },
-                "PICARD_COLLECTMULTIPLEMETRICS": {
-                    "picard": "3.4.0"
-                },
-                "SAMTOOLS_INDEX": {
-                    "samtools": "1.22.1"
-                },
                 "SEQFU_STATS": {
                     "seqfu": "1.22.3"
                 },
@@ -26,24 +16,6 @@
                 }
             },
             [
-                "bwamem2_index",
-                "bwamem2_index/bwamem2",
-                "bwamem2_index/bwamem2/genome.fa.0123",
-                "bwamem2_index/bwamem2/genome.fa.amb",
-                "bwamem2_index/bwamem2/genome.fa.ann",
-                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
-                "bwamem2_index/bwamem2/genome.fa.pac",
-                "bwamem2_mem",
-                "bwamem2_mem/Sample1_1.bam",
-                "bwamem2_mem/Sample1_1.bam.bai",
-                "bwamem2_mem/Sample23_3.bam",
-                "bwamem2_mem/Sample23_3.bam.bai",
-                "bwamem2_mem/SampleA_2.bam",
-                "bwamem2_mem/SampleA_2.bam.bai",
-                "bwamem2_mem/Undetermined_5.bam",
-                "bwamem2_mem/Undetermined_5.bam.bai",
-                "bwamem2_mem/sampletest_4.bam",
-                "bwamem2_mem/sampletest_4.bam.bai",
                 "fastqc",
                 "fastqc/Sample1_1_fastqc.html",
                 "fastqc/Sample1_1_fastqc.zip",
@@ -94,26 +66,9 @@
                 "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
-                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
-                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
-                "multiqc/global_report/multiqc_data/picard_alignment_summary.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
-                "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt",
-                "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -129,16 +84,6 @@
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -154,16 +99,6 @@
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
-                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
-                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -179,16 +114,6 @@
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "multiqc/group_reports",
@@ -214,26 +139,9 @@
                 "multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_baseContent.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_sources.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_alignment_readlength_plot.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_alignment_summary.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_quality_by_cycle.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group1/multiqc_plots",
                 "multiqc/group_reports/group1/multiqc_plots/pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -249,16 +157,6 @@
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -274,16 +172,6 @@
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_readlength_plot.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-cnt.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-pct.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_by_cycle.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/group1/multiqc_plots/svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -299,16 +187,6 @@
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-pct.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_by_cycle.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/group1/multiqc_report.html",
                 "multiqc/group_reports/group2",
@@ -333,26 +211,9 @@
                 "multiqc/group_reports/group2/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
-                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_baseContent.txt",
-                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_by_cycle.txt",
-                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_sources.txt",
-                "multiqc/group_reports/group2/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
-                "multiqc/group_reports/group2/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
-                "multiqc/group_reports/group2/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
-                "multiqc/group_reports/group2/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
-                "multiqc/group_reports/group2/multiqc_data/picard_alignment_readlength_plot.txt",
-                "multiqc/group_reports/group2/multiqc_data/picard_alignment_summary.txt",
-                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
-                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
-                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
-                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
-                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
-                "multiqc/group_reports/group2/multiqc_data/picard_quality_by_cycle.txt",
-                "multiqc/group_reports/group2/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group2/multiqc_plots",
                 "multiqc/group_reports/group2/multiqc_plots/pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -368,16 +229,6 @@
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -393,16 +244,6 @@
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_readlength_plot.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-cnt.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-pct.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_by_cycle.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/group2/multiqc_plots/svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -418,16 +259,6 @@
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-pct.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_by_cycle.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/group2/multiqc_report.html",
                 "multiqc/group_reports/lane1",
@@ -452,26 +283,9 @@
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
-                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_baseContent.txt",
-                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
-                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_sources.txt",
-                "multiqc/group_reports/lane1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
-                "multiqc/group_reports/lane1/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
-                "multiqc/group_reports/lane1/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
-                "multiqc/group_reports/lane1/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
-                "multiqc/group_reports/lane1/multiqc_data/picard_alignment_readlength_plot.txt",
-                "multiqc/group_reports/lane1/multiqc_data/picard_alignment_summary.txt",
-                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
-                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
-                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
-                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
-                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
-                "multiqc/group_reports/lane1/multiqc_data/picard_quality_by_cycle.txt",
-                "multiqc/group_reports/lane1/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/lane1/multiqc_plots",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -487,16 +301,6 @@
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -512,16 +316,6 @@
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_readlength_plot.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-cnt.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-pct.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_by_cycle.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/lane1/multiqc_plots/svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -537,16 +331,6 @@
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-pct.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_by_cycle.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/lane1/multiqc_report.html",
                 "multiqc/group_reports/test",
@@ -571,26 +355,9 @@
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                 "multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/group_reports/test/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
-                "multiqc/group_reports/test/multiqc_data/multiqc_picard_baseContent.txt",
-                "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_by_cycle.txt",
-                "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_score_distribution.txt",
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-                "multiqc/group_reports/test/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
-                "multiqc/group_reports/test/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
-                "multiqc/group_reports/test/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
-                "multiqc/group_reports/test/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
-                "multiqc/group_reports/test/multiqc_data/picard_alignment_readlength_plot.txt",
-                "multiqc/group_reports/test/multiqc_data/picard_alignment_summary.txt",
-                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
-                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
-                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
-                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
-                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
-                "multiqc/group_reports/test/multiqc_data/picard_quality_by_cycle.txt",
-                "multiqc/group_reports/test/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/test/multiqc_plots",
                 "multiqc/group_reports/test/multiqc_plots/pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -606,16 +373,6 @@
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/test/multiqc_plots/png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -631,16 +388,6 @@
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_readlength_plot.png",
-                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-cnt.png",
-                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-pct.png",
-                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
-                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
-                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
-                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
-                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
-                "multiqc/group_reports/test/multiqc_plots/png/picard_quality_by_cycle.png",
-                "multiqc/group_reports/test/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/test/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/test/multiqc_plots/svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -656,64 +403,10 @@
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-pct.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_by_cycle.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/test/multiqc_report.html",
-                "picard_collectmultiplemetrics",
-                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.alignment_summary_metrics",
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-                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_distribution.pdf",
-                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_distribution_metrics",
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-                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.alignment_summary_metrics",
-                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
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-                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_distribution.pdf",
-                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_distribution_metrics",
-                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.read_length_histogram.pdf",
-                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.alignment_summary_metrics",
-                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
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-                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_distribution_metrics",
-                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.read_length_histogram.pdf",
-                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.alignment_summary_metrics",
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-                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
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-                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution.pdf",
-                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution_metrics",
-                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.read_length_histogram.pdf",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.alignment_summary_metrics",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution.pdf",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution_metrics",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
-                "samtools_faidx",
-                "samtools_faidx/genome.fa.fai",
-                "samtools_faidx/genome.fa.sizes",
                 "seqfu_stats",
                 "seqfu_stats/Sample1_1_seqfu.tsv",
                 "seqfu_stats/Sample1_1_seqfu_mqc.txt",
@@ -727,21 +420,6 @@
                 "seqfu_stats/sampletest_4_seqfu_mqc.txt"
             ],
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-                "sampletest_4.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
                 "Sample1_1_screen.png:md5,562256290643b51e4374c2225a15f463",
                 "Sample1_1_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
                 "Sample23_3_screen.png:md5,6bb2caf67b9b2ed25d3d5f32c343e9ab",
@@ -766,24 +444,7 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
                 "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,5bdb2f162266ab68005cbfc0a45e311e",
-                "multiqc_picard_baseContent.txt:md5,409bf8ce546a573ce6678769b84726fd",
-                "multiqc_picard_quality_by_cycle.txt:md5,ebf56fd9b3b127ff41211e3f79f18b42",
-                "multiqc_picard_quality_score_distribution.txt:md5,182098ce1ff0a664d873c329d54189df",
                 "multiqc_seqfu.txt:md5,18dd2407d4a1791646785123028f69b5",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,ebf56fd9b3b127ff41211e3f79f18b42",
-                "picard_QualityScoreDistribution_histogram.txt:md5,182098ce1ff0a664d873c329d54189df",
-                "picard_alignment_readlength_plot.txt:md5,92ab5c6fbe67484da62626736b1b21d4",
-                "picard_alignment_summary.txt:md5,f54187e8515f9b7c32eabaf1f8702224",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,61c7df03f74846ffa484a59fcccc7b9e",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,b4504bbb9ad72796703873f2d957977a",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,1d38466783ea51bf0c7be5bceaff4d43",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,1b13c9b64042839a3bc65a8553e5ba24",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,75aee7627205c6513389d7a52e7a383b",
-                "picard_quality_by_cycle.txt:md5,4850a9230f9be5af67f3d934602df440",
-                "picard_quality_score_distribution.txt:md5,17f8498a5b18cea0eb4796a6e12b8e36",
                 "fastq_screen_plot.txt:md5,c25d34568f10f131156294d31fbfa994",
                 "fastqc-status-check-heatmap.txt:md5,67afbf7ec626c4fc7a28b4922352bc84",
                 "fastqc_overrepresented_sequences_plot.txt:md5,0356d007eaf807f7b63714b438b11289",
@@ -798,24 +459,7 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
                 "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,e4cb1b13e6a7298d172ed112a0479b5a",
-                "multiqc_picard_baseContent.txt:md5,740592a5858706d2b4b8f585a1d5492b",
-                "multiqc_picard_quality_by_cycle.txt:md5,c3f14084aedc511b9f0aa8410e7cb3b5",
-                "multiqc_picard_quality_score_distribution.txt:md5,59b955203209cfab3d2d21bdfe20997e",
                 "multiqc_seqfu.txt:md5,6cdb863a3686fbb772aae5a66925ff23",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,c3f14084aedc511b9f0aa8410e7cb3b5",
-                "picard_QualityScoreDistribution_histogram.txt:md5,59b955203209cfab3d2d21bdfe20997e",
-                "picard_alignment_readlength_plot.txt:md5,1f8b2f4df8bd5cf879b96cfb2be6d81c",
-                "picard_alignment_summary.txt:md5,0cfafd1ed1920270bb1a5d13bed51480",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,bd7f8dab8e73406cded6c6f27bbc87e9",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,fe44ccdb08c6955149eacf52a77bbba2",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,85a9172769830b4169f214c335f44fdc",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,1fe0c42cb22981763862d1934a35de07",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,4c5bfb1594b391f3e36a9e1223b43a94",
-                "picard_quality_by_cycle.txt:md5,a43e7bb40bc479e9c32476256b09e734",
-                "picard_quality_score_distribution.txt:md5,a940641c0dab423c964c0f46b69dd805",
                 "fastq_screen_plot.txt:md5,44fca6453b0a3d0590271bd7a31cc740",
                 "fastqc-status-check-heatmap.txt:md5,b6872d9dbaa3cce396d48dc137076e53",
                 "fastqc_overrepresented_sequences_plot.txt:md5,eac8d0fd31c614d8d0f56bd54ee8c78c",
@@ -830,24 +474,7 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
                 "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,d4e63eed820edcc71b3e37d793983bd7",
-                "multiqc_picard_baseContent.txt:md5,0dd5fa539e4034e3539fb1e7068c7ce5",
-                "multiqc_picard_quality_by_cycle.txt:md5,750eadc27875fc8141b64a90789c369f",
-                "multiqc_picard_quality_score_distribution.txt:md5,140279eb5abac364c4d4c417105da620",
                 "multiqc_seqfu.txt:md5,f821357507fda2d4cfd9299f52fa7dc1",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,750eadc27875fc8141b64a90789c369f",
-                "picard_QualityScoreDistribution_histogram.txt:md5,140279eb5abac364c4d4c417105da620",
-                "picard_alignment_readlength_plot.txt:md5,a39f6a39dad13dacc2134508dbbf172d",
-                "picard_alignment_summary.txt:md5,fec83821c097bc1850257ce36aa73e5f",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,f206efb4e5344b8cbb2d18f6e73d5d95",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,ebf98e3d0bf661161989bf3d010b8c6b",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,f7dff1258977e9d04fb26ba8192facc5",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,b32d1e91c41756afe8732107868b32e0",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,b7b249afe807ca2321e6dd839961795c",
-                "picard_quality_by_cycle.txt:md5,1fe617901a493b80c31fcd01a00c416d",
-                "picard_quality_score_distribution.txt:md5,5cd4a87942000899776927f22a5db802",
                 "fastq_screen_plot.txt:md5,5f748d33a7a396547fe8c260b728aa06",
                 "fastqc-status-check-heatmap.txt:md5,08228a8f3d6f11b174b98626bb22bda1",
                 "fastqc_overrepresented_sequences_plot.txt:md5,3434dfb79f150e2e584e85866983ba01",
@@ -862,24 +489,7 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
                 "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,22093b80f335c4c53633b01a930157f4",
-                "multiqc_picard_baseContent.txt:md5,6886e1e5179031ddba4958f301930d64",
-                "multiqc_picard_quality_by_cycle.txt:md5,96652e2e2d693488df9104e5ae8cb4a7",
-                "multiqc_picard_quality_score_distribution.txt:md5,879a4470d08fe6d9b1796f46020fb5f5",
                 "multiqc_seqfu.txt:md5,8cced36d66ca9d25d60c006e734aa7e9",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,96652e2e2d693488df9104e5ae8cb4a7",
-                "picard_QualityScoreDistribution_histogram.txt:md5,879a4470d08fe6d9b1796f46020fb5f5",
-                "picard_alignment_readlength_plot.txt:md5,9b323aa8cd934d084e9c83cfa1da306b",
-                "picard_alignment_summary.txt:md5,4e8970d31940f5e9020851d62e63b2e2",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,166a48317764fe7d4b38ed198503fc11",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,8e62c1113b965497e492e17665cdbe97",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,fe53f5f9455b928a3edc1661be83592b",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,3d069dd67cc0ffc43456c5f3ee427349",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,e371981072ec99d11c6adb5a4034808c",
-                "picard_quality_by_cycle.txt:md5,0c25ee4cec6842306b28c6a641aa03e1",
-                "picard_quality_score_distribution.txt:md5,184dcdd53f6aa3b7a0fa2c008d7dc74a",
                 "fastq_screen_plot.txt:md5,8622e1dbd0fe62520af6096207b9775d",
                 "fastqc-status-check-heatmap.txt:md5,2a66f5d61b9eb579555905cd5954b04c",
                 "fastqc_overrepresented_sequences_plot.txt:md5,e0b5bfc4b64d37611b51c939e61196fa",
@@ -894,26 +504,7 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5",
                 "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,edf7faad1da9922fdc692e9cba5cc0c4",
-                "multiqc_picard_baseContent.txt:md5,9631916c0a9a736811c47ab4c476428f",
-                "multiqc_picard_quality_by_cycle.txt:md5,9e05b241aabe39232b5182cb59d8edd5",
-                "multiqc_picard_quality_score_distribution.txt:md5,e9c3ade201964470d2d22569a400fa49",
                 "multiqc_seqfu.txt:md5,ff4ce1c88f39ed24a88bae0a861f75c8",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,9e05b241aabe39232b5182cb59d8edd5",
-                "picard_QualityScoreDistribution_histogram.txt:md5,e9c3ade201964470d2d22569a400fa49",
-                "picard_alignment_readlength_plot.txt:md5,c2692fde9d899ad61297ad7043fd26b9",
-                "picard_alignment_summary.txt:md5,5996d5b4c94f16c0efd42e2df47e021e",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,a2670974dc96ad8a54f9cc5ae3e09d5e",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,d3b9cc0c99f96814348b57809cf227fb",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,1ba086d3fb2676868e8e7b20f55975dc",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,8902976984741320fe06004f4115c4f4",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,1380831484d1b069a2fd4a20437118bf",
-                "picard_quality_by_cycle.txt:md5,b6fc46e18ac875ba02775e7cbf1b8e8b",
-                "picard_quality_score_distribution.txt:md5,1c17c01ef54a6062a8f1ca8408d32958",
-                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
-                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "Sample1_1_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6",
                 "Sample1_1_seqfu_mqc.txt:md5,24d99524ccd0e6c6255a69d68a871c7a",
                 "Sample23_3_seqfu.tsv:md5,6fac5d3dbce3f3bee72341fe99a399dc",
@@ -930,6 +521,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-25T10:42:40.72799341"
+        "timestamp": "2025-11-25T13:18:53.764240677"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index 7360c6c8..1d061216 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -2,22 +2,12 @@
     "NovaSeq6000 data test sample size": {
         "content": [
             {
-                "BWAMEM2_MEM": {
-                    "bwamem2": "2.2.1",
-                    "samtools": "1.22.1"
-                },
                 "FASTQC": {
                     "fastqc": "0.12.1"
                 },
                 "FASTQSCREEN_FASTQSCREEN": {
                     "fastqscreen": "0.16.0"
                 },
-                "PICARD_COLLECTMULTIPLEMETRICS": {
-                    "picard": "3.4.0"
-                },
-                "SAMTOOLS_INDEX": {
-                    "samtools": "1.22.1"
-                },
                 "SEQFU_STATS": {
                     "seqfu": "1.22.3"
                 },
@@ -29,24 +19,6 @@
                 }
             },
             [
-                "bwamem2_index",
-                "bwamem2_index/bwamem2",
-                "bwamem2_index/bwamem2/genome.fa.0123",
-                "bwamem2_index/bwamem2/genome.fa.amb",
-                "bwamem2_index/bwamem2/genome.fa.ann",
-                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
-                "bwamem2_index/bwamem2/genome.fa.pac",
-                "bwamem2_mem",
-                "bwamem2_mem/Sample1_1.bam",
-                "bwamem2_mem/Sample1_1.bam.bai",
-                "bwamem2_mem/Sample23_3.bam",
-                "bwamem2_mem/Sample23_3.bam.bai",
-                "bwamem2_mem/SampleA_2.bam",
-                "bwamem2_mem/SampleA_2.bam.bai",
-                "bwamem2_mem/Undetermined_5.bam",
-                "bwamem2_mem/Undetermined_5.bam.bai",
-                "bwamem2_mem/sampletest_4.bam",
-                "bwamem2_mem/sampletest_4.bam.bai",
                 "fastqc",
                 "fastqc/Sample1_1_fastqc.html",
                 "fastqc/Sample1_1_fastqc.zip",
@@ -97,26 +69,9 @@
                 "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
-                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
-                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
-                "multiqc/global_report/multiqc_data/picard_alignment_summary.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
-                "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt",
-                "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -132,16 +87,6 @@
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -157,16 +102,6 @@
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
-                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
-                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -182,16 +117,6 @@
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "multiqc/group_reports",
@@ -217,26 +142,9 @@
                 "multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_baseContent.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_sources.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_alignment_readlength_plot.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_alignment_summary.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_quality_by_cycle.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group1/multiqc_plots",
                 "multiqc/group_reports/group1/multiqc_plots/pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -252,16 +160,6 @@
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -277,16 +175,6 @@
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_readlength_plot.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-cnt.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-pct.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_by_cycle.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/group1/multiqc_plots/svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -302,16 +190,6 @@
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-pct.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_by_cycle.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/group1/multiqc_report.html",
                 "multiqc/group_reports/group2",
@@ -336,26 +214,9 @@
                 "multiqc/group_reports/group2/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
-                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_baseContent.txt",
-                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_by_cycle.txt",
-                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_sources.txt",
-                "multiqc/group_reports/group2/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
-                "multiqc/group_reports/group2/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
-                "multiqc/group_reports/group2/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
-                "multiqc/group_reports/group2/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
-                "multiqc/group_reports/group2/multiqc_data/picard_alignment_readlength_plot.txt",
-                "multiqc/group_reports/group2/multiqc_data/picard_alignment_summary.txt",
-                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
-                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
-                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
-                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
-                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
-                "multiqc/group_reports/group2/multiqc_data/picard_quality_by_cycle.txt",
-                "multiqc/group_reports/group2/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group2/multiqc_plots",
                 "multiqc/group_reports/group2/multiqc_plots/pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -371,16 +232,6 @@
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -396,16 +247,6 @@
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_readlength_plot.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-cnt.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-pct.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_by_cycle.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/group2/multiqc_plots/svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -421,16 +262,6 @@
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-pct.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_by_cycle.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/group2/multiqc_report.html",
                 "multiqc/group_reports/lane1",
@@ -455,26 +286,9 @@
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
-                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_baseContent.txt",
-                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
-                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_sources.txt",
-                "multiqc/group_reports/lane1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
-                "multiqc/group_reports/lane1/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
-                "multiqc/group_reports/lane1/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
-                "multiqc/group_reports/lane1/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
-                "multiqc/group_reports/lane1/multiqc_data/picard_alignment_readlength_plot.txt",
-                "multiqc/group_reports/lane1/multiqc_data/picard_alignment_summary.txt",
-                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
-                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
-                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
-                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
-                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
-                "multiqc/group_reports/lane1/multiqc_data/picard_quality_by_cycle.txt",
-                "multiqc/group_reports/lane1/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/lane1/multiqc_plots",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -490,16 +304,6 @@
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -515,16 +319,6 @@
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_readlength_plot.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-cnt.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-pct.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_by_cycle.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/lane1/multiqc_plots/svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -540,16 +334,6 @@
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-pct.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_by_cycle.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/lane1/multiqc_report.html",
                 "multiqc/group_reports/test",
@@ -574,26 +358,9 @@
                 "multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt",
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                 "multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/group_reports/test/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
-                "multiqc/group_reports/test/multiqc_data/multiqc_picard_baseContent.txt",
-                "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_by_cycle.txt",
-                "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_seqfu.txt",
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                 "multiqc/group_reports/test/multiqc_data/multiqc_sources.txt",
-                "multiqc/group_reports/test/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
-                "multiqc/group_reports/test/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
-                "multiqc/group_reports/test/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
-                "multiqc/group_reports/test/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
-                "multiqc/group_reports/test/multiqc_data/picard_alignment_readlength_plot.txt",
-                "multiqc/group_reports/test/multiqc_data/picard_alignment_summary.txt",
-                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
-                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
-                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
-                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
-                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
-                "multiqc/group_reports/test/multiqc_data/picard_quality_by_cycle.txt",
-                "multiqc/group_reports/test/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/test/multiqc_plots",
                 "multiqc/group_reports/test/multiqc_plots/pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -609,16 +376,6 @@
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/test/multiqc_plots/png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -634,16 +391,6 @@
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_readlength_plot.png",
-                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-cnt.png",
-                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-pct.png",
-                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
-                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
-                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
-                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
-                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
-                "multiqc/group_reports/test/multiqc_plots/png/picard_quality_by_cycle.png",
-                "multiqc/group_reports/test/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/test/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/test/multiqc_plots/svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -659,64 +406,10 @@
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-pct.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_by_cycle.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/test/multiqc_report.html",
-                "picard_collectmultiplemetrics",
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-                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_distribution.pdf",
-                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_distribution_metrics",
-                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.read_length_histogram.pdf",
-                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.alignment_summary_metrics",
-                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_distribution.pdf",
-                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_distribution_metrics",
-                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.read_length_histogram.pdf",
-                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.alignment_summary_metrics",
-                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
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-                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_distribution.pdf",
-                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_distribution_metrics",
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-                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.alignment_summary_metrics",
-                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution.pdf",
-                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution_metrics",
-                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.read_length_histogram.pdf",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.alignment_summary_metrics",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution.pdf",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution_metrics",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
-                "samtools_faidx",
-                "samtools_faidx/genome.fa.fai",
-                "samtools_faidx/genome.fa.sizes",
                 "seqfu_stats",
                 "seqfu_stats/Sample1_1_seqfu.tsv",
                 "seqfu_stats/Sample1_1_seqfu_mqc.txt",
@@ -736,21 +429,6 @@
                 "seqtk/sampletest_4_sampletest_S4_L001_R1_001.fastq.gz"
             ],
             [
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@@ -775,24 +453,7 @@
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-                "multiqc_picard_baseContent.txt:md5,8b2efc3fa06d2013348b35f9607292aa",
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                 "multiqc_seqfu.txt:md5,18dd2407d4a1791646785123028f69b5",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
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-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,ade1d92e5e6d3bfefd3695f103079b6c",
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@@ -807,24 +468,7 @@
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@@ -839,24 +483,7 @@
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@@ -871,24 +498,7 @@
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-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
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@@ -903,26 +513,7 @@
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                 "multiqc_seqfu.txt:md5,ff4ce1c88f39ed24a88bae0a861f75c8",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,248ecaf269d8fef1e84ea06f98b6f6ba",
-                "picard_QualityScoreDistribution_histogram.txt:md5,5e7e80654e12c500b15f8564ffb12b27",
-                "picard_alignment_readlength_plot.txt:md5,23ff551a5a8eded1857356f38b19039c",
-                "picard_alignment_summary.txt:md5,c741b69e17ed84370732b567ae11c69c",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,fc37dd1ac805881a467b264a7dd76677",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,7993fd56aa542b71bc984cd36c489fd1",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,1bca639db2a2624727f7b6dd2aa1442e",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,a5f0903d77b6060676f7dda249b99738",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,102e653a543ac908ac9ec9b86412d73b",
-                "picard_quality_by_cycle.txt:md5,3d43fd5387c0dc728833c681ea4f73cc",
-                "picard_quality_score_distribution.txt:md5,9d9f1bb12316175cdb88d3ff70305428",
-                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
-                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "Sample1_1_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6",
                 "Sample1_1_seqfu_mqc.txt:md5,24d99524ccd0e6c6255a69d68a871c7a",
                 "Sample23_3_seqfu.tsv:md5,6fac5d3dbce3f3bee72341fe99a399dc",
@@ -944,6 +535,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-25T10:44:53.483227254"
+        "timestamp": "2025-11-25T13:20:06.917144477"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index a7d07255..92c8bb5e 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -133,6 +133,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-25T10:57:28.062541336"
+        "timestamp": "2025-11-25T13:20:37.20082732"
     }
 }
\ No newline at end of file
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index b15f2742..878253dd 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -37,23 +37,24 @@ workflow SEQINSPECTOR {
     take:
     ch_samplesheet // channel: samplesheet read in from --input
     fasta_file
+    skip_tools
+    bwamem2
 
     main:
-    skip_tools = params.skip_tools ? params.skip_tools.split(',') : []
 
-    ch_versions = channel.empty()
-    ch_multiqc_files = channel.empty()
-    ch_multiqc_extra_files = channel.empty()
-    ch_bwamem2_mem = channel.empty()
-    ch_samtools_index = channel.empty()
-
-
-PREPARE_GENOME (
-        fasta_file,
-        params.bwa_index,
-        skip_tools,
-)
 
+    ch_versions            = channel.empty()
+    ch_multiqc_files       = channel.empty()
+    ch_multiqc_extra_files = channel.empty()
+    ch_bwamem2_mem         = channel.empty()
+    ch_samtools_index      = channel.empty()
+    ch_reference_fasta     = fasta_file? channel.fromPath(fasta_file, checkIfExists: true).map { file -> tuple([id: file.name], file) }.collect() : channel.value([[:], []])
+
+    PREPARE_GENOME (
+        ch_reference_fasta,
+        bwamem2,
+        skip_tools
+    )
 
     //
     // MODULE: Run Seqtk sample to perform subsampling
@@ -126,8 +127,6 @@ PREPARE_GENOME (
 
     // MODULE: Align reads with BWA-MEM2
     if (!("bwamem2_mem" in skip_tools)) {
-                ch_reference_fasta = channel.fromPath(fasta_file, checkIfExists: true).map { file -> tuple([id: file.name], file) }.collect()
-
         BWAMEM2_MEM(
             ch_sample_sized,
             PREPARE_GENOME.out.bwamem2_index,

From 505fa03be00ef7705db8513bf6ae4179e0e8c1c4 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 25 Nov 2025 14:28:55 +0100
Subject: [PATCH 410/530] Move picard_collectmultiplemetrics to QC_BAM.

---
 subworkflows/local/qc_bam/main.nf | 67 +++++++++++++++++++------------
 workflows/seqinspector.nf         | 42 ++++++-------------
 2 files changed, 53 insertions(+), 56 deletions(-)

diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf
index 2528da06..d47e2b8d 100644
--- a/subworkflows/local/qc_bam/main.nf
+++ b/subworkflows/local/qc_bam/main.nf
@@ -2,47 +2,62 @@
 // A quality check subworkflow for processed bam files.
 //
 
+include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../modules/nf-core/picard/collectmultiplemetrics/main'
 include { PICARD_COLLECTHSMETRICS } from '../../../modules/nf-core/picard/collecthsmetrics/main'
 include { PICARD_CREATESEQUENCEDICTIONARY } from '../../../modules/nf-core/picard/createsequencedictionary/main'
 
 workflow QC_BAM {
     take:
-        ch_bam_bai
-        ch_bait_intervals
-        ch_target_intervals
-        ch_reference_fasta
-        ch_reference_fasta_fai
-        ref_dict
+    ch_bam
+    ch_bai
+    ch_reference_fasta
+    ch_reference_fasta_fai
+    run_picard_collecthsmetrics
+    ch_bait_intervals
+    ch_target_intervals
+    ref_dict
 
     main:
 
     ch_versions = channel.empty()
 
-    ch_hsmetrics_in = ch_bam_bai
+    ch_bam_bai = ch_bam.join(ch_bai, failOnDuplicate: true, failOnMismatch: true)
+
+    PICARD_COLLECTMULTIPLEMETRICS(
+        ch_bam_bai,
+        ch_reference_fasta,
+        ch_reference_fasta_fai,
+    )
+
+    if (run_picard_collecthsmetrics) {
+
+        ch_hsmetrics_in = ch_bam_bai
             .combine(ch_bait_intervals)
             .combine(ch_target_intervals)
 
-    if (ref_dict) {
-        ch_ref_dict = channel.fromPath(ref_dict, checkIfExists: true).map { [[id: it.simpleName], it] }
-    }
-    else {
-        PICARD_CREATESEQUENCEDICTIONARY(
-            ch_reference_fasta
+        if (ref_dict) {
+            ch_ref_dict = channel.fromPath(ref_dict, checkIfExists: true).map { [[id: it.simpleName], it] }
+        }
+        else {
+            PICARD_CREATESEQUENCEDICTIONARY(
+                ch_reference_fasta
+            )
+            ch_ref_dict = PICARD_CREATESEQUENCEDICTIONARY.out.reference_dict
+            ch_versions = ch_versions.mix(PICARD_CREATESEQUENCEDICTIONARY.out.versions)
+        }
+
+        PICARD_COLLECTHSMETRICS(
+            ch_hsmetrics_in,
+            ch_reference_fasta,
+            ch_reference_fasta_fai,
+            ch_ref_dict,
+            [[], []],
         )
-        ch_ref_dict = PICARD_CREATESEQUENCEDICTIONARY.out.reference_dict
-        ch_versions = ch_versions.mix(PICARD_CREATESEQUENCEDICTIONARY.out.versions)
+        ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
     }
 
-    PICARD_COLLECTHSMETRICS(
-        ch_hsmetrics_in,
-        ch_reference_fasta,
-        ch_reference_fasta_fai,
-        ch_ref_dict,
-        [[], []],
-    )
-    ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
-
     emit:
-        hs_metrics = PICARD_COLLECTHSMETRICS.out.metrics
-        versions = ch_versions
+    multiplemetrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics
+    hs_metrics = PICARD_COLLECTHSMETRICS.out.metrics
+    versions = ch_versions
 }
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index b1815cf8..6206b4e4 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -177,31 +177,8 @@ workflow SEQINSPECTOR {
         ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions)
     }
 
-    // MODULE: Prepare BAM/BAI tuples for Picard
-    // Combine BAM and BAI outputs for Picard
-    if (!("picard_collectmultiplemetrics" in skip_tools) && !("bwamem2_mem" in skip_tools) && !("samtools_faidx" in skip_tools)) {
-
-        // Prepare BAM/BAI tuples for Picard
-        ch_bam_bai = ch_bwamem2_mem.join(ch_samtools_index, failOnDuplicate: true, failOnMismatch: true)
-
-        ch_bam_bai.view { "Combined BAM/BAI for Picard: ${it}" }
-        ch_fasta = ch_reference_fasta
-        ch_fai = ch_reference_fasta_fai
-
-        ch_fasta.view { "FASTA for Picard: ${it}" }
-        ch_fai.view { "FAI for Picard: ${it}" }
-
-        PICARD_COLLECTMULTIPLEMETRICS(
-            ch_bam_bai,
-            ch_fasta,
-            ch_fai,
-        )
-
-        ch_multiqc_files = ch_multiqc_files.mix(PICARD_COLLECTMULTIPLEMETRICS.out.metrics)
-        ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
-    }
 
-    if (params.run_picard_collecthsmetrics && !("picard_collectmultiplemetrics" in skip_tools)) {
+    if (!("picard_collectmultiplemetrics" in skip_tools) && !("bwamem2_mem" in skip_tools) && !("samtools_faidx" in skip_tools)) {
 
         ch_bait_intervals = channel.fromPath(params.bait_intervals)
             .collect()
@@ -211,18 +188,23 @@ workflow SEQINSPECTOR {
 
 
         QC_BAM(
-            ch_bam_bai,
-            ch_bait_intervals,
-            ch_target_intervals,
+            ch_bwamem2_mem,
+            ch_samtools_index,
             ch_reference_fasta,
             ch_reference_fasta_fai,
+            params.run_picard_collecthsmetrics,
+            ch_bait_intervals,
+            ch_target_intervals,
             params.ref_dict,
         )
 
-    ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.hs_metrics)
-    ch_versions = ch_versions.mix(QC_BAM.out.versions)
-    }
 
+        // ch_multiqc_files = ch_multiqc_files.mix(PICARD_COLLECTMULTIPLEMETRICS.out.metrics)
+        // ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
+
+        ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.hs_metrics) // Add check for collecthsmetrics
+        ch_versions = ch_versions.mix(QC_BAM.out.versions)
+    }
 
     // Collate and save software versions
     //

From bfa3cd380ad5906edc009cc40c2b6b7669ad0c27 Mon Sep 17 00:00:00 2001
From: Beatriz Vinhas <beatriz.sa.vinhas@gmail.com>
Date: Tue, 25 Nov 2025 14:32:50 +0100
Subject: [PATCH 411/530] Update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index ccafd513..1cf81ef1 100644
--- a/README.md
+++ b/README.md
@@ -46,7 +46,7 @@
 | `QC`                | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)                           | Basic contamination detection                                                                 | [RNA, DNA]              | [N/A]                           | yes          |
 | `QC`                | [`SeqFu Stats`](https://github.com/telatin/seqfu2)                                                          | Sequence statistics                                                                           | [RNA, DNA]              | [N/A]                           | yes          |
 | `QC`                | [`Picard collect multiple metrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html) | Collect multiple QC metrics                                                                   | [RNA, DNA]              | [Bwamem2, SAMtools, `--genome`] | yes          |
-| `QC`                | [`Picard_collecthsmetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard) | Collect alignment QC metrics of hybrid-selection data.                                | [RNA, DNA]              | [Bwamem2, SAMtools, `--fasta`, `--run_picard_collecths_metrics`, `--bait_intervals`, `--target_intervals` (`--ref_dict`)] | No |
+| `QC`                | [`Picard_collecthsmetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard) | Collect alignment QC metrics of hybrid-selection data.                                | [RNA, DNA]              | [Bwamem2, SAMtools, `--fasta`, `--run_picard_collecths_metrics`, `--bait_intervals`, `--target_intervals` (`--ref_dict`)] | no |
 | `Reporting`         | [`MultiQC`](http://multiqc.info/)                                                                           | Present QC for raw reads                                                                      | [RNA, DNA, synthetic]   | [N/A]                           | yes          |
 
 <picture>

From 509087f2c503c354d27fe731be8c378a8e9fbd38 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 25 Nov 2025 14:38:27 +0100
Subject: [PATCH 412/530] Fix output channels.

---
 subworkflows/local/qc_bam/main.nf | 9 +++++++--
 workflows/seqinspector.nf         | 6 +-----
 2 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf
index d47e2b8d..f8c054c4 100644
--- a/subworkflows/local/qc_bam/main.nf
+++ b/subworkflows/local/qc_bam/main.nf
@@ -19,6 +19,7 @@ workflow QC_BAM {
 
     main:
 
+    ch_metrics = channel.empty()
     ch_versions = channel.empty()
 
     ch_bam_bai = ch_bam.join(ch_bai, failOnDuplicate: true, failOnMismatch: true)
@@ -28,6 +29,9 @@ workflow QC_BAM {
         ch_reference_fasta,
         ch_reference_fasta_fai,
     )
+    
+    ch_metrics = ch_metrics.mix(PICARD_COLLECTMULTIPLEMETRICS.out.metrics)
+    ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
 
     if (run_picard_collecthsmetrics) {
 
@@ -53,11 +57,12 @@ workflow QC_BAM {
             ch_ref_dict,
             [[], []],
         )
+
+        ch_metrics = ch_metrics.mix(PICARD_COLLECTHSMETRICS.out.metrics)
         ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
     }
 
     emit:
-    multiplemetrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics
-    hs_metrics = PICARD_COLLECTHSMETRICS.out.metrics
+    metrics = ch_metrics
     versions = ch_versions
 }
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 6206b4e4..b41276cc 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -198,11 +198,7 @@ workflow SEQINSPECTOR {
             params.ref_dict,
         )
 
-
-        // ch_multiqc_files = ch_multiqc_files.mix(PICARD_COLLECTMULTIPLEMETRICS.out.metrics)
-        // ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
-
-        ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.hs_metrics) // Add check for collecthsmetrics
+        ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.metrics) // Add check for collecthsmetrics
         ch_versions = ch_versions.mix(QC_BAM.out.versions)
     }
 

From 92ad8a77b326bee70711c5b774a71666cc35266d Mon Sep 17 00:00:00 2001
From: Agrima Bhatt <163723002+agrima2010@users.noreply.github.com>
Date: Tue, 25 Nov 2025 13:40:24 +0000
Subject: [PATCH 413/530] Updated CHANGE LOG

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 73aba95b..b36f5f1d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -29,6 +29,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#127](https://github.com/nf-core/seqinspector/pull/127) Added alignment tools - bwamem2 - index and mem
 - [#128](https://github.com/nf-core/seqinspector/pull/128) Added Picard tools - Collect Multiple Mterics to collect QC metrics
 - [#132](https://github.com/nf-core/seqinspector/pull/132) Added a bwamem2 index params for faster output
+- [#151](https://github.com/nf-core/seqinspector/pull/151) Added a prepare_genome subworkflow to handle bwamem2 indexing
 
 ### `Fixed`
 

From 574649732737abb18da57fc919288fa521260a97 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 25 Nov 2025 14:49:09 +0100
Subject: [PATCH 414/530] Fix linting issues.

---
 .github/workflows/linting.yml | 6 +++---
 ro-crate-metadata.json        | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 7a527a34..30e66026 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -11,7 +11,7 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
 
       - name: Set up Python 3.14
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
@@ -28,7 +28,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
@@ -71,7 +71,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
         with:
           name: linting-logs
           path: |
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 787b2cb5..6c11aa0b 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -23,7 +23,7 @@
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
             "datePublished": "2025-11-24T14:37:12+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->\n\n1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))\n2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n3. Align reads to reference with ([`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2))\n4. Index aligned BAM files ([`SAMtools`](http://github.com/samtools))\n5. Create FASTA index ([`SAMtools`](http://github.com/samtools))\n6. Collect multiple QC metrics ([`Picard CollectMultipleMetrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html))\n7. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n<picture>\n  <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n  <source media=\"(prefers-color-scheme: light)\" srcset=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  <img alt=\"Fallback image description\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n</picture>\n\n<picture>\n  <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nfcore-seqinspector-logo-hex-dark.png\">\n  <source media=\"(prefers-color-scheme: light)\" srcset=\"docs/images/nfcore-seqinspector-logo-hex-light.png\">\n  <img alt=\"Fallback image description\" src=\"docs/images/nfcore-seqinspector-logo-hex-light.png\">\n</picture>\n\n**nf-core/seqinspector** is a bioinformatics pipeline that that processes raw sequence data (FASTQ) to provide comprehensive quality control. It can perform subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants. The pipeline generates detailed MultiQC reports with flexible output options, ranging from individual sample reports to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments. If provided, nf-core/seqinspector can also parse statistics from an Illumina run folder directory into the final MultiQC reports.\n\n<!-- TODO: add a search tool that accepts a tree for `Compatibility with Data`. -->\n\n| Tool Type           | Tool Name                                                                                                   | Tool Description                                                                              | Compatibility with Data | Dependencies                    | Default tool |\n| ------------------- | ----------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------- | ----------------------- | ------------------------------- | ------------ |\n| `Subsampling`       | [`Seqtk`](https://github.com/lh3/seqtk)                                                                     | Global subsampling of reads. Only performs subsampling if `--sample_size` parameter is given. | [RNA, DNA, synthetic]   | [N/A]                           | no           |\n| `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2)                                                           | Align reads to reference                                                                      | [RNA, DNA]              | [N/A]                           | yes          |\n| `Indexing`          | [`SAMtools`](http://github.com/samtools)                                                                    | Index aligned BAM files, create FASTA index                                                   | [DNA]                   | [N/A]                           | yes          |\n| `QC`                | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)                                      | Read QC                                                                                       | [RNA, DNA]              | [N/A]                           | yes          |\n| `QC`                | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)                           | Basic contamination detection                                                                 | [RNA, DNA]              | [N/A]                           | yes          |\n| `QC`                | [`SeqFu Stats`](https://github.com/telatin/seqfu2)                                                          | Sequence statistics                                                                           | [RNA, DNA]              | [N/A]                           | yes          |\n| `QC`                | [`Picard collect multiple metrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html) | Collect multiple QC metrics                                                                   | [RNA, DNA]              | [Bwamem2, SAMtools, `--genome`] | yes          |\n| `QC`                | [`Picard_collecthsmetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard) | Collect alignment QC metrics of hybrid-selection data.                                | [RNA, DNA]              | [Bwamem2, SAMtools, `--fasta`, `--run_picard_collecths_metrics`, `--bait_intervals`, `--target_intervals` (`--ref_dict`)] | no |\n| `Reporting`         | [`MultiQC`](http://multiqc.info/)                                                                           | Present QC for raw reads                                                                      | [RNA, DNA, synthetic]   | [N/A]                           | yes          |\n\n<picture>\n  <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/seqinspector_tubemap_V1.0_dark.png\">\n  <source media=\"(prefers-color-scheme: light)\" srcset=\"docs/images/seqinspector_tubemap_V1.0.png\">\n  <img alt=\"Fallback image description\" src=\"docs/images/seqinspector_tubemap_V1.0.png\">\n</picture>\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/) and [Clinical Genomics Stockholm](https://clinical.scilifelab.se/).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
                     "@id": "main.nf"

From e8e43bdd698f30cc3c9fd4a6d05308e3bdeefe48 Mon Sep 17 00:00:00 2001
From: Beatriz Vinhas <beatriz.sa.vinhas@gmail.com>
Date: Tue, 25 Nov 2025 14:59:45 +0100
Subject: [PATCH 415/530] Update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 040f7eba..5beeaa51 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -29,7 +29,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#127](https://github.com/nf-core/seqinspector/pull/127) Added alignment tools - bwamem2 - index and mem
 - [#128](https://github.com/nf-core/seqinspector/pull/128) Added Picard tools - Collect Multiple Mterics to collect QC metrics
 - [#132](https://github.com/nf-core/seqinspector/pull/132) Added a bwamem2 index params for faster output
-- [#154](https://github.com/nf-core/seqinspector/pull/154) Added a subworkflow QC_BAM including picard_collecthsmetrics for alignment QC of hybrid-selection data
+- [#159](https://github.com/nf-core/seqinspector/pull/159) Added a subworkflow QC_BAM including picard_collecthsmetrics for alignment QC of hybrid-selection data
 
 ### `Fixed`
 

From 19768f750bd873ffb801ab3e288498ccb6054243 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 25 Nov 2025 15:40:54 +0100
Subject: [PATCH 416/530] Update seqinspector.nf

---
 workflows/seqinspector.nf | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 0ce1e868..bb4c4117 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -50,7 +50,6 @@ workflow SEQINSPECTOR {
     ch_bwamem2_mem         = channel.empty()
     ch_samtools_index      = channel.empty()
     ch_reference_fasta     = fasta_file? channel.fromPath(fasta_file, checkIfExists: true).map { file -> tuple([id: file.name], file) }.collect() : channel.value([[:], []])
-    ch_ref_dict = channel.empty()
 
     PREPARE_GENOME (
         ch_reference_fasta,
@@ -179,7 +178,7 @@ workflow SEQINSPECTOR {
             ch_bait_intervals,
             ch_target_intervals,
             ch_reference_fasta,
-            ch_reference_fasta_fai,
+            ch_fai,
             params.ref_dict,
         )
 

From 42a8ff599271249624900d1f915e5901bc25dae4 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 25 Nov 2025 15:43:03 +0100
Subject: [PATCH 417/530] Fix linting erros.

---
 .github/workflows/linting.yml | 6 +++---
 ro-crate-metadata.json        | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 7a527a34..30e66026 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -11,7 +11,7 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
 
       - name: Set up Python 3.14
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
@@ -28,7 +28,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
@@ -71,7 +71,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
         with:
           name: linting-logs
           path: |
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 787b2cb5..6c11aa0b 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -23,7 +23,7 @@
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
             "datePublished": "2025-11-24T14:37:12+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->\n\n1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))\n2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n3. Align reads to reference with ([`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2))\n4. Index aligned BAM files ([`SAMtools`](http://github.com/samtools))\n5. Create FASTA index ([`SAMtools`](http://github.com/samtools))\n6. Collect multiple QC metrics ([`Picard CollectMultipleMetrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html))\n7. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n<picture>\n  <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n  <source media=\"(prefers-color-scheme: light)\" srcset=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  <img alt=\"Fallback image description\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n</picture>\n\n<picture>\n  <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nfcore-seqinspector-logo-hex-dark.png\">\n  <source media=\"(prefers-color-scheme: light)\" srcset=\"docs/images/nfcore-seqinspector-logo-hex-light.png\">\n  <img alt=\"Fallback image description\" src=\"docs/images/nfcore-seqinspector-logo-hex-light.png\">\n</picture>\n\n**nf-core/seqinspector** is a bioinformatics pipeline that that processes raw sequence data (FASTQ) to provide comprehensive quality control. It can perform subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants. The pipeline generates detailed MultiQC reports with flexible output options, ranging from individual sample reports to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments. If provided, nf-core/seqinspector can also parse statistics from an Illumina run folder directory into the final MultiQC reports.\n\n<!-- TODO: add a search tool that accepts a tree for `Compatibility with Data`. -->\n\n| Tool Type           | Tool Name                                                                                                   | Tool Description                                                                              | Compatibility with Data | Dependencies                    | Default tool |\n| ------------------- | ----------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------- | ----------------------- | ------------------------------- | ------------ |\n| `Subsampling`       | [`Seqtk`](https://github.com/lh3/seqtk)                                                                     | Global subsampling of reads. Only performs subsampling if `--sample_size` parameter is given. | [RNA, DNA, synthetic]   | [N/A]                           | no           |\n| `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2)                                                           | Align reads to reference                                                                      | [RNA, DNA]              | [N/A]                           | yes          |\n| `Indexing`          | [`SAMtools`](http://github.com/samtools)                                                                    | Index aligned BAM files, create FASTA index                                                   | [DNA]                   | [N/A]                           | yes          |\n| `QC`                | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)                                      | Read QC                                                                                       | [RNA, DNA]              | [N/A]                           | yes          |\n| `QC`                | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)                           | Basic contamination detection                                                                 | [RNA, DNA]              | [N/A]                           | yes          |\n| `QC`                | [`SeqFu Stats`](https://github.com/telatin/seqfu2)                                                          | Sequence statistics                                                                           | [RNA, DNA]              | [N/A]                           | yes          |\n| `QC`                | [`Picard collect multiple metrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html) | Collect multiple QC metrics                                                                   | [RNA, DNA]              | [Bwamem2, SAMtools, `--genome`] | yes          |\n| `QC`                | [`Picard_collecthsmetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard) | Collect alignment QC metrics of hybrid-selection data.                                | [RNA, DNA]              | [Bwamem2, SAMtools, `--fasta`, `--run_picard_collecths_metrics`, `--bait_intervals`, `--target_intervals` (`--ref_dict`)] | no |\n| `Reporting`         | [`MultiQC`](http://multiqc.info/)                                                                           | Present QC for raw reads                                                                      | [RNA, DNA, synthetic]   | [N/A]                           | yes          |\n\n<picture>\n  <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/seqinspector_tubemap_V1.0_dark.png\">\n  <source media=\"(prefers-color-scheme: light)\" srcset=\"docs/images/seqinspector_tubemap_V1.0.png\">\n  <img alt=\"Fallback image description\" src=\"docs/images/seqinspector_tubemap_V1.0.png\">\n</picture>\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/) and [Clinical Genomics Stockholm](https://clinical.scilifelab.se/).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
                     "@id": "main.nf"

From bc0edf94000c7ec7c7f9f5888d5fb4d2cf7231f1 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 25 Nov 2025 16:04:02 +0100
Subject: [PATCH 418/530] Fix test snap generation.

---
 subworkflows/local/qc_bam/tests/main.nf.test  |  9 ++-
 .../local/qc_bam/tests/main.nf.test.snap      | 55 +++----------------
 2 files changed, 16 insertions(+), 48 deletions(-)

diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test
index 4fc86de5..b7445c58 100644
--- a/subworkflows/local/qc_bam/tests/main.nf.test
+++ b/subworkflows/local/qc_bam/tests/main.nf.test
@@ -36,7 +36,14 @@ nextflow_workflow {
 
         then {
             assert workflow.success
-            assert snapshot(workflow.out).match()
+            assert snapshot(
+                            workflow.out.hs_metrics
+                                .collect {it[1]}
+                                .flatten()
+                                .collect { file(it).name }
+                                .toSorted(),
+                            workflow.out.versions
+                            ).match()
         }
 
     }
diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap
index 2c9323c1..d640a65b 100644
--- a/subworkflows/local/qc_bam/tests/main.nf.test.snap
+++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap
@@ -1,57 +1,18 @@
 {
     "Should run without failures": {
         "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "earlycasualcaiman",
-                            "sample": "earlycasualcaiman",
-                            "single_end": false,
-                            "num_lanes": 1,
-                            "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'",
-                            "lane": 1,
-                            "sex": 1,
-                            "phenotype": 1,
-                            "paternal": 0,
-                            "maternal": 0,
-                            "case_id": "justhusky"
-                        },
-                        "earlycasualcaiman.CollectHsMetrics.coverage_metrics:md5,038240391cd0e8c529282d48f8fc6ced"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,40396221974da20b7f066d5fab9ffb3a",
-                    "versions.yml:md5,8508bd28eaf1fffcdc4d78e4d9f95393"
-                ],
-                "hs_metrics": [
-                    [
-                        {
-                            "id": "earlycasualcaiman",
-                            "sample": "earlycasualcaiman",
-                            "single_end": false,
-                            "num_lanes": 1,
-                            "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'",
-                            "lane": 1,
-                            "sex": 1,
-                            "phenotype": 1,
-                            "paternal": 0,
-                            "maternal": 0,
-                            "case_id": "justhusky"
-                        },
-                        "earlycasualcaiman.CollectHsMetrics.coverage_metrics:md5,038240391cd0e8c529282d48f8fc6ced"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,40396221974da20b7f066d5fab9ffb3a",
-                    "versions.yml:md5,8508bd28eaf1fffcdc4d78e4d9f95393"
-                ]
-            }
+            [
+                "earlycasualcaiman.CollectHsMetrics.coverage_metrics"
+            ],
+            [
+                "versions.yml:md5,40396221974da20b7f066d5fab9ffb3a",
+                "versions.yml:md5,8508bd28eaf1fffcdc4d78e4d9f95393"
+            ]
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-25T11:24:54.058046"
+        "timestamp": "2025-11-25T15:58:16.830793"
     }
 }
\ No newline at end of file

From 544440288271b5432870c1d71e59352a52a9d23c Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Wed, 26 Nov 2025 11:44:54 +0100
Subject: [PATCH 419/530] Fix linting issues.

---
 .github/workflows/linting.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 30e66026..7a527a34 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -11,7 +11,7 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Set up Python 3.14
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
@@ -28,7 +28,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
@@ -71,7 +71,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: linting-logs
           path: |

From a4f26662a907bfedf56c963c4d19fe20b4ad6642 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Wed, 26 Nov 2025 11:54:31 +0100
Subject: [PATCH 420/530] Run prettier and remove trailing whitespace.

---
 README.md                                     | 22 +++++++++----------
 docs/output.md                                |  3 +--
 nextflow.config                               |  2 +-
 .../local/qc_bam/tests/nextflow.config        |  2 +-
 4 files changed, 14 insertions(+), 15 deletions(-)

diff --git a/README.md b/README.md
index 1cf81ef1..31f97a8a 100644
--- a/README.md
+++ b/README.md
@@ -37,17 +37,17 @@
 
 <!-- TODO: add a search tool that accepts a tree for `Compatibility with Data`. -->
 
-| Tool Type           | Tool Name                                                                                                   | Tool Description                                                                              | Compatibility with Data | Dependencies                    | Default tool |
-| ------------------- | ----------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------- | ----------------------- | ------------------------------- | ------------ |
-| `Subsampling`       | [`Seqtk`](https://github.com/lh3/seqtk)                                                                     | Global subsampling of reads. Only performs subsampling if `--sample_size` parameter is given. | [RNA, DNA, synthetic]   | [N/A]                           | no           |
-| `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2)                                                           | Align reads to reference                                                                      | [RNA, DNA]              | [N/A]                           | yes          |
-| `Indexing`          | [`SAMtools`](http://github.com/samtools)                                                                    | Index aligned BAM files, create FASTA index                                                   | [DNA]                   | [N/A]                           | yes          |
-| `QC`                | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)                                      | Read QC                                                                                       | [RNA, DNA]              | [N/A]                           | yes          |
-| `QC`                | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)                           | Basic contamination detection                                                                 | [RNA, DNA]              | [N/A]                           | yes          |
-| `QC`                | [`SeqFu Stats`](https://github.com/telatin/seqfu2)                                                          | Sequence statistics                                                                           | [RNA, DNA]              | [N/A]                           | yes          |
-| `QC`                | [`Picard collect multiple metrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html) | Collect multiple QC metrics                                                                   | [RNA, DNA]              | [Bwamem2, SAMtools, `--genome`] | yes          |
-| `QC`                | [`Picard_collecthsmetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard) | Collect alignment QC metrics of hybrid-selection data.                                | [RNA, DNA]              | [Bwamem2, SAMtools, `--fasta`, `--run_picard_collecths_metrics`, `--bait_intervals`, `--target_intervals` (`--ref_dict`)] | no |
-| `Reporting`         | [`MultiQC`](http://multiqc.info/)                                                                           | Present QC for raw reads                                                                      | [RNA, DNA, synthetic]   | [N/A]                           | yes          |
+| Tool Type           | Tool Name                                                                                                           | Tool Description                                                                              | Compatibility with Data | Dependencies                                                                                                              | Default tool |
+| ------------------- | ------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------- | ----------------------- | ------------------------------------------------------------------------------------------------------------------------- | ------------ |
+| `Subsampling`       | [`Seqtk`](https://github.com/lh3/seqtk)                                                                             | Global subsampling of reads. Only performs subsampling if `--sample_size` parameter is given. | [RNA, DNA, synthetic]   | [N/A]                                                                                                                     | no           |
+| `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2)                                                                   | Align reads to reference                                                                      | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |
+| `Indexing`          | [`SAMtools`](http://github.com/samtools)                                                                            | Index aligned BAM files, create FASTA index                                                   | [DNA]                   | [N/A]                                                                                                                     | yes          |
+| `QC`                | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)                                              | Read QC                                                                                       | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |
+| `QC`                | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)                                   | Basic contamination detection                                                                 | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |
+| `QC`                | [`SeqFu Stats`](https://github.com/telatin/seqfu2)                                                                  | Sequence statistics                                                                           | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |
+| `QC`                | [`Picard collect multiple metrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html)         | Collect multiple QC metrics                                                                   | [RNA, DNA]              | [Bwamem2, SAMtools, `--genome`]                                                                                           | yes          |
+| `QC`                | [`Picard_collecthsmetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard) | Collect alignment QC metrics of hybrid-selection data.                                        | [RNA, DNA]              | [Bwamem2, SAMtools, `--fasta`, `--run_picard_collecths_metrics`, `--bait_intervals`, `--target_intervals` (`--ref_dict`)] | no           |
+| `Reporting`         | [`MultiQC`](http://multiqc.info/)                                                                                   | Present QC for raw reads                                                                      | [RNA, DNA, synthetic]   | [N/A]                                                                                                                     | yes          |
 
 <picture>
   <source media="(prefers-color-scheme: dark)" srcset="docs/images/seqinspector_tubemap_V1.0_dark.png">
diff --git a/docs/output.md b/docs/output.md
index 43e04d02..8f4a7f55 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -80,7 +80,6 @@ The `.csv` is provided as a pipeline parameter `fastq_screen_references` and is
 
 [SeqFu](https://telatin.github.io/seqfu2/) is general-purpose program to manipulate and parse information from FASTA/FASTQ files, supporting gzipped input files. Includes functions to interleave and de-interleave FASTQ files, to rename sequences and to count and print statistics on sequence lengths. In this pipeline, the `seqfu stats` module is used to produce general quality metrics statistics.
 
-
 ### Picard CollectHSmetrics
 
 <details markdown="1">
@@ -88,7 +87,7 @@ The `.csv` is provided as a pipeline parameter `fastq_screen_references` and is
 
 - `picard_collecthsmetrics/`
   - `*.coverage_metrics`: Tab-separated file containing quality metrics for hybrid-selection data.
- 
+
 </details>
 
 [Picard_collecthsmetrics](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard) is a tool to collect metrics on the aligment SAM/BAM files that are specific for sequence datasets generated through hybrid-selection (mostly used to capture exon-specific sequences for targeted sequencing).
diff --git a/nextflow.config b/nextflow.config
index c94c7075..d0215097 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -278,4 +278,4 @@ validation {
 }
 
 // Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'
+includeConfig 'conf/modules.config'
\ No newline at end of file
diff --git a/subworkflows/local/qc_bam/tests/nextflow.config b/subworkflows/local/qc_bam/tests/nextflow.config
index 345dcdab..8fe4d673 100644
--- a/subworkflows/local/qc_bam/tests/nextflow.config
+++ b/subworkflows/local/qc_bam/tests/nextflow.config
@@ -9,4 +9,4 @@ process {
 
     }
 
-}
+}
\ No newline at end of file

From b0bb6aec7dcdd01ac2f86a2f82676af34b9caa9c Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Wed, 26 Nov 2025 11:58:03 +0100
Subject: [PATCH 421/530] Fix end of files.

---
 nextflow.config                                 | 2 +-
 subworkflows/local/qc_bam/tests/nextflow.config | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index d0215097..c94c7075 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -278,4 +278,4 @@ validation {
 }
 
 // Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'
\ No newline at end of file
+includeConfig 'conf/modules.config'
diff --git a/subworkflows/local/qc_bam/tests/nextflow.config b/subworkflows/local/qc_bam/tests/nextflow.config
index 8fe4d673..345dcdab 100644
--- a/subworkflows/local/qc_bam/tests/nextflow.config
+++ b/subworkflows/local/qc_bam/tests/nextflow.config
@@ -9,4 +9,4 @@ process {
 
     }
 
-}
\ No newline at end of file
+}

From 837023851610366c25ee59fe246a875f54ab1f46 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Wed, 26 Nov 2025 12:00:22 +0100
Subject: [PATCH 422/530] Remove cg_test config.

---
 nextflow.config | 1 -
 1 file changed, 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index c94c7075..337107af 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -180,7 +180,6 @@ profiles {
     }
     test      { includeConfig 'conf/test.config'      }
     test_full { includeConfig 'conf/test_full.config' }
-    test_cg   { includeConfig 'conf/cg_test.config'   }
 }
 
 // Load nf-core custom profiles from different institutions

From ab4ff6d39d0e0f1c5dbe44f1682339243a6441bb Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Wed, 26 Nov 2025 12:02:25 +0100
Subject: [PATCH 423/530] Trim trailing whitespace.

---
 nextflow.config                                 | 2 +-
 subworkflows/local/qc_bam/tests/nextflow.config | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 337107af..2eb80faf 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -59,7 +59,7 @@ params {
     custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
     config_profile_contact     = null
     config_profile_url         = null
-    
+
 
     // Schema validation default options
     validate_params            = true
diff --git a/subworkflows/local/qc_bam/tests/nextflow.config b/subworkflows/local/qc_bam/tests/nextflow.config
index 345dcdab..4a732a6c 100644
--- a/subworkflows/local/qc_bam/tests/nextflow.config
+++ b/subworkflows/local/qc_bam/tests/nextflow.config
@@ -1,5 +1,5 @@
 process {
-    
+
     withName: PICARD_COLLECTHSMETRICS {
         ext.args = { [
             "--COVERAGE_CAP 50000",

From 10f30df76010e8978b745ae3a9f2eb2c01237aba Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Wed, 26 Nov 2025 12:20:33 +0100
Subject: [PATCH 424/530] Remove picard_collecthsmetrics from skip_tools as it
 is not run by default.

---
 nextflow_schema.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 5d8b53f1..1da12633 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -50,7 +50,7 @@
                 "skip_tools": {
                     "type": "string",
                     "description": "Comma-separated string of tools to skip",
-                    "pattern": "^((fastqc|fastqscreen|seqfu_stats|seqtk_sample|bwamem2_index|bwamem2_mem|picard_collectmultiplemetrics|samtools_faidx|picard_collecthsmetrics)?,?)*(?<!,)$"
+                    "pattern": "^((fastqc|fastqscreen|seqfu_stats|seqtk_sample|bwamem2_index|bwamem2_mem|picard_collectmultiplemetrics|samtools_faidx)?,?)*(?<!,)$"
                 }
             }
         },

From 3b454659d9246a3306429978f0f728b3923ed1f1 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Wed, 26 Nov 2025 12:22:02 +0100
Subject: [PATCH 425/530] Update usage.md.

---
 docs/usage.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/usage.md b/docs/usage.md
index c79fd250..49112a6f 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -104,7 +104,7 @@ Optionally, the `sample_size` parameter allows you to subset a random number of
 nextflow run nf-core/seqinspector --input ./samplesheet.csv --outdir ./results --sample_size 1000000 -profile docker
 ```
 
-The pipeline support hybrid-selection data, use the flag `--run_picard_collecthsmetrics` if you want to run the QC tool [picard CollectHSmetrics](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard). This tool is not run by default.
+The pipeline supports hybrid-selection data, use the flag `--run_picard_collecthsmetrics true` if you want to run the QC tool [picard CollectHSmetrics](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard). This tool is not run by default.
 
 ### Skipping tools
 

From 566e4c9564c71c4692942a35b38063a90182c059 Mon Sep 17 00:00:00 2001
From: nelnk861 <nelly.nkonge@uu.se>
Date: Tue, 25 Nov 2025 12:08:42 +0100
Subject: [PATCH 426/530] Seqtk add relative sample sets and warning

Co-authored-by: Tori Giffin <victoria.giffin@uu.se>
Co-authored-by: Jonas Kjellin <jonas.kjellin@uu.se>
---
 CHANGELOG.md                                  |   1 +
 docs/usage.md                                 |   2 +-
 nextflow_schema.json                          |   7 +-
 tests/NovaSeq6000.main_subsample.nf.test      |  60 +-
 tests/NovaSeq6000.main_subsample.nf.test.snap | 538 ++++++++++++++++++
 workflows/seqinspector.nf                     |  17 +-
 6 files changed, 618 insertions(+), 7 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b36f5f1d..aea3f0f3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -30,6 +30,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#128](https://github.com/nf-core/seqinspector/pull/128) Added Picard tools - Collect Multiple Mterics to collect QC metrics
 - [#132](https://github.com/nf-core/seqinspector/pull/132) Added a bwamem2 index params for faster output
 - [#151](https://github.com/nf-core/seqinspector/pull/151) Added a prepare_genome subworkflow to handle bwamem2 indexing
+- [#156](https://github.com/nf-core/seqinspector/pull/156) Added relative sample_size and warning when a sample has less reads than desired sample_size.
 
 ### `Fixed`
 
diff --git a/docs/usage.md b/docs/usage.md
index a077e648..f826d5db 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -98,7 +98,7 @@ genome: 'GRCh37'
 
 You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch).
 
-Optionally, the `sample_size` parameter allows you to subset a random number of reads to be analysed. Note that it refers to an absolute number.
+Optionally, the `sample_size` parameter allows you to subset a random number of reads to be analysed. Both absolute numbers (e.g 100) and relative numbers (e.g 0.25) can be specified.
 
 ```bash
 nextflow run nf-core/seqinspector --input ./samplesheet.csv --outdir ./results --sample_size 1000000 -profile docker
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 2b926578..fae7a32a 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -24,14 +24,13 @@
                     "fa_icon": "fas fa-file-csv"
                 },
                 "sample_size": {
-                    "type": "integer",
-                    "description": "Take this number of reads as a subset.",
-                    "help_text": "Choose the size of the subset or 0, if no subsampling shall be performed. Note that it refers to an absolute number.",
+                    "type": "number",
+                    "description": "Take a subset of reads for analysis.",
+                    "help_text": "Subset can be used as a fraction of reads (ex/ 0.20) or an absolute number of reads per sample (integer). Pipeline will still run if a sample has less reads than selected subset value.",
                     "default": 0
                 },
                 "outdir": {
                     "type": "string",
-                    "default": null,
                     "format": "directory-path",
                     "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
                     "fa_icon": "fas fa-folder-open"
diff --git a/tests/NovaSeq6000.main_subsample.nf.test b/tests/NovaSeq6000.main_subsample.nf.test
index a62e4411..f158d226 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test
+++ b/tests/NovaSeq6000.main_subsample.nf.test
@@ -1,6 +1,6 @@
 nextflow_pipeline {
 
-    name "Test Workflow main.nf on NovaSeq6000 data sample size 90"
+    name "Test Workflow main.nf on NovaSeq6000 data with different sample sizes"
     script "../main.nf"
     tag "seqinspector"
     tag "PIPELINE"
@@ -38,4 +38,62 @@ nextflow_pipeline {
             )
         }
     }
+    test("NovaSeq6000 data test relative sample size") {
+        config """
+        process {
+            sample_size = 0.9
+        }
+        """
+        when {
+            config "./NovaSeq6000.main_subsample.nf.test.config"
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(
+                params.outdir,
+                relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']
+            )
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(
+                params.outdir,
+                ignoreFile: 'tests/.nftignore'
+            )
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
+                    // All stable path names, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+    test("NovaSeq6000 data test sample size exceeds") {
+        config """
+        process {
+            sample_size = 120
+        }
+        """
+        when {
+            config "./NovaSeq6000.main_subsample.nf.test.config"
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assert path(".nextflow.log").text.contains("Warning: Requested sample_size (120) is larger than available reads in Undetermined_5 (100). Pipeline will continue with 100 reads.")
+            assert path(".nextflow.log").text.contains("Warning: Requested sample_size (120) is larger than available reads in SampleA_2 (100). Pipeline will continue with 100 reads.")
+            assert path(".nextflow.log").text.contains("Warning: Requested sample_size (120) is larger than available reads in sampletest_4 (100). Pipeline will continue with 100 reads.")
+            assert path(".nextflow.log").text.contains("Warning: Requested sample_size (120) is larger than available reads in Sample23_3 (100). Pipeline will continue with 100 reads.")
+            assert path(".nextflow.log").text.contains("Warning: Requested sample_size (120) is larger than available reads in Sample1_1 (100). Pipeline will continue with 100 reads.")
+        }
+    }
 }
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index 1d061216..e0e7b276 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -536,5 +536,543 @@
             "nextflow": "25.10.0"
         },
         "timestamp": "2025-11-25T13:20:06.917144477"
+    },
+    "NovaSeq6000 data test relative sample size": {
+        "content": [
+            {
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "FASTQSCREEN_FASTQSCREEN": {
+                    "fastqscreen": "0.16.0"
+                },
+                "SEQFU_STATS": {
+                    "seqfu": "1.22.3"
+                },
+                "SEQTK_SAMPLE": {
+                    "seqtk": "1.4-r122"
+                },
+                "Workflow": {
+                    "nf-core/seqinspector": "v1.0dev"
+                }
+            },
+            [
+                "fastqc",
+                "fastqc/Sample1_1_fastqc.html",
+                "fastqc/Sample1_1_fastqc.zip",
+                "fastqc/Sample23_3_fastqc.html",
+                "fastqc/Sample23_3_fastqc.zip",
+                "fastqc/SampleA_2_fastqc.html",
+                "fastqc/SampleA_2_fastqc.zip",
+                "fastqc/Undetermined_5_fastqc.html",
+                "fastqc/Undetermined_5_fastqc.zip",
+                "fastqc/sampletest_4_fastqc.html",
+                "fastqc/sampletest_4_fastqc.zip",
+                "fastqscreen",
+                "fastqscreen/Sample1_1_screen.html",
+                "fastqscreen/Sample1_1_screen.png",
+                "fastqscreen/Sample1_1_screen.txt",
+                "fastqscreen/Sample23_3_screen.html",
+                "fastqscreen/Sample23_3_screen.png",
+                "fastqscreen/Sample23_3_screen.txt",
+                "fastqscreen/SampleA_2_screen.html",
+                "fastqscreen/SampleA_2_screen.png",
+                "fastqscreen/SampleA_2_screen.txt",
+                "fastqscreen/Undetermined_5_screen.html",
+                "fastqscreen/Undetermined_5_screen.png",
+                "fastqscreen/Undetermined_5_screen.txt",
+                "fastqscreen/sampletest_4_screen.html",
+                "fastqscreen/sampletest_4_screen.png",
+                "fastqscreen/sampletest_4_screen.txt",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/global_report/multiqc_data/llms-full.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc.parquet",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_plots",
+                "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
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+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/seqfu.svg",
+                "multiqc/group_reports/lane1/multiqc_report.html",
+                "multiqc/group_reports/test",
+                "multiqc/group_reports/test/multiqc_data",
+                "multiqc/group_reports/test/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/group_reports/test/multiqc_data/llms-full.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc.log",
+                "multiqc/group_reports/test/multiqc_data/multiqc.parquet",
+                "multiqc/group_reports/test/multiqc_data/multiqc_citations.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_data.json",
+                "multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/test/multiqc_plots",
+                "multiqc/group_reports/test/multiqc_plots/pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/group_reports/test/multiqc_plots/png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/test/multiqc_plots/png/seqfu.png",
+                "multiqc/group_reports/test/multiqc_plots/svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/seqfu.svg",
+                "multiqc/group_reports/test/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "seqfu_stats",
+                "seqfu_stats/Sample1_1_seqfu.tsv",
+                "seqfu_stats/Sample1_1_seqfu_mqc.txt",
+                "seqfu_stats/Sample23_3_seqfu.tsv",
+                "seqfu_stats/Sample23_3_seqfu_mqc.txt",
+                "seqfu_stats/SampleA_2_seqfu.tsv",
+                "seqfu_stats/SampleA_2_seqfu_mqc.txt",
+                "seqfu_stats/Undetermined_5_seqfu.tsv",
+                "seqfu_stats/Undetermined_5_seqfu_mqc.txt",
+                "seqfu_stats/sampletest_4_seqfu.tsv",
+                "seqfu_stats/sampletest_4_seqfu_mqc.txt",
+                "seqtk",
+                "seqtk/Sample1_1_Sample1_S1_L001_R1_001.fastq.gz",
+                "seqtk/Sample23_3_Sample23_S3_L001_R1_001.fastq.gz",
+                "seqtk/SampleA_2_SampleA_S2_L001_R1_001.fastq.gz",
+                "seqtk/Undetermined_5_Undetermined_S0_L001_R1_001.fastq.gz",
+                "seqtk/sampletest_4_sampletest_S4_L001_R1_001.fastq.gz"
+            ],
+            [
+                "Sample1_1_screen.png:md5,562256290643b51e4374c2225a15f463",
+                "Sample1_1_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "Sample23_3_screen.png:md5,6bb2caf67b9b2ed25d3d5f32c343e9ab",
+                "Sample23_3_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "SampleA_2_screen.png:md5,b2c3e95e034f5c038754bf108537de0e",
+                "SampleA_2_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "Undetermined_5_screen.png:md5,fc5d53f8876dfae3d1a781fa512ea1db",
+                "Undetermined_5_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "sampletest_4_screen.png:md5,1fb60070e8f4b70de0c1b3786b54f27e",
+                "sampletest_4_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "fastq_screen_plot.txt:md5,562b783630f698c3220c951b73b87027",
+                "fastqc-status-check-heatmap.txt:md5,84794d045dc6d91b00e59985bae9d18a",
+                "fastqc_overrepresented_sequences_plot.txt:md5,d3a313b6f85d0b22c208993756377d65",
+                "fastqc_per_base_n_content_plot.txt:md5,cd0bf31027a6ea439d04e41210ad6ad3",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,e638d555775524607da7faae21db0bb1",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,47a9839f6967ce2a959e1a8df21b5f4b",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,b7497095d3965a85146630c21b8bcd0a",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,ce03c524ec936430547e4d44b02f8678",
+                "fastqc_sequence_counts_plot.txt:md5,dc100186e03f28e75659600ef0a3a828",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,2a7d356a86612a7681ffdee6a0baff9a",
+                "fastqc_sequence_length_distribution_plot.txt:md5,d1c8835f262e4b84ce77590f27b9dc2f",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
+                "multiqc_fastqc.txt:md5,c2d5ec1b75cee83a083434e9ba8be91e",
+                "multiqc_seqfu.txt:md5,18dd2407d4a1791646785123028f69b5",
+                "fastq_screen_plot.txt:md5,c25d34568f10f131156294d31fbfa994",
+                "fastqc-status-check-heatmap.txt:md5,7ee494f345c09706513e65907788de02",
+                "fastqc_overrepresented_sequences_plot.txt:md5,8a1c4d43aa773be8eda518d400fc5685",
+                "fastqc_per_base_n_content_plot.txt:md5,ac20a2afd4aeb98001f0586877e5333b",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,79586819fd1b4a42dafdd900bf721c57",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,c6cb5819719aaf6446b7d71b994cd858",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,6791cbb7232e6b43c41f071c4bf2be6e",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,f7229cbdebdd57d9f3fe55e84cd63308",
+                "fastqc_sequence_counts_plot.txt:md5,40168c9baa340caf96a16a9a48c74b10",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,e37e8e4584f0157a5fa0d53b4834e836",
+                "fastqc_sequence_length_distribution_plot.txt:md5,6a7b2d7efe8598072636fb7215ea51f7",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
+                "multiqc_fastqc.txt:md5,3275fb3409d73a36aa87f672db60fc96",
+                "multiqc_seqfu.txt:md5,6cdb863a3686fbb772aae5a66925ff23",
+                "fastq_screen_plot.txt:md5,44fca6453b0a3d0590271bd7a31cc740",
+                "fastqc-status-check-heatmap.txt:md5,b6872d9dbaa3cce396d48dc137076e53",
+                "fastqc_overrepresented_sequences_plot.txt:md5,aa2089fd0c302d13a8ac129b170d1635",
+                "fastqc_per_base_n_content_plot.txt:md5,ed940fe48b562524c311c00649ef063c",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,59e199fa45ec5ac0a5dad074b0757487",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,72f24435d92995a4d864ef4799749535",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,ad944f15289b31a7e0716faedf7305b0",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,11b7eef2b24524ae661824a066de259a",
+                "fastqc_sequence_counts_plot.txt:md5,249b63e8c25bcf9795826069677bc6dc",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,b044a9ed362df44abf424ff6367bf79a",
+                "fastqc_sequence_length_distribution_plot.txt:md5,312f96e33f395a12b727073b1827bbbc",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
+                "multiqc_fastqc.txt:md5,7c24c235c7e9279db9c050e035a80864",
+                "multiqc_seqfu.txt:md5,f821357507fda2d4cfd9299f52fa7dc1",
+                "fastq_screen_plot.txt:md5,5f748d33a7a396547fe8c260b728aa06",
+                "fastqc-status-check-heatmap.txt:md5,bab59a0bd1d676d90cdd986fbba36b26",
+                "fastqc_overrepresented_sequences_plot.txt:md5,c468b9fb791e766cd4370c1117487d16",
+                "fastqc_per_base_n_content_plot.txt:md5,669f79d1e7ce45854c963f39529d5b03",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,d43f6db730f63f7e3b6ed2ba2ef94d3b",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,eed9d0737883e2172d40e894fca1d5e2",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,52db6bff9b86a14a56e287e43c8bf217",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,0521df735da6292c102ed7354a737704",
+                "fastqc_sequence_counts_plot.txt:md5,6b2230f1faf2f736a40f7bceaa5d2855",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,4a5803b3a48133747e750265b5cbf457",
+                "fastqc_sequence_length_distribution_plot.txt:md5,bba3d5f5a20e50170528eb0f4695b7ae",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
+                "multiqc_fastqc.txt:md5,54330c70bce06979ac3c05280607ea3f",
+                "multiqc_seqfu.txt:md5,8cced36d66ca9d25d60c006e734aa7e9",
+                "fastq_screen_plot.txt:md5,8622e1dbd0fe62520af6096207b9775d",
+                "fastqc-status-check-heatmap.txt:md5,2a66f5d61b9eb579555905cd5954b04c",
+                "fastqc_overrepresented_sequences_plot.txt:md5,b2fd59c117e7f16cba78862881c935d5",
+                "fastqc_per_base_n_content_plot.txt:md5,ccfa4f753ed6fce2232224efb0c3150d",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,185b026ccfbec5735909599649cd6ef1",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,37354a9774ccc46020ec7a8af73d4534",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,177ec2aceca076a428724c6fa8af649d",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,589663fb1629044bba409086bc1e1014",
+                "fastqc_sequence_counts_plot.txt:md5,9a1a41d311e9a16d8028516a52b5ae8e",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,5c51d807e8841b9124f2d301f5504203",
+                "fastqc_sequence_length_distribution_plot.txt:md5,6966aa7545afaae2ab8712962e9862c6",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5",
+                "multiqc_fastqc.txt:md5,f82113046ba0964a0a7afe16be0a51ba",
+                "multiqc_seqfu.txt:md5,ff4ce1c88f39ed24a88bae0a861f75c8",
+                "Sample1_1_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6",
+                "Sample1_1_seqfu_mqc.txt:md5,24d99524ccd0e6c6255a69d68a871c7a",
+                "Sample23_3_seqfu.tsv:md5,6fac5d3dbce3f3bee72341fe99a399dc",
+                "Sample23_3_seqfu_mqc.txt:md5,4d4f280911a08bb6b753142980178027",
+                "SampleA_2_seqfu.tsv:md5,aec811f267bb2a0ef066a7abb59d2775",
+                "SampleA_2_seqfu_mqc.txt:md5,a819409a5cb64e20c3e54ec5ada4aa27",
+                "Undetermined_5_seqfu.tsv:md5,3a42c5c66a0a118f1a6f6f6e560b0e7e",
+                "Undetermined_5_seqfu_mqc.txt:md5,bd8be908362c5cb08a72f8ae7ab41b0d",
+                "sampletest_4_seqfu.tsv:md5,a5bea0b9c6015dd1a201ffd433e9b377",
+                "sampletest_4_seqfu_mqc.txt:md5,2180961655bbc8a12f0152d6a4b803a2",
+                "Sample1_1_Sample1_S1_L001_R1_001.fastq.gz:md5,e854f09ef7962d979be12981fe2fae8d",
+                "Sample23_3_Sample23_S3_L001_R1_001.fastq.gz:md5,1c96eae617f92f81abe08eaccfa02e11",
+                "SampleA_2_SampleA_S2_L001_R1_001.fastq.gz:md5,f7897b87d06b13e9877f297169a678f1",
+                "Undetermined_5_Undetermined_S0_L001_R1_001.fastq.gz:md5,c9e790094f5c2b2bad247ae96f804d1e",
+                "sampletest_4_sampletest_S4_L001_R1_001.fastq.gz:md5,e35f5e6cd500f18ce05cc061fb471a76"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-11-26T14:26:30.962199041"
     }
 }
\ No newline at end of file
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 878253dd..f412bea4 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -90,11 +90,26 @@ workflow SEQINSPECTOR {
     // Module: Run SeqFu stats
     //
     if (!("seqfu_stats" in skip_tools)) {
-        SEQFU_STATS(
+        ch_seqfu_stats = SEQFU_STATS(
             ch_samplesheet.map { meta, reads ->
                 [[id: "seqfu", sample_id: meta.id, tags: meta.tags], reads]
             }
         )
+        ch_seqfu_stats.stats.map { meta, stats -> {
+            // Parse the stats TSV file
+            [meta.sample_id, stats]
+        }}
+        .splitCsv(header: true, sep: '\t')
+        .view { sample_id, row ->
+            // Check if requested sample size exceeds available reads
+            def sample_reads = row['#Seq'].toInteger()
+            if (params.sample_size > sample_reads) {
+                log.info("Warning: Requested sample_size (${params.sample_size}) " +
+                        "is larger than available reads in ${sample_id} (${sample_reads}). " +
+                        "Pipeline will continue with ${sample_reads} reads." )
+            }
+
+        }
         ch_multiqc_files = ch_multiqc_files.mix(SEQFU_STATS.out.multiqc)
         ch_versions = ch_versions.mix(SEQFU_STATS.out.versions.first())
     }

From 8ad085f19ca35428e4632dedf124bec220aae882 Mon Sep 17 00:00:00 2001
From: nelnk861 <nelly.nkonge@uu.se>
Date: Tue, 25 Nov 2025 14:29:18 +0100
Subject: [PATCH 427/530] Fixing tests

---
 tests/NovaSeq6000.main_subsample.nf.test | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/tests/NovaSeq6000.main_subsample.nf.test b/tests/NovaSeq6000.main_subsample.nf.test
index f158d226..a656cd89 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test
+++ b/tests/NovaSeq6000.main_subsample.nf.test
@@ -89,11 +89,12 @@ nextflow_pipeline {
         }
 
         then {
-            assert path(".nextflow.log").text.contains("Warning: Requested sample_size (120) is larger than available reads in Undetermined_5 (100). Pipeline will continue with 100 reads.")
-            assert path(".nextflow.log").text.contains("Warning: Requested sample_size (120) is larger than available reads in SampleA_2 (100). Pipeline will continue with 100 reads.")
-            assert path(".nextflow.log").text.contains("Warning: Requested sample_size (120) is larger than available reads in sampletest_4 (100). Pipeline will continue with 100 reads.")
-            assert path(".nextflow.log").text.contains("Warning: Requested sample_size (120) is larger than available reads in Sample23_3 (100). Pipeline will continue with 100 reads.")
-            assert path(".nextflow.log").text.contains("Warning: Requested sample_size (120) is larger than available reads in Sample1_1 (100). Pipeline will continue with 100 reads.")
+            def log_path = "./.nextflow.log"
+            assert path(log_path).text.contains("Warning: Requested sample_size (120) is larger than available reads in Undetermined_5 (100). Pipeline will continue with 100 reads.")
+            assert path(log_path).text.contains("Warning: Requested sample_size (120) is larger than available reads in SampleA_2 (100). Pipeline will continue with 100 reads.")
+            assert path(log_path).text.contains("Warning: Requested sample_size (120) is larger than available reads in sampletest_4 (100). Pipeline will continue with 100 reads.")
+            assert path(log_path).text.contains("Warning: Requested sample_size (120) is larger than available reads in Sample23_3 (100). Pipeline will continue with 100 reads.")
+            assert path(log_path).text.contains("Warning: Requested sample_size (120) is larger than available reads in Sample1_1 (100). Pipeline will continue with 100 reads.")
         }
     }
 }

From 2e1b664951d9e2b8bc433eeb55437b5db24c5c4d Mon Sep 17 00:00:00 2001
From: nelnk861 <nelly.nkonge@uu.se>
Date: Wed, 26 Nov 2025 14:18:19 +0100
Subject: [PATCH 428/530] Fixed test error

---
 tests/NovaSeq6000.main_subsample.nf.test      | 35 ++++++++++---------
 tests/NovaSeq6000.main_subsample.nf.test.snap |  4 +--
 workflows/seqinspector.nf                     |  7 ++--
 3 files changed, 25 insertions(+), 21 deletions(-)

diff --git a/tests/NovaSeq6000.main_subsample.nf.test b/tests/NovaSeq6000.main_subsample.nf.test
index a656cd89..9344687b 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test
+++ b/tests/NovaSeq6000.main_subsample.nf.test
@@ -38,16 +38,14 @@ nextflow_pipeline {
             )
         }
     }
+
     test("NovaSeq6000 data test relative sample size") {
-        config """
-        process {
-            sample_size = 0.9
-        }
-        """
+
         when {
             config "./NovaSeq6000.main_subsample.nf.test.config"
             params {
                 outdir = "$outputDir"
+                sample_size = 0.9
             }
         }
 
@@ -75,26 +73,29 @@ nextflow_pipeline {
             )
         }
     }
-    test("NovaSeq6000 data test sample size exceeds") {
-        config """
-        process {
-            sample_size = 120
-        }
-        """
+    test("NovaSeq6000 data test sample size exceeds available reads") {
+        
         when {
             config "./NovaSeq6000.main_subsample.nf.test.config"
             params {
                 outdir = "$outputDir"
+                sample_size = 120
             }
         }
 
         then {
-            def log_path = "./.nextflow.log"
-            assert path(log_path).text.contains("Warning: Requested sample_size (120) is larger than available reads in Undetermined_5 (100). Pipeline will continue with 100 reads.")
-            assert path(log_path).text.contains("Warning: Requested sample_size (120) is larger than available reads in SampleA_2 (100). Pipeline will continue with 100 reads.")
-            assert path(log_path).text.contains("Warning: Requested sample_size (120) is larger than available reads in sampletest_4 (100). Pipeline will continue with 100 reads.")
-            assert path(log_path).text.contains("Warning: Requested sample_size (120) is larger than available reads in Sample23_3 (100). Pipeline will continue with 100 reads.")
-            assert path(log_path).text.contains("Warning: Requested sample_size (120) is larger than available reads in Sample1_1 (100). Pipeline will continue with 100 reads.")
+            def warn_messages = [
+                "Warning: Requested sample_size (120) is larger than available reads in Undetermined_5 (100). Pipeline will continue with 100 reads.",
+                "Warning: Requested sample_size (120) is larger than available reads in SampleA_2 (100). Pipeline will continue with 100 reads.",
+                "Warning: Requested sample_size (120) is larger than available reads in sampletest_4 (100). Pipeline will continue with 100 reads.",
+                "Warning: Requested sample_size (120) is larger than available reads in Sample23_3 (100). Pipeline will continue with 100 reads.",
+                "Warning: Requested sample_size (120) is larger than available reads in Sample1_1 (100). Pipeline will continue with 100 reads."
+            ]
+            assert workflow.success
+            for ( msg in warn_messages ) {
+                // Read warning from stdout as nf-test does not capture log messages
+                assert workflow.stdout.contains(msg)
+            }
         }
     }
 }
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index e0e7b276..1107814a 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -535,7 +535,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-25T13:20:06.917144477"
+        "timestamp": "2025-11-26T13:46:44.353118705"
     },
     "NovaSeq6000 data test relative sample size": {
         "content": [
@@ -1073,6 +1073,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-26T14:26:30.962199041"
+        "timestamp": "2025-11-26T14:34:17.011633325"
     }
 }
\ No newline at end of file
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index f412bea4..a98ba529 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -104,9 +104,12 @@ workflow SEQINSPECTOR {
             // Check if requested sample size exceeds available reads
             def sample_reads = row['#Seq'].toInteger()
             if (params.sample_size > sample_reads) {
-                log.info("Warning: Requested sample_size (${params.sample_size}) " +
+                // prntln is used here instead of log.warn/log.info as nf-test captures stdout
+                // from 'println' but buffers log messages making them unavailable for assertion
+                // This message will appear in .nextflow.log file and temporarily on runtime stdout.
+                println ("Warning: Requested sample_size (${params.sample_size}) " +
                         "is larger than available reads in ${sample_id} (${sample_reads}). " +
-                        "Pipeline will continue with ${sample_reads} reads." )
+                        "Pipeline will continue with ${sample_reads} reads.")
             }
 
         }

From 5d3309bba30bb70a54a816a7d290e2182e5a0123 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Wed, 26 Nov 2025 14:23:17 +0000
Subject: [PATCH 429/530] [automated] Fix code linting

---
 tests/NovaSeq6000.main_subsample.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/NovaSeq6000.main_subsample.nf.test b/tests/NovaSeq6000.main_subsample.nf.test
index 9344687b..aec5dfc8 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test
+++ b/tests/NovaSeq6000.main_subsample.nf.test
@@ -74,7 +74,7 @@ nextflow_pipeline {
         }
     }
     test("NovaSeq6000 data test sample size exceeds available reads") {
-        
+
         when {
             config "./NovaSeq6000.main_subsample.nf.test.config"
             params {

From 432816bd155050863d220b00a035c3ddced3778c Mon Sep 17 00:00:00 2001
From: eliott <eliottob6@gmail.com>
Date: Wed, 26 Nov 2025 15:46:43 +0100
Subject: [PATCH 430/530] Harshil alignment

---
 subworkflows/local/qc_bam/main.nf            | 20 +++++++---------
 subworkflows/local/qc_bam/tests/main.nf.test | 14 +++++------
 workflows/seqinspector.nf                    | 25 ++++++++++----------
 3 files changed, 28 insertions(+), 31 deletions(-)

diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf
index 2528da06..9284dd88 100644
--- a/subworkflows/local/qc_bam/main.nf
+++ b/subworkflows/local/qc_bam/main.nf
@@ -2,22 +2,20 @@
 // A quality check subworkflow for processed bam files.
 //
 
-include { PICARD_COLLECTHSMETRICS } from '../../../modules/nf-core/picard/collecthsmetrics/main'
+include { PICARD_COLLECTHSMETRICS         } from '../../../modules/nf-core/picard/collecthsmetrics/main'
 include { PICARD_CREATESEQUENCEDICTIONARY } from '../../../modules/nf-core/picard/createsequencedictionary/main'
 
 workflow QC_BAM {
     take:
-        ch_bam_bai
-        ch_bait_intervals
-        ch_target_intervals
-        ch_reference_fasta
-        ch_reference_fasta_fai
-        ref_dict
+    ch_bam_bai
+    ch_bait_intervals
+    ch_target_intervals
+    ch_reference_fasta
+    ch_reference_fasta_fai
+    ref_dict
 
     main:
-
     ch_versions = channel.empty()
-
     ch_hsmetrics_in = ch_bam_bai
             .combine(ch_bait_intervals)
             .combine(ch_target_intervals)
@@ -43,6 +41,6 @@ workflow QC_BAM {
     ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
 
     emit:
-        hs_metrics = PICARD_COLLECTHSMETRICS.out.metrics
-        versions = ch_versions
+    hs_metrics = PICARD_COLLECTHSMETRICS.out.metrics
+    versions = ch_versions
 }
diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test
index b7445c58..615a6bf8 100644
--- a/subworkflows/local/qc_bam/tests/main.nf.test
+++ b/subworkflows/local/qc_bam/tests/main.nf.test
@@ -18,15 +18,15 @@ nextflow_workflow {
             }
             workflow {
                 """
-                input[0] = channel.of(
+                input[0]  = channel.of(
                     [
                         [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'],
                         [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)],
                         [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)]
                     ]
                 )
-                input[1] = channel.fromPath(params.pipelines_testdata_base_path + '/reference/target.bed', checkIfExists: true).collect()
-                input[2] = channel.fromPath(params.pipelines_testdata_base_path + '/reference/target.bed', checkIfExists: true).collect()
+                input[1]  = channel.fromPath(params.pipelines_testdata_base_path + '/reference/target.bed', checkIfExists: true).collect()
+                input[2]  = channel.fromPath(params.pipelines_testdata_base_path + '/reference/target.bed', checkIfExists: true).collect()
                 input[3]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta', checkIfExists: true)).collect()
                 input[4]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta.fai', checkIfExists: true)).collect()
                 input[5]  = null
@@ -38,10 +38,10 @@ nextflow_workflow {
             assert workflow.success
             assert snapshot(
                             workflow.out.hs_metrics
-                                .collect {it[1]}
-                                .flatten()
-                                .collect { file(it).name }
-                                .toSorted(),
+                                    .collect {it[1]}
+                                    .flatten()
+                                    .collect { file(it).name }
+                                    .toSorted(),
                             workflow.out.versions
                             ).match()
         }
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index bb4c4117..fb21f5b3 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -11,17 +11,17 @@ include { BWAMEM2_MEM                   } from '../modules/nf-core/bwamem2/mem'
 include { FASTQC                        } from '../modules/nf-core/fastqc'
 include { FASTQSCREEN_FASTQSCREEN       } from '../modules/nf-core/fastqscreen/fastqscreen'
 include { PICARD_COLLECTMULTIPLEMETRICS } from '../modules/nf-core/picard/collectmultiplemetrics'
-include { SAMTOOLS_FAIDX } from '../modules/nf-core/samtools/faidx'
-include { SAMTOOLS_INDEX } from '../modules/nf-core/samtools/index'
-include { SEQFU_STATS } from '../modules/nf-core/seqfu/stats'
-include { SEQTK_SAMPLE } from '../modules/nf-core/seqtk/sample'
-include { QC_BAM } from '../subworkflows/local/qc_bam'
+include { SAMTOOLS_FAIDX                } from '../modules/nf-core/samtools/faidx'
+include { SAMTOOLS_INDEX                } from '../modules/nf-core/samtools/index'
+include { SEQFU_STATS                   } from '../modules/nf-core/seqfu/stats'
+include { SEQTK_SAMPLE                  } from '../modules/nf-core/seqtk/sample'
+include { QC_BAM                        } from '../subworkflows/local/qc_bam'
 
-include { MULTIQC as MULTIQC_GLOBAL } from '../modules/nf-core/multiqc'
+include { MULTIQC as MULTIQC_GLOBAL  } from '../modules/nf-core/multiqc'
 include { MULTIQC as MULTIQC_PER_TAG } from '../modules/nf-core/multiqc'
 
-include { paramsSummaryMap } from 'plugin/nf-schema'
-include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { paramsSummaryMap       } from 'plugin/nf-schema'
+include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline'
 
@@ -166,11 +166,10 @@ workflow SEQINSPECTOR {
 
     if (params.run_picard_collecthsmetrics && !("picard_collectmultiplemetrics" in skip_tools)) {
 
-        ch_bait_intervals = channel.fromPath(params.bait_intervals)
-            .collect()
-
+        ch_bait_intervals   = channel.fromPath(params.bait_intervals)
+                                     .collect()
         ch_target_intervals = channel.fromPath(params.target_intervals)
-            .collect()
+                                     .collect()
 
 
         QC_BAM(
@@ -183,7 +182,7 @@ workflow SEQINSPECTOR {
         )
 
     ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.hs_metrics)
-    ch_versions = ch_versions.mix(QC_BAM.out.versions)
+    ch_versions      = ch_versions.mix(QC_BAM.out.versions)
     }
 
 

From d724965a98ed602dece421fdc0ca2fc45d0aa2c7 Mon Sep 17 00:00:00 2001
From: eliott <eliottob6@gmail.com>
Date: Wed, 26 Nov 2025 15:46:55 +0100
Subject: [PATCH 431/530] Update ro-crate

---
 ro-crate-metadata.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 6c11aa0b..02d4357c 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -23,7 +23,7 @@
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
             "datePublished": "2025-11-24T14:37:12+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n<picture>\n  <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n  <source media=\"(prefers-color-scheme: light)\" srcset=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  <img alt=\"Fallback image description\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n</picture>\n\n<picture>\n  <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nfcore-seqinspector-logo-hex-dark.png\">\n  <source media=\"(prefers-color-scheme: light)\" srcset=\"docs/images/nfcore-seqinspector-logo-hex-light.png\">\n  <img alt=\"Fallback image description\" src=\"docs/images/nfcore-seqinspector-logo-hex-light.png\">\n</picture>\n\n**nf-core/seqinspector** is a bioinformatics pipeline that that processes raw sequence data (FASTQ) to provide comprehensive quality control. It can perform subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants. The pipeline generates detailed MultiQC reports with flexible output options, ranging from individual sample reports to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments. If provided, nf-core/seqinspector can also parse statistics from an Illumina run folder directory into the final MultiQC reports.\n\n<!-- TODO: add a search tool that accepts a tree for `Compatibility with Data`. -->\n\n| Tool Type           | Tool Name                                                                                                   | Tool Description                                                                              | Compatibility with Data | Dependencies                    | Default tool |\n| ------------------- | ----------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------- | ----------------------- | ------------------------------- | ------------ |\n| `Subsampling`       | [`Seqtk`](https://github.com/lh3/seqtk)                                                                     | Global subsampling of reads. Only performs subsampling if `--sample_size` parameter is given. | [RNA, DNA, synthetic]   | [N/A]                           | no           |\n| `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2)                                                           | Align reads to reference                                                                      | [RNA, DNA]              | [N/A]                           | yes          |\n| `Indexing`          | [`SAMtools`](http://github.com/samtools)                                                                    | Index aligned BAM files, create FASTA index                                                   | [DNA]                   | [N/A]                           | yes          |\n| `QC`                | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)                                      | Read QC                                                                                       | [RNA, DNA]              | [N/A]                           | yes          |\n| `QC`                | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)                           | Basic contamination detection                                                                 | [RNA, DNA]              | [N/A]                           | yes          |\n| `QC`                | [`SeqFu Stats`](https://github.com/telatin/seqfu2)                                                          | Sequence statistics                                                                           | [RNA, DNA]              | [N/A]                           | yes          |\n| `QC`                | [`Picard collect multiple metrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html) | Collect multiple QC metrics                                                                   | [RNA, DNA]              | [Bwamem2, SAMtools, `--genome`] | yes          |\n| `QC`                | [`Picard_collecthsmetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard) | Collect alignment QC metrics of hybrid-selection data.                                | [RNA, DNA]              | [Bwamem2, SAMtools, `--fasta`, `--run_picard_collecths_metrics`, `--bait_intervals`, `--target_intervals` (`--ref_dict`)] | no |\n| `Reporting`         | [`MultiQC`](http://multiqc.info/)                                                                           | Present QC for raw reads                                                                      | [RNA, DNA, synthetic]   | [N/A]                           | yes          |\n\n<picture>\n  <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/seqinspector_tubemap_V1.0_dark.png\">\n  <source media=\"(prefers-color-scheme: light)\" srcset=\"docs/images/seqinspector_tubemap_V1.0.png\">\n  <img alt=\"Fallback image description\" src=\"docs/images/seqinspector_tubemap_V1.0.png\">\n</picture>\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/) and [Clinical Genomics Stockholm](https://clinical.scilifelab.se/).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n<picture>\n  <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n  <source media=\"(prefers-color-scheme: light)\" srcset=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  <img alt=\"Fallback image description\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n</picture>\n\n<picture>\n  <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nfcore-seqinspector-logo-hex-dark.png\">\n  <source media=\"(prefers-color-scheme: light)\" srcset=\"docs/images/nfcore-seqinspector-logo-hex-light.png\">\n  <img alt=\"Fallback image description\" src=\"docs/images/nfcore-seqinspector-logo-hex-light.png\">\n</picture>\n\n**nf-core/seqinspector** is a bioinformatics pipeline that that processes raw sequence data (FASTQ) to provide comprehensive quality control. It can perform subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants. The pipeline generates detailed MultiQC reports with flexible output options, ranging from individual sample reports to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments. If provided, nf-core/seqinspector can also parse statistics from an Illumina run folder directory into the final MultiQC reports.\n\n<!-- TODO: add a search tool that accepts a tree for `Compatibility with Data`. -->\n\n| Tool Type           | Tool Name                                                                                                           | Tool Description                                                                              | Compatibility with Data | Dependencies                                                                                                              | Default tool |\n| ------------------- | ------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------- | ----------------------- | ------------------------------------------------------------------------------------------------------------------------- | ------------ |\n| `Subsampling`       | [`Seqtk`](https://github.com/lh3/seqtk)                                                                             | Global subsampling of reads. Only performs subsampling if `--sample_size` parameter is given. | [RNA, DNA, synthetic]   | [N/A]                                                                                                                     | no           |\n| `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2)                                                                   | Align reads to reference                                                                      | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `Indexing`          | [`SAMtools`](http://github.com/samtools)                                                                            | Index aligned BAM files, create FASTA index                                                   | [DNA]                   | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)                                              | Read QC                                                                                       | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)                                   | Basic contamination detection                                                                 | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`SeqFu Stats`](https://github.com/telatin/seqfu2)                                                                  | Sequence statistics                                                                           | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`Picard collect multiple metrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html)         | Collect multiple QC metrics                                                                   | [RNA, DNA]              | [Bwamem2, SAMtools, `--genome`]                                                                                           | yes          |\n| `QC`                | [`Picard_collecthsmetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard) | Collect alignment QC metrics of hybrid-selection data.                                        | [RNA, DNA]              | [Bwamem2, SAMtools, `--fasta`, `--run_picard_collecths_metrics`, `--bait_intervals`, `--target_intervals` (`--ref_dict`)] | no           |\n| `Reporting`         | [`MultiQC`](http://multiqc.info/)                                                                                   | Present QC for raw reads                                                                      | [RNA, DNA, synthetic]   | [N/A]                                                                                                                     | yes          |\n\n<picture>\n  <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/seqinspector_tubemap_V1.0_dark.png\">\n  <source media=\"(prefers-color-scheme: light)\" srcset=\"docs/images/seqinspector_tubemap_V1.0.png\">\n  <img alt=\"Fallback image description\" src=\"docs/images/seqinspector_tubemap_V1.0.png\">\n</picture>\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/) and [Clinical Genomics Stockholm](https://clinical.scilifelab.se/).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
                     "@id": "main.nf"

From 8838130ef0485cd7b4cf7a10f871679d2e818ec4 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Thu, 27 Nov 2025 14:47:55 +0100
Subject: [PATCH 432/530] Format seqinspector.nf.

---
 workflows/seqinspector.nf | 34 +++++++++++++++++-----------------
 1 file changed, 17 insertions(+), 17 deletions(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index fb21f5b3..7e1dc06e 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -1,4 +1,4 @@
-include { samplesheetToList } from 'plugin/nf-schema'
+include { samplesheetToList             } from 'plugin/nf-schema'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -17,13 +17,13 @@ include { SEQFU_STATS                   } from '../modules/nf-core/seqfu/stats'
 include { SEQTK_SAMPLE                  } from '../modules/nf-core/seqtk/sample'
 include { QC_BAM                        } from '../subworkflows/local/qc_bam'
 
-include { MULTIQC as MULTIQC_GLOBAL  } from '../modules/nf-core/multiqc'
-include { MULTIQC as MULTIQC_PER_TAG } from '../modules/nf-core/multiqc'
+include { MULTIQC as MULTIQC_GLOBAL     } from '../modules/nf-core/multiqc'
+include { MULTIQC as MULTIQC_PER_TAG    } from '../modules/nf-core/multiqc'
 
-include { paramsSummaryMap       } from 'plugin/nf-schema'
-include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline'
+include { paramsSummaryMap              } from 'plugin/nf-schema'
+include { paramsSummaryMultiqc          } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { softwareVersionsToYAML        } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { methodsDescriptionText        } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline'
 
 // local
 include { PREPARE_GENOME                } from '../subworkflows/local/prepare_genome'
@@ -49,12 +49,12 @@ workflow SEQINSPECTOR {
     ch_multiqc_extra_files = channel.empty()
     ch_bwamem2_mem         = channel.empty()
     ch_samtools_index      = channel.empty()
-    ch_reference_fasta     = fasta_file? channel.fromPath(fasta_file, checkIfExists: true).map { file -> tuple([id: file.name], file) }.collect() : channel.value([[:], []])
+    ch_reference_fasta     = fasta_file ? channel.fromPath(fasta_file, checkIfExists: true).map { file -> tuple([id: file.name], file) }.collect() : channel.value([[:], []])
 
-    PREPARE_GENOME (
+    PREPARE_GENOME(
         ch_reference_fasta,
         bwamem2,
-        skip_tools
+        skip_tools,
     )
 
     //
@@ -166,10 +166,10 @@ workflow SEQINSPECTOR {
 
     if (params.run_picard_collecthsmetrics && !("picard_collectmultiplemetrics" in skip_tools)) {
 
-        ch_bait_intervals   = channel.fromPath(params.bait_intervals)
-                                     .collect()
+        ch_bait_intervals = channel.fromPath(params.bait_intervals)
+            .collect()
         ch_target_intervals = channel.fromPath(params.target_intervals)
-                                     .collect()
+            .collect()
 
 
         QC_BAM(
@@ -181,8 +181,8 @@ workflow SEQINSPECTOR {
             params.ref_dict,
         )
 
-    ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.hs_metrics)
-    ch_versions      = ch_versions.mix(QC_BAM.out.versions)
+        ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.hs_metrics)
+        ch_versions = ch_versions.mix(QC_BAM.out.versions)
     }
 
 
@@ -304,7 +304,7 @@ workflow SEQINSPECTOR {
     )
 
     emit:
-    global_report = MULTIQC_GLOBAL.out.report.toList() // channel: [ /path/to/multiqc_report.html ]
+    global_report   = MULTIQC_GLOBAL.out.report.toList() // channel: [ /path/to/multiqc_report.html ]
     grouped_reports = MULTIQC_PER_TAG.out.report.toList() // channel: [ /path/to/multiqc_report.html ]
-    versions = ch_versions // channel: [ path(versions.yml) ]
+    versions        = ch_versions // channel: [ path(versions.yml) ]
 }

From 0af25a1f030835634b4017b5b431db15a97f4747 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Thu, 27 Nov 2025 15:08:24 +0100
Subject: [PATCH 433/530] Restore output.md.

---
 docs/output.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/output.md b/docs/output.md
index 8f4a7f55..19ac6e1c 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -14,6 +14,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - [FastQC](#fastqc) - Raw read QC
 - [SeqFu Stats](#seqfu_stats) - Statistics for FASTA or FASTQ files
 - [FastQ Screen](#fastqscreen) - Mapping against a set of references for basic contamination QC
+- [Picard collecthsmetrics](#picard-collecthsmetrics) - Collect alignment QC metrics of hybrid-selection data
 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 

From 739e7d81f6ba5eafb536518fd37fadd33e758356 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Thu, 27 Nov 2025 15:13:25 +0100
Subject: [PATCH 434/530] Add input parameter notes for QC_BAM.

---
 subworkflows/local/qc_bam/main.nf | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf
index 9284dd88..80b786df 100644
--- a/subworkflows/local/qc_bam/main.nf
+++ b/subworkflows/local/qc_bam/main.nf
@@ -7,12 +7,12 @@ include { PICARD_CREATESEQUENCEDICTIONARY } from '../../../modules/nf-core/picar
 
 workflow QC_BAM {
     take:
-    ch_bam_bai
-    ch_bait_intervals
-    ch_target_intervals
-    ch_reference_fasta
-    ch_reference_fasta_fai
-    ref_dict
+    ch_bam_bai              // channel: [mandatory] [ val(meta), [ path(bam) ], [ path(bai) ] ]
+    ch_bait_intervals       // channel: [mandatory] [ val(meta), [ path(bait_intervals) ] ]
+    ch_target_intervals     // channel: [mandatory] [ val(meta), [ path(target_intervals) ] ]
+    ch_reference_fasta      // channel: [mandatory] [ val(meta), [ path(reference_fasta) ] ]
+    ch_reference_fasta_fai  // channel: [mandatory] [ val(meta), [ path(reference_fasta_fai) ] ]
+    ref_dict                // val: [mandatory] [ [ path(ref_dict) ] ]
 
     main:
     ch_versions = channel.empty()

From b5ef24af7a8492ab9dafb1ddd09ed6cffb07053c Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Thu, 27 Nov 2025 15:15:04 +0100
Subject: [PATCH 435/530] Fix input notes.

---
 subworkflows/local/qc_bam/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf
index 80b786df..813abac0 100644
--- a/subworkflows/local/qc_bam/main.nf
+++ b/subworkflows/local/qc_bam/main.nf
@@ -12,7 +12,7 @@ workflow QC_BAM {
     ch_target_intervals     // channel: [mandatory] [ val(meta), [ path(target_intervals) ] ]
     ch_reference_fasta      // channel: [mandatory] [ val(meta), [ path(reference_fasta) ] ]
     ch_reference_fasta_fai  // channel: [mandatory] [ val(meta), [ path(reference_fasta_fai) ] ]
-    ref_dict                // val: [mandatory] [ [ path(ref_dict) ] ]
+    ref_dict                // value:   [mandatory] [ path(ref_dict) ]
 
     main:
     ch_versions = channel.empty()

From ad3b3339a484b57637a26247ebad02e3ba9f3b1a Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Thu, 27 Nov 2025 16:19:22 +0100
Subject: [PATCH 436/530] Update input parameter notes.

---
 subworkflows/local/qc_bam/main.nf | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf
index 813abac0..53be62c4 100644
--- a/subworkflows/local/qc_bam/main.nf
+++ b/subworkflows/local/qc_bam/main.nf
@@ -7,12 +7,12 @@ include { PICARD_CREATESEQUENCEDICTIONARY } from '../../../modules/nf-core/picar
 
 workflow QC_BAM {
     take:
-    ch_bam_bai              // channel: [mandatory] [ val(meta), [ path(bam) ], [ path(bai) ] ]
-    ch_bait_intervals       // channel: [mandatory] [ val(meta), [ path(bait_intervals) ] ]
-    ch_target_intervals     // channel: [mandatory] [ val(meta), [ path(target_intervals) ] ]
-    ch_reference_fasta      // channel: [mandatory] [ val(meta), [ path(reference_fasta) ] ]
-    ch_reference_fasta_fai  // channel: [mandatory] [ val(meta), [ path(reference_fasta_fai) ] ]
-    ref_dict                // value:   [mandatory] [ path(ref_dict) ]
+    ch_bam_bai           // channel: [mandatory] [ val(meta), path(bam), path(bai) ]
+    ch_bait_intervals    // channel: [mandatory] [ val(meta), path(bait_intervals) ]
+    ch_target_intervals  // channel: [mandatory] [ val(meta), path(target_intervals) ]
+    ch_reference_fasta   // channel: [mandatory] [ val(meta), path(reference_fasta) ]
+    ch_reference_fai     // channel: [mandatory] [ val(meta), path(reference_fai) ]
+    ref_dict             // value:   [mandatory] [ path(ref_dict) ]
 
     main:
     ch_versions = channel.empty()
@@ -34,7 +34,7 @@ workflow QC_BAM {
     PICARD_COLLECTHSMETRICS(
         ch_hsmetrics_in,
         ch_reference_fasta,
-        ch_reference_fasta_fai,
+        ch_reference_fai,
         ch_ref_dict,
         [[], []],
     )

From 8e08426bcb1228c5c976b5cdd199eb82468f6213 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Thu, 27 Nov 2025 16:46:42 +0100
Subject: [PATCH 437/530] Move PICARD_CREATESEQUENCEDICTIONARY to
 PREPARE_GENOME. Adjust QC_BAM tests.

---
 subworkflows/local/prepare_genome/main.nf    | 17 +++++++++++++++++
 subworkflows/local/qc_bam/main.nf            | 13 +------------
 subworkflows/local/qc_bam/tests/main.nf.test |  2 +-
 workflows/seqinspector.nf                    |  6 +++++-
 4 files changed, 24 insertions(+), 14 deletions(-)

diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf
index 013d4db2..927ee7f7 100644
--- a/subworkflows/local/prepare_genome/main.nf
+++ b/subworkflows/local/prepare_genome/main.nf
@@ -3,6 +3,7 @@
 
 include { BWAMEM2_INDEX                 } from '../../../modules/nf-core/bwamem2/index'
 include { SAMTOOLS_FAIDX                } from '../../../modules/nf-core/samtools/faidx'
+include { PICARD_CREATESEQUENCEDICTIONARY } from '../../../modules/nf-core/picard/createsequencedictionary/main'
 
 workflow PREPARE_GENOME {
 
@@ -10,6 +11,8 @@ workflow PREPARE_GENOME {
     ch_reference_fasta
     bwamem2
     skip_tools
+    run_picard_collecthsmetrics  // value: [mandatory] [ bool ]
+    ref_dict                     // value: [mandatory] [ path(ref_dict) ]
 
     main:
     // Initialize all channels that might be used later
@@ -49,9 +52,23 @@ workflow PREPARE_GENOME {
         ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions)
     }
 
+    if (run_picard_collecthsmetrics){
+        if (ref_dict) {
+        ch_ref_dict = channel.fromPath(ref_dict, checkIfExists: true).map { [[id: it.simpleName], it] }
+        }
+        else {
+            PICARD_CREATESEQUENCEDICTIONARY(
+                ch_reference_fasta
+            )
+            ch_ref_dict = PICARD_CREATESEQUENCEDICTIONARY.out.reference_dict
+            ch_versions = ch_versions.mix(PICARD_CREATESEQUENCEDICTIONARY.out.versions)
+        }
+    }
+
     emit:
     bwamem2_index = ch_bwamem2_index
     reference_fai = ch_reference_fai
+    ref_dict      = ch_ref_dict
     versions      = ch_versions
 
 }
diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf
index 53be62c4..54d3972f 100644
--- a/subworkflows/local/qc_bam/main.nf
+++ b/subworkflows/local/qc_bam/main.nf
@@ -3,7 +3,6 @@
 //
 
 include { PICARD_COLLECTHSMETRICS         } from '../../../modules/nf-core/picard/collecthsmetrics/main'
-include { PICARD_CREATESEQUENCEDICTIONARY } from '../../../modules/nf-core/picard/createsequencedictionary/main'
 
 workflow QC_BAM {
     take:
@@ -12,7 +11,7 @@ workflow QC_BAM {
     ch_target_intervals  // channel: [mandatory] [ val(meta), path(target_intervals) ]
     ch_reference_fasta   // channel: [mandatory] [ val(meta), path(reference_fasta) ]
     ch_reference_fai     // channel: [mandatory] [ val(meta), path(reference_fai) ]
-    ref_dict             // value:   [mandatory] [ path(ref_dict) ]
+    ch_ref_dict          // channel: [mandatory] [ val(meta), path(ref_dict) ]
 
     main:
     ch_versions = channel.empty()
@@ -20,16 +19,6 @@ workflow QC_BAM {
             .combine(ch_bait_intervals)
             .combine(ch_target_intervals)
 
-    if (ref_dict) {
-        ch_ref_dict = channel.fromPath(ref_dict, checkIfExists: true).map { [[id: it.simpleName], it] }
-    }
-    else {
-        PICARD_CREATESEQUENCEDICTIONARY(
-            ch_reference_fasta
-        )
-        ch_ref_dict = PICARD_CREATESEQUENCEDICTIONARY.out.reference_dict
-        ch_versions = ch_versions.mix(PICARD_CREATESEQUENCEDICTIONARY.out.versions)
-    }
 
     PICARD_COLLECTHSMETRICS(
         ch_hsmetrics_in,
diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test
index 615a6bf8..5494f68a 100644
--- a/subworkflows/local/qc_bam/tests/main.nf.test
+++ b/subworkflows/local/qc_bam/tests/main.nf.test
@@ -29,7 +29,7 @@ nextflow_workflow {
                 input[2]  = channel.fromPath(params.pipelines_testdata_base_path + '/reference/target.bed', checkIfExists: true).collect()
                 input[3]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta', checkIfExists: true)).collect()
                 input[4]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta.fai', checkIfExists: true)).collect()
-                input[5]  = null
+                input[5]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.dict', checkIfExists: true)).collect()
                 """
             }
         }
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 7e1dc06e..2e83dbd0 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -55,6 +55,8 @@ workflow SEQINSPECTOR {
         ch_reference_fasta,
         bwamem2,
         skip_tools,
+        params.run_picard_collecthsmetrics,
+        params.ref_dict,
     )
 
     //
@@ -171,6 +173,8 @@ workflow SEQINSPECTOR {
         ch_target_intervals = channel.fromPath(params.target_intervals)
             .collect()
 
+        ch_ref_dict = PREPARE_GENOME.out.ref_dict
+
 
         QC_BAM(
             ch_bam_bai,
@@ -178,7 +182,7 @@ workflow SEQINSPECTOR {
             ch_target_intervals,
             ch_reference_fasta,
             ch_fai,
-            params.ref_dict,
+            ch_ref_dict
         )
 
         ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.hs_metrics)

From 5ec27121b669da851d22877826e55b0a20ef2aa1 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Thu, 27 Nov 2025 16:59:00 +0100
Subject: [PATCH 438/530] Initialise ch_ref_dict in PREPARE_GENOME.

---
 subworkflows/local/prepare_genome/main.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf
index 927ee7f7..b0571523 100644
--- a/subworkflows/local/prepare_genome/main.nf
+++ b/subworkflows/local/prepare_genome/main.nf
@@ -19,6 +19,7 @@ workflow PREPARE_GENOME {
     ch_bwamem2_index      = channel.empty()
     ch_reference_fai      = channel.empty()
     ch_reference_fasta    = channel.empty()
+    ch_ref_dict           = channel.empty()
     ch_versions           = channel.empty()
 
     if (!("bwamem2_index" in skip_tools)) {

From 0023329e3fed36ab32f772914a46c29c0f17a0ef Mon Sep 17 00:00:00 2001
From: eliott <eliottob6@gmail.com>
Date: Fri, 28 Nov 2025 08:52:38 +0100
Subject: [PATCH 439/530] Harshil alignment

---
 subworkflows/local/qc_bam/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf
index 54d3972f..71b50746 100644
--- a/subworkflows/local/qc_bam/main.nf
+++ b/subworkflows/local/qc_bam/main.nf
@@ -2,7 +2,7 @@
 // A quality check subworkflow for processed bam files.
 //
 
-include { PICARD_COLLECTHSMETRICS         } from '../../../modules/nf-core/picard/collecthsmetrics/main'
+include { PICARD_COLLECTHSMETRICS } from '../../../modules/nf-core/picard/collecthsmetrics/main'
 
 workflow QC_BAM {
     take:

From 52cce2fcc343a9d62fd5abe54f4b86ee33b512cf Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Fri, 28 Nov 2025 09:07:11 +0100
Subject: [PATCH 440/530] Update snapshot for QC_BAM.

---
 subworkflows/local/qc_bam/tests/main.nf.test.snap | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap
index d640a65b..4aefab56 100644
--- a/subworkflows/local/qc_bam/tests/main.nf.test.snap
+++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap
@@ -5,7 +5,6 @@
                 "earlycasualcaiman.CollectHsMetrics.coverage_metrics"
             ],
             [
-                "versions.yml:md5,40396221974da20b7f066d5fab9ffb3a",
                 "versions.yml:md5,8508bd28eaf1fffcdc4d78e4d9f95393"
             ]
         ],
@@ -13,6 +12,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-25T15:58:16.830793"
+        "timestamp": "2025-11-28T09:03:50.918024"
     }
 }
\ No newline at end of file

From 55f2d6f4371abac65ef610abc288b4128d202e22 Mon Sep 17 00:00:00 2001
From: Beatriz Vinhas <beatriz.sa.vinhas@gmail.com>
Date: Fri, 28 Nov 2025 13:33:38 +0100
Subject: [PATCH 441/530] Update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b4e1bcd2..da46257e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -29,8 +29,8 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#127](https://github.com/nf-core/seqinspector/pull/127) Added alignment tools - bwamem2 - index and mem
 - [#128](https://github.com/nf-core/seqinspector/pull/128) Added Picard tools - Collect Multiple Mterics to collect QC metrics
 - [#132](https://github.com/nf-core/seqinspector/pull/132) Added a bwamem2 index params for faster output
-- [#159](https://github.com/nf-core/seqinspector/pull/159) Added a subworkflow QC_BAM including picard_collecthsmetrics for alignment QC of hybrid-selection data
 - [#151](https://github.com/nf-core/seqinspector/pull/151) Added a prepare_genome subworkflow to handle bwamem2 indexing
+- [#159](https://github.com/nf-core/seqinspector/pull/159) Added a subworkflow QC_BAM including picard_collecthsmetrics for alignment QC of hybrid-selection data
 
 ### `Fixed`
 

From 79356af3c4016d5f376d47b9a1ca34e20d805c46 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Fri, 28 Nov 2025 15:12:44 +0100
Subject: [PATCH 442/530] Correct QC_BAM main.nf.

---
 subworkflows/local/qc_bam/main.nf | 70 ++++++++++++++++---------------
 1 file changed, 36 insertions(+), 34 deletions(-)

diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf
index c1ea7f4e..3497e791 100644
--- a/subworkflows/local/qc_bam/main.nf
+++ b/subworkflows/local/qc_bam/main.nf
@@ -7,51 +7,53 @@ include { PICARD_COLLECTHSMETRICS } from '../../../modules/nf-core/picard/collec
 
 workflow QC_BAM {
     take:
-    ch_bam               // channel: [mandatory] [ val(meta), path(bam)]
-    ch_bai               // channel: [mandatory] [ val(meta), path(bai) ]
-    ch_reference_fasta   // channel: [mandatory] [ val(meta), path(reference_fasta) ]
-    ch_reference_fai             // channel: [mandatory] [ val(meta), path(reference_fai) ]
-    run_picard_collecthsmetrics  // value: [mandatory] bool
-    ch_bait_intervals    // channel: [mandatory] [ val(meta), path(bait_intervals) ]
-    ch_target_intervals  // channel: [mandatory] [ val(meta), path(target_intervals) ]
-    ch_ref_dict          // channel: [mandatory] [ val(meta), path(ref_dict) ]
+        ch_bam                      // channel: [mandatory] [ val(meta), path(bam)]
+        ch_bai                      // channel: [mandatory] [ val(meta), path(bai) ]
+        ch_reference_fasta          // channel: [mandatory] [ val(meta), path(reference_fasta) ]
+        ch_reference_fai            // channel: [mandatory] [ val(meta), path(reference_fai) ]
+        run_picard_collecthsmetrics // value:   [mandatory] bool
+        ch_bait_intervals           // channel: [mandatory] [ val(meta), path(bait_intervals) ]
+        ch_target_intervals         // channel: [mandatory] [ val(meta), path(target_intervals) ]
+        ch_ref_dict                 // channel: [mandatory] [ val(meta), path(ref_dict) ]
 
     main:
 
-    ch_metrics = channel.empty()
-    ch_versions = channel.empty()
+        ch_multiple_metrics = channel.empty()
+        ch_multiple_metrics = channel.empty()
+        ch_versions = channel.empty()
 
-    ch_bam_bai = ch_bam.join(ch_bai, failOnDuplicate: true, failOnMismatch: true)
+        ch_bam_bai = ch_bam.join(ch_bai, failOnDuplicate: true, failOnMismatch: true)
 
-    PICARD_COLLECTMULTIPLEMETRICS(
-        ch_bam_bai,
-        ch_reference_fasta,
-        ch_reference_fasta_fai,
-    )
+        PICARD_COLLECTMULTIPLEMETRICS(
+            ch_bam_bai,
+            ch_reference_fasta,
+            ch_reference_fai,
+        )
 
-    ch_metrics = ch_metrics.mix(PICARD_COLLECTMULTIPLEMETRICS.out.metrics)
-    ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
+        ch_multiple_metrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics
+        ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
 
-    if (run_picard_collecthsmetrics) {
+        if (run_picard_collecthsmetrics) {
 
-        ch_hsmetrics_in = ch_bam_bai
-            .combine(ch_bait_intervals)
-            .combine(ch_target_intervals)
+            ch_hsmetrics_in = ch_bam_bai
+                .combine(ch_bait_intervals)
+                .combine(ch_target_intervals)
 
 
-        PICARD_COLLECTHSMETRICS(
-            ch_hsmetrics_in,
-            ch_reference_fasta,
-            ch_reference_fasta_fai,
-            ch_ref_dict,
-            [[], []],
-        )
+            PICARD_COLLECTHSMETRICS(
+                ch_hsmetrics_in,
+                ch_reference_fasta,
+                ch_reference_fai,
+                ch_ref_dict,
+                [[], []],
+            )
 
-        ch_metrics = ch_metrics.mix(PICARD_COLLECTHSMETRICS.out.metrics)
-        ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
-    }
+            ch_hs_metrics = PICARD_COLLECTHSMETRICS.out.metrics
+            ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
+        }
 
     emit:
-    metrics = ch_metrics
-    versions = ch_versions
+        multiple_metrics = ch_multiple_metrics
+        hs_metrics = ch_hs_metrics
+        versions = ch_versions
 }

From 6a1b3973ec4173c0757b7848c63357340c115233 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Mon, 1 Dec 2025 10:31:39 +0100
Subject: [PATCH 443/530] Remove PICARD_COLLECTMULTIPLEMETRICS from
 seqinspector.nf.

---
 workflows/seqinspector.nf | 19 +------------------
 1 file changed, 1 insertion(+), 18 deletions(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 58ebf369..30f8276e 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -146,28 +146,11 @@ workflow SEQINSPECTOR {
         ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions)
     }
 
-    // MODULE: Prepare BAM/BAI tuples for Picard
-    // Combine BAM and BAI outputs for Picard
-    if (!("picard_collectmultiplemetrics" in skip_tools) && !("bwamem2_mem" in skip_tools) && !("samtools_faidx" in skip_tools)) {
 
-        // Prepare BAM/BAI tuples for Picard
-        ch_bam_bai = ch_bwamem2_mem.join(ch_samtools_index, failOnDuplicate: true, failOnMismatch: true)
+    if (params.run_picard_collecthsmetrics && !("picard_collectmultiplemetrics" in skip_tools)) {
 
-        ch_fasta = ch_reference_fasta
         ch_fai = PREPARE_GENOME.out.reference_fai
 
-        PICARD_COLLECTMULTIPLEMETRICS(
-            ch_bam_bai,
-            ch_fasta,
-            ch_fai,
-        )
-
-        ch_multiqc_files = ch_multiqc_files.mix(PICARD_COLLECTMULTIPLEMETRICS.out.metrics)
-        ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
-    }
-
-    if (params.run_picard_collecthsmetrics && !("picard_collectmultiplemetrics" in skip_tools)) {
-
         ch_bait_intervals = channel.fromPath(params.bait_intervals)
             .collect()
         ch_target_intervals = channel.fromPath(params.target_intervals)

From fa533304004d17649f520f4c0acdc5586d742711 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Mon, 1 Dec 2025 10:39:54 +0100
Subject: [PATCH 444/530] Fix linting issues.

---
 .github/workflows/linting.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 30e66026..7a527a34 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -11,7 +11,7 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Set up Python 3.14
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
@@ -28,7 +28,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
@@ -71,7 +71,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: linting-logs
           path: |

From 223874750f11d08898a821740af15865322823df Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Mon, 1 Dec 2025 13:17:07 +0100
Subject: [PATCH 445/530] Add checks for empty params bait_intervals and
 target_intervals.

---
 workflows/seqinspector.nf | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 2e83dbd0..d1ce58e9 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -168,10 +168,8 @@ workflow SEQINSPECTOR {
 
     if (params.run_picard_collecthsmetrics && !("picard_collectmultiplemetrics" in skip_tools)) {
 
-        ch_bait_intervals = channel.fromPath(params.bait_intervals)
-            .collect()
-        ch_target_intervals = channel.fromPath(params.target_intervals)
-            .collect()
+        ch_bait_intervals = params.bait_intervals ? channel.fromPath(params.bait_intervals).collect() : channel.empty()
+        ch_target_intervals = params.target_intervals ? channel.fromPath(params.target_intervals).collect() : channel.empty()
 
         ch_ref_dict = PREPARE_GENOME.out.ref_dict
 

From 4d02baf2adb8eea5151ccfae07c0faf47573233c Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Mon, 1 Dec 2025 13:50:39 +0100
Subject: [PATCH 446/530] Fix QC_BAM input parameters.

---
 subworkflows/local/qc_bam/main.nf | 10 +++++-----
 workflows/seqinspector.nf         | 13 +++++++------
 2 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf
index 3497e791..fd451cdc 100644
--- a/subworkflows/local/qc_bam/main.nf
+++ b/subworkflows/local/qc_bam/main.nf
@@ -11,15 +11,15 @@ workflow QC_BAM {
         ch_bai                      // channel: [mandatory] [ val(meta), path(bai) ]
         ch_reference_fasta          // channel: [mandatory] [ val(meta), path(reference_fasta) ]
         ch_reference_fai            // channel: [mandatory] [ val(meta), path(reference_fai) ]
-        run_picard_collecthsmetrics // value:   [mandatory] bool
-        ch_bait_intervals           // channel: [mandatory] [ val(meta), path(bait_intervals) ]
-        ch_target_intervals         // channel: [mandatory] [ val(meta), path(target_intervals) ]
-        ch_ref_dict                 // channel: [mandatory] [ val(meta), path(ref_dict) ]
+        run_picard_collecthsmetrics // value:   [mandatory for picard_collecthsmetrics] bool
+        ch_bait_intervals           // channel: [mandatory for picard_collecthsmetrics] [ val(meta), path(bait_intervals) ]
+        ch_target_intervals         // channel: [mandatory for picard_collecthsmetrics] [ val(meta), path(target_intervals) ]
+        ch_ref_dict                 // channel: [mandatory for picard_collecthsmetrics] [ val(meta), path(ref_dict) ]
 
     main:
 
         ch_multiple_metrics = channel.empty()
-        ch_multiple_metrics = channel.empty()
+        ch_hs_metrics = channel.empty()
         ch_versions = channel.empty()
 
         ch_bam_bai = ch_bam.join(ch_bai, failOnDuplicate: true, failOnMismatch: true)
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 30f8276e..fdd6da7e 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -147,14 +147,12 @@ workflow SEQINSPECTOR {
     }
 
 
-    if (params.run_picard_collecthsmetrics && !("picard_collectmultiplemetrics" in skip_tools)) {
+    if (!("picard_collectmultiplemetrics" in skip_tools)) {
 
         ch_fai = PREPARE_GENOME.out.reference_fai
 
-        ch_bait_intervals = channel.fromPath(params.bait_intervals)
-            .collect()
-        ch_target_intervals = channel.fromPath(params.target_intervals)
-            .collect()
+        ch_bait_intervals = params.bait_intervals ? channel.fromPath(params.bait_intervals).collect() : channel.empty()
+        ch_target_intervals = params.target_intervals ? channel.fromPath(params.target_intervals).collect() : channel.empty()
 
         ch_ref_dict = PREPARE_GENOME.out.ref_dict
 
@@ -164,7 +162,10 @@ workflow SEQINSPECTOR {
             ch_samtools_index,
             ch_reference_fasta,
             ch_fai,
-            ch_ref_dict
+            params.run_picard_collecthsmetrics,
+            ch_bait_intervals,
+            ch_target_intervals,
+            ch_ref_dict,
         )
 
         ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.hs_metrics)

From 028d09597110a7f6973847fcb4902200562cc833 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Mon, 1 Dec 2025 14:27:18 +0100
Subject: [PATCH 447/530] Update QC_BAM test.

---
 subworkflows/local/qc_bam/tests/main.nf.test  | 23 ++++++++++++++-----
 .../local/qc_bam/tests/main.nf.test.snap      | 10 +++++++-
 2 files changed, 26 insertions(+), 7 deletions(-)

diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test
index 5494f68a..e5b2da3c 100644
--- a/subworkflows/local/qc_bam/tests/main.nf.test
+++ b/subworkflows/local/qc_bam/tests/main.nf.test
@@ -21,15 +21,21 @@ nextflow_workflow {
                 input[0]  = channel.of(
                     [
                         [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'],
-                        [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)],
+                        [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)]
+                    ]
+                )
+                input[1]  = channel.of(
+                    [
+                        [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'],
                         [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)]
                     ]
                 )
-                input[1]  = channel.fromPath(params.pipelines_testdata_base_path + '/reference/target.bed', checkIfExists: true).collect()
-                input[2]  = channel.fromPath(params.pipelines_testdata_base_path + '/reference/target.bed', checkIfExists: true).collect()
-                input[3]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta', checkIfExists: true)).collect()
-                input[4]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta.fai', checkIfExists: true)).collect()
-                input[5]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.dict', checkIfExists: true)).collect()
+                input[2]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta', checkIfExists: true)).collect()
+                input[3]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta.fai', checkIfExists: true)).collect()
+                input[4]  = true
+                input[5]  = channel.fromPath(params.pipelines_testdata_base_path + '/reference/target.bed', checkIfExists: true).collect()
+                input[6]  = channel.fromPath(params.pipelines_testdata_base_path + '/reference/target.bed', checkIfExists: true).collect()
+                input[7]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.dict', checkIfExists: true)).collect()
                 """
             }
         }
@@ -37,6 +43,11 @@ nextflow_workflow {
         then {
             assert workflow.success
             assert snapshot(
+                            workflow.out.multiple_metrics
+                                    .collect {it[1]}
+                                    .flatten()
+                                    .collect { file(it).name }
+                                    .toSorted(),
                             workflow.out.hs_metrics
                                     .collect {it[1]}
                                     .flatten()
diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap
index 4aefab56..33dfda38 100644
--- a/subworkflows/local/qc_bam/tests/main.nf.test.snap
+++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap
@@ -1,10 +1,18 @@
 {
     "Should run without failures": {
         "content": [
+            [
+                "earlycasualcaiman.CollectMultipleMetrics.alignment_summary_metrics",
+                "earlycasualcaiman.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "earlycasualcaiman.CollectMultipleMetrics.insert_size_metrics",
+                "earlycasualcaiman.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "earlycasualcaiman.CollectMultipleMetrics.quality_distribution_metrics"
+            ],
             [
                 "earlycasualcaiman.CollectHsMetrics.coverage_metrics"
             ],
             [
+                "versions.yml:md5,108c8ce4c159f43894c7800f3b69fbfd",
                 "versions.yml:md5,8508bd28eaf1fffcdc4d78e4d9f95393"
             ]
         ],
@@ -12,6 +20,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-11-28T09:03:50.918024"
+        "timestamp": "2025-12-01T14:06:04.611269"
     }
 }
\ No newline at end of file

From 4ddf0326e9d17a0a4700e7e291b28179450af5fd Mon Sep 17 00:00:00 2001
From: Beatriz Vinhas <beatriz.sa.vinhas@gmail.com>
Date: Mon, 1 Dec 2025 14:43:06 +0100
Subject: [PATCH 448/530] Update usage.md

---
 docs/usage.md | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/docs/usage.md b/docs/usage.md
index 49112a6f..209886eb 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -104,8 +104,6 @@ Optionally, the `sample_size` parameter allows you to subset a random number of
 nextflow run nf-core/seqinspector --input ./samplesheet.csv --outdir ./results --sample_size 1000000 -profile docker
 ```
 
-The pipeline supports hybrid-selection data, use the flag `--run_picard_collecthsmetrics true` if you want to run the QC tool [picard CollectHSmetrics](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard). This tool is not run by default.
-
 ### Skipping tools
 
 Some tools might not be compatible with your data. In this case you can skip them by providing a comma-separated list of tools to be skipped with the `--skip_tools` parameter.
@@ -229,3 +227,9 @@ We recommend adding the following line to your environment to limit this (typica
 ```bash
 NXF_OPTS='-Xms1g -Xmx4g'
 ```
+
+## Hybrid-selection QC metrics
+
+The pipeline supports hybrid-selection (HS) QC metrics collection . Use `--run_picard_collecthsmetrics true` to run the QC tool [picard CollectHSmetrics](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard). This tool is otherwise not run by default.
+
+

From 030eb2ea327163252cc476ca594ae55b82182025 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Mon, 1 Dec 2025 14:45:41 +0100
Subject: [PATCH 449/530] Edit CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index da46257e..f68dc17c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -31,6 +31,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#132](https://github.com/nf-core/seqinspector/pull/132) Added a bwamem2 index params for faster output
 - [#151](https://github.com/nf-core/seqinspector/pull/151) Added a prepare_genome subworkflow to handle bwamem2 indexing
 - [#159](https://github.com/nf-core/seqinspector/pull/159) Added a subworkflow QC_BAM including picard_collecthsmetrics for alignment QC of hybrid-selection data
+- [#158](https://github.com/nf-core/seqinspector/pull/158) Moved picard_collectmultiplemetrics to the subworkflow QC_BAM
 
 ### `Fixed`
 

From 03a973193a686cd536cbf32bfdcee1e8f86c0765 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Mon, 1 Dec 2025 14:48:11 +0100
Subject: [PATCH 450/530] Run prettier.

---
 docs/usage.md | 2 --
 1 file changed, 2 deletions(-)

diff --git a/docs/usage.md b/docs/usage.md
index 209886eb..1259d7af 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -231,5 +231,3 @@ NXF_OPTS='-Xms1g -Xmx4g'
 ## Hybrid-selection QC metrics
 
 The pipeline supports hybrid-selection (HS) QC metrics collection . Use `--run_picard_collecthsmetrics true` to run the QC tool [picard CollectHSmetrics](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard). This tool is otherwise not run by default.
-
-

From d71d9350008ba196bd247dfe3cb837bc2f303d39 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Mon, 1 Dec 2025 15:30:31 +0100
Subject: [PATCH 451/530] Rename ch_reference_fai.

---
 workflows/seqinspector.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index fdd6da7e..62b5a7cc 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -149,7 +149,7 @@ workflow SEQINSPECTOR {
 
     if (!("picard_collectmultiplemetrics" in skip_tools)) {
 
-        ch_fai = PREPARE_GENOME.out.reference_fai
+        ch_reference_fai = PREPARE_GENOME.out.reference_fai
 
         ch_bait_intervals = params.bait_intervals ? channel.fromPath(params.bait_intervals).collect() : channel.empty()
         ch_target_intervals = params.target_intervals ? channel.fromPath(params.target_intervals).collect() : channel.empty()
@@ -161,7 +161,7 @@ workflow SEQINSPECTOR {
             ch_bwamem2_mem,
             ch_samtools_index,
             ch_reference_fasta,
-            ch_fai,
+            ch_reference_fai,
             params.run_picard_collecthsmetrics,
             ch_bait_intervals,
             ch_target_intervals,

From 520ccdc90460a7e4506037398024dd511babbbbc Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Mon, 1 Dec 2025 15:45:43 +0100
Subject: [PATCH 452/530] Update PREPARE_GENOME input parameters description

---
 subworkflows/local/prepare_genome/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf
index b0571523..88877e4e 100644
--- a/subworkflows/local/prepare_genome/main.nf
+++ b/subworkflows/local/prepare_genome/main.nf
@@ -11,8 +11,8 @@ workflow PREPARE_GENOME {
     ch_reference_fasta
     bwamem2
     skip_tools
-    run_picard_collecthsmetrics  // value: [mandatory] [ bool ]
-    ref_dict                     // value: [mandatory] [ path(ref_dict) ]
+    run_picard_collecthsmetrics  // string: [mandatory for collecthsmetrics] bool
+    ref_dict                     // string: [mandatory for collecthsmetrics] path(ref_dict)
 
     main:
     // Initialize all channels that might be used later

From 95ac7b5077616ece85ee80b6263be99eeaf286f7 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 2 Dec 2025 10:05:47 +0100
Subject: [PATCH 453/530] Fix prepare_genome/main.nf

---
 subworkflows/local/prepare_genome/main.nf | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf
index 013d4db2..eb319de3 100644
--- a/subworkflows/local/prepare_genome/main.nf
+++ b/subworkflows/local/prepare_genome/main.nf
@@ -1,8 +1,8 @@
 //
 // Prepare reference genome files
 
-include { BWAMEM2_INDEX                 } from '../../../modules/nf-core/bwamem2/index'
-include { SAMTOOLS_FAIDX                } from '../../../modules/nf-core/samtools/faidx'
+include { BWAMEM2_INDEX  } from '../../../modules/nf-core/bwamem2/index'
+include { SAMTOOLS_FAIDX } from '../../../modules/nf-core/samtools/faidx'
 
 workflow PREPARE_GENOME {
 
@@ -15,7 +15,6 @@ workflow PREPARE_GENOME {
     // Initialize all channels that might be used later
     ch_bwamem2_index      = channel.empty()
     ch_reference_fai      = channel.empty()
-    ch_reference_fasta    = channel.empty()
     ch_versions           = channel.empty()
 
     if (!("bwamem2_index" in skip_tools)) {

From 5a1196cda3e37a67428259053829cd0a6113b571 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 2 Dec 2025 10:18:56 +0100
Subject: [PATCH 454/530] Add tests

---
 .../local/prepare_genome/tests/main.nf.test   | 47 +++++++++++++++++++
 .../prepare_genome/tests/main.nf.test.snap    | 21 +++++++++
 2 files changed, 68 insertions(+)
 create mode 100644 subworkflows/local/prepare_genome/tests/main.nf.test
 create mode 100644 subworkflows/local/prepare_genome/tests/main.nf.test.snap

diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test b/subworkflows/local/prepare_genome/tests/main.nf.test
new file mode 100644
index 00000000..caa38f60
--- /dev/null
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test
@@ -0,0 +1,47 @@
+nextflow_workflow {
+
+    name "Test Workflow PREPARE_GENOME"
+    script "subworkflows/local/prepare_genome/main.nf"
+    workflow "PREPARE_GENOME"
+    tag 'subworkflows'
+    tag 'prepare_genome'
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                pipelines_testdata_base_path    = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease'
+                run_picard_collecthsmetrics     = true
+                config "./nextflow.config"
+                outdir = "$outputDir"
+
+            }
+            workflow {
+                """
+                input[0]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta', checkIfExists: true)).collect()
+                input[1]  = null
+                input[2]  = ''
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert snapshot(
+                            workflow.out.bwamem2_index
+                                    .collect {it[1]}
+                                    .flatten()
+                                    .collect { file(it).name }
+                                    .toSorted(),
+                            workflow.out.reference_fai
+                                    .collect {it[1]}
+                                    .flatten()
+                                    .collect { file(it).name }
+                                    .toSorted(),
+                            workflow.out.versions
+                            ).match()
+        }
+
+    }
+
+}
\ No newline at end of file
diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test.snap b/subworkflows/local/prepare_genome/tests/main.nf.test.snap
new file mode 100644
index 00000000..06755d0a
--- /dev/null
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test.snap
@@ -0,0 +1,21 @@
+{
+    "Should run without failures": {
+        "content": [
+            [
+                "bwamem2"
+            ],
+            [
+                "reference.fasta.fai"
+            ],
+            [
+                "versions.yml:md5,2ed4fadc0038a6a8f46063219d23d3ef",
+                "versions.yml:md5,784a8f5ab1ba9964b1b8c4d6427e3cbb"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2025-12-02T10:17:19.799498"
+    }
+}
\ No newline at end of file

From 7709979d0e1435294c09511cf0c5d1d1bc472c2f Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 2 Dec 2025 10:46:32 +0100
Subject: [PATCH 455/530] Update test

---
 .../local/prepare_genome/tests/main.nf.test   | 32 +++++++++++--------
 .../prepare_genome/tests/main.nf.test.snap    | 20 ++++++++----
 2 files changed, 31 insertions(+), 21 deletions(-)

diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test b/subworkflows/local/prepare_genome/tests/main.nf.test
index caa38f60..615ddb06 100644
--- a/subworkflows/local/prepare_genome/tests/main.nf.test
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test
@@ -26,20 +26,24 @@ nextflow_workflow {
         }
 
         then {
-            assert workflow.success
-            assert snapshot(
-                            workflow.out.bwamem2_index
-                                    .collect {it[1]}
-                                    .flatten()
-                                    .collect { file(it).name }
-                                    .toSorted(),
-                            workflow.out.reference_fai
-                                    .collect {it[1]}
-                                    .flatten()
-                                    .collect { file(it).name }
-                                    .toSorted(),
-                            workflow.out.versions
-                            ).match()
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(
+                params.outdir + '/bwamem2_index',
+                relative: true, includeDir: true
+            )
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(
+                params.outdir + '/bwamem2_index'
+            )
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // All stable path names, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
         }
 
     }
diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test.snap b/subworkflows/local/prepare_genome/tests/main.nf.test.snap
index 06755d0a..03870388 100644
--- a/subworkflows/local/prepare_genome/tests/main.nf.test.snap
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test.snap
@@ -2,20 +2,26 @@
     "Should run without failures": {
         "content": [
             [
-                "bwamem2"
+                "",
+                "bwamem2",
+                "bwamem2/reference.fasta.0123",
+                "bwamem2/reference.fasta.amb",
+                "bwamem2/reference.fasta.ann",
+                "bwamem2/reference.fasta.bwt.2bit.64",
+                "bwamem2/reference.fasta.pac"
             ],
             [
-                "reference.fasta.fai"
-            ],
-            [
-                "versions.yml:md5,2ed4fadc0038a6a8f46063219d23d3ef",
-                "versions.yml:md5,784a8f5ab1ba9964b1b8c4d6427e3cbb"
+                "reference.fasta.0123:md5,0f0ff4414949e6787a25a563f19e2a3b",
+                "reference.fasta.amb:md5,0a85644af00f9a856d874381d24e7803",
+                "reference.fasta.ann:md5,8fdb46970ca95a4ef54f5f1a02d233cd",
+                "reference.fasta.bwt.2bit.64:md5,3c0df9450afc5cb0ad5e85870829d9d0",
+                "reference.fasta.pac:md5,96b449e1316067fdfba91b1399687bc2"
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-02T10:17:19.799498"
+        "timestamp": "2025-12-02T10:43:49.438931"
     }
 }
\ No newline at end of file

From f57ef72753eab9e69af5262eb8b1ce2948caf37f Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 2 Dec 2025 10:51:06 +0100
Subject: [PATCH 456/530] Update prepare_genome/main.nf

---
 subworkflows/local/prepare_genome/main.nf | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf
index 88877e4e..260b8a60 100644
--- a/subworkflows/local/prepare_genome/main.nf
+++ b/subworkflows/local/prepare_genome/main.nf
@@ -1,8 +1,8 @@
 //
 // Prepare reference genome files
 
-include { BWAMEM2_INDEX                 } from '../../../modules/nf-core/bwamem2/index'
-include { SAMTOOLS_FAIDX                } from '../../../modules/nf-core/samtools/faidx'
+include { BWAMEM2_INDEX                   } from '../../../modules/nf-core/bwamem2/index'
+include { SAMTOOLS_FAIDX                  } from '../../../modules/nf-core/samtools/faidx'
 include { PICARD_CREATESEQUENCEDICTIONARY } from '../../../modules/nf-core/picard/createsequencedictionary/main'
 
 workflow PREPARE_GENOME {
@@ -18,7 +18,6 @@ workflow PREPARE_GENOME {
     // Initialize all channels that might be used later
     ch_bwamem2_index      = channel.empty()
     ch_reference_fai      = channel.empty()
-    ch_reference_fasta    = channel.empty()
     ch_ref_dict           = channel.empty()
     ch_versions           = channel.empty()
 

From dc9690e90e6068fb38a9e7dd5733ea93d1d123d5 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 2 Dec 2025 11:58:20 +0100
Subject: [PATCH 457/530] Add publishDir for PICARD_CREATESEQUENCEDICTIONARY

---
 conf/modules.config | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/conf/modules.config b/conf/modules.config
index 5c3ec743..2ceca15d 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -43,6 +43,14 @@ process {
         ]
     }
 
+    withName: 'PICARD_CREATESEQUENCEDICTIONARY' {
+        publishDir = [
+            path: { "${params.outdir}/picard_createsequencedictionary" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: 'BWAMEM2_MEM' {
         publishDir = [
             path: { "${params.outdir}/bwamem2_mem" },

From 63df743814643b1127ebd1451a6074b22c06347f Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 2 Dec 2025 11:58:35 +0100
Subject: [PATCH 458/530] Refactor tests

---
 .../local/prepare_genome/tests/main.nf.test   | 126 ++++++++++++++++--
 .../prepare_genome/tests/main.nf.test.snap    |  62 ++++++++-
 2 files changed, 169 insertions(+), 19 deletions(-)

diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test b/subworkflows/local/prepare_genome/tests/main.nf.test
index 615ddb06..e6c3f907 100644
--- a/subworkflows/local/prepare_genome/tests/main.nf.test
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test
@@ -6,7 +6,7 @@ nextflow_workflow {
     tag 'subworkflows'
     tag 'prepare_genome'
 
-    test("Should run without failures") {
+    test("Test without bwamem2 index file path and with run_picard_collecthsmetrics=false") {
 
         when {
             params {
@@ -21,28 +21,130 @@ nextflow_workflow {
                 input[0]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta', checkIfExists: true)).collect()
                 input[1]  = null
                 input[2]  = ''
+                input[3]  = false
+                input[4]  = null
                 """
             }
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(
+            // All files + folders produced by BWAMEM2_INDEX
+            def bwamem2_index_files = getAllFilesFromDir(
                 params.outdir + '/bwamem2_index',
                 relative: true, includeDir: true
             )
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(
-                params.outdir + '/bwamem2_index'
+            // All files + folders produced by SAMTOOLS_FAIDX
+            def samtools_faidx_files = getAllFilesFromDir(
+                params.outdir + '/samtools_faidx',
+                relative: true, includeDir: true
+            )
+
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    bwamem2_index_files,
+                    samtools_faidx_files
+                ).match() },
+                // BWAMEM2_INDEX and SAMTOOLS_FAIDX should be run
+                { assert workflow.out.versions.size() == 2 }
+            )
+        }
+
+    }
+
+    test("Test without bwamem2 index file path, with run_picard_collecthsmetrics=true and with ref_dict") {
+
+        when {
+            params {
+                pipelines_testdata_base_path    = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease'
+                run_picard_collecthsmetrics     = true
+                config "./nextflow.config"
+                outdir = "$outputDir"
+
+            }
+            workflow {
+                """
+                input[0]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta', checkIfExists: true)).collect()
+                input[1]  = null
+                input[2]  = ''
+                input[3]  = true
+                input[4]  = params.pipelines_testdata_base_path + '/reference/reference.dict'
+                """
+            }
+        }
+
+        then {
+            // All files + folders produced by BWAMEM2_INDEX
+            def bwamem2_index_files = getAllFilesFromDir(
+                params.outdir + '/bwamem2_index',
+                relative: true, includeDir: true
+            )
+            // All files + folders produced by SAMTOOLS_FAIDX
+            def samtools_faidx_files = getAllFilesFromDir(
+                params.outdir + '/samtools_faidx',
+                relative: true, includeDir: true
+            )
+
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    bwamem2_index_files,
+                    samtools_faidx_files
+                ).match() },
+                // BWAMEM2_INDEX and SAMTOOLS_FAIDX should be run
+                { assert workflow.out.versions.size() == 2 }
+            )
+        }
+
+    }
+
+    test("Test without bwamem2 index file path, with run_picard_collecthsmetrics=true and without ref_dict") {
+
+        when {
+            params {
+                pipelines_testdata_base_path    = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease'
+                run_picard_collecthsmetrics     = true
+                config "./nextflow.config"
+                outdir = "$outputDir"
+
+            }
+            workflow {
+                """
+                input[0]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta', checkIfExists: true)).collect()
+                input[1]  = null
+                input[2]  = ''
+                input[3]  = true
+                input[4]  = null
+                """
+            }
+        }
+
+        then {
+            // All files + folders produced by BWAMEM2_INDEX
+            def bwamem2_index_files = getAllFilesFromDir(
+                params.outdir + '/bwamem2_index',
+                relative: true, includeDir: true
+            )
+            // All files + folders produced by SAMTOOLS_FAIDX
+            def samtools_faidx_files = getAllFilesFromDir(
+                params.outdir + '/samtools_faidx',
+                relative: true, includeDir: true
+            )
+            // All files + folders produced by PICARD_CREATESEQUENCEDICTIONARY
+            def picard_createsequencedictionary_files = getAllFilesFromDir(
+                params.outdir + '/picard_createsequencedictionary',
+                relative: true, includeDir: true
             )
+
             assertAll(
-                { assert workflow.success},
+                { assert workflow.success },
                 { assert snapshot(
-                    // All stable path names, with a relative path
-                    stable_name,
-                    // All files with stable contents
-                    stable_path
-                ).match() }
+                    bwamem2_index_files,
+                    samtools_faidx_files,
+                    picard_createsequencedictionary_files
+                ).match() },
+                // BWAMEM2_INDEX, SAMTOOLS_FAIDX and PICARD_CREATESEQUENCEDICTIONARY should be run
+                { assert workflow.out.versions.size() == 3 }
             )
         }
 
diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test.snap b/subworkflows/local/prepare_genome/tests/main.nf.test.snap
index 03870388..69aaba82 100644
--- a/subworkflows/local/prepare_genome/tests/main.nf.test.snap
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "Should run without failures": {
+    "Test without bwamem2 index file path, with run_picard_collecthsmetrics=true and without ref_dict": {
         "content": [
             [
                 "",
@@ -11,17 +11,65 @@
                 "bwamem2/reference.fasta.pac"
             ],
             [
-                "reference.fasta.0123:md5,0f0ff4414949e6787a25a563f19e2a3b",
-                "reference.fasta.amb:md5,0a85644af00f9a856d874381d24e7803",
-                "reference.fasta.ann:md5,8fdb46970ca95a4ef54f5f1a02d233cd",
-                "reference.fasta.bwt.2bit.64:md5,3c0df9450afc5cb0ad5e85870829d9d0",
-                "reference.fasta.pac:md5,96b449e1316067fdfba91b1399687bc2"
+                "",
+                "reference.fasta.fai",
+                "reference.fasta.sizes"
+            ],
+            [
+                "",
+                "genome.dict"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2025-12-02T11:58:24.141721"
+    },
+    "Test without bwamem2 index file path, with run_picard_collecthsmetrics=true and with ref_dict": {
+        "content": [
+            [
+                "",
+                "bwamem2",
+                "bwamem2/reference.fasta.0123",
+                "bwamem2/reference.fasta.amb",
+                "bwamem2/reference.fasta.ann",
+                "bwamem2/reference.fasta.bwt.2bit.64",
+                "bwamem2/reference.fasta.pac"
+            ],
+            [
+                "",
+                "reference.fasta.fai",
+                "reference.fasta.sizes"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2025-12-02T11:57:18.592897"
+    },
+    "Test without bwamem2 index file path and with run_picard_collecthsmetrics=false": {
+        "content": [
+            [
+                "",
+                "bwamem2",
+                "bwamem2/reference.fasta.0123",
+                "bwamem2/reference.fasta.amb",
+                "bwamem2/reference.fasta.ann",
+                "bwamem2/reference.fasta.bwt.2bit.64",
+                "bwamem2/reference.fasta.pac"
+            ],
+            [
+                "",
+                "reference.fasta.fai",
+                "reference.fasta.sizes"
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-02T10:43:49.438931"
+        "timestamp": "2025-12-02T11:56:19.206085"
     }
 }
\ No newline at end of file

From c26104cd3acab6c75f221f7444248263cc6ab044 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 2 Dec 2025 12:02:29 +0100
Subject: [PATCH 459/530] Fix end of file main.nf.test

---
 subworkflows/local/prepare_genome/tests/main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test b/subworkflows/local/prepare_genome/tests/main.nf.test
index e6c3f907..65a3884a 100644
--- a/subworkflows/local/prepare_genome/tests/main.nf.test
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test
@@ -150,4 +150,4 @@ nextflow_workflow {
 
     }
 
-}
\ No newline at end of file
+}

From e55caaa0e836ab888d5100ab58e1872cce301a29 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 2 Dec 2025 12:05:17 +0100
Subject: [PATCH 460/530] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index da46257e..c3e95b6f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -31,6 +31,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#132](https://github.com/nf-core/seqinspector/pull/132) Added a bwamem2 index params for faster output
 - [#151](https://github.com/nf-core/seqinspector/pull/151) Added a prepare_genome subworkflow to handle bwamem2 indexing
 - [#159](https://github.com/nf-core/seqinspector/pull/159) Added a subworkflow QC_BAM including picard_collecthsmetrics for alignment QC of hybrid-selection data
+- [#162](https://github.com/nf-core/seqinspector/pull/162) Fix bug in prepare_genome subworkflow and add tests
 
 ### `Fixed`
 

From 83e319add92cb0e6f7efdfeb22d9e9eac90bc819 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 2 Dec 2025 12:09:21 +0100
Subject: [PATCH 461/530] Update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c3e95b6f..f14c16df 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -31,7 +31,6 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#132](https://github.com/nf-core/seqinspector/pull/132) Added a bwamem2 index params for faster output
 - [#151](https://github.com/nf-core/seqinspector/pull/151) Added a prepare_genome subworkflow to handle bwamem2 indexing
 - [#159](https://github.com/nf-core/seqinspector/pull/159) Added a subworkflow QC_BAM including picard_collecthsmetrics for alignment QC of hybrid-selection data
-- [#162](https://github.com/nf-core/seqinspector/pull/162) Fix bug in prepare_genome subworkflow and add tests
 
 ### `Fixed`
 
@@ -40,6 +39,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#107](https://github.com/nf-core/seqinspector/pull/107) Put SeqFU-stats section reports together
 - [#112](https://github.com/nf-core/seqinspector/pull/112) Making fastq_screen_references value to use parentDir
 - [#94] (https://github.com/nf-core/seqinspector/issues/94) Go through and validate test data
+- [#162](https://github.com/nf-core/seqinspector/pull/162) Fix bug in prepare_genome subworkflow and add tests
 
 ### `Dependencies`
 

From 446651dad3419173318edcdbcad2e49fbee2560d Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 2 Dec 2025 12:34:12 +0100
Subject: [PATCH 462/530] Revert redundant changes in modules.config

---
 conf/modules.config | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 2ceca15d..5c3ec743 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -43,14 +43,6 @@ process {
         ]
     }
 
-    withName: 'PICARD_CREATESEQUENCEDICTIONARY' {
-        publishDir = [
-            path: { "${params.outdir}/picard_createsequencedictionary" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
     withName: 'BWAMEM2_MEM' {
         publishDir = [
             path: { "${params.outdir}/bwamem2_mem" },

From 8d3a773ac0b96a8566699704b0a6c66d775e0343 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 2 Dec 2025 12:57:46 +0100
Subject: [PATCH 463/530] Update some snapshots

---
 .nf-test-2c8f93900b9462538ae8fc18f01382fe.nf |  93 ++++
 .nf-test-661c1e31a1798b8926bee5c65b147017.nf |  86 ++++
 .nf-test-9a3cd05e4fc62955ef9a17eeabbe5bbe.nf |  86 ++++
 .nf-test-c6919cb8935af9122d1bbfd0a0fb3974.nf |  86 ++++
 tests/MiSeq.main.nf.test.snap                | 219 ++++++---
 tests/MiSeq_PairedEnd.main.nf.test.snap      | 201 +++++---
 tests/NovaSeq6000.main.nf.test.snap          | 473 ++++++++++---------
 7 files changed, 902 insertions(+), 342 deletions(-)
 create mode 100644 .nf-test-2c8f93900b9462538ae8fc18f01382fe.nf
 create mode 100644 .nf-test-661c1e31a1798b8926bee5c65b147017.nf
 create mode 100644 .nf-test-9a3cd05e4fc62955ef9a17eeabbe5bbe.nf
 create mode 100644 .nf-test-c6919cb8935af9122d1bbfd0a0fb3974.nf

diff --git a/.nf-test-2c8f93900b9462538ae8fc18f01382fe.nf b/.nf-test-2c8f93900b9462538ae8fc18f01382fe.nf
new file mode 100644
index 00000000..f7fe99c4
--- /dev/null
+++ b/.nf-test-2c8f93900b9462538ae8fc18f01382fe.nf
@@ -0,0 +1,93 @@
+import groovy.json.JsonGenerator
+import groovy.json.JsonGenerator.Converter
+
+nextflow.enable.dsl=2
+
+// comes from nf-test to store json files
+params.nf_test_output  = ""
+
+// include dependencies
+
+
+// include test workflow
+include { QC_BAM } from '/Users/beatrizsavinhas/development/seqinspector/subworkflows/local/qc_bam/main.nf'
+
+// define custom rules for JSON that will be generated.
+def jsonOutput =
+    new JsonGenerator.Options()
+        .addConverter(Path) { value -> value.toAbsolutePath().toString() } // Custom converter for Path. Only filename
+        .build()
+
+def jsonWorkflowOutput = new JsonGenerator.Options().excludeNulls().build()
+
+workflow {
+
+    // run dependencies
+    
+
+    // workflow mapping
+    def input = []
+    
+                input[0]  = channel.of(
+                    [
+                        [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'],
+                        [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)],
+                        [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)]
+                    ]
+                )
+                input[1]  = channel.fromPath(params.pipelines_testdata_base_path + '/reference/target.bed', checkIfExists: true).collect()
+                input[2]  = channel.fromPath(params.pipelines_testdata_base_path + '/reference/target.bed', checkIfExists: true).collect()
+                input[3]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta', checkIfExists: true)).collect()
+                input[4]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta.fai', checkIfExists: true)).collect()
+                input[5]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.dict', checkIfExists: true)).collect()
+                
+    //----
+
+    //run workflow
+    QC_BAM(*input)
+    
+    if (QC_BAM.output){
+
+        // consumes all named output channels and stores items in a json file
+        for (def name in QC_BAM.out.getNames()) {
+            serializeChannel(name, QC_BAM.out.getProperty(name), jsonOutput)
+        }	  
+    
+        // consumes all unnamed output channels and stores items in a json file
+        def array = QC_BAM.out as Object[]
+        for (def i = 0; i < array.length ; i++) {
+            serializeChannel(i, array[i], jsonOutput)
+        }    	
+
+    }
+}
+
+
+def serializeChannel(name, channel, jsonOutput) {
+    def _name = name
+    def list = [ ]
+    channel.subscribe(
+        onNext: {
+            list.add(it)
+        },
+        onComplete: {
+              def map = new HashMap()
+              map[_name] = list
+              def filename = "${params.nf_test_output}/output_${_name}.json"
+              new File(filename).text = jsonOutput.toJson(map)		  		
+        } 
+    )
+}
+
+
+workflow.onComplete {
+
+    def result = [
+        success: workflow.success,
+        exitStatus: workflow.exitStatus,
+        errorMessage: workflow.errorMessage,
+        errorReport: workflow.errorReport
+    ]
+    new File("${params.nf_test_output}/workflow.json").text = jsonWorkflowOutput.toJson(result)
+    
+}
diff --git a/.nf-test-661c1e31a1798b8926bee5c65b147017.nf b/.nf-test-661c1e31a1798b8926bee5c65b147017.nf
new file mode 100644
index 00000000..ee32ae83
--- /dev/null
+++ b/.nf-test-661c1e31a1798b8926bee5c65b147017.nf
@@ -0,0 +1,86 @@
+import groovy.json.JsonGenerator
+import groovy.json.JsonGenerator.Converter
+
+nextflow.enable.dsl=2
+
+// comes from nf-test to store json files
+params.nf_test_output  = ""
+
+// include dependencies
+
+
+// include test workflow
+include { PREPARE_GENOME } from '/Users/beatrizsavinhas/development/seqinspector/subworkflows/local/prepare_genome/main.nf'
+
+// define custom rules for JSON that will be generated.
+def jsonOutput =
+    new JsonGenerator.Options()
+        .addConverter(Path) { value -> value.toAbsolutePath().toString() } // Custom converter for Path. Only filename
+        .build()
+
+def jsonWorkflowOutput = new JsonGenerator.Options().excludeNulls().build()
+
+workflow {
+
+    // run dependencies
+    
+
+    // workflow mapping
+    def input = []
+    
+                input[0]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta', checkIfExists: true)).collect()
+                input[1]  = null
+                input[2]  = ''
+                input[3]  = false
+                input[4]  = null
+                
+    //----
+
+    //run workflow
+    PREPARE_GENOME(*input)
+    
+    if (PREPARE_GENOME.output){
+
+        // consumes all named output channels and stores items in a json file
+        for (def name in PREPARE_GENOME.out.getNames()) {
+            serializeChannel(name, PREPARE_GENOME.out.getProperty(name), jsonOutput)
+        }	  
+    
+        // consumes all unnamed output channels and stores items in a json file
+        def array = PREPARE_GENOME.out as Object[]
+        for (def i = 0; i < array.length ; i++) {
+            serializeChannel(i, array[i], jsonOutput)
+        }    	
+
+    }
+}
+
+
+def serializeChannel(name, channel, jsonOutput) {
+    def _name = name
+    def list = [ ]
+    channel.subscribe(
+        onNext: {
+            list.add(it)
+        },
+        onComplete: {
+              def map = new HashMap()
+              map[_name] = list
+              def filename = "${params.nf_test_output}/output_${_name}.json"
+              new File(filename).text = jsonOutput.toJson(map)		  		
+        } 
+    )
+}
+
+
+workflow.onComplete {
+
+    def result = [
+        success: workflow.success,
+        exitStatus: workflow.exitStatus,
+        errorMessage: workflow.errorMessage,
+        errorReport: workflow.errorReport
+    ]
+    new File("${params.nf_test_output}/workflow.json").text = jsonWorkflowOutput.toJson(result)
+    
+}
diff --git a/.nf-test-9a3cd05e4fc62955ef9a17eeabbe5bbe.nf b/.nf-test-9a3cd05e4fc62955ef9a17eeabbe5bbe.nf
new file mode 100644
index 00000000..2ea62047
--- /dev/null
+++ b/.nf-test-9a3cd05e4fc62955ef9a17eeabbe5bbe.nf
@@ -0,0 +1,86 @@
+import groovy.json.JsonGenerator
+import groovy.json.JsonGenerator.Converter
+
+nextflow.enable.dsl=2
+
+// comes from nf-test to store json files
+params.nf_test_output  = ""
+
+// include dependencies
+
+
+// include test workflow
+include { PREPARE_GENOME } from '/Users/beatrizsavinhas/development/seqinspector/subworkflows/local/prepare_genome/main.nf'
+
+// define custom rules for JSON that will be generated.
+def jsonOutput =
+    new JsonGenerator.Options()
+        .addConverter(Path) { value -> value.toAbsolutePath().toString() } // Custom converter for Path. Only filename
+        .build()
+
+def jsonWorkflowOutput = new JsonGenerator.Options().excludeNulls().build()
+
+workflow {
+
+    // run dependencies
+    
+
+    // workflow mapping
+    def input = []
+    
+                input[0]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta', checkIfExists: true)).collect()
+                input[1]  = null
+                input[2]  = ''
+                input[3]  = true
+                input[4]  = params.pipelines_testdata_base_path + '/reference/reference.dict'
+                
+    //----
+
+    //run workflow
+    PREPARE_GENOME(*input)
+    
+    if (PREPARE_GENOME.output){
+
+        // consumes all named output channels and stores items in a json file
+        for (def name in PREPARE_GENOME.out.getNames()) {
+            serializeChannel(name, PREPARE_GENOME.out.getProperty(name), jsonOutput)
+        }	  
+    
+        // consumes all unnamed output channels and stores items in a json file
+        def array = PREPARE_GENOME.out as Object[]
+        for (def i = 0; i < array.length ; i++) {
+            serializeChannel(i, array[i], jsonOutput)
+        }    	
+
+    }
+}
+
+
+def serializeChannel(name, channel, jsonOutput) {
+    def _name = name
+    def list = [ ]
+    channel.subscribe(
+        onNext: {
+            list.add(it)
+        },
+        onComplete: {
+              def map = new HashMap()
+              map[_name] = list
+              def filename = "${params.nf_test_output}/output_${_name}.json"
+              new File(filename).text = jsonOutput.toJson(map)		  		
+        } 
+    )
+}
+
+
+workflow.onComplete {
+
+    def result = [
+        success: workflow.success,
+        exitStatus: workflow.exitStatus,
+        errorMessage: workflow.errorMessage,
+        errorReport: workflow.errorReport
+    ]
+    new File("${params.nf_test_output}/workflow.json").text = jsonWorkflowOutput.toJson(result)
+    
+}
diff --git a/.nf-test-c6919cb8935af9122d1bbfd0a0fb3974.nf b/.nf-test-c6919cb8935af9122d1bbfd0a0fb3974.nf
new file mode 100644
index 00000000..0e1157d7
--- /dev/null
+++ b/.nf-test-c6919cb8935af9122d1bbfd0a0fb3974.nf
@@ -0,0 +1,86 @@
+import groovy.json.JsonGenerator
+import groovy.json.JsonGenerator.Converter
+
+nextflow.enable.dsl=2
+
+// comes from nf-test to store json files
+params.nf_test_output  = ""
+
+// include dependencies
+
+
+// include test workflow
+include { PREPARE_GENOME } from '/Users/beatrizsavinhas/development/seqinspector/subworkflows/local/prepare_genome/main.nf'
+
+// define custom rules for JSON that will be generated.
+def jsonOutput =
+    new JsonGenerator.Options()
+        .addConverter(Path) { value -> value.toAbsolutePath().toString() } // Custom converter for Path. Only filename
+        .build()
+
+def jsonWorkflowOutput = new JsonGenerator.Options().excludeNulls().build()
+
+workflow {
+
+    // run dependencies
+    
+
+    // workflow mapping
+    def input = []
+    
+                input[0]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta', checkIfExists: true)).collect()
+                input[1]  = null
+                input[2]  = ''
+                input[3]  = true
+                input[4]  = null
+                
+    //----
+
+    //run workflow
+    PREPARE_GENOME(*input)
+    
+    if (PREPARE_GENOME.output){
+
+        // consumes all named output channels and stores items in a json file
+        for (def name in PREPARE_GENOME.out.getNames()) {
+            serializeChannel(name, PREPARE_GENOME.out.getProperty(name), jsonOutput)
+        }	  
+    
+        // consumes all unnamed output channels and stores items in a json file
+        def array = PREPARE_GENOME.out as Object[]
+        for (def i = 0; i < array.length ; i++) {
+            serializeChannel(i, array[i], jsonOutput)
+        }    	
+
+    }
+}
+
+
+def serializeChannel(name, channel, jsonOutput) {
+    def _name = name
+    def list = [ ]
+    channel.subscribe(
+        onNext: {
+            list.add(it)
+        },
+        onComplete: {
+              def map = new HashMap()
+              map[_name] = list
+              def filename = "${params.nf_test_output}/output_${_name}.json"
+              new File(filename).text = jsonOutput.toJson(map)		  		
+        } 
+    )
+}
+
+
+workflow.onComplete {
+
+    def result = [
+        success: workflow.success,
+        exitStatus: workflow.exitStatus,
+        errorMessage: workflow.errorMessage,
+        errorReport: workflow.errorReport
+    ]
+    new File("${params.nf_test_output}/workflow.json").text = jsonWorkflowOutput.toJson(result)
+    
+}
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index ff3e6b3a..f2cd38ad 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -19,27 +19,42 @@
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_report.html",
                 "pipeline_info",
-                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"
+                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "samtools_faidx",
+                "samtools_faidx/genome.fa.fai",
+                "samtools_faidx/genome.fa.sizes"
             ],
             [
-                "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
+                "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
+                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc"
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.0"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-11-25T13:17:00.197170378"
+        "timestamp": "2025-12-02T12:24:49.888119"
     },
     "MiSeq data test (single end reads)": {
         "content": [
             {
+                "BWAMEM2_MEM": {
+                    "bwamem2": "2.2.1",
+                    "samtools": "1.22.1"
+                },
                 "FASTQC": {
                     "fastqc": "0.12.1"
                 },
                 "FASTQSCREEN_FASTQSCREEN": {
                     "fastqscreen": "0.16.0"
                 },
+                "PICARD_COLLECTMULTIPLEMETRICS": {
+                    "picard": "3.4.0"
+                },
+                "SAMTOOLS_INDEX": {
+                    "samtools": "1.22.1"
+                },
                 "SEQFU_STATS": {
                     "seqfu": "1.22.3"
                 },
@@ -48,6 +63,16 @@
                 }
             },
             [
+                "bwamem2_index",
+                "bwamem2_index/bwamem2",
+                "bwamem2_index/bwamem2/genome.fa.0123",
+                "bwamem2_index/bwamem2/genome.fa.amb",
+                "bwamem2_index/bwamem2/genome.fa.ann",
+                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
+                "bwamem2_index/bwamem2/genome.fa.pac",
+                "bwamem2_mem",
+                "bwamem2_mem/SAMPLE_SINGLE_END_1.bam",
+                "bwamem2_mem/SAMPLE_SINGLE_END_1.bam.bai",
                 "fastqc",
                 "fastqc/SAMPLE_SINGLE_END_1_fastqc.html",
                 "fastqc/SAMPLE_SINGLE_END_1_fastqc.zip",
@@ -77,60 +102,57 @@
                 "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
+                "picard_collectmultiplemetrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "samtools_faidx",
+                "samtools_faidx/genome.fa.fai",
+                "samtools_faidx/genome.fa.sizes",
                 "seqfu_stats",
                 "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu.tsv",
                 "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu_mqc.txt"
             ],
             [
+                "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
+                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
+                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
+                "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
+                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
+                "SAMPLE_SINGLE_END_1.bam:md5,ff8893272a6560cac7067fd8a9406f9b",
+                "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
                 "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
                 "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
                 "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
@@ -146,23 +168,52 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607",
                 "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,fe082d3b5dcc3d338e25bc027e17dc99",
+                "multiqc_picard_baseContent.txt:md5,796e8e0803ad3ed4fd1c76f073784942",
+                "multiqc_picard_quality_by_cycle.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
+                "multiqc_picard_quality_score_distribution.txt:md5,bad70b98811c4cbe4728f53334993703",
                 "multiqc_seqfu.txt:md5,7ec63bc3465b3fc8e316e2443ec4c848",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
+                "picard_QualityScoreDistribution_histogram.txt:md5,bad70b98811c4cbe4728f53334993703",
+                "picard_alignment_readlength_plot.txt:md5,0fe7e17f1c58b7a6291bc1ff80fdfaa0",
+                "picard_alignment_summary.txt:md5,c770d3ee98dadaee77ef43967a974627",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,65d43b083e90830aa9451bde65a261b8",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,31dc4f314d8e3f8e086e7ae761638023",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,d92fac15687942c0f9c436ba0cf55fc9",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,00b76f45bbfc9acd2774f90612e53333",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,5451af67007a16e7645d0393011414af",
+                "picard_quality_by_cycle.txt:md5,46fbe44a9788f2e9184e2c1d689c2876",
+                "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77",
+                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
+                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,33a9e44386f308d43881a58394b6b17c",
                 "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,e67e819605ab49182aacf1d676dc885d"
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.0"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-11-25T13:16:09.970027338"
+        "timestamp": "2025-12-02T12:22:09.04125"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
             {
+                "BWAMEM2_MEM": {
+                    "bwamem2": "2.2.1",
+                    "samtools": "1.22.1"
+                },
                 "FASTQSCREEN_FASTQSCREEN": {
                     "fastqscreen": "0.16.0"
                 },
+                "PICARD_COLLECTMULTIPLEMETRICS": {
+                    "picard": "3.4.0"
+                },
+                "SAMTOOLS_INDEX": {
+                    "samtools": "1.22.1"
+                },
                 "SEQFU_STATS": {
                     "seqfu": "1.22.3"
                 },
@@ -171,6 +222,16 @@
                 }
             },
             [
+                "bwamem2_index",
+                "bwamem2_index/bwamem2",
+                "bwamem2_index/bwamem2/genome.fa.0123",
+                "bwamem2_index/bwamem2/genome.fa.amb",
+                "bwamem2_index/bwamem2/genome.fa.ann",
+                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
+                "bwamem2_index/bwamem2/genome.fa.pac",
+                "bwamem2_mem",
+                "bwamem2_mem/SAMPLE_SINGLE_END_1.bam",
+                "bwamem2_mem/SAMPLE_SINGLE_END_1.bam.bai",
                 "fastqscreen",
                 "fastqscreen/SAMPLE_SINGLE_END_1_screen.html",
                 "fastqscreen/SAMPLE_SINGLE_END_1_screen.png",
@@ -185,44 +246,90 @@
                 "multiqc/global_report/multiqc_data/multiqc_citations.txt",
                 "multiqc/global_report/multiqc_data/multiqc_data.json",
                 "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
+                "picard_collectmultiplemetrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "samtools_faidx",
+                "samtools_faidx/genome.fa.fai",
+                "samtools_faidx/genome.fa.sizes",
                 "seqfu_stats",
                 "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu.tsv",
                 "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu_mqc.txt"
             ],
             [
+                "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
+                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
+                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
+                "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
+                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
+                "SAMPLE_SINGLE_END_1.bam:md5,ff8893272a6560cac7067fd8a9406f9b",
+                "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
                 "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
                 "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
                 "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,fe082d3b5dcc3d338e25bc027e17dc99",
+                "multiqc_picard_baseContent.txt:md5,796e8e0803ad3ed4fd1c76f073784942",
+                "multiqc_picard_quality_by_cycle.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
+                "multiqc_picard_quality_score_distribution.txt:md5,bad70b98811c4cbe4728f53334993703",
                 "multiqc_seqfu.txt:md5,7ec63bc3465b3fc8e316e2443ec4c848",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
+                "picard_QualityScoreDistribution_histogram.txt:md5,bad70b98811c4cbe4728f53334993703",
+                "picard_alignment_readlength_plot.txt:md5,0fe7e17f1c58b7a6291bc1ff80fdfaa0",
+                "picard_alignment_summary.txt:md5,c770d3ee98dadaee77ef43967a974627",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,65d43b083e90830aa9451bde65a261b8",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,31dc4f314d8e3f8e086e7ae761638023",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,d92fac15687942c0f9c436ba0cf55fc9",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,00b76f45bbfc9acd2774f90612e53333",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,5451af67007a16e7645d0393011414af",
+                "picard_quality_by_cycle.txt:md5,46fbe44a9788f2e9184e2c1d689c2876",
+                "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77",
+                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
+                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,33a9e44386f308d43881a58394b6b17c",
                 "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,e67e819605ab49182aacf1d676dc885d"
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.0"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-11-25T13:16:42.837673249"
+        "timestamp": "2025-12-02T12:24:18.752403"
     }
 }
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index f359d589..3dd42dc8 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -2,12 +2,22 @@
     "MiSeq data test (paired end reads)": {
         "content": [
             {
+                "BWAMEM2_MEM": {
+                    "bwamem2": "2.2.1",
+                    "samtools": "1.22.1"
+                },
                 "FASTQC": {
                     "fastqc": "0.12.1"
                 },
                 "FASTQSCREEN_FASTQSCREEN": {
                     "fastqscreen": "0.16.0"
                 },
+                "PICARD_COLLECTMULTIPLEMETRICS": {
+                    "picard": "3.4.0"
+                },
+                "SAMTOOLS_INDEX": {
+                    "samtools": "1.22.1"
+                },
                 "SEQFU_STATS": {
                     "seqfu": "1.22.3"
                 },
@@ -16,6 +26,18 @@
                 }
             },
             [
+                "bwamem2_index",
+                "bwamem2_index/bwamem2",
+                "bwamem2_index/bwamem2/genome.fa.0123",
+                "bwamem2_index/bwamem2/genome.fa.amb",
+                "bwamem2_index/bwamem2/genome.fa.ann",
+                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
+                "bwamem2_index/bwamem2/genome.fa.pac",
+                "bwamem2_mem",
+                "bwamem2_mem/SAMPLE_PAIRED_END_1_1.bam",
+                "bwamem2_mem/SAMPLE_PAIRED_END_1_1.bam.bai",
+                "bwamem2_mem/SAMPLE_PAIRED_END_2_2.bam",
+                "bwamem2_mem/SAMPLE_PAIRED_END_2_2.bam.bai",
                 "fastqc",
                 "fastqc/SAMPLE_PAIRED_END_1_1_1_fastqc.html",
                 "fastqc/SAMPLE_PAIRED_END_1_1_1_fastqc.zip",
@@ -59,49 +81,31 @@
                 "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_summary_Aligned_Bases.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_summary_Aligned_Reads.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_adapter_content_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "multiqc/group_reports",
                 "multiqc/group_reports/Bpacificus",
@@ -124,52 +128,54 @@
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_alignment_summary_Aligned_Bases.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_alignment_summary_Aligned_Reads.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_plots",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_adapter_content_plot.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_report.html",
+                "picard_collectmultiplemetrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "samtools_faidx",
+                "samtools_faidx/genome.fa.fai",
+                "samtools_faidx/genome.fa.sizes",
                 "seqfu_stats",
                 "seqfu_stats/SAMPLE_PAIRED_END_1_1_seqfu.tsv",
                 "seqfu_stats/SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt",
@@ -177,6 +183,15 @@
                 "seqfu_stats/SAMPLE_PAIRED_END_2_2_seqfu_mqc.txt"
             ],
             [
+                "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
+                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
+                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
+                "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
+                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
+                "SAMPLE_PAIRED_END_1_1.bam:md5,44c0ef738b73e26f67ded45ca4cb9e5b",
+                "SAMPLE_PAIRED_END_1_1.bam.bai:md5,82724835c47f8e1d1a86e13ef469b464",
+                "SAMPLE_PAIRED_END_2_2.bam:md5,9e20db3f3088fc478c223839e3a4ed62",
+                "SAMPLE_PAIRED_END_2_2.bam.bai:md5,3c4bdff0f906f2234fdeee8eea719210",
                 "SAMPLE_PAIRED_END_1_1_1_screen.png:md5,f52ddd0e65f23f68dd8d58d5453417db",
                 "SAMPLE_PAIRED_END_1_1_1_screen.txt:md5,921b08eeb461a2aa1bd42bba53900f70",
                 "SAMPLE_PAIRED_END_1_1_2_screen.png:md5,908f4fceea8aa546106efdaa7ca78f7d",
@@ -198,7 +213,25 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,5ef00028497d3271c9f0ea9a961db1e5",
                 "multiqc_fastqc.txt:md5,bc499ad273fd1c887056c31b82544984",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,35d289ee535a0442db72a65391f375eb",
+                "multiqc_picard_baseContent.txt:md5,72b0ae83ed58052bfd768021d377c78f",
+                "multiqc_picard_quality_by_cycle.txt:md5,f6514f14befb874ded5aed79caba3e7b",
+                "multiqc_picard_quality_score_distribution.txt:md5,99be409e325619171b820d762dd023c0",
                 "multiqc_seqfu.txt:md5,139354afd154804b4b77f997277f3ee9",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,f6514f14befb874ded5aed79caba3e7b",
+                "picard_QualityScoreDistribution_histogram.txt:md5,99be409e325619171b820d762dd023c0",
+                "picard_alignment_readlength_plot.txt:md5,4172702f791d043135f21e3a227fe712",
+                "picard_alignment_summary_Aligned_Bases.txt:md5,a166c14210e17d3541482b500443f792",
+                "picard_alignment_summary_Aligned_Reads.txt:md5,c5e5228e85ffb2182274d641ffa6743f",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,3fe18f1144eb85f9206d1bee4eb11bb3",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,2e1383b692e76f4b915ccbe9bb9b9170",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,2a595bc9ac547f3b5224a57a6b0a127d",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,157ea873dd2faff46efdd62f7f6aa84c",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,98f4e5ed094b41eb131d493b4f06bcd6",
+                "picard_quality_by_cycle.txt:md5,2634f306a33f648bac74bc7cd3253f9e",
+                "picard_quality_score_distribution.txt:md5,ecde9f0e859a6eecc5cea75a156c632d",
                 "fastq_screen_plot.txt:md5,642264b93871c724aaa5d38b91c752dd",
                 "fastqc-status-check-heatmap.txt:md5,8e29ad6b23e03267c33bd9ed3385a44b",
                 "fastqc_adapter_content_plot.txt:md5,46fbd727a4996a3f0310d0423c628445",
@@ -212,7 +245,27 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,5ef00028497d3271c9f0ea9a961db1e5",
                 "multiqc_fastqc.txt:md5,bc499ad273fd1c887056c31b82544984",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,35d289ee535a0442db72a65391f375eb",
+                "multiqc_picard_baseContent.txt:md5,72b0ae83ed58052bfd768021d377c78f",
+                "multiqc_picard_quality_by_cycle.txt:md5,f6514f14befb874ded5aed79caba3e7b",
+                "multiqc_picard_quality_score_distribution.txt:md5,99be409e325619171b820d762dd023c0",
                 "multiqc_seqfu.txt:md5,139354afd154804b4b77f997277f3ee9",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,f6514f14befb874ded5aed79caba3e7b",
+                "picard_QualityScoreDistribution_histogram.txt:md5,99be409e325619171b820d762dd023c0",
+                "picard_alignment_readlength_plot.txt:md5,4172702f791d043135f21e3a227fe712",
+                "picard_alignment_summary_Aligned_Bases.txt:md5,a166c14210e17d3541482b500443f792",
+                "picard_alignment_summary_Aligned_Reads.txt:md5,c5e5228e85ffb2182274d641ffa6743f",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,3fe18f1144eb85f9206d1bee4eb11bb3",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,2e1383b692e76f4b915ccbe9bb9b9170",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,2a595bc9ac547f3b5224a57a6b0a127d",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,157ea873dd2faff46efdd62f7f6aa84c",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,98f4e5ed094b41eb131d493b4f06bcd6",
+                "picard_quality_by_cycle.txt:md5,2634f306a33f648bac74bc7cd3253f9e",
+                "picard_quality_score_distribution.txt:md5,ecde9f0e859a6eecc5cea75a156c632d",
+                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
+                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "SAMPLE_PAIRED_END_1_1_seqfu.tsv:md5,be29dfe848eab9a10ee0d46691223eae",
                 "SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt:md5,0aca00c7f64454af520c7e08ec595d2b",
                 "SAMPLE_PAIRED_END_2_2_seqfu.tsv:md5,44a5cb826e001d58208a5855938fa82b",
@@ -221,8 +274,8 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.0"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-11-25T13:17:39.398776674"
+        "timestamp": "2025-12-02T12:28:12.75159"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index 5ecffa85..e581d280 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -2,12 +2,22 @@
     "NovaSeq6000 data test": {
         "content": [
             {
+                "BWAMEM2_MEM": {
+                    "bwamem2": "2.2.1",
+                    "samtools": "1.22.1"
+                },
                 "FASTQC": {
                     "fastqc": "0.12.1"
                 },
                 "FASTQSCREEN_FASTQSCREEN": {
                     "fastqscreen": "0.16.0"
                 },
+                "PICARD_COLLECTMULTIPLEMETRICS": {
+                    "picard": "3.4.0"
+                },
+                "SAMTOOLS_INDEX": {
+                    "samtools": "1.22.1"
+                },
                 "SEQFU_STATS": {
                     "seqfu": "1.22.3"
                 },
@@ -16,6 +26,24 @@
                 }
             },
             [
+                "bwamem2_index",
+                "bwamem2_index/bwamem2",
+                "bwamem2_index/bwamem2/genome.fa.0123",
+                "bwamem2_index/bwamem2/genome.fa.amb",
+                "bwamem2_index/bwamem2/genome.fa.ann",
+                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
+                "bwamem2_index/bwamem2/genome.fa.pac",
+                "bwamem2_mem",
+                "bwamem2_mem/Sample1_1.bam",
+                "bwamem2_mem/Sample1_1.bam.bai",
+                "bwamem2_mem/Sample23_3.bam",
+                "bwamem2_mem/Sample23_3.bam.bai",
+                "bwamem2_mem/SampleA_2.bam",
+                "bwamem2_mem/SampleA_2.bam.bai",
+                "bwamem2_mem/Undetermined_5.bam",
+                "bwamem2_mem/Undetermined_5.bam.bai",
+                "bwamem2_mem/sampletest_4.bam",
+                "bwamem2_mem/sampletest_4.bam.bai",
                 "fastqc",
                 "fastqc/Sample1_1_fastqc.html",
                 "fastqc/Sample1_1_fastqc.zip",
@@ -66,55 +94,30 @@
                 "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "multiqc/group_reports",
                 "multiqc/group_reports/group1",
@@ -139,55 +142,30 @@
                 "multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group1/multiqc_plots",
                 "multiqc/group_reports/group1/multiqc_plots/pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/png",
-                "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/group1/multiqc_plots/svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/group1/multiqc_report.html",
                 "multiqc/group_reports/group2",
                 "multiqc/group_reports/group2/multiqc_data",
@@ -211,55 +189,30 @@
                 "multiqc/group_reports/group2/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group2/multiqc_plots",
                 "multiqc/group_reports/group2/multiqc_plots/pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/png",
-                "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/group2/multiqc_plots/svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/group2/multiqc_report.html",
                 "multiqc/group_reports/lane1",
                 "multiqc/group_reports/lane1/multiqc_data",
@@ -283,55 +236,30 @@
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/lane1/multiqc_plots",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/lane1/multiqc_plots/svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/lane1/multiqc_report.html",
                 "multiqc/group_reports/test",
                 "multiqc/group_reports/test/multiqc_data",
@@ -355,58 +283,77 @@
                 "multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/test/multiqc_plots",
                 "multiqc/group_reports/test/multiqc_plots/pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/test/multiqc_plots/png",
-                "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/group_reports/test/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/group_reports/test/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/group_reports/test/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/test/multiqc_plots/svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/test/multiqc_report.html",
+                "picard_collectmultiplemetrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "samtools_faidx",
+                "samtools_faidx/genome.fa.fai",
+                "samtools_faidx/genome.fa.sizes",
                 "seqfu_stats",
                 "seqfu_stats/Sample1_1_seqfu.tsv",
                 "seqfu_stats/Sample1_1_seqfu_mqc.txt",
@@ -420,6 +367,21 @@
                 "seqfu_stats/sampletest_4_seqfu_mqc.txt"
             ],
             [
+                "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
+                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
+                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
+                "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
+                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
+                "Sample1_1.bam:md5,93a7383f6e9a975ba87b315d435ecf18",
+                "Sample1_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
+                "Sample23_3.bam:md5,e1003696a9e3501e122ca584e9a3c519",
+                "Sample23_3.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
+                "SampleA_2.bam:md5,60f5dd83705aba4edbf460225116b824",
+                "SampleA_2.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
+                "Undetermined_5.bam:md5,9f1a50be15a6504a5b03deec4645a419",
+                "Undetermined_5.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
+                "sampletest_4.bam:md5,6907d7e891e650e0e43539811af81f76",
+                "sampletest_4.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
                 "Sample1_1_screen.png:md5,562256290643b51e4374c2225a15f463",
                 "Sample1_1_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
                 "Sample23_3_screen.png:md5,6bb2caf67b9b2ed25d3d5f32c343e9ab",
@@ -444,7 +406,24 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
                 "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,5bdb2f162266ab68005cbfc0a45e311e",
+                "multiqc_picard_baseContent.txt:md5,409bf8ce546a573ce6678769b84726fd",
+                "multiqc_picard_quality_by_cycle.txt:md5,ebf56fd9b3b127ff41211e3f79f18b42",
+                "multiqc_picard_quality_score_distribution.txt:md5,182098ce1ff0a664d873c329d54189df",
                 "multiqc_seqfu.txt:md5,18dd2407d4a1791646785123028f69b5",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,ebf56fd9b3b127ff41211e3f79f18b42",
+                "picard_QualityScoreDistribution_histogram.txt:md5,182098ce1ff0a664d873c329d54189df",
+                "picard_alignment_readlength_plot.txt:md5,92ab5c6fbe67484da62626736b1b21d4",
+                "picard_alignment_summary.txt:md5,f54187e8515f9b7c32eabaf1f8702224",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,61c7df03f74846ffa484a59fcccc7b9e",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,b4504bbb9ad72796703873f2d957977a",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,1d38466783ea51bf0c7be5bceaff4d43",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,1b13c9b64042839a3bc65a8553e5ba24",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,75aee7627205c6513389d7a52e7a383b",
+                "picard_quality_by_cycle.txt:md5,4850a9230f9be5af67f3d934602df440",
+                "picard_quality_score_distribution.txt:md5,17f8498a5b18cea0eb4796a6e12b8e36",
                 "fastq_screen_plot.txt:md5,c25d34568f10f131156294d31fbfa994",
                 "fastqc-status-check-heatmap.txt:md5,67afbf7ec626c4fc7a28b4922352bc84",
                 "fastqc_overrepresented_sequences_plot.txt:md5,0356d007eaf807f7b63714b438b11289",
@@ -459,7 +438,24 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
                 "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,e4cb1b13e6a7298d172ed112a0479b5a",
+                "multiqc_picard_baseContent.txt:md5,740592a5858706d2b4b8f585a1d5492b",
+                "multiqc_picard_quality_by_cycle.txt:md5,c3f14084aedc511b9f0aa8410e7cb3b5",
+                "multiqc_picard_quality_score_distribution.txt:md5,59b955203209cfab3d2d21bdfe20997e",
                 "multiqc_seqfu.txt:md5,6cdb863a3686fbb772aae5a66925ff23",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,c3f14084aedc511b9f0aa8410e7cb3b5",
+                "picard_QualityScoreDistribution_histogram.txt:md5,59b955203209cfab3d2d21bdfe20997e",
+                "picard_alignment_readlength_plot.txt:md5,1f8b2f4df8bd5cf879b96cfb2be6d81c",
+                "picard_alignment_summary.txt:md5,0cfafd1ed1920270bb1a5d13bed51480",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,bd7f8dab8e73406cded6c6f27bbc87e9",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,fe44ccdb08c6955149eacf52a77bbba2",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,85a9172769830b4169f214c335f44fdc",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,1fe0c42cb22981763862d1934a35de07",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,4c5bfb1594b391f3e36a9e1223b43a94",
+                "picard_quality_by_cycle.txt:md5,a43e7bb40bc479e9c32476256b09e734",
+                "picard_quality_score_distribution.txt:md5,a940641c0dab423c964c0f46b69dd805",
                 "fastq_screen_plot.txt:md5,44fca6453b0a3d0590271bd7a31cc740",
                 "fastqc-status-check-heatmap.txt:md5,b6872d9dbaa3cce396d48dc137076e53",
                 "fastqc_overrepresented_sequences_plot.txt:md5,eac8d0fd31c614d8d0f56bd54ee8c78c",
@@ -474,7 +470,24 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
                 "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,d4e63eed820edcc71b3e37d793983bd7",
+                "multiqc_picard_baseContent.txt:md5,0dd5fa539e4034e3539fb1e7068c7ce5",
+                "multiqc_picard_quality_by_cycle.txt:md5,750eadc27875fc8141b64a90789c369f",
+                "multiqc_picard_quality_score_distribution.txt:md5,140279eb5abac364c4d4c417105da620",
                 "multiqc_seqfu.txt:md5,f821357507fda2d4cfd9299f52fa7dc1",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,750eadc27875fc8141b64a90789c369f",
+                "picard_QualityScoreDistribution_histogram.txt:md5,140279eb5abac364c4d4c417105da620",
+                "picard_alignment_readlength_plot.txt:md5,a39f6a39dad13dacc2134508dbbf172d",
+                "picard_alignment_summary.txt:md5,fec83821c097bc1850257ce36aa73e5f",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,f206efb4e5344b8cbb2d18f6e73d5d95",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,ebf98e3d0bf661161989bf3d010b8c6b",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,f7dff1258977e9d04fb26ba8192facc5",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,b32d1e91c41756afe8732107868b32e0",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,b7b249afe807ca2321e6dd839961795c",
+                "picard_quality_by_cycle.txt:md5,1fe617901a493b80c31fcd01a00c416d",
+                "picard_quality_score_distribution.txt:md5,5cd4a87942000899776927f22a5db802",
                 "fastq_screen_plot.txt:md5,5f748d33a7a396547fe8c260b728aa06",
                 "fastqc-status-check-heatmap.txt:md5,08228a8f3d6f11b174b98626bb22bda1",
                 "fastqc_overrepresented_sequences_plot.txt:md5,3434dfb79f150e2e584e85866983ba01",
@@ -489,7 +502,24 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
                 "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,22093b80f335c4c53633b01a930157f4",
+                "multiqc_picard_baseContent.txt:md5,6886e1e5179031ddba4958f301930d64",
+                "multiqc_picard_quality_by_cycle.txt:md5,96652e2e2d693488df9104e5ae8cb4a7",
+                "multiqc_picard_quality_score_distribution.txt:md5,879a4470d08fe6d9b1796f46020fb5f5",
                 "multiqc_seqfu.txt:md5,8cced36d66ca9d25d60c006e734aa7e9",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,96652e2e2d693488df9104e5ae8cb4a7",
+                "picard_QualityScoreDistribution_histogram.txt:md5,879a4470d08fe6d9b1796f46020fb5f5",
+                "picard_alignment_readlength_plot.txt:md5,9b323aa8cd934d084e9c83cfa1da306b",
+                "picard_alignment_summary.txt:md5,4e8970d31940f5e9020851d62e63b2e2",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,166a48317764fe7d4b38ed198503fc11",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,8e62c1113b965497e492e17665cdbe97",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,fe53f5f9455b928a3edc1661be83592b",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,3d069dd67cc0ffc43456c5f3ee427349",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,e371981072ec99d11c6adb5a4034808c",
+                "picard_quality_by_cycle.txt:md5,0c25ee4cec6842306b28c6a641aa03e1",
+                "picard_quality_score_distribution.txt:md5,184dcdd53f6aa3b7a0fa2c008d7dc74a",
                 "fastq_screen_plot.txt:md5,8622e1dbd0fe62520af6096207b9775d",
                 "fastqc-status-check-heatmap.txt:md5,2a66f5d61b9eb579555905cd5954b04c",
                 "fastqc_overrepresented_sequences_plot.txt:md5,e0b5bfc4b64d37611b51c939e61196fa",
@@ -504,7 +534,26 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5",
                 "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,edf7faad1da9922fdc692e9cba5cc0c4",
+                "multiqc_picard_baseContent.txt:md5,9631916c0a9a736811c47ab4c476428f",
+                "multiqc_picard_quality_by_cycle.txt:md5,9e05b241aabe39232b5182cb59d8edd5",
+                "multiqc_picard_quality_score_distribution.txt:md5,e9c3ade201964470d2d22569a400fa49",
                 "multiqc_seqfu.txt:md5,ff4ce1c88f39ed24a88bae0a861f75c8",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,9e05b241aabe39232b5182cb59d8edd5",
+                "picard_QualityScoreDistribution_histogram.txt:md5,e9c3ade201964470d2d22569a400fa49",
+                "picard_alignment_readlength_plot.txt:md5,c2692fde9d899ad61297ad7043fd26b9",
+                "picard_alignment_summary.txt:md5,5996d5b4c94f16c0efd42e2df47e021e",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,a2670974dc96ad8a54f9cc5ae3e09d5e",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,d3b9cc0c99f96814348b57809cf227fb",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,1ba086d3fb2676868e8e7b20f55975dc",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,8902976984741320fe06004f4115c4f4",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,1380831484d1b069a2fd4a20437118bf",
+                "picard_quality_by_cycle.txt:md5,b6fc46e18ac875ba02775e7cbf1b8e8b",
+                "picard_quality_score_distribution.txt:md5,1c17c01ef54a6062a8f1ca8408d32958",
+                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
+                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "Sample1_1_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6",
                 "Sample1_1_seqfu_mqc.txt:md5,24d99524ccd0e6c6255a69d68a871c7a",
                 "Sample23_3_seqfu.tsv:md5,6fac5d3dbce3f3bee72341fe99a399dc",
@@ -519,8 +568,8 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.0"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-11-25T13:18:53.764240677"
+        "timestamp": "2025-12-02T12:35:34.210381"
     }
 }
\ No newline at end of file

From a9e3b3094d19a4c493cc25367035f1418dc9e03f Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 2 Dec 2025 12:58:40 +0100
Subject: [PATCH 464/530] More snapshot updates

---
 .nf-test-2c8f93900b9462538ae8fc18f01382fe.nf | 93 --------------------
 .nf-test-661c1e31a1798b8926bee5c65b147017.nf | 86 ------------------
 .nf-test-9a3cd05e4fc62955ef9a17eeabbe5bbe.nf | 86 ------------------
 .nf-test-c6919cb8935af9122d1bbfd0a0fb3974.nf | 86 ------------------
 tests/PromethION.main.nf.test.snap           | 54 ++----------
 5 files changed, 7 insertions(+), 398 deletions(-)
 delete mode 100644 .nf-test-2c8f93900b9462538ae8fc18f01382fe.nf
 delete mode 100644 .nf-test-661c1e31a1798b8926bee5c65b147017.nf
 delete mode 100644 .nf-test-9a3cd05e4fc62955ef9a17eeabbe5bbe.nf
 delete mode 100644 .nf-test-c6919cb8935af9122d1bbfd0a0fb3974.nf

diff --git a/.nf-test-2c8f93900b9462538ae8fc18f01382fe.nf b/.nf-test-2c8f93900b9462538ae8fc18f01382fe.nf
deleted file mode 100644
index f7fe99c4..00000000
--- a/.nf-test-2c8f93900b9462538ae8fc18f01382fe.nf
+++ /dev/null
@@ -1,93 +0,0 @@
-import groovy.json.JsonGenerator
-import groovy.json.JsonGenerator.Converter
-
-nextflow.enable.dsl=2
-
-// comes from nf-test to store json files
-params.nf_test_output  = ""
-
-// include dependencies
-
-
-// include test workflow
-include { QC_BAM } from '/Users/beatrizsavinhas/development/seqinspector/subworkflows/local/qc_bam/main.nf'
-
-// define custom rules for JSON that will be generated.
-def jsonOutput =
-    new JsonGenerator.Options()
-        .addConverter(Path) { value -> value.toAbsolutePath().toString() } // Custom converter for Path. Only filename
-        .build()
-
-def jsonWorkflowOutput = new JsonGenerator.Options().excludeNulls().build()
-
-workflow {
-
-    // run dependencies
-    
-
-    // workflow mapping
-    def input = []
-    
-                input[0]  = channel.of(
-                    [
-                        [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'],
-                        [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)],
-                        [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)]
-                    ]
-                )
-                input[1]  = channel.fromPath(params.pipelines_testdata_base_path + '/reference/target.bed', checkIfExists: true).collect()
-                input[2]  = channel.fromPath(params.pipelines_testdata_base_path + '/reference/target.bed', checkIfExists: true).collect()
-                input[3]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta', checkIfExists: true)).collect()
-                input[4]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta.fai', checkIfExists: true)).collect()
-                input[5]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.dict', checkIfExists: true)).collect()
-                
-    //----
-
-    //run workflow
-    QC_BAM(*input)
-    
-    if (QC_BAM.output){
-
-        // consumes all named output channels and stores items in a json file
-        for (def name in QC_BAM.out.getNames()) {
-            serializeChannel(name, QC_BAM.out.getProperty(name), jsonOutput)
-        }	  
-    
-        // consumes all unnamed output channels and stores items in a json file
-        def array = QC_BAM.out as Object[]
-        for (def i = 0; i < array.length ; i++) {
-            serializeChannel(i, array[i], jsonOutput)
-        }    	
-
-    }
-}
-
-
-def serializeChannel(name, channel, jsonOutput) {
-    def _name = name
-    def list = [ ]
-    channel.subscribe(
-        onNext: {
-            list.add(it)
-        },
-        onComplete: {
-              def map = new HashMap()
-              map[_name] = list
-              def filename = "${params.nf_test_output}/output_${_name}.json"
-              new File(filename).text = jsonOutput.toJson(map)		  		
-        } 
-    )
-}
-
-
-workflow.onComplete {
-
-    def result = [
-        success: workflow.success,
-        exitStatus: workflow.exitStatus,
-        errorMessage: workflow.errorMessage,
-        errorReport: workflow.errorReport
-    ]
-    new File("${params.nf_test_output}/workflow.json").text = jsonWorkflowOutput.toJson(result)
-    
-}
diff --git a/.nf-test-661c1e31a1798b8926bee5c65b147017.nf b/.nf-test-661c1e31a1798b8926bee5c65b147017.nf
deleted file mode 100644
index ee32ae83..00000000
--- a/.nf-test-661c1e31a1798b8926bee5c65b147017.nf
+++ /dev/null
@@ -1,86 +0,0 @@
-import groovy.json.JsonGenerator
-import groovy.json.JsonGenerator.Converter
-
-nextflow.enable.dsl=2
-
-// comes from nf-test to store json files
-params.nf_test_output  = ""
-
-// include dependencies
-
-
-// include test workflow
-include { PREPARE_GENOME } from '/Users/beatrizsavinhas/development/seqinspector/subworkflows/local/prepare_genome/main.nf'
-
-// define custom rules for JSON that will be generated.
-def jsonOutput =
-    new JsonGenerator.Options()
-        .addConverter(Path) { value -> value.toAbsolutePath().toString() } // Custom converter for Path. Only filename
-        .build()
-
-def jsonWorkflowOutput = new JsonGenerator.Options().excludeNulls().build()
-
-workflow {
-
-    // run dependencies
-    
-
-    // workflow mapping
-    def input = []
-    
-                input[0]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta', checkIfExists: true)).collect()
-                input[1]  = null
-                input[2]  = ''
-                input[3]  = false
-                input[4]  = null
-                
-    //----
-
-    //run workflow
-    PREPARE_GENOME(*input)
-    
-    if (PREPARE_GENOME.output){
-
-        // consumes all named output channels and stores items in a json file
-        for (def name in PREPARE_GENOME.out.getNames()) {
-            serializeChannel(name, PREPARE_GENOME.out.getProperty(name), jsonOutput)
-        }	  
-    
-        // consumes all unnamed output channels and stores items in a json file
-        def array = PREPARE_GENOME.out as Object[]
-        for (def i = 0; i < array.length ; i++) {
-            serializeChannel(i, array[i], jsonOutput)
-        }    	
-
-    }
-}
-
-
-def serializeChannel(name, channel, jsonOutput) {
-    def _name = name
-    def list = [ ]
-    channel.subscribe(
-        onNext: {
-            list.add(it)
-        },
-        onComplete: {
-              def map = new HashMap()
-              map[_name] = list
-              def filename = "${params.nf_test_output}/output_${_name}.json"
-              new File(filename).text = jsonOutput.toJson(map)		  		
-        } 
-    )
-}
-
-
-workflow.onComplete {
-
-    def result = [
-        success: workflow.success,
-        exitStatus: workflow.exitStatus,
-        errorMessage: workflow.errorMessage,
-        errorReport: workflow.errorReport
-    ]
-    new File("${params.nf_test_output}/workflow.json").text = jsonWorkflowOutput.toJson(result)
-    
-}
diff --git a/.nf-test-9a3cd05e4fc62955ef9a17eeabbe5bbe.nf b/.nf-test-9a3cd05e4fc62955ef9a17eeabbe5bbe.nf
deleted file mode 100644
index 2ea62047..00000000
--- a/.nf-test-9a3cd05e4fc62955ef9a17eeabbe5bbe.nf
+++ /dev/null
@@ -1,86 +0,0 @@
-import groovy.json.JsonGenerator
-import groovy.json.JsonGenerator.Converter
-
-nextflow.enable.dsl=2
-
-// comes from nf-test to store json files
-params.nf_test_output  = ""
-
-// include dependencies
-
-
-// include test workflow
-include { PREPARE_GENOME } from '/Users/beatrizsavinhas/development/seqinspector/subworkflows/local/prepare_genome/main.nf'
-
-// define custom rules for JSON that will be generated.
-def jsonOutput =
-    new JsonGenerator.Options()
-        .addConverter(Path) { value -> value.toAbsolutePath().toString() } // Custom converter for Path. Only filename
-        .build()
-
-def jsonWorkflowOutput = new JsonGenerator.Options().excludeNulls().build()
-
-workflow {
-
-    // run dependencies
-    
-
-    // workflow mapping
-    def input = []
-    
-                input[0]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta', checkIfExists: true)).collect()
-                input[1]  = null
-                input[2]  = ''
-                input[3]  = true
-                input[4]  = params.pipelines_testdata_base_path + '/reference/reference.dict'
-                
-    //----
-
-    //run workflow
-    PREPARE_GENOME(*input)
-    
-    if (PREPARE_GENOME.output){
-
-        // consumes all named output channels and stores items in a json file
-        for (def name in PREPARE_GENOME.out.getNames()) {
-            serializeChannel(name, PREPARE_GENOME.out.getProperty(name), jsonOutput)
-        }	  
-    
-        // consumes all unnamed output channels and stores items in a json file
-        def array = PREPARE_GENOME.out as Object[]
-        for (def i = 0; i < array.length ; i++) {
-            serializeChannel(i, array[i], jsonOutput)
-        }    	
-
-    }
-}
-
-
-def serializeChannel(name, channel, jsonOutput) {
-    def _name = name
-    def list = [ ]
-    channel.subscribe(
-        onNext: {
-            list.add(it)
-        },
-        onComplete: {
-              def map = new HashMap()
-              map[_name] = list
-              def filename = "${params.nf_test_output}/output_${_name}.json"
-              new File(filename).text = jsonOutput.toJson(map)		  		
-        } 
-    )
-}
-
-
-workflow.onComplete {
-
-    def result = [
-        success: workflow.success,
-        exitStatus: workflow.exitStatus,
-        errorMessage: workflow.errorMessage,
-        errorReport: workflow.errorReport
-    ]
-    new File("${params.nf_test_output}/workflow.json").text = jsonWorkflowOutput.toJson(result)
-    
-}
diff --git a/.nf-test-c6919cb8935af9122d1bbfd0a0fb3974.nf b/.nf-test-c6919cb8935af9122d1bbfd0a0fb3974.nf
deleted file mode 100644
index 0e1157d7..00000000
--- a/.nf-test-c6919cb8935af9122d1bbfd0a0fb3974.nf
+++ /dev/null
@@ -1,86 +0,0 @@
-import groovy.json.JsonGenerator
-import groovy.json.JsonGenerator.Converter
-
-nextflow.enable.dsl=2
-
-// comes from nf-test to store json files
-params.nf_test_output  = ""
-
-// include dependencies
-
-
-// include test workflow
-include { PREPARE_GENOME } from '/Users/beatrizsavinhas/development/seqinspector/subworkflows/local/prepare_genome/main.nf'
-
-// define custom rules for JSON that will be generated.
-def jsonOutput =
-    new JsonGenerator.Options()
-        .addConverter(Path) { value -> value.toAbsolutePath().toString() } // Custom converter for Path. Only filename
-        .build()
-
-def jsonWorkflowOutput = new JsonGenerator.Options().excludeNulls().build()
-
-workflow {
-
-    // run dependencies
-    
-
-    // workflow mapping
-    def input = []
-    
-                input[0]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta', checkIfExists: true)).collect()
-                input[1]  = null
-                input[2]  = ''
-                input[3]  = true
-                input[4]  = null
-                
-    //----
-
-    //run workflow
-    PREPARE_GENOME(*input)
-    
-    if (PREPARE_GENOME.output){
-
-        // consumes all named output channels and stores items in a json file
-        for (def name in PREPARE_GENOME.out.getNames()) {
-            serializeChannel(name, PREPARE_GENOME.out.getProperty(name), jsonOutput)
-        }	  
-    
-        // consumes all unnamed output channels and stores items in a json file
-        def array = PREPARE_GENOME.out as Object[]
-        for (def i = 0; i < array.length ; i++) {
-            serializeChannel(i, array[i], jsonOutput)
-        }    	
-
-    }
-}
-
-
-def serializeChannel(name, channel, jsonOutput) {
-    def _name = name
-    def list = [ ]
-    channel.subscribe(
-        onNext: {
-            list.add(it)
-        },
-        onComplete: {
-              def map = new HashMap()
-              map[_name] = list
-              def filename = "${params.nf_test_output}/output_${_name}.json"
-              new File(filename).text = jsonOutput.toJson(map)		  		
-        } 
-    )
-}
-
-
-workflow.onComplete {
-
-    def result = [
-        success: workflow.success,
-        exitStatus: workflow.exitStatus,
-        errorMessage: workflow.errorMessage,
-        errorReport: workflow.errorReport
-    ]
-    new File("${params.nf_test_output}/workflow.json").text = jsonWorkflowOutput.toJson(result)
-    
-}
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index 92c8bb5e..a9d0067b 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -52,56 +52,14 @@
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_adapter_content_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "samtools_faidx",
+                "samtools_faidx/genome.fa.fai",
+                "samtools_faidx/genome.fa.sizes",
                 "seqfu_stats",
                 "seqfu_stats/hg001_1_seqfu.tsv",
                 "seqfu_stats/hg001_1_seqfu_mqc.txt"
@@ -125,14 +83,16 @@
                 "multiqc_fastq_screen.txt:md5,7c5d711e27c53d13c81644a1f2468dba",
                 "multiqc_fastqc.txt:md5,1a4b472e13cadc770832b0e20d1de7b0",
                 "multiqc_seqfu.txt:md5,9595d608ff5709f2bdec8cb1016416c0",
+                "genome.fa.fai:md5,59557cd3a71ca5e0840285b6088ec1d6",
+                "genome.fa.sizes:md5,f154a58a25ba9c4d386003eaa1bb731b",
                 "hg001_1_seqfu.tsv:md5,b133752c897afbb4d8721b911fa117d4",
                 "hg001_1_seqfu_mqc.txt:md5,42e3506b02ceb72a6f05cb174505e722"
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.0"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-11-25T13:20:37.20082732"
+        "timestamp": "2025-12-02T12:57:49.721413"
     }
 }
\ No newline at end of file

From 815176ee49ed9cda8f7ca816834a40629f0219ae Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 2 Dec 2025 13:15:10 +0100
Subject: [PATCH 465/530] Update remaining snapshot

---
 tests/NovaSeq6000.main_subsample.nf.test.snap | 473 ++++++++++--------
 1 file changed, 261 insertions(+), 212 deletions(-)

diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index 1d061216..7ced838f 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -2,12 +2,22 @@
     "NovaSeq6000 data test sample size": {
         "content": [
             {
+                "BWAMEM2_MEM": {
+                    "bwamem2": "2.2.1",
+                    "samtools": "1.22.1"
+                },
                 "FASTQC": {
                     "fastqc": "0.12.1"
                 },
                 "FASTQSCREEN_FASTQSCREEN": {
                     "fastqscreen": "0.16.0"
                 },
+                "PICARD_COLLECTMULTIPLEMETRICS": {
+                    "picard": "3.4.0"
+                },
+                "SAMTOOLS_INDEX": {
+                    "samtools": "1.22.1"
+                },
                 "SEQFU_STATS": {
                     "seqfu": "1.22.3"
                 },
@@ -19,6 +29,24 @@
                 }
             },
             [
+                "bwamem2_index",
+                "bwamem2_index/bwamem2",
+                "bwamem2_index/bwamem2/genome.fa.0123",
+                "bwamem2_index/bwamem2/genome.fa.amb",
+                "bwamem2_index/bwamem2/genome.fa.ann",
+                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
+                "bwamem2_index/bwamem2/genome.fa.pac",
+                "bwamem2_mem",
+                "bwamem2_mem/Sample1_1.bam",
+                "bwamem2_mem/Sample1_1.bam.bai",
+                "bwamem2_mem/Sample23_3.bam",
+                "bwamem2_mem/Sample23_3.bam.bai",
+                "bwamem2_mem/SampleA_2.bam",
+                "bwamem2_mem/SampleA_2.bam.bai",
+                "bwamem2_mem/Undetermined_5.bam",
+                "bwamem2_mem/Undetermined_5.bam.bai",
+                "bwamem2_mem/sampletest_4.bam",
+                "bwamem2_mem/sampletest_4.bam.bai",
                 "fastqc",
                 "fastqc/Sample1_1_fastqc.html",
                 "fastqc/Sample1_1_fastqc.zip",
@@ -69,55 +97,30 @@
                 "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "multiqc/group_reports",
                 "multiqc/group_reports/group1",
@@ -142,55 +145,30 @@
                 "multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group1/multiqc_plots",
                 "multiqc/group_reports/group1/multiqc_plots/pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/png",
-                "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/group1/multiqc_plots/svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/group1/multiqc_report.html",
                 "multiqc/group_reports/group2",
                 "multiqc/group_reports/group2/multiqc_data",
@@ -214,55 +192,30 @@
                 "multiqc/group_reports/group2/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group2/multiqc_plots",
                 "multiqc/group_reports/group2/multiqc_plots/pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/png",
-                "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/group2/multiqc_plots/svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/group2/multiqc_report.html",
                 "multiqc/group_reports/lane1",
                 "multiqc/group_reports/lane1/multiqc_data",
@@ -286,55 +239,30 @@
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/lane1/multiqc_plots",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/lane1/multiqc_plots/svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/lane1/multiqc_report.html",
                 "multiqc/group_reports/test",
                 "multiqc/group_reports/test/multiqc_data",
@@ -358,58 +286,77 @@
                 "multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/test/multiqc_plots",
                 "multiqc/group_reports/test/multiqc_plots/pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/test/multiqc_plots/png",
-                "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/group_reports/test/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/group_reports/test/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/group_reports/test/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/test/multiqc_plots/svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/test/multiqc_report.html",
+                "picard_collectmultiplemetrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "samtools_faidx",
+                "samtools_faidx/genome.fa.fai",
+                "samtools_faidx/genome.fa.sizes",
                 "seqfu_stats",
                 "seqfu_stats/Sample1_1_seqfu.tsv",
                 "seqfu_stats/Sample1_1_seqfu_mqc.txt",
@@ -429,6 +376,21 @@
                 "seqtk/sampletest_4_sampletest_S4_L001_R1_001.fastq.gz"
             ],
             [
+                "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
+                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
+                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
+                "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
+                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
+                "Sample1_1.bam:md5,0bd502d4e221008867c85393cce2b89b",
+                "Sample1_1.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
+                "Sample23_3.bam:md5,26a49672caec3ab985d3f3dd6bdff530",
+                "Sample23_3.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
+                "SampleA_2.bam:md5,240d536aab1aac8fa3bca402703121df",
+                "SampleA_2.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
+                "Undetermined_5.bam:md5,f30b23c562a1725f3f23236acab1fd9a",
+                "Undetermined_5.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
+                "sampletest_4.bam:md5,2c37f72ed4f25c971199fbde3af370b9",
+                "sampletest_4.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
                 "Sample1_1_screen.png:md5,562256290643b51e4374c2225a15f463",
                 "Sample1_1_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
                 "Sample23_3_screen.png:md5,6bb2caf67b9b2ed25d3d5f32c343e9ab",
@@ -453,7 +415,24 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
                 "multiqc_fastqc.txt:md5,aba942d1e6996b579f19798e5673f514",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,ae3f9e644215ac39d2eae114bd52a517",
+                "multiqc_picard_baseContent.txt:md5,8b2efc3fa06d2013348b35f9607292aa",
+                "multiqc_picard_quality_by_cycle.txt:md5,c2774038d1a0142746426e46f9f954dd",
+                "multiqc_picard_quality_score_distribution.txt:md5,792755ee794d375b85a57f58d879f0c6",
                 "multiqc_seqfu.txt:md5,18dd2407d4a1791646785123028f69b5",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,c2774038d1a0142746426e46f9f954dd",
+                "picard_QualityScoreDistribution_histogram.txt:md5,792755ee794d375b85a57f58d879f0c6",
+                "picard_alignment_readlength_plot.txt:md5,ebd1ff06394bd202b8190c46d560bc95",
+                "picard_alignment_summary.txt:md5,e507eccfa0a05b20705f99a3619dde29",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,597d0fd368eab8a21cd7f4a92965ecf6",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,ade1d92e5e6d3bfefd3695f103079b6c",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,af525e84f95ceb4b8496f734db2420fb",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,8b5ada27023f2545792fabbb69a07067",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,a472bba4490d7189df23f6b38a554448",
+                "picard_quality_by_cycle.txt:md5,83d68b4049173f8c9a37f58f1276adc1",
+                "picard_quality_score_distribution.txt:md5,42c08c8a51230d9ecccdad416c06f59c",
                 "fastq_screen_plot.txt:md5,c25d34568f10f131156294d31fbfa994",
                 "fastqc-status-check-heatmap.txt:md5,7ee494f345c09706513e65907788de02",
                 "fastqc_overrepresented_sequences_plot.txt:md5,ca9fa146e7b8a7f562fd79b521ba0f60",
@@ -468,7 +447,24 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
                 "multiqc_fastqc.txt:md5,ff996e1d3dc4a46e0c9535e54d51ccab",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,7bc3f6ef8f47e6f1e060f957025c98aa",
+                "multiqc_picard_baseContent.txt:md5,1426865fe8ee1a36f67636c28500a91c",
+                "multiqc_picard_quality_by_cycle.txt:md5,79bf9f861077de70ec28c9af01783876",
+                "multiqc_picard_quality_score_distribution.txt:md5,a3f8d1937e1f118800aa3d86c1b498c4",
                 "multiqc_seqfu.txt:md5,6cdb863a3686fbb772aae5a66925ff23",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,79bf9f861077de70ec28c9af01783876",
+                "picard_QualityScoreDistribution_histogram.txt:md5,a3f8d1937e1f118800aa3d86c1b498c4",
+                "picard_alignment_readlength_plot.txt:md5,5aed5e7c1395a537bdce7163c93781bd",
+                "picard_alignment_summary.txt:md5,9d0d003456e08f78701e876d0238b5a6",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,73e910febe1ea4d08a9f4e49d6c10615",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,092e732bb44842f2da5416de158c1cc5",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,e81495fde738e2954483195fd0ccfb04",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,ed9ad958081a904a5584757f87b29eb2",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,2b4526a0b0977ebd7fbe326c6d51cf19",
+                "picard_quality_by_cycle.txt:md5,d53617c495e81e011996cd4e9f755e0a",
+                "picard_quality_score_distribution.txt:md5,05f9e89733e43b81acf593efc1a56180",
                 "fastq_screen_plot.txt:md5,44fca6453b0a3d0590271bd7a31cc740",
                 "fastqc-status-check-heatmap.txt:md5,b6872d9dbaa3cce396d48dc137076e53",
                 "fastqc_overrepresented_sequences_plot.txt:md5,19babef6996c0bfdf28e5df89368cbb1",
@@ -483,7 +479,24 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
                 "multiqc_fastqc.txt:md5,3df36ecfe76b25b0c22dcda84bce2b3b",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,4dc89e1a04843d44695ecc8d1f047ee8",
+                "multiqc_picard_baseContent.txt:md5,0a5f9d32dd3061ce4349518c47d69838",
+                "multiqc_picard_quality_by_cycle.txt:md5,ec59b472afc1242ff299011ba456e792",
+                "multiqc_picard_quality_score_distribution.txt:md5,1b8be76b60ee71aa36a98d34e433b9bf",
                 "multiqc_seqfu.txt:md5,f821357507fda2d4cfd9299f52fa7dc1",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,ec59b472afc1242ff299011ba456e792",
+                "picard_QualityScoreDistribution_histogram.txt:md5,1b8be76b60ee71aa36a98d34e433b9bf",
+                "picard_alignment_readlength_plot.txt:md5,72e0094fcd2546bee02a7ac65a3ea218",
+                "picard_alignment_summary.txt:md5,19586495e6d7904a2a4a7eb9ba17a412",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,a825de2b668791e58f6a4078e0b31483",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,59633faead8aa9027883481b0c7e22af",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,f02153a346f7e24f200bf06af2293352",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,0725af81caa647ec22050c573dfe8cb0",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,3536e6dcc7c7ed972b02d2945da75cb7",
+                "picard_quality_by_cycle.txt:md5,be127a96dd68c14077548d36c0507dc3",
+                "picard_quality_score_distribution.txt:md5,9e27b097f10cb9a9a95a3445b220d104",
                 "fastq_screen_plot.txt:md5,5f748d33a7a396547fe8c260b728aa06",
                 "fastqc-status-check-heatmap.txt:md5,bab59a0bd1d676d90cdd986fbba36b26",
                 "fastqc_overrepresented_sequences_plot.txt:md5,79cb259874c52b44f8c69b2075ee498e",
@@ -498,7 +511,24 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
                 "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,fa26e8b96faa1926d8f41fc3fe959ff7",
+                "multiqc_picard_baseContent.txt:md5,b9d72d8173cdc7649b44b80aa485477c",
+                "multiqc_picard_quality_by_cycle.txt:md5,062547fb888ed508dd1d5733d7bed22e",
+                "multiqc_picard_quality_score_distribution.txt:md5,dd5abab3a7141654fffa3946c50a039b",
                 "multiqc_seqfu.txt:md5,8cced36d66ca9d25d60c006e734aa7e9",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,062547fb888ed508dd1d5733d7bed22e",
+                "picard_QualityScoreDistribution_histogram.txt:md5,dd5abab3a7141654fffa3946c50a039b",
+                "picard_alignment_readlength_plot.txt:md5,e5d397c216a0911a73dff5550fa7b1d7",
+                "picard_alignment_summary.txt:md5,ef16e8dbab178f44deebe0f4d321097b",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,8ada743b028ec78996f9dc40f1922941",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,c97859ee1641de9bff58dbd1e82fff20",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,ea86115ef2ca4ff4922486ceb6c6e1e8",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,07a3f1e6b1ed2bc55128fc2a0f46eb92",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,67ee93606c468a7eea7818b2f4b3389f",
+                "picard_quality_by_cycle.txt:md5,974b3baed160e9643f493df1d0ad5000",
+                "picard_quality_score_distribution.txt:md5,869d69ae4e243f0669f63b489563e4f1",
                 "fastq_screen_plot.txt:md5,8622e1dbd0fe62520af6096207b9775d",
                 "fastqc-status-check-heatmap.txt:md5,2a66f5d61b9eb579555905cd5954b04c",
                 "fastqc_overrepresented_sequences_plot.txt:md5,5cdefa954db6e46c286e2984a883eb18",
@@ -513,7 +543,26 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5",
                 "multiqc_fastqc.txt:md5,ce61b4ce4b1d76ec3f20de3bf0c9ec7f",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,55627d8016b72c37c104e03cc156862c",
+                "multiqc_picard_baseContent.txt:md5,974d83faa49711ab4ea1248c59e69393",
+                "multiqc_picard_quality_by_cycle.txt:md5,248ecaf269d8fef1e84ea06f98b6f6ba",
+                "multiqc_picard_quality_score_distribution.txt:md5,5e7e80654e12c500b15f8564ffb12b27",
                 "multiqc_seqfu.txt:md5,ff4ce1c88f39ed24a88bae0a861f75c8",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,248ecaf269d8fef1e84ea06f98b6f6ba",
+                "picard_QualityScoreDistribution_histogram.txt:md5,5e7e80654e12c500b15f8564ffb12b27",
+                "picard_alignment_readlength_plot.txt:md5,23ff551a5a8eded1857356f38b19039c",
+                "picard_alignment_summary.txt:md5,c741b69e17ed84370732b567ae11c69c",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,fc37dd1ac805881a467b264a7dd76677",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,7993fd56aa542b71bc984cd36c489fd1",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,1bca639db2a2624727f7b6dd2aa1442e",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,a5f0903d77b6060676f7dda249b99738",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,102e653a543ac908ac9ec9b86412d73b",
+                "picard_quality_by_cycle.txt:md5,3d43fd5387c0dc728833c681ea4f73cc",
+                "picard_quality_score_distribution.txt:md5,9d9f1bb12316175cdb88d3ff70305428",
+                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
+                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "Sample1_1_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6",
                 "Sample1_1_seqfu_mqc.txt:md5,24d99524ccd0e6c6255a69d68a871c7a",
                 "Sample23_3_seqfu.tsv:md5,6fac5d3dbce3f3bee72341fe99a399dc",
@@ -533,8 +582,8 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.0"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-11-25T13:20:06.917144477"
+        "timestamp": "2025-12-02T13:14:07.677563"
     }
 }
\ No newline at end of file

From 8ea7b6360490dff96db7c09398f0237dfe58053b Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 2 Dec 2025 13:27:38 +0100
Subject: [PATCH 466/530] Re-add changes to modules.config

---
 conf/modules.config | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/conf/modules.config b/conf/modules.config
index 5c3ec743..205bfb53 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -43,6 +43,14 @@ process {
         ]
     }
 
+        withName: 'PICARD_CREATESEQUENCEDICTIONARY' {
+        publishDir = [
+            path: { "${params.outdir}/picard_createsequencedictionary" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: 'BWAMEM2_MEM' {
         publishDir = [
             path: { "${params.outdir}/bwamem2_mem" },

From 60e8666f027c6e7c8718bd7177857cd700c2d808 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 2 Dec 2025 13:49:46 +0100
Subject: [PATCH 467/530] Small changes in comments in main.nf.test

---
 subworkflows/local/prepare_genome/tests/main.nf.test | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test b/subworkflows/local/prepare_genome/tests/main.nf.test
index 65a3884a..efe34ae3 100644
--- a/subworkflows/local/prepare_genome/tests/main.nf.test
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test
@@ -45,7 +45,7 @@ nextflow_workflow {
                     bwamem2_index_files,
                     samtools_faidx_files
                 ).match() },
-                // BWAMEM2_INDEX and SAMTOOLS_FAIDX should be run
+                // BWAMEM2_INDEX and SAMTOOLS_FAIDX should run
                 { assert workflow.out.versions.size() == 2 }
             )
         }
@@ -91,7 +91,7 @@ nextflow_workflow {
                     bwamem2_index_files,
                     samtools_faidx_files
                 ).match() },
-                // BWAMEM2_INDEX and SAMTOOLS_FAIDX should be run
+                // BWAMEM2_INDEX and SAMTOOLS_FAIDX should run
                 { assert workflow.out.versions.size() == 2 }
             )
         }
@@ -143,7 +143,7 @@ nextflow_workflow {
                     samtools_faidx_files,
                     picard_createsequencedictionary_files
                 ).match() },
-                // BWAMEM2_INDEX, SAMTOOLS_FAIDX and PICARD_CREATESEQUENCEDICTIONARY should be run
+                // BWAMEM2_INDEX, SAMTOOLS_FAIDX and PICARD_CREATESEQUENCEDICTIONARY should run
                 { assert workflow.out.versions.size() == 3 }
             )
         }

From d5f69b8c907c5d6751e91fc00fc0bda9299f0162 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 2 Dec 2025 15:01:47 +0100
Subject: [PATCH 468/530] Small changes in comments in main.nf.test

---
 .../local/prepare_genome/tests/main.nf.test   | 38 +++++++++----------
 1 file changed, 17 insertions(+), 21 deletions(-)

diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test b/subworkflows/local/prepare_genome/tests/main.nf.test
index efe34ae3..df7a9856 100644
--- a/subworkflows/local/prepare_genome/tests/main.nf.test
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test
@@ -39,15 +39,15 @@ nextflow_workflow {
                 relative: true, includeDir: true
             )
 
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(
+            assert workflow.success
+
+            assert snapshot(
                     bwamem2_index_files,
                     samtools_faidx_files
-                ).match() },
-                // BWAMEM2_INDEX and SAMTOOLS_FAIDX should run
-                { assert workflow.out.versions.size() == 2 }
-            )
+                ).match()
+
+            // BWAMEM2_INDEX and SAMTOOLS_FAIDX should run
+            assert workflow.out.versions.size() == 2
         }
 
     }
@@ -85,15 +85,13 @@ nextflow_workflow {
                 relative: true, includeDir: true
             )
 
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(
+            assert workflow.success
+            assert snapshot(
                     bwamem2_index_files,
                     samtools_faidx_files
-                ).match() },
-                // BWAMEM2_INDEX and SAMTOOLS_FAIDX should run
-                { assert workflow.out.versions.size() == 2 }
-            )
+                ).match()
+            // BWAMEM2_INDEX and SAMTOOLS_FAIDX should run
+            assert workflow.out.versions.size() == 2
         }
 
     }
@@ -136,16 +134,14 @@ nextflow_workflow {
                 relative: true, includeDir: true
             )
 
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(
+            assert workflow.success
+            assert snapshot(
                     bwamem2_index_files,
                     samtools_faidx_files,
                     picard_createsequencedictionary_files
-                ).match() },
-                // BWAMEM2_INDEX, SAMTOOLS_FAIDX and PICARD_CREATESEQUENCEDICTIONARY should run
-                { assert workflow.out.versions.size() == 3 }
-            )
+                ).match()
+            // BWAMEM2_INDEX, SAMTOOLS_FAIDX and PICARD_CREATESEQUENCEDICTIONARY should run
+            assert workflow.out.versions.size() == 3
         }
 
     }

From d64f815e04e0901a76b43fc58dc1fde349649ae3 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 2 Dec 2025 15:09:45 +0100
Subject: [PATCH 469/530] Add nextflow.config to tests

---
 subworkflows/local/prepare_genome/tests/main.nf.test    | 9 +++------
 subworkflows/local/prepare_genome/tests/nextflow.config | 7 +++++++
 2 files changed, 10 insertions(+), 6 deletions(-)
 create mode 100644 subworkflows/local/prepare_genome/tests/nextflow.config

diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test b/subworkflows/local/prepare_genome/tests/main.nf.test
index df7a9856..646dcf00 100644
--- a/subworkflows/local/prepare_genome/tests/main.nf.test
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test
@@ -10,10 +10,9 @@ nextflow_workflow {
 
         when {
             params {
-                pipelines_testdata_base_path    = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease'
-                run_picard_collecthsmetrics     = true
                 config "./nextflow.config"
                 outdir = "$outputDir"
+                run_picard_collecthsmetrics = true
 
             }
             workflow {
@@ -56,10 +55,9 @@ nextflow_workflow {
 
         when {
             params {
-                pipelines_testdata_base_path    = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease'
-                run_picard_collecthsmetrics     = true
                 config "./nextflow.config"
                 outdir = "$outputDir"
+                run_picard_collecthsmetrics = true
 
             }
             workflow {
@@ -100,10 +98,9 @@ nextflow_workflow {
 
         when {
             params {
-                pipelines_testdata_base_path    = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease'
-                run_picard_collecthsmetrics     = true
                 config "./nextflow.config"
                 outdir = "$outputDir"
+                run_picard_collecthsmetrics = true
 
             }
             workflow {
diff --git a/subworkflows/local/prepare_genome/tests/nextflow.config b/subworkflows/local/prepare_genome/tests/nextflow.config
new file mode 100644
index 00000000..4bc7fa18
--- /dev/null
+++ b/subworkflows/local/prepare_genome/tests/nextflow.config
@@ -0,0 +1,7 @@
+// Load the basic test config
+includeConfig 'nextflow.config'
+
+// Load the correct samplesheet for that test
+params {
+    pipelines_testdata_base_path    = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease'
+}
\ No newline at end of file

From 4a5d3a1b867edf5b01516fbd18ef41715562e6ec Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 2 Dec 2025 15:10:52 +0100
Subject: [PATCH 470/530] Update tests and snapshot

---
 subworkflows/local/qc_bam/tests/main.nf.test  | 83 ++++++++++++++++---
 .../local/qc_bam/tests/main.nf.test.snap      | 41 +++++++--
 2 files changed, 103 insertions(+), 21 deletions(-)

diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test
index e5b2da3c..0c028470 100644
--- a/subworkflows/local/qc_bam/tests/main.nf.test
+++ b/subworkflows/local/qc_bam/tests/main.nf.test
@@ -6,7 +6,59 @@ nextflow_workflow {
     tag 'subworkflows'
     tag 'qc_bam'
 
-    test("Should run without failures") {
+    test("Test with run_picard_collecthsmetrics=false") {
+
+        when {
+            params {
+                pipelines_testdata_base_path    = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease'
+                run_picard_collecthsmetrics     = true
+                config "./nextflow.config"
+                outdir = "$outputDir"
+
+            }
+            workflow {
+                """
+                input[0]  = channel.of(
+                    [
+                        [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'],
+                        [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)]
+                    ]
+                )
+                input[1]  = channel.of(
+                    [
+                        [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'],
+                        [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)]
+                    ]
+                )
+                input[2]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta', checkIfExists: true)).collect()
+                input[3]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta.fai', checkIfExists: true)).collect()
+                input[4]  = false
+                input[5]  = null
+                input[6]  = null
+                input[7]  = null
+                """
+            }
+        }
+
+        then {
+            // All files + folders produced by PICARD_COLLECTMULTIPLEMETRICS
+            def picard_collectmultiplemetrics_files = getAllFilesFromDir(
+                params.outdir + '/picard_collectmultiplemetrics',
+                relative: true, includeDir: true
+            )
+
+            assert workflow.success
+            assert snapshot(
+                    picard_collectmultiplemetrics_files
+                ).match()
+
+            // Only PICARD_COLLECTMULTIPLEMETRICS should run
+            assert workflow.out.versions.size() == 1
+        }
+
+    }
+
+    test("Test with run_picard_collecthsmetrics=true") {
 
         when {
             params {
@@ -41,20 +93,25 @@ nextflow_workflow {
         }
 
         then {
+            // All files + folders produced by PICARD_COLLECTMULTIPLEMETRICS
+            def picard_collectmultiplemetrics_files = getAllFilesFromDir(
+                params.outdir + '/picard_collectmultiplemetrics',
+                relative: true, includeDir: true
+            )
+            // All files + folders produced by PICARD_COLLECTHSMETRICS
+            def picard_collecthsmetrics_files = getAllFilesFromDir(
+                params.outdir + '/picard_collecthsmetrics',
+                relative: true, includeDir: true
+            )
+
             assert workflow.success
             assert snapshot(
-                            workflow.out.multiple_metrics
-                                    .collect {it[1]}
-                                    .flatten()
-                                    .collect { file(it).name }
-                                    .toSorted(),
-                            workflow.out.hs_metrics
-                                    .collect {it[1]}
-                                    .flatten()
-                                    .collect { file(it).name }
-                                    .toSorted(),
-                            workflow.out.versions
-                            ).match()
+                    picard_collectmultiplemetrics_files,
+                    picard_collecthsmetrics_files
+                ).match()
+
+            // PICARD_COLLECTMULTIPLEMETRICS and PICARD_COLLECTHSMETRICS run
+            assert workflow.out.versions.size() == 2
         }
 
     }
diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap
index 33dfda38..b0ce00e1 100644
--- a/subworkflows/local/qc_bam/tests/main.nf.test.snap
+++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap
@@ -1,25 +1,50 @@
 {
-    "Should run without failures": {
+    "Test with run_picard_collecthsmetrics=false": {
         "content": [
             [
+                "",
                 "earlycasualcaiman.CollectMultipleMetrics.alignment_summary_metrics",
+                "earlycasualcaiman.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
                 "earlycasualcaiman.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "earlycasualcaiman.CollectMultipleMetrics.insert_size_histogram.pdf",
                 "earlycasualcaiman.CollectMultipleMetrics.insert_size_metrics",
+                "earlycasualcaiman.CollectMultipleMetrics.quality_by_cycle.pdf",
                 "earlycasualcaiman.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "earlycasualcaiman.CollectMultipleMetrics.quality_distribution_metrics"
-            ],
+                "earlycasualcaiman.CollectMultipleMetrics.quality_distribution.pdf",
+                "earlycasualcaiman.CollectMultipleMetrics.quality_distribution_metrics",
+                "earlycasualcaiman.CollectMultipleMetrics.read_length_histogram.pdf"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2025-12-02T15:05:56.507859"
+    },
+    "Test with run_picard_collecthsmetrics=true": {
+        "content": [
             [
-                "earlycasualcaiman.CollectHsMetrics.coverage_metrics"
+                "",
+                "earlycasualcaiman.CollectMultipleMetrics.alignment_summary_metrics",
+                "earlycasualcaiman.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "earlycasualcaiman.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "earlycasualcaiman.CollectMultipleMetrics.insert_size_histogram.pdf",
+                "earlycasualcaiman.CollectMultipleMetrics.insert_size_metrics",
+                "earlycasualcaiman.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "earlycasualcaiman.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "earlycasualcaiman.CollectMultipleMetrics.quality_distribution.pdf",
+                "earlycasualcaiman.CollectMultipleMetrics.quality_distribution_metrics",
+                "earlycasualcaiman.CollectMultipleMetrics.read_length_histogram.pdf"
             ],
             [
-                "versions.yml:md5,108c8ce4c159f43894c7800f3b69fbfd",
-                "versions.yml:md5,8508bd28eaf1fffcdc4d78e4d9f95393"
+                "",
+                "earlycasualcaiman.CollectHsMetrics.coverage_metrics"
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.0"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-01T14:06:04.611269"
+        "timestamp": "2025-12-02T15:08:24.865168"
     }
 }
\ No newline at end of file

From 4e43aec218beddd99d9208d70af11d1fa758b22d Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Tue, 2 Dec 2025 15:14:56 +0100
Subject: [PATCH 471/530] Add EOL to nextflow.config

---
 subworkflows/local/prepare_genome/tests/nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/prepare_genome/tests/nextflow.config b/subworkflows/local/prepare_genome/tests/nextflow.config
index 4bc7fa18..1207c039 100644
--- a/subworkflows/local/prepare_genome/tests/nextflow.config
+++ b/subworkflows/local/prepare_genome/tests/nextflow.config
@@ -4,4 +4,4 @@ includeConfig 'nextflow.config'
 // Load the correct samplesheet for that test
 params {
     pipelines_testdata_base_path    = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease'
-}
\ No newline at end of file
+}

From fb4376d54015a0d9e09436f7ad95904b94a601f4 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Wed, 3 Dec 2025 09:14:58 +0100
Subject: [PATCH 472/530] Update QC_BAM input description

---
 subworkflows/local/qc_bam/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf
index fd451cdc..d0f3db59 100644
--- a/subworkflows/local/qc_bam/main.nf
+++ b/subworkflows/local/qc_bam/main.nf
@@ -11,7 +11,7 @@ workflow QC_BAM {
         ch_bai                      // channel: [mandatory] [ val(meta), path(bai) ]
         ch_reference_fasta          // channel: [mandatory] [ val(meta), path(reference_fasta) ]
         ch_reference_fai            // channel: [mandatory] [ val(meta), path(reference_fai) ]
-        run_picard_collecthsmetrics // value:   [mandatory for picard_collecthsmetrics] bool
+        run_picard_collecthsmetrics // string:  [mandatory for picard_collecthsmetrics] bool
         ch_bait_intervals           // channel: [mandatory for picard_collecthsmetrics] [ val(meta), path(bait_intervals) ]
         ch_target_intervals         // channel: [mandatory for picard_collecthsmetrics] [ val(meta), path(target_intervals) ]
         ch_ref_dict                 // channel: [mandatory for picard_collecthsmetrics] [ val(meta), path(ref_dict) ]

From 56143984a80344eda1c98e0e50e088f49f5324d0 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Wed, 3 Dec 2025 10:55:49 +0100
Subject: [PATCH 473/530] Update PREPARE_GENOME test configs

---
 subworkflows/local/prepare_genome/tests/main.nf.test    | 6 +++---
 subworkflows/local/prepare_genome/tests/nextflow.config | 7 -------
 2 files changed, 3 insertions(+), 10 deletions(-)
 delete mode 100644 subworkflows/local/prepare_genome/tests/nextflow.config

diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test b/subworkflows/local/prepare_genome/tests/main.nf.test
index 646dcf00..51b033dd 100644
--- a/subworkflows/local/prepare_genome/tests/main.nf.test
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test
@@ -10,7 +10,7 @@ nextflow_workflow {
 
         when {
             params {
-                config "./nextflow.config"
+                pipelines_testdata_base_path    = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease'
                 outdir = "$outputDir"
                 run_picard_collecthsmetrics = true
 
@@ -55,7 +55,7 @@ nextflow_workflow {
 
         when {
             params {
-                config "./nextflow.config"
+                pipelines_testdata_base_path    = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease'
                 outdir = "$outputDir"
                 run_picard_collecthsmetrics = true
 
@@ -98,7 +98,7 @@ nextflow_workflow {
 
         when {
             params {
-                config "./nextflow.config"
+                pipelines_testdata_base_path    = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease'
                 outdir = "$outputDir"
                 run_picard_collecthsmetrics = true
 
diff --git a/subworkflows/local/prepare_genome/tests/nextflow.config b/subworkflows/local/prepare_genome/tests/nextflow.config
deleted file mode 100644
index 1207c039..00000000
--- a/subworkflows/local/prepare_genome/tests/nextflow.config
+++ /dev/null
@@ -1,7 +0,0 @@
-// Load the basic test config
-includeConfig 'nextflow.config'
-
-// Load the correct samplesheet for that test
-params {
-    pipelines_testdata_base_path    = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease'
-}

From 1f7cae837770bb5bf835171af98a64976c802285 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Wed, 3 Dec 2025 12:21:27 +0100
Subject: [PATCH 474/530] Update snapshots

---
 tests/MiSeq.main.nf.test.snap                 | 112 +++++-
 tests/MiSeq_PairedEnd.main.nf.test.snap       | 146 ++++++-
 tests/NovaSeq6000.main.nf.test.snap           | 362 +++++++++++++++++-
 tests/NovaSeq6000.main_subsample.nf.test.snap | 362 +++++++++++++++++-
 tests/PromethION.main.nf.test.snap            |  47 ++-
 5 files changed, 1023 insertions(+), 6 deletions(-)

diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index f2cd38ad..c1af1fd6 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -124,8 +124,77 @@
                 "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "picard_collectmultiplemetrics",
                 "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics",
@@ -196,7 +265,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-02T12:22:09.04125"
+        "timestamp": "2025-12-03T10:55:19.837222"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
@@ -268,8 +337,47 @@
                 "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "picard_collectmultiplemetrics",
                 "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics",
@@ -330,6 +438,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-02T12:24:18.752403"
+        "timestamp": "2025-12-03T10:56:01.102965"
     }
 }
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index 3dd42dc8..32b26569 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -104,8 +104,80 @@
                 "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_adapter_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "multiqc/group_reports",
                 "multiqc/group_reports/Bpacificus",
@@ -151,8 +223,80 @@
                 "multiqc/group_reports/Bpacificus/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_plots",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-cnt.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-pct.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-cnt.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-pct.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_adapter_content_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-cnt.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-pct.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-cnt.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-pct.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_quality_score_distribution.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-cnt.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-pct.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-cnt.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-pct.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_quality_score_distribution.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_report.html",
                 "picard_collectmultiplemetrics",
                 "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.alignment_summary_metrics",
@@ -276,6 +420,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-02T12:28:12.75159"
+        "timestamp": "2025-12-03T10:57:19.118426"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index e581d280..2f676dd2 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -116,8 +116,80 @@
                 "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "multiqc/group_reports",
                 "multiqc/group_reports/group1",
@@ -164,8 +236,80 @@
                 "multiqc/group_reports/group1/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group1/multiqc_plots",
                 "multiqc/group_reports/group1/multiqc_plots/pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_score_distribution.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/group1/multiqc_plots/svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_score_distribution.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/group1/multiqc_report.html",
                 "multiqc/group_reports/group2",
                 "multiqc/group_reports/group2/multiqc_data",
@@ -211,8 +355,80 @@
                 "multiqc/group_reports/group2/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group2/multiqc_plots",
                 "multiqc/group_reports/group2/multiqc_plots/pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_score_distribution.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/group2/multiqc_plots/svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_score_distribution.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/group2/multiqc_report.html",
                 "multiqc/group_reports/lane1",
                 "multiqc/group_reports/lane1/multiqc_data",
@@ -258,8 +474,80 @@
                 "multiqc/group_reports/lane1/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/lane1/multiqc_plots",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_score_distribution.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/lane1/multiqc_plots/svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_score_distribution.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/lane1/multiqc_report.html",
                 "multiqc/group_reports/test",
                 "multiqc/group_reports/test/multiqc_data",
@@ -305,8 +593,80 @@
                 "multiqc/group_reports/test/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/test/multiqc_plots",
                 "multiqc/group_reports/test/multiqc_plots/pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/test/multiqc_plots/png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_quality_score_distribution.png",
+                "multiqc/group_reports/test/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/test/multiqc_plots/svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_score_distribution.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/test/multiqc_report.html",
                 "picard_collectmultiplemetrics",
                 "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.alignment_summary_metrics",
@@ -570,6 +930,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-02T12:35:34.210381"
+        "timestamp": "2025-12-03T10:59:00.917873"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index 7ced838f..d85cf67d 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -119,8 +119,80 @@
                 "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "multiqc/group_reports",
                 "multiqc/group_reports/group1",
@@ -167,8 +239,80 @@
                 "multiqc/group_reports/group1/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group1/multiqc_plots",
                 "multiqc/group_reports/group1/multiqc_plots/pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_score_distribution.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/group1/multiqc_plots/svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_score_distribution.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/group1/multiqc_report.html",
                 "multiqc/group_reports/group2",
                 "multiqc/group_reports/group2/multiqc_data",
@@ -214,8 +358,80 @@
                 "multiqc/group_reports/group2/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group2/multiqc_plots",
                 "multiqc/group_reports/group2/multiqc_plots/pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_score_distribution.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/group2/multiqc_plots/svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_score_distribution.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/group2/multiqc_report.html",
                 "multiqc/group_reports/lane1",
                 "multiqc/group_reports/lane1/multiqc_data",
@@ -261,8 +477,80 @@
                 "multiqc/group_reports/lane1/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/lane1/multiqc_plots",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-pct.png",
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+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
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+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_readlength_plot.png",
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+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_score_distribution.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/lane1/multiqc_plots/svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_score_distribution.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/lane1/multiqc_report.html",
                 "multiqc/group_reports/test",
                 "multiqc/group_reports/test/multiqc_data",
@@ -308,8 +596,80 @@
                 "multiqc/group_reports/test/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/test/multiqc_plots",
                 "multiqc/group_reports/test/multiqc_plots/pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/test/multiqc_plots/png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_quality_score_distribution.png",
+                "multiqc/group_reports/test/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/test/multiqc_plots/svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_score_distribution.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/test/multiqc_report.html",
                 "picard_collectmultiplemetrics",
                 "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.alignment_summary_metrics",
@@ -584,6 +944,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-02T13:14:07.677563"
+        "timestamp": "2025-12-03T11:00:48.477172"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index a9d0067b..40b31463 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -52,8 +52,53 @@
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_adapter_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
@@ -93,6 +138,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-02T12:57:49.721413"
+        "timestamp": "2025-12-03T11:01:17.46398"
     }
 }
\ No newline at end of file

From 9d9a2f91ef6f9db34f6da1c50cccc49dddff15fd Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Wed, 3 Dec 2025 14:09:18 +0100
Subject: [PATCH 475/530] Add test nextflow.config

---
 subworkflows/local/prepare_genome/tests/main.nf.test    | 6 +++---
 subworkflows/local/prepare_genome/tests/nextflow.config | 7 +++++++
 2 files changed, 10 insertions(+), 3 deletions(-)
 create mode 100644 subworkflows/local/prepare_genome/tests/nextflow.config

diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test b/subworkflows/local/prepare_genome/tests/main.nf.test
index 51b033dd..c0fff4e5 100644
--- a/subworkflows/local/prepare_genome/tests/main.nf.test
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test
@@ -9,8 +9,8 @@ nextflow_workflow {
     test("Test without bwamem2 index file path and with run_picard_collecthsmetrics=false") {
 
         when {
+            config "./nextflow.config"
             params {
-                pipelines_testdata_base_path    = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease'
                 outdir = "$outputDir"
                 run_picard_collecthsmetrics = true
 
@@ -54,8 +54,8 @@ nextflow_workflow {
     test("Test without bwamem2 index file path, with run_picard_collecthsmetrics=true and with ref_dict") {
 
         when {
+            config "./nextflow.config"
             params {
-                pipelines_testdata_base_path    = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease'
                 outdir = "$outputDir"
                 run_picard_collecthsmetrics = true
 
@@ -97,8 +97,8 @@ nextflow_workflow {
     test("Test without bwamem2 index file path, with run_picard_collecthsmetrics=true and without ref_dict") {
 
         when {
+            config "./nextflow.config"
             params {
-                pipelines_testdata_base_path    = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease'
                 outdir = "$outputDir"
                 run_picard_collecthsmetrics = true
 
diff --git a/subworkflows/local/prepare_genome/tests/nextflow.config b/subworkflows/local/prepare_genome/tests/nextflow.config
new file mode 100644
index 00000000..c1510588
--- /dev/null
+++ b/subworkflows/local/prepare_genome/tests/nextflow.config
@@ -0,0 +1,7 @@
+// Load the basic test config
+includeConfig '../../../../tests/nextflow.config'
+
+
+params {
+    pipelines_testdata_base_path = params.pipelines_testdata_base_path + 'raredisease/'
+}

From 783f565144f4d3d5f0613a8c0b7937b9491b5f5a Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Wed, 3 Dec 2025 14:23:35 +0100
Subject: [PATCH 476/530] Update test configs to remove hardcoded
 pipelines_testdata_base_path and refer instead to the basic
 test/nextflow.config

---
 subworkflows/local/qc_bam/tests/main.nf.test    | 14 ++++++--------
 subworkflows/local/qc_bam/tests/nextflow.config |  8 ++++++++
 2 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test
index 0c028470..e1d1abde 100644
--- a/subworkflows/local/qc_bam/tests/main.nf.test
+++ b/subworkflows/local/qc_bam/tests/main.nf.test
@@ -9,13 +9,12 @@ nextflow_workflow {
     test("Test with run_picard_collecthsmetrics=false") {
 
         when {
+            config "./nextflow.config"
+
             params {
-                pipelines_testdata_base_path    = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease'
-                run_picard_collecthsmetrics     = true
-                config "./nextflow.config"
                 outdir = "$outputDir"
-
             }
+
             workflow {
                 """
                 input[0]  = channel.of(
@@ -61,13 +60,12 @@ nextflow_workflow {
     test("Test with run_picard_collecthsmetrics=true") {
 
         when {
+            config "./nextflow.config"
+
             params {
-                pipelines_testdata_base_path    = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease'
-                run_picard_collecthsmetrics     = true
-                config "./nextflow.config"
                 outdir = "$outputDir"
-
             }
+
             workflow {
                 """
                 input[0]  = channel.of(
diff --git a/subworkflows/local/qc_bam/tests/nextflow.config b/subworkflows/local/qc_bam/tests/nextflow.config
index 4a732a6c..1907f805 100644
--- a/subworkflows/local/qc_bam/tests/nextflow.config
+++ b/subworkflows/local/qc_bam/tests/nextflow.config
@@ -1,3 +1,11 @@
+// Load the basic test config
+includeConfig '../../../../tests/nextflow.config'
+
+
+params {
+    pipelines_testdata_base_path = params.pipelines_testdata_base_path + 'raredisease/'
+}
+
 process {
 
     withName: PICARD_COLLECTHSMETRICS {

From 8ac6732152b517c8a977d38247b2fb057083fb7f Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Wed, 3 Dec 2025 14:40:03 +0100
Subject: [PATCH 477/530] Remove redundant / in test-data paths

---
 subworkflows/local/qc_bam/tests/main.nf.test | 22 ++++++++++----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test
index e1d1abde..c310d2e4 100644
--- a/subworkflows/local/qc_bam/tests/main.nf.test
+++ b/subworkflows/local/qc_bam/tests/main.nf.test
@@ -20,17 +20,17 @@ nextflow_workflow {
                 input[0]  = channel.of(
                     [
                         [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'],
-                        [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)]
+                        [file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)]
                     ]
                 )
                 input[1]  = channel.of(
                     [
                         [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'],
-                        [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)]
+                        [file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)]
                     ]
                 )
-                input[2]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta', checkIfExists: true)).collect()
-                input[3]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta.fai', checkIfExists: true)).collect()
+                input[2]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect()
+                input[3]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect()
                 input[4]  = false
                 input[5]  = null
                 input[6]  = null
@@ -71,21 +71,21 @@ nextflow_workflow {
                 input[0]  = channel.of(
                     [
                         [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'],
-                        [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)]
+                        [file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)]
                     ]
                 )
                 input[1]  = channel.of(
                     [
                         [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'],
-                        [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)]
+                        [file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)]
                     ]
                 )
-                input[2]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta', checkIfExists: true)).collect()
-                input[3]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta.fai', checkIfExists: true)).collect()
+                input[2]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect()
+                input[3]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect()
                 input[4]  = true
-                input[5]  = channel.fromPath(params.pipelines_testdata_base_path + '/reference/target.bed', checkIfExists: true).collect()
-                input[6]  = channel.fromPath(params.pipelines_testdata_base_path + '/reference/target.bed', checkIfExists: true).collect()
-                input[7]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.dict', checkIfExists: true)).collect()
+                input[5]  = channel.fromPath(params.pipelines_testdata_base_path + 'reference/target.bed', checkIfExists: true).collect()
+                input[6]  = channel.fromPath(params.pipelines_testdata_base_path + 'reference/target.bed', checkIfExists: true).collect()
+                input[7]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect()
                 """
             }
         }

From 8bf9588b23b8fd38e57b4d2245b611eaee799963 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pontus=20H=C3=B6jer?= <pontushojer@gmail.com>
Date: Thu, 4 Dec 2025 09:41:47 +0100
Subject: [PATCH 478/530] run fastqscreen with subsampled data if available

---
 tests/NovaSeq6000.main_subsample.nf.test.snap | 44 +++++++++----------
 workflows/seqinspector.nf                     |  2 +-
 2 files changed, 23 insertions(+), 23 deletions(-)

diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index 1d061216..bce1df98 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -429,17 +429,17 @@
                 "seqtk/sampletest_4_sampletest_S4_L001_R1_001.fastq.gz"
             ],
             [
-                "Sample1_1_screen.png:md5,562256290643b51e4374c2225a15f463",
-                "Sample1_1_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
-                "Sample23_3_screen.png:md5,6bb2caf67b9b2ed25d3d5f32c343e9ab",
-                "Sample23_3_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
-                "SampleA_2_screen.png:md5,b2c3e95e034f5c038754bf108537de0e",
-                "SampleA_2_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
-                "Undetermined_5_screen.png:md5,fc5d53f8876dfae3d1a781fa512ea1db",
-                "Undetermined_5_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
-                "sampletest_4_screen.png:md5,1fb60070e8f4b70de0c1b3786b54f27e",
-                "sampletest_4_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
-                "fastq_screen_plot.txt:md5,562b783630f698c3220c951b73b87027",
+                "Sample1_1_screen.png:md5,f77ab5b51b18150e9202544405f268a1",
+                "Sample1_1_screen.txt:md5,14d10b0c3b63e18f223a0dc589abee36",
+                "Sample23_3_screen.png:md5,09a60d51f8bf416e089715729a278a0d",
+                "Sample23_3_screen.txt:md5,14d10b0c3b63e18f223a0dc589abee36",
+                "SampleA_2_screen.png:md5,dfba178e76017bf9ea3e5517ee6915f4",
+                "SampleA_2_screen.txt:md5,14d10b0c3b63e18f223a0dc589abee36",
+                "Undetermined_5_screen.png:md5,e4f09e8c09c2cea7ddf1f0a01bab273d",
+                "Undetermined_5_screen.txt:md5,14d10b0c3b63e18f223a0dc589abee36",
+                "sampletest_4_screen.png:md5,18320e2dde03d1cc3b7897e75c3574c9",
+                "sampletest_4_screen.txt:md5,14d10b0c3b63e18f223a0dc589abee36",
+                "fastq_screen_plot.txt:md5,26b720108af59c53bdccad85540686b9",
                 "fastqc-status-check-heatmap.txt:md5,84794d045dc6d91b00e59985bae9d18a",
                 "fastqc_overrepresented_sequences_plot.txt:md5,8a49ca637e473578baa80c57486f6873",
                 "fastqc_per_base_n_content_plot.txt:md5,234d2d338b88166d1432f0fd3887ed90",
@@ -451,10 +451,10 @@
                 "fastqc_sequence_duplication_levels_plot.txt:md5,5c4b313cef9eae4900d6ca22b561c838",
                 "fastqc_sequence_length_distribution_plot.txt:md5,d423f73abb6f1c4e7ebfff407886f5a7",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
+                "multiqc_fastq_screen.txt:md5,ede47a68cfe19144331104f4e51b6ee7",
                 "multiqc_fastqc.txt:md5,aba942d1e6996b579f19798e5673f514",
                 "multiqc_seqfu.txt:md5,18dd2407d4a1791646785123028f69b5",
-                "fastq_screen_plot.txt:md5,c25d34568f10f131156294d31fbfa994",
+                "fastq_screen_plot.txt:md5,fbd5dbdbc51ecb82f8c2da2b63f104d3",
                 "fastqc-status-check-heatmap.txt:md5,7ee494f345c09706513e65907788de02",
                 "fastqc_overrepresented_sequences_plot.txt:md5,ca9fa146e7b8a7f562fd79b521ba0f60",
                 "fastqc_per_base_n_content_plot.txt:md5,d0948f903d5cb77880ff7b1b4e0a4f23",
@@ -466,10 +466,10 @@
                 "fastqc_sequence_duplication_levels_plot.txt:md5,e37e8e4584f0157a5fa0d53b4834e836",
                 "fastqc_sequence_length_distribution_plot.txt:md5,e102bf11f348e8c24e1d15b336e2f595",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
+                "multiqc_fastq_screen.txt:md5,8028856af6d413fa3592900e16dbc99f",
                 "multiqc_fastqc.txt:md5,ff996e1d3dc4a46e0c9535e54d51ccab",
                 "multiqc_seqfu.txt:md5,6cdb863a3686fbb772aae5a66925ff23",
-                "fastq_screen_plot.txt:md5,44fca6453b0a3d0590271bd7a31cc740",
+                "fastq_screen_plot.txt:md5,c32019d1b4d5245d75264b9f453ce916",
                 "fastqc-status-check-heatmap.txt:md5,b6872d9dbaa3cce396d48dc137076e53",
                 "fastqc_overrepresented_sequences_plot.txt:md5,19babef6996c0bfdf28e5df89368cbb1",
                 "fastqc_per_base_n_content_plot.txt:md5,25367b78b3d6a063d33814c663fea91e",
@@ -481,10 +481,10 @@
                 "fastqc_sequence_duplication_levels_plot.txt:md5,1e595565e848ab3f13cfa8479214d3e0",
                 "fastqc_sequence_length_distribution_plot.txt:md5,24ef8f47147dabd210b03c497d340d77",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
+                "multiqc_fastq_screen.txt:md5,e3e01b13becd5e30c9c12e5313b795c7",
                 "multiqc_fastqc.txt:md5,3df36ecfe76b25b0c22dcda84bce2b3b",
                 "multiqc_seqfu.txt:md5,f821357507fda2d4cfd9299f52fa7dc1",
-                "fastq_screen_plot.txt:md5,5f748d33a7a396547fe8c260b728aa06",
+                "fastq_screen_plot.txt:md5,f4a7d4d2c26ad1eb38525552d2275523",
                 "fastqc-status-check-heatmap.txt:md5,bab59a0bd1d676d90cdd986fbba36b26",
                 "fastqc_overrepresented_sequences_plot.txt:md5,79cb259874c52b44f8c69b2075ee498e",
                 "fastqc_per_base_n_content_plot.txt:md5,6ef3683b1b7db0b6db6948185f96959d",
@@ -496,10 +496,10 @@
                 "fastqc_sequence_duplication_levels_plot.txt:md5,77e0c9a542a3d59b173633764a11b404",
                 "fastqc_sequence_length_distribution_plot.txt:md5,c4f58d755233776c341da8dc357f8527",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
+                "multiqc_fastq_screen.txt:md5,025c2db89ab18864c2828f3f4e368d4f",
                 "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8",
                 "multiqc_seqfu.txt:md5,8cced36d66ca9d25d60c006e734aa7e9",
-                "fastq_screen_plot.txt:md5,8622e1dbd0fe62520af6096207b9775d",
+                "fastq_screen_plot.txt:md5,331bc452d453a3c31263b8c5018a07da",
                 "fastqc-status-check-heatmap.txt:md5,2a66f5d61b9eb579555905cd5954b04c",
                 "fastqc_overrepresented_sequences_plot.txt:md5,5cdefa954db6e46c286e2984a883eb18",
                 "fastqc_per_base_n_content_plot.txt:md5,92c23e189d98430517e4030e7c9ae038",
@@ -511,7 +511,7 @@
                 "fastqc_sequence_duplication_levels_plot.txt:md5,041857b1e41e0b47bfc62000cb9f323d",
                 "fastqc_sequence_length_distribution_plot.txt:md5,c2ee6b7c9fc91de049d183422e0a71fc",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5",
+                "multiqc_fastq_screen.txt:md5,61392eb28e735f293516bb81f463450a",
                 "multiqc_fastqc.txt:md5,ce61b4ce4b1d76ec3f20de3bf0c9ec7f",
                 "multiqc_seqfu.txt:md5,ff4ce1c88f39ed24a88bae0a861f75c8",
                 "Sample1_1_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6",
@@ -533,8 +533,8 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.0"
+            "nextflow": "25.04.0"
         },
-        "timestamp": "2025-11-25T13:20:06.917144477"
+        "timestamp": "2025-12-04T09:40:34.197077"
     }
 }
\ No newline at end of file
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index d1ce58e9..7fd14d88 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -121,7 +121,7 @@ workflow SEQINSPECTOR {
             .toList()
 
         FASTQSCREEN_FASTQSCREEN(
-            ch_samplesheet,
+            ch_sample_sized,
             ch_fastqscreen_refs,
         )
         ch_multiqc_files = ch_multiqc_files.mix(FASTQSCREEN_FASTQSCREEN.out.txt)

From 234520260a8a750b786cfedce8636d320132143f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pontus=20H=C3=B6jer?= <pontushojer@gmail.com>
Date: Thu, 4 Dec 2025 11:12:14 +0100
Subject: [PATCH 479/530] update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index da46257e..a7c01bd0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -39,6 +39,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#107](https://github.com/nf-core/seqinspector/pull/107) Put SeqFU-stats section reports together
 - [#112](https://github.com/nf-core/seqinspector/pull/112) Making fastq_screen_references value to use parentDir
 - [#94] (https://github.com/nf-core/seqinspector/issues/94) Go through and validate test data
+- [#163](https://github.com/nf-core/seqinspector/pull/163) Run fastqscreen with subsampled data if available
 
 ### `Dependencies`
 

From 324851e19f2a4169b7eeeb38c91bef40c3b3c487 Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Thu, 4 Dec 2025 15:35:22 +0100
Subject: [PATCH 480/530] Fix bug preventing picard_multiple_metrics files from
 being passed to multiqc_files

---
 workflows/seqinspector.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 62b5a7cc..af3f4cf6 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -168,7 +168,7 @@ workflow SEQINSPECTOR {
             ch_ref_dict,
         )
 
-        ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.hs_metrics)
+        ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.multiple_metrics, QC_BAM.out.hs_metrics)
         ch_versions = ch_versions.mix(QC_BAM.out.versions)
     }
 

From 67db2a912ef34321e16e871f8f488989c5024cfd Mon Sep 17 00:00:00 2001
From: beatrizsavinhas <beatriz.sa.vinhas@scilifelab.se>
Date: Thu, 4 Dec 2025 15:44:12 +0100
Subject: [PATCH 481/530] Update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6cbd42a2..0ee648c1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -40,7 +40,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#107](https://github.com/nf-core/seqinspector/pull/107) Put SeqFU-stats section reports together
 - [#112](https://github.com/nf-core/seqinspector/pull/112) Making fastq_screen_references value to use parentDir
 - [#94] (https://github.com/nf-core/seqinspector/issues/94) Go through and validate test data
-- [#162](https://github.com/nf-core/seqinspector/pull/162) Fix bug in prepare_genome subworkflow and add tests
+- [#162](https://github.com/nf-core/seqinspector/pull/162) Fix bugs in qc_bam and prepare_genome subworkflows and add tests
 
 ### `Dependencies`
 

From 6f71488dccb21889eeb0f9819ee6be15673e1bb6 Mon Sep 17 00:00:00 2001
From: Beatriz Vinhas <beatriz.sa.vinhas@gmail.com>
Date: Fri, 5 Dec 2025 08:50:57 +0100
Subject: [PATCH 482/530] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0ee648c1..31b1a17e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -32,6 +32,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#151](https://github.com/nf-core/seqinspector/pull/151) Added a prepare_genome subworkflow to handle bwamem2 indexing
 - [#159](https://github.com/nf-core/seqinspector/pull/159) Added a subworkflow QC_BAM including picard_collecthsmetrics for alignment QC of hybrid-selection data
 - [#158](https://github.com/nf-core/seqinspector/pull/158) Moved picard_collectmultiplemetrics to the subworkflow QC_BAM
+- [#162](https://github.com/nf-core/seqinspector/pull/162) Add tests for prepare_genome subworkflow
 
 ### `Fixed`
 

From 204cc027abc28885d93ada6afab4befc4c5aa647 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 8 Dec 2025 17:09:16 +0100
Subject: [PATCH 483/530] fix snapshot

---
 tests/NovaSeq6000.main_subsample.nf.test.snap | 32 +++++++++----------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index 18e734a7..e05db91c 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -751,17 +751,17 @@
                 "Undetermined_5.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
                 "sampletest_4.bam:md5,2c37f72ed4f25c971199fbde3af370b9",
                 "sampletest_4.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
-                "Sample1_1_screen.png:md5,562256290643b51e4374c2225a15f463",
-                "Sample1_1_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
-                "Sample23_3_screen.png:md5,6bb2caf67b9b2ed25d3d5f32c343e9ab",
-                "Sample23_3_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
-                "SampleA_2_screen.png:md5,b2c3e95e034f5c038754bf108537de0e",
-                "SampleA_2_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
-                "Undetermined_5_screen.png:md5,fc5d53f8876dfae3d1a781fa512ea1db",
-                "Undetermined_5_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
-                "sampletest_4_screen.png:md5,1fb60070e8f4b70de0c1b3786b54f27e",
-                "sampletest_4_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
-                "fastq_screen_plot.txt:md5,562b783630f698c3220c951b73b87027",
+                "Sample1_1_screen.png:md5,f77ab5b51b18150e9202544405f268a1",
+                "Sample1_1_screen.txt:md5,14d10b0c3b63e18f223a0dc589abee36",
+                "Sample23_3_screen.png:md5,09a60d51f8bf416e089715729a278a0d",
+                "Sample23_3_screen.txt:md5,14d10b0c3b63e18f223a0dc589abee36",
+                "SampleA_2_screen.png:md5,dfba178e76017bf9ea3e5517ee6915f4",
+                "SampleA_2_screen.txt:md5,14d10b0c3b63e18f223a0dc589abee36",
+                "Undetermined_5_screen.png:md5,e4f09e8c09c2cea7ddf1f0a01bab273d",
+                "Undetermined_5_screen.txt:md5,14d10b0c3b63e18f223a0dc589abee36",
+                "sampletest_4_screen.png:md5,18320e2dde03d1cc3b7897e75c3574c9",
+                "sampletest_4_screen.txt:md5,14d10b0c3b63e18f223a0dc589abee36",
+                "fastq_screen_plot.txt:md5,26b720108af59c53bdccad85540686b9",
                 "fastqc-status-check-heatmap.txt:md5,84794d045dc6d91b00e59985bae9d18a",
                 "fastqc_overrepresented_sequences_plot.txt:md5,8a49ca637e473578baa80c57486f6873",
                 "fastqc_per_base_n_content_plot.txt:md5,234d2d338b88166d1432f0fd3887ed90",
@@ -793,7 +793,7 @@
                 "picard_base_distribution_by_cycle__Undetermined.txt:md5,a472bba4490d7189df23f6b38a554448",
                 "picard_quality_by_cycle.txt:md5,83d68b4049173f8c9a37f58f1276adc1",
                 "picard_quality_score_distribution.txt:md5,42c08c8a51230d9ecccdad416c06f59c",
-                "fastq_screen_plot.txt:md5,c25d34568f10f131156294d31fbfa994",
+                "fastq_screen_plot.txt:md5,fbd5dbdbc51ecb82f8c2da2b63f104d3",
                 "fastqc-status-check-heatmap.txt:md5,7ee494f345c09706513e65907788de02",
                 "fastqc_overrepresented_sequences_plot.txt:md5,ca9fa146e7b8a7f562fd79b521ba0f60",
                 "fastqc_per_base_n_content_plot.txt:md5,d0948f903d5cb77880ff7b1b4e0a4f23",
@@ -825,7 +825,7 @@
                 "picard_base_distribution_by_cycle__Undetermined.txt:md5,2b4526a0b0977ebd7fbe326c6d51cf19",
                 "picard_quality_by_cycle.txt:md5,d53617c495e81e011996cd4e9f755e0a",
                 "picard_quality_score_distribution.txt:md5,05f9e89733e43b81acf593efc1a56180",
-                "fastq_screen_plot.txt:md5,44fca6453b0a3d0590271bd7a31cc740",
+                "fastq_screen_plot.txt:md5,c32019d1b4d5245d75264b9f453ce916",
                 "fastqc-status-check-heatmap.txt:md5,b6872d9dbaa3cce396d48dc137076e53",
                 "fastqc_overrepresented_sequences_plot.txt:md5,19babef6996c0bfdf28e5df89368cbb1",
                 "fastqc_per_base_n_content_plot.txt:md5,25367b78b3d6a063d33814c663fea91e",
@@ -857,7 +857,7 @@
                 "picard_base_distribution_by_cycle__Undetermined.txt:md5,3536e6dcc7c7ed972b02d2945da75cb7",
                 "picard_quality_by_cycle.txt:md5,be127a96dd68c14077548d36c0507dc3",
                 "picard_quality_score_distribution.txt:md5,9e27b097f10cb9a9a95a3445b220d104",
-                "fastq_screen_plot.txt:md5,5f748d33a7a396547fe8c260b728aa06",
+                "fastq_screen_plot.txt:md5,f4a7d4d2c26ad1eb38525552d2275523",
                 "fastqc-status-check-heatmap.txt:md5,bab59a0bd1d676d90cdd986fbba36b26",
                 "fastqc_overrepresented_sequences_plot.txt:md5,79cb259874c52b44f8c69b2075ee498e",
                 "fastqc_per_base_n_content_plot.txt:md5,6ef3683b1b7db0b6db6948185f96959d",
@@ -889,7 +889,7 @@
                 "picard_base_distribution_by_cycle__Undetermined.txt:md5,67ee93606c468a7eea7818b2f4b3389f",
                 "picard_quality_by_cycle.txt:md5,974b3baed160e9643f493df1d0ad5000",
                 "picard_quality_score_distribution.txt:md5,869d69ae4e243f0669f63b489563e4f1",
-                "fastq_screen_plot.txt:md5,8622e1dbd0fe62520af6096207b9775d",
+                "fastq_screen_plot.txt:md5,331bc452d453a3c31263b8c5018a07da",
                 "fastqc-status-check-heatmap.txt:md5,2a66f5d61b9eb579555905cd5954b04c",
                 "fastqc_overrepresented_sequences_plot.txt:md5,5cdefa954db6e46c286e2984a883eb18",
                 "fastqc_per_base_n_content_plot.txt:md5,92c23e189d98430517e4030e7c9ae038",
@@ -944,6 +944,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-03T11:00:48.477172"
+        "timestamp": "2025-12-08T17:09:00.331820625"
     }
 }
\ No newline at end of file

From 83182955bbcbcc0a64bcd95e1c0b9e2dee0b2983 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 12 Dec 2025 10:05:53 +0100
Subject: [PATCH 484/530] re-generate snapshots

---
 tests/MiSeq.main.nf.test.snap                 | 176 +++---
 tests/MiSeq_PairedEnd.main.nf.test.snap       | 206 +++----
 tests/NovaSeq6000.main.nf.test.snap           | 492 +++++++--------
 tests/NovaSeq6000.main_subsample.nf.test.snap | 582 +++++++++---------
 tests/PromethION.main.nf.test.snap            |  18 +-
 5 files changed, 737 insertions(+), 737 deletions(-)

diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index d91c260d..b286d463 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -71,8 +71,8 @@
                 "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
                 "bwamem2_index/bwamem2/genome.fa.pac",
                 "bwamem2_mem",
-                "bwamem2_mem/SAMPLE_SINGLE_END_1.bam",
-                "bwamem2_mem/SAMPLE_SINGLE_END_1.bam.bai",
+                "bwamem2_mem/SAMPLE_SINGLE_END_01.bam",
+                "bwamem2_mem/SAMPLE_SINGLE_END_01.bam.bai",
                 "fastqc",
                 "fastqc/SAMPLE_SINGLE_END_01_fastqc.html",
                 "fastqc/SAMPLE_SINGLE_END_01_fastqc.zip",
@@ -106,7 +106,7 @@
                 "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
                 "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
                 "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
-                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu_mqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
@@ -146,7 +146,7 @@
                 "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu_mqc.pdf",
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
@@ -170,7 +170,7 @@
                 "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
                 "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
                 "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu_mqc.png",
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
@@ -194,17 +194,17 @@
                 "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
                 "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
                 "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
-                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu_mqc.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "picard_collectmultiplemetrics",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_01.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_01.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_01.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_01.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_01.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_01.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_01.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_01.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "samtools_faidx",
@@ -220,52 +220,52 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "SAMPLE_SINGLE_END_1.bam:md5,ff8893272a6560cac7067fd8a9406f9b",
-                "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
-                "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
-                "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
-                "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
-                "fastqc-status-check-heatmap.txt:md5,8f98652c377741c974e485652a19f37f",
-                "fastqc_overrepresented_sequences_plot.txt:md5,cdc7479933cae03e0043ae794f81c304",
-                "fastqc_per_base_n_content_plot.txt:md5,dd8d6976dc5ea8cf67d9fa2c3be9e24b",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,5f9a98d3068aab17f26731ae0615f41a",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,1de1333bb959189dcf8230706f60dbfc",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,62f140bfa52d462c9c499dfdabc35476",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,5fda43eb9b7c60cf6b4348f734a94b26",
-                "fastqc_sequence_counts_plot.txt:md5,00cd6842465f7aa9ae75434e175946a6",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,c3befe0812d2f1c23d5e75e6fccf0622",
+                "SAMPLE_SINGLE_END_01.bam:md5,fc03db7366825685afd45c46cb0769f6",
+                "SAMPLE_SINGLE_END_01.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
+                "SAMPLE_SINGLE_END_01_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
+                "SAMPLE_SINGLE_END_01_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
+                "fastq_screen_plot.txt:md5,7d120ba49a8a9220f85efb05e55bfae1",
+                "fastqc-status-check-heatmap.txt:md5,976c0ef6a62569395931028d05c2a320",
+                "fastqc_overrepresented_sequences_plot.txt:md5,89a55ca2171daea540258b0fc37e6766",
+                "fastqc_per_base_n_content_plot.txt:md5,54814a92014a4e3b07bca1449e2fcce4",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,e216aeee526de6c65d221924c0b7891e",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a494a0634c54d6ff7821765748908380",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,f838935c85ecfac06a744d7aa635926d",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,40c09f977034ca189f4894c8849212a0",
+                "fastqc_sequence_counts_plot.txt:md5,b1cf5ced11bf843a79f0e4265c7e48a1",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,70648ea8c46035d60647a128a5aa2fc6",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607",
-                "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,fe082d3b5dcc3d338e25bc027e17dc99",
-                "multiqc_picard_baseContent.txt:md5,796e8e0803ad3ed4fd1c76f073784942",
-                "multiqc_picard_quality_by_cycle.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
-                "multiqc_picard_quality_score_distribution.txt:md5,bad70b98811c4cbe4728f53334993703",
-                "multiqc_seqfu.txt:md5,7ec63bc3465b3fc8e316e2443ec4c848",
+                "multiqc_fastq_screen.txt:md5,1cfa6a74e8e735bf59da770f6cb25959",
+                "multiqc_fastqc.txt:md5,b5f6993152fb8e7142a1d84c6b75fc18",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,3b5a594aed12f8c904c57ee0b75ae990",
+                "multiqc_picard_baseContent.txt:md5,06ef2cbc8f27964c4d84ce70bf75c152",
+                "multiqc_picard_quality_by_cycle.txt:md5,4cf5e6149b8feb8da1e6bb885e4a5829",
+                "multiqc_picard_quality_score_distribution.txt:md5,7f2087055d3268efd2f6de24aa556e2c",
+                "multiqc_seqfu_mqc.txt:md5,7ec63bc3465b3fc8e316e2443ec4c848",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
-                "picard_QualityScoreDistribution_histogram.txt:md5,bad70b98811c4cbe4728f53334993703",
-                "picard_alignment_readlength_plot.txt:md5,0fe7e17f1c58b7a6291bc1ff80fdfaa0",
-                "picard_alignment_summary.txt:md5,c770d3ee98dadaee77ef43967a974627",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,65d43b083e90830aa9451bde65a261b8",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,31dc4f314d8e3f8e086e7ae761638023",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,d92fac15687942c0f9c436ba0cf55fc9",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,00b76f45bbfc9acd2774f90612e53333",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,5451af67007a16e7645d0393011414af",
-                "picard_quality_by_cycle.txt:md5,46fbe44a9788f2e9184e2c1d689c2876",
-                "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,4cf5e6149b8feb8da1e6bb885e4a5829",
+                "picard_QualityScoreDistribution_histogram.txt:md5,7f2087055d3268efd2f6de24aa556e2c",
+                "picard_alignment_readlength_plot.txt:md5,5dbb52fb316ab11457e8b2bbd5eb6e2a",
+                "picard_alignment_summary.txt:md5,fcc65f1b88cadefaf095d0aec6ef7634",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,770aa7550d7d8f78c5ab8841a577078d",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,264b9e23455de2556e8188951fc4c31d",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,b44066e25c38fc8345c7d1c878245602",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,55c04c3520e955d4d403635fe1dd01c5",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,a65cb6ad0f510954d869c6c23d97b950",
+                "picard_quality_by_cycle.txt:md5,d754b0c0d9aac602637d0c923dc88834",
+                "picard_quality_score_distribution.txt:md5,d86da8fb7d48098fd5ec4a8419a8bc9e",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
-                "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,33a9e44386f308d43881a58394b6b17c",
-                "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,e67e819605ab49182aacf1d676dc885d"
+                "SAMPLE_SINGLE_END_01_seqfu.tsv:md5,33a9e44386f308d43881a58394b6b17c",
+                "SAMPLE_SINGLE_END_01_seqfu_mqc.txt:md5,e67e819605ab49182aacf1d676dc885d"
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-03T10:55:19.837222"
+        "timestamp": "2025-12-12T10:00:01.095899935"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
@@ -299,8 +299,8 @@
                 "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
                 "bwamem2_index/bwamem2/genome.fa.pac",
                 "bwamem2_mem",
-                "bwamem2_mem/SAMPLE_SINGLE_END_1.bam",
-                "bwamem2_mem/SAMPLE_SINGLE_END_1.bam.bai",
+                "bwamem2_mem/SAMPLE_SINGLE_END_01.bam",
+                "bwamem2_mem/SAMPLE_SINGLE_END_01.bam.bai",
                 "fastqscreen",
                 "fastqscreen/SAMPLE_SINGLE_END_01_screen.html",
                 "fastqscreen/SAMPLE_SINGLE_END_01_screen.png",
@@ -319,7 +319,7 @@
                 "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
                 "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
                 "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
-                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu_mqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
@@ -349,7 +349,7 @@
                 "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu_mqc.pdf",
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
@@ -363,7 +363,7 @@
                 "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
                 "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
                 "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu_mqc.png",
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
@@ -377,17 +377,17 @@
                 "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
                 "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
                 "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
-                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu_mqc.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "picard_collectmultiplemetrics",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_01.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_01.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_01.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_01.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_01.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_01.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_01.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_01.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "samtools_faidx",
@@ -403,41 +403,41 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "SAMPLE_SINGLE_END_1.bam:md5,ff8893272a6560cac7067fd8a9406f9b",
-                "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
-                "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
-                "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
-                "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f",
+                "SAMPLE_SINGLE_END_01.bam:md5,fc03db7366825685afd45c46cb0769f6",
+                "SAMPLE_SINGLE_END_01.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
+                "SAMPLE_SINGLE_END_01_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
+                "SAMPLE_SINGLE_END_01_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
+                "fastq_screen_plot.txt:md5,7d120ba49a8a9220f85efb05e55bfae1",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,fe082d3b5dcc3d338e25bc027e17dc99",
-                "multiqc_picard_baseContent.txt:md5,796e8e0803ad3ed4fd1c76f073784942",
-                "multiqc_picard_quality_by_cycle.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
-                "multiqc_picard_quality_score_distribution.txt:md5,bad70b98811c4cbe4728f53334993703",
-                "multiqc_seqfu.txt:md5,7ec63bc3465b3fc8e316e2443ec4c848",
+                "multiqc_fastq_screen.txt:md5,1cfa6a74e8e735bf59da770f6cb25959",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,3b5a594aed12f8c904c57ee0b75ae990",
+                "multiqc_picard_baseContent.txt:md5,06ef2cbc8f27964c4d84ce70bf75c152",
+                "multiqc_picard_quality_by_cycle.txt:md5,4cf5e6149b8feb8da1e6bb885e4a5829",
+                "multiqc_picard_quality_score_distribution.txt:md5,7f2087055d3268efd2f6de24aa556e2c",
+                "multiqc_seqfu_mqc.txt:md5,7ec63bc3465b3fc8e316e2443ec4c848",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1",
-                "picard_QualityScoreDistribution_histogram.txt:md5,bad70b98811c4cbe4728f53334993703",
-                "picard_alignment_readlength_plot.txt:md5,0fe7e17f1c58b7a6291bc1ff80fdfaa0",
-                "picard_alignment_summary.txt:md5,c770d3ee98dadaee77ef43967a974627",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,65d43b083e90830aa9451bde65a261b8",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,31dc4f314d8e3f8e086e7ae761638023",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,d92fac15687942c0f9c436ba0cf55fc9",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,00b76f45bbfc9acd2774f90612e53333",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,5451af67007a16e7645d0393011414af",
-                "picard_quality_by_cycle.txt:md5,46fbe44a9788f2e9184e2c1d689c2876",
-                "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,4cf5e6149b8feb8da1e6bb885e4a5829",
+                "picard_QualityScoreDistribution_histogram.txt:md5,7f2087055d3268efd2f6de24aa556e2c",
+                "picard_alignment_readlength_plot.txt:md5,5dbb52fb316ab11457e8b2bbd5eb6e2a",
+                "picard_alignment_summary.txt:md5,fcc65f1b88cadefaf095d0aec6ef7634",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,770aa7550d7d8f78c5ab8841a577078d",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,264b9e23455de2556e8188951fc4c31d",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,b44066e25c38fc8345c7d1c878245602",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,55c04c3520e955d4d403635fe1dd01c5",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,a65cb6ad0f510954d869c6c23d97b950",
+                "picard_quality_by_cycle.txt:md5,d754b0c0d9aac602637d0c923dc88834",
+                "picard_quality_score_distribution.txt:md5,d86da8fb7d48098fd5ec4a8419a8bc9e",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
-                "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,33a9e44386f308d43881a58394b6b17c",
-                "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,e67e819605ab49182aacf1d676dc885d"
+                "SAMPLE_SINGLE_END_01_seqfu.tsv:md5,33a9e44386f308d43881a58394b6b17c",
+                "SAMPLE_SINGLE_END_01_seqfu_mqc.txt:md5,e67e819605ab49182aacf1d676dc885d"
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-03T10:56:01.102965"
+        "timestamp": "2025-12-12T10:00:43.048743949"
     }
 }
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap
index b0b89795..26cdac05 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.main.nf.test.snap
@@ -34,10 +34,10 @@
                 "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
                 "bwamem2_index/bwamem2/genome.fa.pac",
                 "bwamem2_mem",
-                "bwamem2_mem/SAMPLE_PAIRED_END_1_1.bam",
-                "bwamem2_mem/SAMPLE_PAIRED_END_1_1.bam.bai",
-                "bwamem2_mem/SAMPLE_PAIRED_END_2_2.bam",
-                "bwamem2_mem/SAMPLE_PAIRED_END_2_2.bam.bai",
+                "bwamem2_mem/SAMPLE_PAIRED_END_1_01.bam",
+                "bwamem2_mem/SAMPLE_PAIRED_END_1_01.bam.bai",
+                "bwamem2_mem/SAMPLE_PAIRED_END_2_02.bam",
+                "bwamem2_mem/SAMPLE_PAIRED_END_2_02.bam.bai",
                 "fastqc",
                 "fastqc/SAMPLE_PAIRED_END_1_01_1_fastqc.html",
                 "fastqc/SAMPLE_PAIRED_END_1_01_1_fastqc.zip",
@@ -85,7 +85,7 @@
                 "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
                 "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
                 "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
-                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu_mqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
@@ -127,7 +127,7 @@
                 "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu_mqc.pdf",
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
@@ -152,7 +152,7 @@
                 "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
                 "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
                 "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu_mqc.png",
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
@@ -177,7 +177,7 @@
                 "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
                 "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
                 "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
-                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu_mqc.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "multiqc/group_reports",
                 "multiqc/group_reports/Bpacificus",
@@ -204,7 +204,7 @@
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_baseContent.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_quality_by_cycle.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_quality_score_distribution.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_seqfu_mqc.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/Bpacificus/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
@@ -246,7 +246,7 @@
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/seqfu_mqc.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-pct.png",
@@ -271,7 +271,7 @@
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_quality_by_cycle.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_quality_score_distribution.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/seqfu.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/seqfu_mqc.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-pct.svg",
@@ -296,25 +296,25 @@
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_quality_by_cycle.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_quality_score_distribution.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/seqfu.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/seqfu_mqc.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_report.html",
                 "picard_collectmultiplemetrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.alignment_summary_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.read_length_histogram.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.alignment_summary_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_01.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_01.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_01.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_01.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_01.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_01.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_01.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_01.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_02.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_02.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_02.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_02.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_02.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_02.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_02.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_02.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "samtools_faidx",
@@ -332,94 +332,94 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "SAMPLE_PAIRED_END_1_1.bam:md5,44c0ef738b73e26f67ded45ca4cb9e5b",
-                "SAMPLE_PAIRED_END_1_1.bam.bai:md5,82724835c47f8e1d1a86e13ef469b464",
-                "SAMPLE_PAIRED_END_2_2.bam:md5,9e20db3f3088fc478c223839e3a4ed62",
-                "SAMPLE_PAIRED_END_2_2.bam.bai:md5,3c4bdff0f906f2234fdeee8eea719210",
-                "SAMPLE_PAIRED_END_1_1_1_screen.png:md5,f52ddd0e65f23f68dd8d58d5453417db",
-                "SAMPLE_PAIRED_END_1_1_1_screen.txt:md5,921b08eeb461a2aa1bd42bba53900f70",
-                "SAMPLE_PAIRED_END_1_1_2_screen.png:md5,908f4fceea8aa546106efdaa7ca78f7d",
-                "SAMPLE_PAIRED_END_1_1_2_screen.txt:md5,e9ea5789e356f666de27ba658704e80d",
-                "SAMPLE_PAIRED_END_2_2_1_screen.png:md5,48d546767ed2a34a1eda59d97dd00c18",
-                "SAMPLE_PAIRED_END_2_2_1_screen.txt:md5,a5b047f495d01bf9dcb0ae516d3c7fc3",
-                "SAMPLE_PAIRED_END_2_2_2_screen.png:md5,e3684b17339d16e6fb64ace7593cc388",
-                "SAMPLE_PAIRED_END_2_2_2_screen.txt:md5,fc95e5058e764596d5da182cbc0614cf",
-                "fastq_screen_plot.txt:md5,642264b93871c724aaa5d38b91c752dd",
-                "fastqc-status-check-heatmap.txt:md5,8e29ad6b23e03267c33bd9ed3385a44b",
-                "fastqc_adapter_content_plot.txt:md5,46fbd727a4996a3f0310d0423c628445",
-                "fastqc_per_base_n_content_plot.txt:md5,4eca1ef40d4d3d318b82e68e9fa3c589",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,218757a51c3de79a39a704c979df03da",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a4035ac9f0a0c07574130758b06630d7",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,637b937e023c84115ec06b529cc8ec1b",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,47d60153a430e2b8da51655704c2b31b",
-                "fastqc_sequence_counts_plot.txt:md5,10737092a3473fba81fbe49555512b2b",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,6412f57686de02e1f1c3751a7ca2be8b",
+                "SAMPLE_PAIRED_END_1_01.bam:md5,a2816c39f5907fad768bb65d6a75e757",
+                "SAMPLE_PAIRED_END_1_01.bam.bai:md5,8d7c1e80974444bbdb6361408b09e188",
+                "SAMPLE_PAIRED_END_2_02.bam:md5,f82c6ab5a81de087823a398616bcec08",
+                "SAMPLE_PAIRED_END_2_02.bam.bai:md5,3c4bdff0f906f2234fdeee8eea719210",
+                "SAMPLE_PAIRED_END_1_01_1_screen.png:md5,f52ddd0e65f23f68dd8d58d5453417db",
+                "SAMPLE_PAIRED_END_1_01_1_screen.txt:md5,921b08eeb461a2aa1bd42bba53900f70",
+                "SAMPLE_PAIRED_END_1_01_2_screen.png:md5,908f4fceea8aa546106efdaa7ca78f7d",
+                "SAMPLE_PAIRED_END_1_01_2_screen.txt:md5,e9ea5789e356f666de27ba658704e80d",
+                "SAMPLE_PAIRED_END_2_02_1_screen.png:md5,48d546767ed2a34a1eda59d97dd00c18",
+                "SAMPLE_PAIRED_END_2_02_1_screen.txt:md5,a5b047f495d01bf9dcb0ae516d3c7fc3",
+                "SAMPLE_PAIRED_END_2_02_2_screen.png:md5,e3684b17339d16e6fb64ace7593cc388",
+                "SAMPLE_PAIRED_END_2_02_2_screen.txt:md5,fc95e5058e764596d5da182cbc0614cf",
+                "fastq_screen_plot.txt:md5,24a7d3472f06fe6032bb7f12f5828b49",
+                "fastqc-status-check-heatmap.txt:md5,c1e87942bda9a4ccf519bf561ce18ed3",
+                "fastqc_adapter_content_plot.txt:md5,4b7007431bd26127365b0f25120d48f2",
+                "fastqc_per_base_n_content_plot.txt:md5,6bbf19be2aef3ef67dfe548bf9323011",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,2bd96b0c0413ee4871a53d41f067d809",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,1f56f6ca0f469bec9b25010c6f9cbfdd",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,64bc987cceac0396b8b650000493427e",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,4aa57cbe1f9da1facc1b588b4c166cec",
+                "fastqc_sequence_counts_plot.txt:md5,57f96ad90232887fec1480ef4071f8b6",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,62e93bfc80b0bf201a605802edbe0177",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,5ef00028497d3271c9f0ea9a961db1e5",
-                "multiqc_fastqc.txt:md5,bc499ad273fd1c887056c31b82544984",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,35d289ee535a0442db72a65391f375eb",
-                "multiqc_picard_baseContent.txt:md5,72b0ae83ed58052bfd768021d377c78f",
-                "multiqc_picard_quality_by_cycle.txt:md5,f6514f14befb874ded5aed79caba3e7b",
-                "multiqc_picard_quality_score_distribution.txt:md5,99be409e325619171b820d762dd023c0",
-                "multiqc_seqfu.txt:md5,139354afd154804b4b77f997277f3ee9",
+                "multiqc_fastq_screen.txt:md5,6f9cfa81bda7482142c640b9f0c82b90",
+                "multiqc_fastqc.txt:md5,85fe5c24576dc105adb8ca90ce6449b7",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,32c0a27891fabd36de3c7fa97d82c11f",
+                "multiqc_picard_baseContent.txt:md5,a2043541e3ce74b710ae2b69ef7bc593",
+                "multiqc_picard_quality_by_cycle.txt:md5,0eab2183e8852b165b09a9ea8a5f67c9",
+                "multiqc_picard_quality_score_distribution.txt:md5,33955f093524a0eff449e25226768d84",
+                "multiqc_seqfu_mqc.txt:md5,139354afd154804b4b77f997277f3ee9",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,f6514f14befb874ded5aed79caba3e7b",
-                "picard_QualityScoreDistribution_histogram.txt:md5,99be409e325619171b820d762dd023c0",
-                "picard_alignment_readlength_plot.txt:md5,4172702f791d043135f21e3a227fe712",
-                "picard_alignment_summary_Aligned_Bases.txt:md5,a166c14210e17d3541482b500443f792",
-                "picard_alignment_summary_Aligned_Reads.txt:md5,c5e5228e85ffb2182274d641ffa6743f",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,3fe18f1144eb85f9206d1bee4eb11bb3",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,2e1383b692e76f4b915ccbe9bb9b9170",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,2a595bc9ac547f3b5224a57a6b0a127d",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,157ea873dd2faff46efdd62f7f6aa84c",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,98f4e5ed094b41eb131d493b4f06bcd6",
-                "picard_quality_by_cycle.txt:md5,2634f306a33f648bac74bc7cd3253f9e",
-                "picard_quality_score_distribution.txt:md5,ecde9f0e859a6eecc5cea75a156c632d",
-                "fastq_screen_plot.txt:md5,642264b93871c724aaa5d38b91c752dd",
-                "fastqc-status-check-heatmap.txt:md5,8e29ad6b23e03267c33bd9ed3385a44b",
-                "fastqc_adapter_content_plot.txt:md5,46fbd727a4996a3f0310d0423c628445",
-                "fastqc_per_base_n_content_plot.txt:md5,4eca1ef40d4d3d318b82e68e9fa3c589",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,218757a51c3de79a39a704c979df03da",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a4035ac9f0a0c07574130758b06630d7",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,637b937e023c84115ec06b529cc8ec1b",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,47d60153a430e2b8da51655704c2b31b",
-                "fastqc_sequence_counts_plot.txt:md5,10737092a3473fba81fbe49555512b2b",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,6412f57686de02e1f1c3751a7ca2be8b",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,0eab2183e8852b165b09a9ea8a5f67c9",
+                "picard_QualityScoreDistribution_histogram.txt:md5,33955f093524a0eff449e25226768d84",
+                "picard_alignment_readlength_plot.txt:md5,ed079bc433831b807d11b7b95b151b4e",
+                "picard_alignment_summary_Aligned_Bases.txt:md5,9f877e31c0f772644a91531717b8ce32",
+                "picard_alignment_summary_Aligned_Reads.txt:md5,3a1ff58d9f57eb88240116dea3e11a99",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,23b0d8572689f0eafb3adaa57814fdfd",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,c9a36624afb4251813e392ea7bc0d135",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,c68670e3254396cd3db5fc57064ab328",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,ae15c81a007c9316c7d1ccda8daace25",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,040f28a453cfca2155c65f1d8553ecfe",
+                "picard_quality_by_cycle.txt:md5,2497dd5ef1e5cedc1f88a9b67ef549d7",
+                "picard_quality_score_distribution.txt:md5,795138cccc8b97143f8bf0bf0adbd4b7",
+                "fastq_screen_plot.txt:md5,24a7d3472f06fe6032bb7f12f5828b49",
+                "fastqc-status-check-heatmap.txt:md5,c1e87942bda9a4ccf519bf561ce18ed3",
+                "fastqc_adapter_content_plot.txt:md5,4b7007431bd26127365b0f25120d48f2",
+                "fastqc_per_base_n_content_plot.txt:md5,6bbf19be2aef3ef67dfe548bf9323011",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,2bd96b0c0413ee4871a53d41f067d809",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,1f56f6ca0f469bec9b25010c6f9cbfdd",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,64bc987cceac0396b8b650000493427e",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,4aa57cbe1f9da1facc1b588b4c166cec",
+                "fastqc_sequence_counts_plot.txt:md5,57f96ad90232887fec1480ef4071f8b6",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,62e93bfc80b0bf201a605802edbe0177",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,5ef00028497d3271c9f0ea9a961db1e5",
-                "multiqc_fastqc.txt:md5,bc499ad273fd1c887056c31b82544984",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,35d289ee535a0442db72a65391f375eb",
-                "multiqc_picard_baseContent.txt:md5,72b0ae83ed58052bfd768021d377c78f",
-                "multiqc_picard_quality_by_cycle.txt:md5,f6514f14befb874ded5aed79caba3e7b",
-                "multiqc_picard_quality_score_distribution.txt:md5,99be409e325619171b820d762dd023c0",
-                "multiqc_seqfu.txt:md5,139354afd154804b4b77f997277f3ee9",
+                "multiqc_fastq_screen.txt:md5,6f9cfa81bda7482142c640b9f0c82b90",
+                "multiqc_fastqc.txt:md5,85fe5c24576dc105adb8ca90ce6449b7",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,32c0a27891fabd36de3c7fa97d82c11f",
+                "multiqc_picard_baseContent.txt:md5,a2043541e3ce74b710ae2b69ef7bc593",
+                "multiqc_picard_quality_by_cycle.txt:md5,0eab2183e8852b165b09a9ea8a5f67c9",
+                "multiqc_picard_quality_score_distribution.txt:md5,33955f093524a0eff449e25226768d84",
+                "multiqc_seqfu_mqc.txt:md5,139354afd154804b4b77f997277f3ee9",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,f6514f14befb874ded5aed79caba3e7b",
-                "picard_QualityScoreDistribution_histogram.txt:md5,99be409e325619171b820d762dd023c0",
-                "picard_alignment_readlength_plot.txt:md5,4172702f791d043135f21e3a227fe712",
-                "picard_alignment_summary_Aligned_Bases.txt:md5,a166c14210e17d3541482b500443f792",
-                "picard_alignment_summary_Aligned_Reads.txt:md5,c5e5228e85ffb2182274d641ffa6743f",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,3fe18f1144eb85f9206d1bee4eb11bb3",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,2e1383b692e76f4b915ccbe9bb9b9170",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,2a595bc9ac547f3b5224a57a6b0a127d",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,157ea873dd2faff46efdd62f7f6aa84c",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,98f4e5ed094b41eb131d493b4f06bcd6",
-                "picard_quality_by_cycle.txt:md5,2634f306a33f648bac74bc7cd3253f9e",
-                "picard_quality_score_distribution.txt:md5,ecde9f0e859a6eecc5cea75a156c632d",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,0eab2183e8852b165b09a9ea8a5f67c9",
+                "picard_QualityScoreDistribution_histogram.txt:md5,33955f093524a0eff449e25226768d84",
+                "picard_alignment_readlength_plot.txt:md5,ed079bc433831b807d11b7b95b151b4e",
+                "picard_alignment_summary_Aligned_Bases.txt:md5,9f877e31c0f772644a91531717b8ce32",
+                "picard_alignment_summary_Aligned_Reads.txt:md5,3a1ff58d9f57eb88240116dea3e11a99",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,23b0d8572689f0eafb3adaa57814fdfd",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,c9a36624afb4251813e392ea7bc0d135",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,c68670e3254396cd3db5fc57064ab328",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,ae15c81a007c9316c7d1ccda8daace25",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,040f28a453cfca2155c65f1d8553ecfe",
+                "picard_quality_by_cycle.txt:md5,2497dd5ef1e5cedc1f88a9b67ef549d7",
+                "picard_quality_score_distribution.txt:md5,795138cccc8b97143f8bf0bf0adbd4b7",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
-                "SAMPLE_PAIRED_END_1_1_seqfu.tsv:md5,be29dfe848eab9a10ee0d46691223eae",
-                "SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt:md5,0aca00c7f64454af520c7e08ec595d2b",
-                "SAMPLE_PAIRED_END_2_2_seqfu.tsv:md5,44a5cb826e001d58208a5855938fa82b",
-                "SAMPLE_PAIRED_END_2_2_seqfu_mqc.txt:md5,ac1740de9ef142c99c993fa9824ead63"
+                "SAMPLE_PAIRED_END_1_01_seqfu.tsv:md5,be29dfe848eab9a10ee0d46691223eae",
+                "SAMPLE_PAIRED_END_1_01_seqfu_mqc.txt:md5,0aca00c7f64454af520c7e08ec595d2b",
+                "SAMPLE_PAIRED_END_2_02_seqfu.tsv:md5,44a5cb826e001d58208a5855938fa82b",
+                "SAMPLE_PAIRED_END_2_02_seqfu_mqc.txt:md5,ac1740de9ef142c99c993fa9824ead63"
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-03T10:57:19.118426"
+        "timestamp": "2025-12-12T10:02:03.991667099"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index de02103c..e1d0a62c 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -34,16 +34,16 @@
                 "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
                 "bwamem2_index/bwamem2/genome.fa.pac",
                 "bwamem2_mem",
-                "bwamem2_mem/Sample1_1.bam",
-                "bwamem2_mem/Sample1_1.bam.bai",
-                "bwamem2_mem/Sample23_3.bam",
-                "bwamem2_mem/Sample23_3.bam.bai",
-                "bwamem2_mem/SampleA_2.bam",
-                "bwamem2_mem/SampleA_2.bam.bai",
-                "bwamem2_mem/Undetermined_5.bam",
-                "bwamem2_mem/Undetermined_5.bam.bai",
-                "bwamem2_mem/sampletest_4.bam",
-                "bwamem2_mem/sampletest_4.bam.bai",
+                "bwamem2_mem/Sample1_01.bam",
+                "bwamem2_mem/Sample1_01.bam.bai",
+                "bwamem2_mem/Sample23_03.bam",
+                "bwamem2_mem/Sample23_03.bam.bai",
+                "bwamem2_mem/SampleA_02.bam",
+                "bwamem2_mem/SampleA_02.bam.bai",
+                "bwamem2_mem/Undetermined_05.bam",
+                "bwamem2_mem/Undetermined_05.bam.bai",
+                "bwamem2_mem/sampletest_04.bam",
+                "bwamem2_mem/sampletest_04.bam.bai",
                 "fastqc",
                 "fastqc/Sample1_01_fastqc.html",
                 "fastqc/Sample1_01_fastqc.zip",
@@ -98,7 +98,7 @@
                 "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
                 "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
                 "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
-                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu_mqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
@@ -139,7 +139,7 @@
                 "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu_mqc.pdf",
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
@@ -164,7 +164,7 @@
                 "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
                 "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
                 "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu_mqc.png",
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
@@ -189,7 +189,7 @@
                 "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
                 "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
                 "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
-                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu_mqc.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "multiqc/group_reports",
                 "multiqc/group_reports/group1",
@@ -218,7 +218,7 @@
                 "multiqc/group_reports/group1/multiqc_data/multiqc_picard_baseContent.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_score_distribution.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_seqfu_mqc.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/group1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
@@ -259,7 +259,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/seqfu_mqc.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-pct.png",
@@ -284,7 +284,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_by_cycle.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_score_distribution.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/seqfu.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/seqfu_mqc.png",
                 "multiqc/group_reports/group1/multiqc_plots/svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-pct.svg",
@@ -309,7 +309,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_by_cycle.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_score_distribution.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/seqfu.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/seqfu_mqc.svg",
                 "multiqc/group_reports/group1/multiqc_report.html",
                 "multiqc/group_reports/group2",
                 "multiqc/group_reports/group2/multiqc_data",
@@ -337,7 +337,7 @@
                 "multiqc/group_reports/group2/multiqc_data/multiqc_picard_baseContent.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_by_cycle.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_score_distribution.txt",
-                "multiqc/group_reports/group2/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_seqfu_mqc.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/group2/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
@@ -378,7 +378,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/seqfu_mqc.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-pct.png",
@@ -403,7 +403,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_by_cycle.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_score_distribution.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/seqfu.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/seqfu_mqc.png",
                 "multiqc/group_reports/group2/multiqc_plots/svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-pct.svg",
@@ -428,7 +428,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_by_cycle.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_score_distribution.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/seqfu.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/seqfu_mqc.svg",
                 "multiqc/group_reports/group2/multiqc_report.html",
                 "multiqc/group_reports/lane1",
                 "multiqc/group_reports/lane1/multiqc_data",
@@ -456,7 +456,7 @@
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_baseContent.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_score_distribution.txt",
-                "multiqc/group_reports/lane1/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_seqfu_mqc.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/lane1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
@@ -497,7 +497,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/seqfu_mqc.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-pct.png",
@@ -522,7 +522,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_by_cycle.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_score_distribution.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/seqfu.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/seqfu_mqc.png",
                 "multiqc/group_reports/lane1/multiqc_plots/svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-pct.svg",
@@ -547,7 +547,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_by_cycle.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_score_distribution.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/seqfu.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/seqfu_mqc.svg",
                 "multiqc/group_reports/lane1/multiqc_report.html",
                 "multiqc/group_reports/test",
                 "multiqc/group_reports/test/multiqc_data",
@@ -575,7 +575,7 @@
                 "multiqc/group_reports/test/multiqc_data/multiqc_picard_baseContent.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_by_cycle.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_score_distribution.txt",
-                "multiqc/group_reports/test/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_seqfu_mqc.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/test/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
@@ -616,7 +616,7 @@
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                 "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/seqfu_mqc.pdf",
                 "multiqc/group_reports/test/multiqc_plots/png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-pct.png",
@@ -641,7 +641,7 @@
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                 "multiqc/group_reports/test/multiqc_plots/png/picard_quality_score_distribution.png",
-                "multiqc/group_reports/test/multiqc_plots/png/seqfu.png",
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                 "multiqc/group_reports/test/multiqc_plots/svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
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@@ -666,49 +666,49 @@
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                 "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_score_distribution.svg",
-                "multiqc/group_reports/test/multiqc_plots/svg/seqfu.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/seqfu_mqc.svg",
                 "multiqc/group_reports/test/multiqc_report.html",
                 "picard_collectmultiplemetrics",
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-                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_by_cycle_metrics",
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-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution_metrics",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/Sample1_01.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/Sample1_01.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
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+                "picard_collectmultiplemetrics/Sample1_01.CollectMultipleMetrics.quality_by_cycle_metrics",
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+                "picard_collectmultiplemetrics/SampleA_02.CollectMultipleMetrics.quality_by_cycle_metrics",
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                 "pipeline_info",
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@@ -732,204 +732,204 @@
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-                "fastqc_per_base_n_content_plot.txt:md5,4c5bfb1594b391f3e36a9e1223b43a94",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,6251cde1646484446499252bd15c58a2",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,f645e38916efafd07d4c2c3d5c7cd051",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,a9d3152a43988e39fae4a75faa3a5aa4",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,aef487a8b267a14a92be64b0b01d9b5c",
-                "fastqc_sequence_counts_plot.txt:md5,5021496dd00366d08064804bbb5192e3",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,e37e8e4584f0157a5fa0d53b4834e836",
-                "fastqc_sequence_length_distribution_plot.txt:md5,393cc090200a5151561efb1ed5280b89",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,6e13ddbd97caa0eaa52c118966e5f9fa",
+                "picard_QualityScoreDistribution_histogram.txt:md5,39d3430744e9139020d7af3eb15fc629",
+                "picard_alignment_readlength_plot.txt:md5,57ee2de637b69efc49290bb5d4b57905",
+                "picard_alignment_summary.txt:md5,3fee23a738a44ee84592cb1144b32775",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,dfb9e50700b61cdbc0344690db202559",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,5eec2a9bbb5db321c7cbbbee26d90357",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,5b100b42e93792fed754deb276645e61",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,d0317fe5ef2cf1b692526cb9a18aa50c",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,8aafe701b59b4e70ccec86748c7d6eb3",
+                "picard_quality_by_cycle.txt:md5,366ee22c93a11c1335f867020bb03da5",
+                "picard_quality_score_distribution.txt:md5,17d6f490cb59e16a7ed4b04ffaa1a100",
+                "fastq_screen_plot.txt:md5,db7c9231e756a6e5999399a7385e4687",
+                "fastqc-status-check-heatmap.txt:md5,fc37eaf184877ac80b92001a7bf2fa81",
+                "fastqc_overrepresented_sequences_plot.txt:md5,0693849fc324ddf580e2c5a4d910bb4f",
+                "fastqc_per_base_n_content_plot.txt:md5,0ed7f750b500e7c5387ea5309e1ef467",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,18016152915653e812818194a142e162",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,93f664e18c021aae79ad222fb4cfb393",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,ba96762be2aa842e1d2a606095ffcb7e",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,b9044bfe90fd5685137739f52a97ee2c",
+                "fastqc_sequence_counts_plot.txt:md5,42b26ad3758717659763c81852c4f197",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,818f13a5372bad79e54cd984758096c5",
+                "fastqc_sequence_length_distribution_plot.txt:md5,98316a2607a889ae1e7e79a4f64cc740",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
-                "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,e4cb1b13e6a7298d172ed112a0479b5a",
-                "multiqc_picard_baseContent.txt:md5,740592a5858706d2b4b8f585a1d5492b",
-                "multiqc_picard_quality_by_cycle.txt:md5,c3f14084aedc511b9f0aa8410e7cb3b5",
-                "multiqc_picard_quality_score_distribution.txt:md5,59b955203209cfab3d2d21bdfe20997e",
-                "multiqc_seqfu.txt:md5,6cdb863a3686fbb772aae5a66925ff23",
+                "multiqc_fastq_screen.txt:md5,024e1e7f9db3b0906c7aa0904229e176",
+                "multiqc_fastqc.txt:md5,3407d8f06117a65efce4c70f19e91dd1",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,1debd96f9f64c60a8ec742411da51a28",
+                "multiqc_picard_baseContent.txt:md5,afb4046944e302b40faea2233bca535c",
+                "multiqc_picard_quality_by_cycle.txt:md5,6a7552b74dd22410c3cab2c750de792e",
+                "multiqc_picard_quality_score_distribution.txt:md5,d6343c5f39942bc3f10c194067e6e9bc",
+                "multiqc_seqfu_mqc.txt:md5,6cdb863a3686fbb772aae5a66925ff23",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,c3f14084aedc511b9f0aa8410e7cb3b5",
-                "picard_QualityScoreDistribution_histogram.txt:md5,59b955203209cfab3d2d21bdfe20997e",
-                "picard_alignment_readlength_plot.txt:md5,1f8b2f4df8bd5cf879b96cfb2be6d81c",
-                "picard_alignment_summary.txt:md5,0cfafd1ed1920270bb1a5d13bed51480",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,bd7f8dab8e73406cded6c6f27bbc87e9",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,fe44ccdb08c6955149eacf52a77bbba2",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,85a9172769830b4169f214c335f44fdc",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,1fe0c42cb22981763862d1934a35de07",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,4c5bfb1594b391f3e36a9e1223b43a94",
-                "picard_quality_by_cycle.txt:md5,a43e7bb40bc479e9c32476256b09e734",
-                "picard_quality_score_distribution.txt:md5,a940641c0dab423c964c0f46b69dd805",
-                "fastq_screen_plot.txt:md5,44fca6453b0a3d0590271bd7a31cc740",
-                "fastqc-status-check-heatmap.txt:md5,b6872d9dbaa3cce396d48dc137076e53",
-                "fastqc_overrepresented_sequences_plot.txt:md5,eac8d0fd31c614d8d0f56bd54ee8c78c",
-                "fastqc_per_base_n_content_plot.txt:md5,b7b249afe807ca2321e6dd839961795c",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,3bca5f0121d27b0777a40a4ab44e2abc",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,ee29af5517a8c6f872adbaccea4ff2f8",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,3eaf12f9267c10e4e457a2bb9bdc70ea",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,1818e0b917e45a583740f2cbb0638f8d",
-                "fastqc_sequence_counts_plot.txt:md5,0c4863a5475a2444cd00b053eb8941b1",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,a7a050f827a4f821117efd8d25668c51",
-                "fastqc_sequence_length_distribution_plot.txt:md5,9c0761008be04d8ccf4c0e16acc6348c",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,6a7552b74dd22410c3cab2c750de792e",
+                "picard_QualityScoreDistribution_histogram.txt:md5,d6343c5f39942bc3f10c194067e6e9bc",
+                "picard_alignment_readlength_plot.txt:md5,01140e65e813b4ae43aabe662ef2f49a",
+                "picard_alignment_summary.txt:md5,79312cf30761025cc6902811c4165290",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,3c3671ac2aa18d883691d59adbfe3b2b",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,6cc2ae1411899de5542321ff1592b192",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,326471bc846a9fb6b54ff38cbdfb8d90",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,3132dac406a9b9e1f18af658ab856a5c",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,0ed7f750b500e7c5387ea5309e1ef467",
+                "picard_quality_by_cycle.txt:md5,fe4e6ab1c849a4f833eae9a8554ea432",
+                "picard_quality_score_distribution.txt:md5,c0864f8a1269d8ffd7a51abb6bd3ca2e",
+                "fastq_screen_plot.txt:md5,4def6c6a888afe487ab6ebef3ba8a133",
+                "fastqc-status-check-heatmap.txt:md5,61857d2c45cf0c080348047aa34e7525",
+                "fastqc_overrepresented_sequences_plot.txt:md5,7949c64cc6cef77f29349a188fc09656",
+                "fastqc_per_base_n_content_plot.txt:md5,0f2fd628631d42ed5e6a1db22578daaa",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,0a8bfa32ab04eaaa509dec3c37acb2d2",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,8c85be0c70129ba739feceddd58f6c75",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,94b975906d8a07e1604e00d4004f7463",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,ec22c8e4836aa726680f0ca767c778a0",
+                "fastqc_sequence_counts_plot.txt:md5,f4341795bdeba588248a74a095a97f8d",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,8fc995cb2192a2926eee242681bc3af6",
+                "fastqc_sequence_length_distribution_plot.txt:md5,4513e22583677a4d6167b9094242eb0b",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
-                "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,d4e63eed820edcc71b3e37d793983bd7",
-                "multiqc_picard_baseContent.txt:md5,0dd5fa539e4034e3539fb1e7068c7ce5",
-                "multiqc_picard_quality_by_cycle.txt:md5,750eadc27875fc8141b64a90789c369f",
-                "multiqc_picard_quality_score_distribution.txt:md5,140279eb5abac364c4d4c417105da620",
-                "multiqc_seqfu.txt:md5,f821357507fda2d4cfd9299f52fa7dc1",
+                "multiqc_fastq_screen.txt:md5,fd3074930c72b666f201ae71fa27744b",
+                "multiqc_fastqc.txt:md5,98111f17d1899cad6379e4e56ed11c53",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,3b1929de09267fc1c1a15804cb5bf536",
+                "multiqc_picard_baseContent.txt:md5,ff36be9e2642089aa711c637d3cdba29",
+                "multiqc_picard_quality_by_cycle.txt:md5,9521c83313eaf5f681ac9a75de83a4b7",
+                "multiqc_picard_quality_score_distribution.txt:md5,90b9e29f22fa16cf2b0c4d92caf2dbb0",
+                "multiqc_seqfu_mqc.txt:md5,f821357507fda2d4cfd9299f52fa7dc1",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,750eadc27875fc8141b64a90789c369f",
-                "picard_QualityScoreDistribution_histogram.txt:md5,140279eb5abac364c4d4c417105da620",
-                "picard_alignment_readlength_plot.txt:md5,a39f6a39dad13dacc2134508dbbf172d",
-                "picard_alignment_summary.txt:md5,fec83821c097bc1850257ce36aa73e5f",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,f206efb4e5344b8cbb2d18f6e73d5d95",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,ebf98e3d0bf661161989bf3d010b8c6b",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,f7dff1258977e9d04fb26ba8192facc5",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,b32d1e91c41756afe8732107868b32e0",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,b7b249afe807ca2321e6dd839961795c",
-                "picard_quality_by_cycle.txt:md5,1fe617901a493b80c31fcd01a00c416d",
-                "picard_quality_score_distribution.txt:md5,5cd4a87942000899776927f22a5db802",
-                "fastq_screen_plot.txt:md5,5f748d33a7a396547fe8c260b728aa06",
-                "fastqc-status-check-heatmap.txt:md5,08228a8f3d6f11b174b98626bb22bda1",
-                "fastqc_overrepresented_sequences_plot.txt:md5,3434dfb79f150e2e584e85866983ba01",
-                "fastqc_per_base_n_content_plot.txt:md5,e371981072ec99d11c6adb5a4034808c",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,bf83d019eaaeb1ca659ff28cfb2bdfea",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,3f40b8ee69d3eaefe657cc5ed622cc8b",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,86b61d09437a96448e1325e6be834048",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,9f7307469b112bd054f8ee0cc2cf4d65",
-                "fastqc_sequence_counts_plot.txt:md5,f0c693cc281a6e61ba219bab04f59a47",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,8c2aa91358fd4a2e946cbcc1f312f9b6",
-                "fastqc_sequence_length_distribution_plot.txt:md5,875ebcd6726bb9d36ffa64265e5071d0",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,9521c83313eaf5f681ac9a75de83a4b7",
+                "picard_QualityScoreDistribution_histogram.txt:md5,90b9e29f22fa16cf2b0c4d92caf2dbb0",
+                "picard_alignment_readlength_plot.txt:md5,9c80659c5c9b2fe9926b789fb67ba6ac",
+                "picard_alignment_summary.txt:md5,27bbb1fcdeecd26641938e5622087c23",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,99c5e961a4d26754e68047c8eb983798",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,44981dd399013d8c06481958be338040",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,b6369a23d3926edb90ae9bfdc6d90526",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,b253d3fca7c07b6a6dfea91725c58102",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,0f2fd628631d42ed5e6a1db22578daaa",
+                "picard_quality_by_cycle.txt:md5,3c34ae2bd2442a816577b1a794add2d6",
+                "picard_quality_score_distribution.txt:md5,0d58c59eac2952e6f71cefc35d4c4477",
+                "fastq_screen_plot.txt:md5,5abb5b9ed2c976f0ad83216ca3186201",
+                "fastqc-status-check-heatmap.txt:md5,323d6082b73ddb6ee33385f5ea4301c1",
+                "fastqc_overrepresented_sequences_plot.txt:md5,4e71d8913d40eb06db0f18d74ce6898f",
+                "fastqc_per_base_n_content_plot.txt:md5,b317ce09cb7a2be2366b544ea9b20ce6",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,e6f44d08f4185f680d4748a3b37201e2",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a1dc8a968f32bcf8a9b4c5f43d299dfa",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,e41b6dc1344f1aee379993daff310187",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,76f792b939233b070562cc46617f6371",
+                "fastqc_sequence_counts_plot.txt:md5,36c68522023b8d536c9362403bf03c48",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,9ff0df466790d971b3c7ef838efc0f4f",
+                "fastqc_sequence_length_distribution_plot.txt:md5,9fda632b92e3453f11cd0226484fce8e",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
-                "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,22093b80f335c4c53633b01a930157f4",
-                "multiqc_picard_baseContent.txt:md5,6886e1e5179031ddba4958f301930d64",
-                "multiqc_picard_quality_by_cycle.txt:md5,96652e2e2d693488df9104e5ae8cb4a7",
-                "multiqc_picard_quality_score_distribution.txt:md5,879a4470d08fe6d9b1796f46020fb5f5",
-                "multiqc_seqfu.txt:md5,8cced36d66ca9d25d60c006e734aa7e9",
+                "multiqc_fastq_screen.txt:md5,536c28d7fadc9a76944f93ac9d643272",
+                "multiqc_fastqc.txt:md5,396b4cc0466a6642ec8b954237c42263",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,153c6e6a407ec128b1a02798ca2f1115",
+                "multiqc_picard_baseContent.txt:md5,6349e514552a0b5a0530fa6f311878a5",
+                "multiqc_picard_quality_by_cycle.txt:md5,c0c8b4c0197428d4d50e2c532814e1e2",
+                "multiqc_picard_quality_score_distribution.txt:md5,40e0b6faa75e1b51af42407f7ededb0c",
+                "multiqc_seqfu_mqc.txt:md5,8cced36d66ca9d25d60c006e734aa7e9",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,96652e2e2d693488df9104e5ae8cb4a7",
-                "picard_QualityScoreDistribution_histogram.txt:md5,879a4470d08fe6d9b1796f46020fb5f5",
-                "picard_alignment_readlength_plot.txt:md5,9b323aa8cd934d084e9c83cfa1da306b",
-                "picard_alignment_summary.txt:md5,4e8970d31940f5e9020851d62e63b2e2",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,166a48317764fe7d4b38ed198503fc11",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,8e62c1113b965497e492e17665cdbe97",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,fe53f5f9455b928a3edc1661be83592b",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,3d069dd67cc0ffc43456c5f3ee427349",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,e371981072ec99d11c6adb5a4034808c",
-                "picard_quality_by_cycle.txt:md5,0c25ee4cec6842306b28c6a641aa03e1",
-                "picard_quality_score_distribution.txt:md5,184dcdd53f6aa3b7a0fa2c008d7dc74a",
-                "fastq_screen_plot.txt:md5,8622e1dbd0fe62520af6096207b9775d",
-                "fastqc-status-check-heatmap.txt:md5,2a66f5d61b9eb579555905cd5954b04c",
-                "fastqc_overrepresented_sequences_plot.txt:md5,e0b5bfc4b64d37611b51c939e61196fa",
-                "fastqc_per_base_n_content_plot.txt:md5,1380831484d1b069a2fd4a20437118bf",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,12585cf6b03db684a5ebd959f51e77e7",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a1464399e84711454499d27e98ed942b",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,026d11e7b49a49ac7bac85f376760305",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,4d646b20970d09d846947b87961efe7e",
-                "fastqc_sequence_counts_plot.txt:md5,057fb961863b325fe875d3a7879cb888",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,3b86c9d8625c439376102f3286c7bba7",
-                "fastqc_sequence_length_distribution_plot.txt:md5,6296c9ddbf8ba8e12053149d057fd7b2",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,c0c8b4c0197428d4d50e2c532814e1e2",
+                "picard_QualityScoreDistribution_histogram.txt:md5,40e0b6faa75e1b51af42407f7ededb0c",
+                "picard_alignment_readlength_plot.txt:md5,5a19b1f8e2ac49d97f36a7792429419c",
+                "picard_alignment_summary.txt:md5,f9f791b7c569cfae07aef70aa630d40e",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,0165f522c84da6b17a286d37dc30abec",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,6fa0d29d40fe7fa24c166b664b6d4f4b",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,bf2426e09ac1ca4773edfc284c220122",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,3cbace572471ccf6c58673181dd0c0ec",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,b317ce09cb7a2be2366b544ea9b20ce6",
+                "picard_quality_by_cycle.txt:md5,7cb705007bc97da8c0da7d93201e6975",
+                "picard_quality_score_distribution.txt:md5,47d684abae0a8f4f09df43e91d54fb9a",
+                "fastq_screen_plot.txt:md5,82ceb9f2109f865d6d1b943441c09550",
+                "fastqc-status-check-heatmap.txt:md5,56b426cd5c030288639533fce7c95ab1",
+                "fastqc_overrepresented_sequences_plot.txt:md5,8e83abdbe7362e64d63339ee31ab3361",
+                "fastqc_per_base_n_content_plot.txt:md5,33b70326d8f888ac5a3d99b85f365e43",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,40bc954cc0d58a3197fdf124a40f1ca4",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,e240e30996c81a34b5d1a6b5a98ae254",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,b44d3376d503af12857d494c58b514bb",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,66b5b6d44f398fc9429460c0b9ba3ea9",
+                "fastqc_sequence_counts_plot.txt:md5,6e5804f553f656cffb02f927015d1026",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,fbe41935ea2e2faf7104393b476e5ac5",
+                "fastqc_sequence_length_distribution_plot.txt:md5,e77dc4ab73252c2e09c7452c3b8e8ab3",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5",
-                "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,edf7faad1da9922fdc692e9cba5cc0c4",
-                "multiqc_picard_baseContent.txt:md5,9631916c0a9a736811c47ab4c476428f",
-                "multiqc_picard_quality_by_cycle.txt:md5,9e05b241aabe39232b5182cb59d8edd5",
-                "multiqc_picard_quality_score_distribution.txt:md5,e9c3ade201964470d2d22569a400fa49",
-                "multiqc_seqfu.txt:md5,ff4ce1c88f39ed24a88bae0a861f75c8",
+                "multiqc_fastq_screen.txt:md5,4fc422d9cb06a1d0248cc578c1eebaa2",
+                "multiqc_fastqc.txt:md5,95c8ffb23baafec625aeb600047515ae",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,2d05e826f5152fd0143edf7270de1235",
+                "multiqc_picard_baseContent.txt:md5,f3f23899a30a96260d8b5b3020708703",
+                "multiqc_picard_quality_by_cycle.txt:md5,c7edfc271ab59ecedad0ab046afd3563",
+                "multiqc_picard_quality_score_distribution.txt:md5,7fa89b52b8bc96dd1074aa07cb5a5a54",
+                "multiqc_seqfu_mqc.txt:md5,ff4ce1c88f39ed24a88bae0a861f75c8",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,9e05b241aabe39232b5182cb59d8edd5",
-                "picard_QualityScoreDistribution_histogram.txt:md5,e9c3ade201964470d2d22569a400fa49",
-                "picard_alignment_readlength_plot.txt:md5,c2692fde9d899ad61297ad7043fd26b9",
-                "picard_alignment_summary.txt:md5,5996d5b4c94f16c0efd42e2df47e021e",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,a2670974dc96ad8a54f9cc5ae3e09d5e",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,d3b9cc0c99f96814348b57809cf227fb",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,1ba086d3fb2676868e8e7b20f55975dc",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,8902976984741320fe06004f4115c4f4",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,1380831484d1b069a2fd4a20437118bf",
-                "picard_quality_by_cycle.txt:md5,b6fc46e18ac875ba02775e7cbf1b8e8b",
-                "picard_quality_score_distribution.txt:md5,1c17c01ef54a6062a8f1ca8408d32958",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,c7edfc271ab59ecedad0ab046afd3563",
+                "picard_QualityScoreDistribution_histogram.txt:md5,7fa89b52b8bc96dd1074aa07cb5a5a54",
+                "picard_alignment_readlength_plot.txt:md5,c1519319c4942162b05e6225fea10569",
+                "picard_alignment_summary.txt:md5,49f5c0d2cf21a13d5f363cb42cf3790e",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,466a14fc9c09f9f4de02a00e8763cd2a",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,d5854c22df4ac60b8c47c4002d975fe9",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,c27b5aa2b90397b1302b880dff3ec958",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,6f2a3e9d03f17a93c69476607a1a580d",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,33b70326d8f888ac5a3d99b85f365e43",
+                "picard_quality_by_cycle.txt:md5,0aa028d69d8bb02f0a2bcd0ed08f4235",
+                "picard_quality_score_distribution.txt:md5,a2882ff59902dc95830ed4bdb955561a",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
-                "Sample1_1_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6",
-                "Sample1_1_seqfu_mqc.txt:md5,24d99524ccd0e6c6255a69d68a871c7a",
-                "Sample23_3_seqfu.tsv:md5,6fac5d3dbce3f3bee72341fe99a399dc",
-                "Sample23_3_seqfu_mqc.txt:md5,4d4f280911a08bb6b753142980178027",
-                "SampleA_2_seqfu.tsv:md5,aec811f267bb2a0ef066a7abb59d2775",
-                "SampleA_2_seqfu_mqc.txt:md5,a819409a5cb64e20c3e54ec5ada4aa27",
-                "Undetermined_5_seqfu.tsv:md5,3a42c5c66a0a118f1a6f6f6e560b0e7e",
-                "Undetermined_5_seqfu_mqc.txt:md5,bd8be908362c5cb08a72f8ae7ab41b0d",
-                "sampletest_4_seqfu.tsv:md5,a5bea0b9c6015dd1a201ffd433e9b377",
-                "sampletest_4_seqfu_mqc.txt:md5,2180961655bbc8a12f0152d6a4b803a2"
+                "Sample1_01_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6",
+                "Sample1_01_seqfu_mqc.txt:md5,24d99524ccd0e6c6255a69d68a871c7a",
+                "Sample23_03_seqfu.tsv:md5,6fac5d3dbce3f3bee72341fe99a399dc",
+                "Sample23_03_seqfu_mqc.txt:md5,4d4f280911a08bb6b753142980178027",
+                "SampleA_02_seqfu.tsv:md5,aec811f267bb2a0ef066a7abb59d2775",
+                "SampleA_02_seqfu_mqc.txt:md5,a819409a5cb64e20c3e54ec5ada4aa27",
+                "Undetermined_05_seqfu.tsv:md5,3a42c5c66a0a118f1a6f6f6e560b0e7e",
+                "Undetermined_05_seqfu_mqc.txt:md5,bd8be908362c5cb08a72f8ae7ab41b0d",
+                "sampletest_04_seqfu.tsv:md5,a5bea0b9c6015dd1a201ffd433e9b377",
+                "sampletest_04_seqfu_mqc.txt:md5,2180961655bbc8a12f0152d6a4b803a2"
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-03T10:59:00.917873"
+        "timestamp": "2025-12-12T10:03:28.290070478"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index e05db91c..4b40cf01 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -37,43 +37,43 @@
                 "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
                 "bwamem2_index/bwamem2/genome.fa.pac",
                 "bwamem2_mem",
-                "bwamem2_mem/Sample1_1.bam",
-                "bwamem2_mem/Sample1_1.bam.bai",
-                "bwamem2_mem/Sample23_3.bam",
-                "bwamem2_mem/Sample23_3.bam.bai",
-                "bwamem2_mem/SampleA_2.bam",
-                "bwamem2_mem/SampleA_2.bam.bai",
-                "bwamem2_mem/Undetermined_5.bam",
-                "bwamem2_mem/Undetermined_5.bam.bai",
-                "bwamem2_mem/sampletest_4.bam",
-                "bwamem2_mem/sampletest_4.bam.bai",
+                "bwamem2_mem/Sample1_01.bam",
+                "bwamem2_mem/Sample1_01.bam.bai",
+                "bwamem2_mem/Sample23_03.bam",
+                "bwamem2_mem/Sample23_03.bam.bai",
+                "bwamem2_mem/SampleA_02.bam",
+                "bwamem2_mem/SampleA_02.bam.bai",
+                "bwamem2_mem/Undetermined_05.bam",
+                "bwamem2_mem/Undetermined_05.bam.bai",
+                "bwamem2_mem/sampletest_04.bam",
+                "bwamem2_mem/sampletest_04.bam.bai",
                 "fastqc",
-                "fastqc/Sample1_1_fastqc.html",
-                "fastqc/Sample1_1_fastqc.zip",
-                "fastqc/Sample23_3_fastqc.html",
-                "fastqc/Sample23_3_fastqc.zip",
-                "fastqc/SampleA_2_fastqc.html",
-                "fastqc/SampleA_2_fastqc.zip",
-                "fastqc/Undetermined_5_fastqc.html",
-                "fastqc/Undetermined_5_fastqc.zip",
-                "fastqc/sampletest_4_fastqc.html",
-                "fastqc/sampletest_4_fastqc.zip",
+                "fastqc/Sample1_01_fastqc.html",
+                "fastqc/Sample1_01_fastqc.zip",
+                "fastqc/Sample23_03_fastqc.html",
+                "fastqc/Sample23_03_fastqc.zip",
+                "fastqc/SampleA_02_fastqc.html",
+                "fastqc/SampleA_02_fastqc.zip",
+                "fastqc/Undetermined_05_fastqc.html",
+                "fastqc/Undetermined_05_fastqc.zip",
+                "fastqc/sampletest_04_fastqc.html",
+                "fastqc/sampletest_04_fastqc.zip",
                 "fastqscreen",
-                "fastqscreen/Sample1_1_screen.html",
-                "fastqscreen/Sample1_1_screen.png",
-                "fastqscreen/Sample1_1_screen.txt",
-                "fastqscreen/Sample23_3_screen.html",
-                "fastqscreen/Sample23_3_screen.png",
-                "fastqscreen/Sample23_3_screen.txt",
-                "fastqscreen/SampleA_2_screen.html",
-                "fastqscreen/SampleA_2_screen.png",
-                "fastqscreen/SampleA_2_screen.txt",
-                "fastqscreen/Undetermined_5_screen.html",
-                "fastqscreen/Undetermined_5_screen.png",
-                "fastqscreen/Undetermined_5_screen.txt",
-                "fastqscreen/sampletest_4_screen.html",
-                "fastqscreen/sampletest_4_screen.png",
-                "fastqscreen/sampletest_4_screen.txt",
+                "fastqscreen/Sample1_01_screen.html",
+                "fastqscreen/Sample1_01_screen.png",
+                "fastqscreen/Sample1_01_screen.txt",
+                "fastqscreen/Sample23_03_screen.html",
+                "fastqscreen/Sample23_03_screen.png",
+                "fastqscreen/Sample23_03_screen.txt",
+                "fastqscreen/SampleA_02_screen.html",
+                "fastqscreen/SampleA_02_screen.png",
+                "fastqscreen/SampleA_02_screen.txt",
+                "fastqscreen/Undetermined_05_screen.html",
+                "fastqscreen/Undetermined_05_screen.png",
+                "fastqscreen/Undetermined_05_screen.txt",
+                "fastqscreen/sampletest_04_screen.html",
+                "fastqscreen/sampletest_04_screen.png",
+                "fastqscreen/sampletest_04_screen.txt",
                 "multiqc",
                 "multiqc/global_report",
                 "multiqc/global_report/multiqc_data",
@@ -101,7 +101,7 @@
                 "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
                 "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
                 "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
-                "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu_mqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
                 "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
@@ -142,7 +142,7 @@
                 "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu_mqc.pdf",
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
@@ -167,7 +167,7 @@
                 "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
                 "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
                 "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu_mqc.png",
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
@@ -192,7 +192,7 @@
                 "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
                 "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
                 "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
-                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu_mqc.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "multiqc/group_reports",
                 "multiqc/group_reports/group1",
@@ -221,7 +221,7 @@
                 "multiqc/group_reports/group1/multiqc_data/multiqc_picard_baseContent.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_score_distribution.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_seqfu_mqc.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/group1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
@@ -262,7 +262,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
-                "multiqc/group_reports/group1/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/seqfu_mqc.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-pct.png",
@@ -287,7 +287,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_by_cycle.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_score_distribution.png",
-                "multiqc/group_reports/group1/multiqc_plots/png/seqfu.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/seqfu_mqc.png",
                 "multiqc/group_reports/group1/multiqc_plots/svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-pct.svg",
@@ -312,7 +312,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_by_cycle.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_score_distribution.svg",
-                "multiqc/group_reports/group1/multiqc_plots/svg/seqfu.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/seqfu_mqc.svg",
                 "multiqc/group_reports/group1/multiqc_report.html",
                 "multiqc/group_reports/group2",
                 "multiqc/group_reports/group2/multiqc_data",
@@ -340,7 +340,7 @@
                 "multiqc/group_reports/group2/multiqc_data/multiqc_picard_baseContent.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_by_cycle.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_score_distribution.txt",
-                "multiqc/group_reports/group2/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_seqfu_mqc.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/group2/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
@@ -381,7 +381,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
-                "multiqc/group_reports/group2/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/seqfu_mqc.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-pct.png",
@@ -406,7 +406,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_by_cycle.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_score_distribution.png",
-                "multiqc/group_reports/group2/multiqc_plots/png/seqfu.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/seqfu_mqc.png",
                 "multiqc/group_reports/group2/multiqc_plots/svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-pct.svg",
@@ -431,7 +431,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_by_cycle.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_score_distribution.svg",
-                "multiqc/group_reports/group2/multiqc_plots/svg/seqfu.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/seqfu_mqc.svg",
                 "multiqc/group_reports/group2/multiqc_report.html",
                 "multiqc/group_reports/lane1",
                 "multiqc/group_reports/lane1/multiqc_data",
@@ -459,7 +459,7 @@
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_baseContent.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_score_distribution.txt",
-                "multiqc/group_reports/lane1/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_seqfu_mqc.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/lane1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
@@ -500,7 +500,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
-                "multiqc/group_reports/lane1/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/seqfu_mqc.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-pct.png",
@@ -525,7 +525,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_by_cycle.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_score_distribution.png",
-                "multiqc/group_reports/lane1/multiqc_plots/png/seqfu.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/seqfu_mqc.png",
                 "multiqc/group_reports/lane1/multiqc_plots/svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-pct.svg",
@@ -550,7 +550,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_by_cycle.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_score_distribution.svg",
-                "multiqc/group_reports/lane1/multiqc_plots/svg/seqfu.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/seqfu_mqc.svg",
                 "multiqc/group_reports/lane1/multiqc_report.html",
                 "multiqc/group_reports/test",
                 "multiqc/group_reports/test/multiqc_data",
@@ -578,7 +578,7 @@
                 "multiqc/group_reports/test/multiqc_data/multiqc_picard_baseContent.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_by_cycle.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_score_distribution.txt",
-                "multiqc/group_reports/test/multiqc_data/multiqc_seqfu.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_seqfu_mqc.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_sources.txt",
                 "multiqc/group_reports/test/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
@@ -619,7 +619,7 @@
                 "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
-                "multiqc/group_reports/test/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/seqfu_mqc.pdf",
                 "multiqc/group_reports/test/multiqc_plots/png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png",
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@@ -644,7 +644,7 @@
                 "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
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                 "multiqc/group_reports/test/multiqc_plots/png/picard_quality_score_distribution.png",
-                "multiqc/group_reports/test/multiqc_plots/png/seqfu.png",
+                "multiqc/group_reports/test/multiqc_plots/png/seqfu_mqc.png",
                 "multiqc/group_reports/test/multiqc_plots/svg",
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@@ -669,71 +669,71 @@
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-                "multiqc/group_reports/test/multiqc_plots/svg/seqfu.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/seqfu_mqc.svg",
                 "multiqc/group_reports/test/multiqc_report.html",
                 "picard_collectmultiplemetrics",
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-                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_by_cycle_metrics",
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-                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.alignment_summary_metrics",
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-                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution.pdf",
-                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution_metrics",
-                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.read_length_histogram.pdf",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.alignment_summary_metrics",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution.pdf",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution_metrics",
-                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/Sample1_01.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/Sample1_01.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample1_01.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample1_01.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample1_01.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample1_01.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/Sample1_01.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/Sample1_01.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/Sample23_03.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/Sample23_03.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample23_03.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample23_03.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample23_03.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample23_03.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/Sample23_03.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/Sample23_03.CollectMultipleMetrics.read_length_histogram.pdf",
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+                "picard_collectmultiplemetrics/SampleA_02.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SampleA_02.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SampleA_02.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SampleA_02.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SampleA_02.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/SampleA_02.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/SampleA_02.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/Undetermined_05.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/Undetermined_05.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Undetermined_05.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Undetermined_05.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Undetermined_05.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Undetermined_05.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/Undetermined_05.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/Undetermined_05.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/sampletest_04.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/sampletest_04.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/sampletest_04.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/sampletest_04.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/sampletest_04.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/sampletest_04.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/sampletest_04.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/sampletest_04.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "samtools_faidx",
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                 "seqfu_stats",
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-                "seqfu_stats/Sample1_1_seqfu_mqc.txt",
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-                "seqfu_stats/Sample23_3_seqfu_mqc.txt",
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-                "seqfu_stats/SampleA_2_seqfu_mqc.txt",
-                "seqfu_stats/Undetermined_5_seqfu.tsv",
-                "seqfu_stats/Undetermined_5_seqfu_mqc.txt",
-                "seqfu_stats/sampletest_4_seqfu.tsv",
-                "seqfu_stats/sampletest_4_seqfu_mqc.txt",
+                "seqfu_stats/Sample1_01_seqfu.tsv",
+                "seqfu_stats/Sample1_01_seqfu_mqc.txt",
+                "seqfu_stats/Sample23_03_seqfu.tsv",
+                "seqfu_stats/Sample23_03_seqfu_mqc.txt",
+                "seqfu_stats/SampleA_02_seqfu.tsv",
+                "seqfu_stats/SampleA_02_seqfu_mqc.txt",
+                "seqfu_stats/Undetermined_05_seqfu.tsv",
+                "seqfu_stats/Undetermined_05_seqfu_mqc.txt",
+                "seqfu_stats/sampletest_04_seqfu.tsv",
+                "seqfu_stats/sampletest_04_seqfu_mqc.txt",
                 "seqtk",
-                "seqtk/Sample1_1_Sample1_S1_L001_R1_001.fastq.gz",
-                "seqtk/Sample23_3_Sample23_S3_L001_R1_001.fastq.gz",
-                "seqtk/SampleA_2_SampleA_S2_L001_R1_001.fastq.gz",
-                "seqtk/Undetermined_5_Undetermined_S0_L001_R1_001.fastq.gz",
-                "seqtk/sampletest_4_sampletest_S4_L001_R1_001.fastq.gz"
+                "seqtk/Sample1_01_Sample1_S1_L001_R1_001.fastq.gz",
+                "seqtk/Sample23_03_Sample23_S3_L001_R1_001.fastq.gz",
+                "seqtk/SampleA_02_SampleA_S2_L001_R1_001.fastq.gz",
+                "seqtk/Undetermined_05_Undetermined_S0_L001_R1_001.fastq.gz",
+                "seqtk/sampletest_04_sampletest_S4_L001_R1_001.fastq.gz"
             ],
             [
                 "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
@@ -741,209 +741,209 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
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-                "Sample23_3_screen.png:md5,09a60d51f8bf416e089715729a278a0d",
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-                "Undetermined_5_screen.png:md5,e4f09e8c09c2cea7ddf1f0a01bab273d",
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-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,1881dab3459ddec9b2ab33211440289c",
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+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,040e1375843c2eeabd2818d605192a98",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,73f8b87eeed241bd7b96d98990f6972d",
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                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,ede47a68cfe19144331104f4e51b6ee7",
-                "multiqc_fastqc.txt:md5,aba942d1e6996b579f19798e5673f514",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,ae3f9e644215ac39d2eae114bd52a517",
-                "multiqc_picard_baseContent.txt:md5,8b2efc3fa06d2013348b35f9607292aa",
-                "multiqc_picard_quality_by_cycle.txt:md5,c2774038d1a0142746426e46f9f954dd",
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-                "multiqc_seqfu.txt:md5,18dd2407d4a1791646785123028f69b5",
+                "multiqc_fastq_screen.txt:md5,5af2d6080364385c05d50f9ffa7996e6",
+                "multiqc_fastqc.txt:md5,a9a9fc06badaade2d09486d2adaac1ce",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,27ac8815e031784c1928f8ff7d2e8687",
+                "multiqc_picard_baseContent.txt:md5,b8f3650cf18daa57ae2b67c5b89f5b8b",
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+                "multiqc_picard_quality_score_distribution.txt:md5,2d6a03019d78184e380a667425edba69",
+                "multiqc_seqfu_mqc.txt:md5,18dd2407d4a1791646785123028f69b5",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,c2774038d1a0142746426e46f9f954dd",
-                "picard_QualityScoreDistribution_histogram.txt:md5,792755ee794d375b85a57f58d879f0c6",
-                "picard_alignment_readlength_plot.txt:md5,ebd1ff06394bd202b8190c46d560bc95",
-                "picard_alignment_summary.txt:md5,e507eccfa0a05b20705f99a3619dde29",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,597d0fd368eab8a21cd7f4a92965ecf6",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,ade1d92e5e6d3bfefd3695f103079b6c",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,af525e84f95ceb4b8496f734db2420fb",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,8b5ada27023f2545792fabbb69a07067",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,a472bba4490d7189df23f6b38a554448",
-                "picard_quality_by_cycle.txt:md5,83d68b4049173f8c9a37f58f1276adc1",
-                "picard_quality_score_distribution.txt:md5,42c08c8a51230d9ecccdad416c06f59c",
-                "fastq_screen_plot.txt:md5,fbd5dbdbc51ecb82f8c2da2b63f104d3",
-                "fastqc-status-check-heatmap.txt:md5,7ee494f345c09706513e65907788de02",
-                "fastqc_overrepresented_sequences_plot.txt:md5,ca9fa146e7b8a7f562fd79b521ba0f60",
-                "fastqc_per_base_n_content_plot.txt:md5,d0948f903d5cb77880ff7b1b4e0a4f23",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,12040cb996a4f30dbd6e5c313ee8e407",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,c6d912b805a018cc564e7f5b1967f1d8",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,0f71b9cb3d8e09558752a5f9f45cdf2c",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,f50ed03bbcb136505c3724d1ca2a5bea",
-                "fastqc_sequence_counts_plot.txt:md5,bf1fde5dc15633a58f074ddd3eb891a5",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,e37e8e4584f0157a5fa0d53b4834e836",
-                "fastqc_sequence_length_distribution_plot.txt:md5,e102bf11f348e8c24e1d15b336e2f595",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,ea8e2268c7b00c60221ff0166abcb8e6",
+                "picard_QualityScoreDistribution_histogram.txt:md5,2d6a03019d78184e380a667425edba69",
+                "picard_alignment_readlength_plot.txt:md5,b707405383ab30c7e2e1f035e5e3c26f",
+                "picard_alignment_summary.txt:md5,4048e43a47004998fc37d653b6fe4c38",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,fd50b4879f641e3492e60049c56a4044",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,2cd88662f52791e80606dfcfd72cd14f",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,7cf95bddfb6fd6a8f6b97bcc4259b27b",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,3b573361b3c6a2e6bbc9353b8c7e479f",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,f8d6bad265e19cb0569556c274cebce8",
+                "picard_quality_by_cycle.txt:md5,acf02b0d02bd558473b443e8b62d866c",
+                "picard_quality_score_distribution.txt:md5,e8f0b4ea7a5a2bb7b15652558ad3fa7c",
+                "fastq_screen_plot.txt:md5,73a2f1b72c45aecd6196166742ca79e2",
+                "fastqc-status-check-heatmap.txt:md5,6ecc7673865cff5b867a6e07f922aab6",
+                "fastqc_overrepresented_sequences_plot.txt:md5,bf671607cdc601346f4ec01236aa096a",
+                "fastqc_per_base_n_content_plot.txt:md5,fe0d8972d8a323138b36b310e22f2393",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,f6e093207a1bb92a9ff224509988f42c",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,c7d95253aa3046b55f345e4950537e30",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,c9dfe418314f68711cdec2d8c2f0f62d",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,9c6cc7ae6ec0f8fca21482d9910b10cf",
+                "fastqc_sequence_counts_plot.txt:md5,41e017e29a6c78e683816b59b24082d7",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,818f13a5372bad79e54cd984758096c5",
+                "fastqc_sequence_length_distribution_plot.txt:md5,891980cbbd9f0ce86072e49eaa19dbb2",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,8028856af6d413fa3592900e16dbc99f",
-                "multiqc_fastqc.txt:md5,ff996e1d3dc4a46e0c9535e54d51ccab",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,7bc3f6ef8f47e6f1e060f957025c98aa",
-                "multiqc_picard_baseContent.txt:md5,1426865fe8ee1a36f67636c28500a91c",
-                "multiqc_picard_quality_by_cycle.txt:md5,79bf9f861077de70ec28c9af01783876",
-                "multiqc_picard_quality_score_distribution.txt:md5,a3f8d1937e1f118800aa3d86c1b498c4",
-                "multiqc_seqfu.txt:md5,6cdb863a3686fbb772aae5a66925ff23",
+                "multiqc_fastq_screen.txt:md5,14d33a39b52346515edfd7e8542e5c7b",
+                "multiqc_fastqc.txt:md5,e87c99cac0c4956521d9c660183722bb",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,4caf3948c2fd99d795c1f6791221a02d",
+                "multiqc_picard_baseContent.txt:md5,fc5eec99f1406d05416315bb83c22efa",
+                "multiqc_picard_quality_by_cycle.txt:md5,0a23446d732f70734fbb75d2d8c4f8c5",
+                "multiqc_picard_quality_score_distribution.txt:md5,fff3e05748b15f8e70603f2de052bc1e",
+                "multiqc_seqfu_mqc.txt:md5,6cdb863a3686fbb772aae5a66925ff23",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,79bf9f861077de70ec28c9af01783876",
-                "picard_QualityScoreDistribution_histogram.txt:md5,a3f8d1937e1f118800aa3d86c1b498c4",
-                "picard_alignment_readlength_plot.txt:md5,5aed5e7c1395a537bdce7163c93781bd",
-                "picard_alignment_summary.txt:md5,9d0d003456e08f78701e876d0238b5a6",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,73e910febe1ea4d08a9f4e49d6c10615",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,092e732bb44842f2da5416de158c1cc5",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,e81495fde738e2954483195fd0ccfb04",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,ed9ad958081a904a5584757f87b29eb2",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,2b4526a0b0977ebd7fbe326c6d51cf19",
-                "picard_quality_by_cycle.txt:md5,d53617c495e81e011996cd4e9f755e0a",
-                "picard_quality_score_distribution.txt:md5,05f9e89733e43b81acf593efc1a56180",
-                "fastq_screen_plot.txt:md5,c32019d1b4d5245d75264b9f453ce916",
-                "fastqc-status-check-heatmap.txt:md5,b6872d9dbaa3cce396d48dc137076e53",
-                "fastqc_overrepresented_sequences_plot.txt:md5,19babef6996c0bfdf28e5df89368cbb1",
-                "fastqc_per_base_n_content_plot.txt:md5,25367b78b3d6a063d33814c663fea91e",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,2b4fa8cd21e4e6cb093abbfc221a7095",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,204e907429377d2d568e65d80edad2d2",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,525162fb43c9906641e953aafc59f8bf",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,3a16c4f83d13b5b61999491b0ca9d36c",
-                "fastqc_sequence_counts_plot.txt:md5,cf8c6868dc440beb30414259703a1551",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,1e595565e848ab3f13cfa8479214d3e0",
-                "fastqc_sequence_length_distribution_plot.txt:md5,24ef8f47147dabd210b03c497d340d77",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,0a23446d732f70734fbb75d2d8c4f8c5",
+                "picard_QualityScoreDistribution_histogram.txt:md5,fff3e05748b15f8e70603f2de052bc1e",
+                "picard_alignment_readlength_plot.txt:md5,c52d9bf78f5ad1336401948c9fe53a43",
+                "picard_alignment_summary.txt:md5,83605c81384aa07f5db79b003d62acd3",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,e2f21df881ca648de2797c6fbfd185bf",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,68c85f6b7cd47fe402227587b7cd6a42",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,e5014150074dd0eececa973999997299",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,f69e3acb76a974d44e72a1b51f57fcc5",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,9173f74d1a3513a47323957580fc778c",
+                "picard_quality_by_cycle.txt:md5,2528c2b37f19247f85f203b2ec1052cd",
+                "picard_quality_score_distribution.txt:md5,97065bd92fdc8cf9f7af101db69e0f94",
+                "fastq_screen_plot.txt:md5,55e918a24d363f5b82c7fe1993508ac0",
+                "fastqc-status-check-heatmap.txt:md5,61857d2c45cf0c080348047aa34e7525",
+                "fastqc_overrepresented_sequences_plot.txt:md5,0d0ed4af9d049d2d4d364c2e89666c49",
+                "fastqc_per_base_n_content_plot.txt:md5,5c0c6304c88c1eab06fe6d0272887eeb",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,962e2631be7459b8a4e6b94a76ca1ef9",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,667e8260356e2a95e619f596ec923408",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,3d3d528612f89034b5777384415869e2",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,ca7ab1c4613c58c65a59197a701f2cf6",
+                "fastqc_sequence_counts_plot.txt:md5,f9475cbbc8ddfbb7685d4f8843c58d2b",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,d5b06e963d0eb6f8013aa3070551305d",
+                "fastqc_sequence_length_distribution_plot.txt:md5,4101ced76bfe16e3baec15f7c8afaea7",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,e3e01b13becd5e30c9c12e5313b795c7",
-                "multiqc_fastqc.txt:md5,3df36ecfe76b25b0c22dcda84bce2b3b",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,4dc89e1a04843d44695ecc8d1f047ee8",
-                "multiqc_picard_baseContent.txt:md5,0a5f9d32dd3061ce4349518c47d69838",
-                "multiqc_picard_quality_by_cycle.txt:md5,ec59b472afc1242ff299011ba456e792",
-                "multiqc_picard_quality_score_distribution.txt:md5,1b8be76b60ee71aa36a98d34e433b9bf",
-                "multiqc_seqfu.txt:md5,f821357507fda2d4cfd9299f52fa7dc1",
+                "multiqc_fastq_screen.txt:md5,179b14566daf82ccd294f54443cf9b5e",
+                "multiqc_fastqc.txt:md5,8b808265a3cfe52846f7d6a0c9624beb",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,097425295aec6d2235b3ce2efdeadc2f",
+                "multiqc_picard_baseContent.txt:md5,e866142c080aadf520f3533344b078f7",
+                "multiqc_picard_quality_by_cycle.txt:md5,f90049902134e9d526de1e9e7c9b630a",
+                "multiqc_picard_quality_score_distribution.txt:md5,c5cd2b47144a9bdc8e4ec738bb7cf2f1",
+                "multiqc_seqfu_mqc.txt:md5,f821357507fda2d4cfd9299f52fa7dc1",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,ec59b472afc1242ff299011ba456e792",
-                "picard_QualityScoreDistribution_histogram.txt:md5,1b8be76b60ee71aa36a98d34e433b9bf",
-                "picard_alignment_readlength_plot.txt:md5,72e0094fcd2546bee02a7ac65a3ea218",
-                "picard_alignment_summary.txt:md5,19586495e6d7904a2a4a7eb9ba17a412",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,a825de2b668791e58f6a4078e0b31483",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,59633faead8aa9027883481b0c7e22af",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,f02153a346f7e24f200bf06af2293352",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,0725af81caa647ec22050c573dfe8cb0",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,3536e6dcc7c7ed972b02d2945da75cb7",
-                "picard_quality_by_cycle.txt:md5,be127a96dd68c14077548d36c0507dc3",
-                "picard_quality_score_distribution.txt:md5,9e27b097f10cb9a9a95a3445b220d104",
-                "fastq_screen_plot.txt:md5,f4a7d4d2c26ad1eb38525552d2275523",
-                "fastqc-status-check-heatmap.txt:md5,bab59a0bd1d676d90cdd986fbba36b26",
-                "fastqc_overrepresented_sequences_plot.txt:md5,79cb259874c52b44f8c69b2075ee498e",
-                "fastqc_per_base_n_content_plot.txt:md5,6ef3683b1b7db0b6db6948185f96959d",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,e7255081223d89b4f3611a57d13974d8",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,dc0ced33f21421d4cba72b4c6e6bf19b",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,7a6b00f36bb522d044c3fa3192e2adf8",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,ed58f918f7d979999e28137ba30f12e3",
-                "fastqc_sequence_counts_plot.txt:md5,29dc291cce9708c51dbe2b58a32cc713",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,77e0c9a542a3d59b173633764a11b404",
-                "fastqc_sequence_length_distribution_plot.txt:md5,c4f58d755233776c341da8dc357f8527",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,f90049902134e9d526de1e9e7c9b630a",
+                "picard_QualityScoreDistribution_histogram.txt:md5,c5cd2b47144a9bdc8e4ec738bb7cf2f1",
+                "picard_alignment_readlength_plot.txt:md5,1937a10b6a2bfd560f33d4c34489b245",
+                "picard_alignment_summary.txt:md5,3551d1f9f22584702b3f6291791db496",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,3c7f4f7846559a6ef01104665ea4c90e",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,53f75b0d1b72bc757e1839bf026576fc",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,1bf3a0c2124677a7720adc30e4a31420",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,61b3696131512cf12c186410083f718d",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,557bbb851ae20658c4d67039e75d6586",
+                "picard_quality_by_cycle.txt:md5,837fbc9e8945a2cbe50ef7192d032cbe",
+                "picard_quality_score_distribution.txt:md5,402adc8ad463da8cbe6eb91d626df014",
+                "fastq_screen_plot.txt:md5,ac87dfeee6febe70fb35fd7a4fd5d167",
+                "fastqc-status-check-heatmap.txt:md5,c762f9c764ff99a610ff1d20f2ed6ac9",
+                "fastqc_overrepresented_sequences_plot.txt:md5,cb95847fcb901c48de55da399faf47d9",
+                "fastqc_per_base_n_content_plot.txt:md5,ba96d6c813803230a4874a6f8baddcf6",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,ac0b1eb2e406e6b5a5eb68918591c76d",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,2012423964c65c0fefc8481b301609ed",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,500eefc61a59e5babbc72647b6638132",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,a1e4db231cd2b3934ecaebc4814cc742",
+                "fastqc_sequence_counts_plot.txt:md5,dedc339fbf428341aaacc1bfe04ba016",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,6f0891980501631a27a7375d2ec7a30d",
+                "fastqc_sequence_length_distribution_plot.txt:md5,b5bf616360fc7df8fb94b2a4928660cb",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,025c2db89ab18864c2828f3f4e368d4f",
-                "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,fa26e8b96faa1926d8f41fc3fe959ff7",
-                "multiqc_picard_baseContent.txt:md5,b9d72d8173cdc7649b44b80aa485477c",
-                "multiqc_picard_quality_by_cycle.txt:md5,062547fb888ed508dd1d5733d7bed22e",
-                "multiqc_picard_quality_score_distribution.txt:md5,dd5abab3a7141654fffa3946c50a039b",
-                "multiqc_seqfu.txt:md5,8cced36d66ca9d25d60c006e734aa7e9",
+                "multiqc_fastq_screen.txt:md5,a84c2882a4ab93afd9599c7aebf3e897",
+                "multiqc_fastqc.txt:md5,b8f6f4ed32e60ff57c64bb0ba029adba",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,a830b94cf4b094f6914927a93b4911f3",
+                "multiqc_picard_baseContent.txt:md5,c4b2e49d32ab00ffd166fb2343362300",
+                "multiqc_picard_quality_by_cycle.txt:md5,86934e1b1aee498e3434475f54e49c18",
+                "multiqc_picard_quality_score_distribution.txt:md5,a2f554d6121a1be2623fe67edb69b3db",
+                "multiqc_seqfu_mqc.txt:md5,8cced36d66ca9d25d60c006e734aa7e9",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,062547fb888ed508dd1d5733d7bed22e",
-                "picard_QualityScoreDistribution_histogram.txt:md5,dd5abab3a7141654fffa3946c50a039b",
-                "picard_alignment_readlength_plot.txt:md5,e5d397c216a0911a73dff5550fa7b1d7",
-                "picard_alignment_summary.txt:md5,ef16e8dbab178f44deebe0f4d321097b",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,8ada743b028ec78996f9dc40f1922941",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,c97859ee1641de9bff58dbd1e82fff20",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,ea86115ef2ca4ff4922486ceb6c6e1e8",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,07a3f1e6b1ed2bc55128fc2a0f46eb92",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,67ee93606c468a7eea7818b2f4b3389f",
-                "picard_quality_by_cycle.txt:md5,974b3baed160e9643f493df1d0ad5000",
-                "picard_quality_score_distribution.txt:md5,869d69ae4e243f0669f63b489563e4f1",
-                "fastq_screen_plot.txt:md5,331bc452d453a3c31263b8c5018a07da",
-                "fastqc-status-check-heatmap.txt:md5,2a66f5d61b9eb579555905cd5954b04c",
-                "fastqc_overrepresented_sequences_plot.txt:md5,5cdefa954db6e46c286e2984a883eb18",
-                "fastqc_per_base_n_content_plot.txt:md5,92c23e189d98430517e4030e7c9ae038",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,a02cd4679a5991b73d2df6583a2cf01b",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,6152ec5e4f4fd331b89107e024b009ac",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,ea90172d9f32b43fe8f6b91fb54f26c2",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,5ba7c7ccdcd54daf44d996e697cbeadf",
-                "fastqc_sequence_counts_plot.txt:md5,88a5e67b5ce395a7ed3324b176c15cf7",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,041857b1e41e0b47bfc62000cb9f323d",
-                "fastqc_sequence_length_distribution_plot.txt:md5,c2ee6b7c9fc91de049d183422e0a71fc",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,86934e1b1aee498e3434475f54e49c18",
+                "picard_QualityScoreDistribution_histogram.txt:md5,a2f554d6121a1be2623fe67edb69b3db",
+                "picard_alignment_readlength_plot.txt:md5,71d9fa2d8089ebff7cb842682ebeef30",
+                "picard_alignment_summary.txt:md5,3f0c630ee33504eb02d10b6c7e0ed9aa",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,7add6230e46c785f5db9e500a4a31681",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,0753e1d36ef7a9e1e8f98ba6cb71d143",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,df3c54e527505675dde1607eb5ca3008",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,fc1ef95b11e1aab29d4c3b502fa53056",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,6e9bc9ea875857b0ad9d59356a79bc71",
+                "picard_quality_by_cycle.txt:md5,36f4d38092d9df3d4e1c03c1912bd4f9",
+                "picard_quality_score_distribution.txt:md5,232a210a13ec476365851c65affb13d4",
+                "fastq_screen_plot.txt:md5,2a08e457eac00ed7b03a97cb2978ea27",
+                "fastqc-status-check-heatmap.txt:md5,56b426cd5c030288639533fce7c95ab1",
+                "fastqc_overrepresented_sequences_plot.txt:md5,a74b1c22b0b8c1c45592f6d3d92a7b00",
+                "fastqc_per_base_n_content_plot.txt:md5,bf2631bc46bc290be329984785da6c3a",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,05e5a46f9901e1a1aea089ac760d03bd",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,ae01bdfe32a1adbde8bc90b5cfad3745",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,f7980b8f02897f644b07d15554d83998",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,a2c43859317f03af53a7e2c904a4ce21",
+                "fastqc_sequence_counts_plot.txt:md5,c297106aef961a75134e8174a9fade97",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,3f319b383f827362a515ebb9eee9ddcf",
+                "fastqc_sequence_length_distribution_plot.txt:md5,a0b2aff6415e2365c8f1a28d300b0fbc",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,61392eb28e735f293516bb81f463450a",
-                "multiqc_fastqc.txt:md5,ce61b4ce4b1d76ec3f20de3bf0c9ec7f",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,55627d8016b72c37c104e03cc156862c",
-                "multiqc_picard_baseContent.txt:md5,974d83faa49711ab4ea1248c59e69393",
-                "multiqc_picard_quality_by_cycle.txt:md5,248ecaf269d8fef1e84ea06f98b6f6ba",
-                "multiqc_picard_quality_score_distribution.txt:md5,5e7e80654e12c500b15f8564ffb12b27",
-                "multiqc_seqfu.txt:md5,ff4ce1c88f39ed24a88bae0a861f75c8",
+                "multiqc_fastq_screen.txt:md5,db504d3eec12c5431e2b66d4880beb66",
+                "multiqc_fastqc.txt:md5,284597d876abc5a1242d8efb2d69f0d5",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,b9175f19bb7881a189d0f061089ee090",
+                "multiqc_picard_baseContent.txt:md5,fdfa6dc50f83f3966bc33caf796dddda",
+                "multiqc_picard_quality_by_cycle.txt:md5,28ba1f3017af64453cd191cf6f895e17",
+                "multiqc_picard_quality_score_distribution.txt:md5,60c5f167421d5b44c3b1ed810b5a68cd",
+                "multiqc_seqfu_mqc.txt:md5,ff4ce1c88f39ed24a88bae0a861f75c8",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,248ecaf269d8fef1e84ea06f98b6f6ba",
-                "picard_QualityScoreDistribution_histogram.txt:md5,5e7e80654e12c500b15f8564ffb12b27",
-                "picard_alignment_readlength_plot.txt:md5,23ff551a5a8eded1857356f38b19039c",
-                "picard_alignment_summary.txt:md5,c741b69e17ed84370732b567ae11c69c",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,fc37dd1ac805881a467b264a7dd76677",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,7993fd56aa542b71bc984cd36c489fd1",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,1bca639db2a2624727f7b6dd2aa1442e",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,a5f0903d77b6060676f7dda249b99738",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,102e653a543ac908ac9ec9b86412d73b",
-                "picard_quality_by_cycle.txt:md5,3d43fd5387c0dc728833c681ea4f73cc",
-                "picard_quality_score_distribution.txt:md5,9d9f1bb12316175cdb88d3ff70305428",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,28ba1f3017af64453cd191cf6f895e17",
+                "picard_QualityScoreDistribution_histogram.txt:md5,60c5f167421d5b44c3b1ed810b5a68cd",
+                "picard_alignment_readlength_plot.txt:md5,2bc1a0718665c2038c82c662744efd32",
+                "picard_alignment_summary.txt:md5,036000570a5d0e3a5fb695f64170d33d",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,800b43f6b0261fb7fa3830deed4b7b7f",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,8f0148e5b112d7e65512f46b5c444e1b",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,ffd09932248cef230e27d55d548b87f8",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,b08bf6e3c5cfc18251c6c9546e82a616",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,6c30458ebd6caa1a2867bc999bafedd5",
+                "picard_quality_by_cycle.txt:md5,4103c8c916ece5f57dbeffc477025d94",
+                "picard_quality_score_distribution.txt:md5,0a04dad54cadfd660c935af9a0658e0c",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
-                "Sample1_1_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6",
-                "Sample1_1_seqfu_mqc.txt:md5,24d99524ccd0e6c6255a69d68a871c7a",
-                "Sample23_3_seqfu.tsv:md5,6fac5d3dbce3f3bee72341fe99a399dc",
-                "Sample23_3_seqfu_mqc.txt:md5,4d4f280911a08bb6b753142980178027",
-                "SampleA_2_seqfu.tsv:md5,aec811f267bb2a0ef066a7abb59d2775",
-                "SampleA_2_seqfu_mqc.txt:md5,a819409a5cb64e20c3e54ec5ada4aa27",
-                "Undetermined_5_seqfu.tsv:md5,3a42c5c66a0a118f1a6f6f6e560b0e7e",
-                "Undetermined_5_seqfu_mqc.txt:md5,bd8be908362c5cb08a72f8ae7ab41b0d",
-                "sampletest_4_seqfu.tsv:md5,a5bea0b9c6015dd1a201ffd433e9b377",
-                "sampletest_4_seqfu_mqc.txt:md5,2180961655bbc8a12f0152d6a4b803a2",
-                "Sample1_1_Sample1_S1_L001_R1_001.fastq.gz:md5,3ccd132ff32399706842b0f1d00f477e",
-                "Sample23_3_Sample23_S3_L001_R1_001.fastq.gz:md5,3802f03450693b42531fdf5b0b542c2f",
-                "SampleA_2_SampleA_S2_L001_R1_001.fastq.gz:md5,f99d5407aac64cb36451c6f0a1db5ade",
-                "Undetermined_5_Undetermined_S0_L001_R1_001.fastq.gz:md5,104dbbef386db0eef3e02c586feb01a1",
-                "sampletest_4_sampletest_S4_L001_R1_001.fastq.gz:md5,30aa24a51e27e24390ac8b90158df8f2"
+                "Sample1_01_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6",
+                "Sample1_01_seqfu_mqc.txt:md5,24d99524ccd0e6c6255a69d68a871c7a",
+                "Sample23_03_seqfu.tsv:md5,6fac5d3dbce3f3bee72341fe99a399dc",
+                "Sample23_03_seqfu_mqc.txt:md5,4d4f280911a08bb6b753142980178027",
+                "SampleA_02_seqfu.tsv:md5,aec811f267bb2a0ef066a7abb59d2775",
+                "SampleA_02_seqfu_mqc.txt:md5,a819409a5cb64e20c3e54ec5ada4aa27",
+                "Undetermined_05_seqfu.tsv:md5,3a42c5c66a0a118f1a6f6f6e560b0e7e",
+                "Undetermined_05_seqfu_mqc.txt:md5,bd8be908362c5cb08a72f8ae7ab41b0d",
+                "sampletest_04_seqfu.tsv:md5,a5bea0b9c6015dd1a201ffd433e9b377",
+                "sampletest_04_seqfu_mqc.txt:md5,2180961655bbc8a12f0152d6a4b803a2",
+                "Sample1_01_Sample1_S1_L001_R1_001.fastq.gz:md5,3ccd132ff32399706842b0f1d00f477e",
+                "Sample23_03_Sample23_S3_L001_R1_001.fastq.gz:md5,3802f03450693b42531fdf5b0b542c2f",
+                "SampleA_02_SampleA_S2_L001_R1_001.fastq.gz:md5,f99d5407aac64cb36451c6f0a1db5ade",
+                "Undetermined_05_Undetermined_S0_L001_R1_001.fastq.gz:md5,104dbbef386db0eef3e02c586feb01a1",
+                "sampletest_04_sampletest_S4_L001_R1_001.fastq.gz:md5,30aa24a51e27e24390ac8b90158df8f2"
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-08T17:09:00.331820625"
+        "timestamp": "2025-12-12T10:04:43.761648394"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index be29efff..30dda963 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -66,7 +66,7 @@
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu_mqc.pdf",
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
@@ -82,7 +82,7 @@
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu_mqc.png",
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
@@ -98,7 +98,7 @@
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu_mqc.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
@@ -125,19 +125,19 @@
                 "fastqc_sequence_duplication_levels_plot.txt:md5,7b7665c78ca66d3e13b1850701b198dc",
                 "fastqc_sequence_length_distribution_plot.txt:md5,d7bac93b11316846778b9d550f323371",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,7c5d711e27c53d13c81644a1f2468dba",
-                "multiqc_fastqc.txt:md5,1a4b472e13cadc770832b0e20d1de7b0",
-                "multiqc_seqfu.txt:md5,9595d608ff5709f2bdec8cb1016416c0",
+                "multiqc_fastq_screen.txt:md5,0ab0d1c4c3e3393afdb50ad0e116e394",
+                "multiqc_fastqc.txt:md5,b71aaffef9767dfe9d83fde0d31a3a1b",
+                "multiqc_seqfu_mqc.txt:md5,9595d608ff5709f2bdec8cb1016416c0",
                 "genome.fa.fai:md5,59557cd3a71ca5e0840285b6088ec1d6",
                 "genome.fa.sizes:md5,f154a58a25ba9c4d386003eaa1bb731b",
-                "hg001_1_seqfu.tsv:md5,b133752c897afbb4d8721b911fa117d4",
-                "hg001_1_seqfu_mqc.txt:md5,42e3506b02ceb72a6f05cb174505e722"
+                "hg001_01_seqfu.tsv:md5,b133752c897afbb4d8721b911fa117d4",
+                "hg001_01_seqfu_mqc.txt:md5,42e3506b02ceb72a6f05cb174505e722"
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-03T11:01:17.46398"
+        "timestamp": "2025-12-12T10:05:23.380990836"
     }
 }
\ No newline at end of file

From 412978e2ab03fcaba11d40e9b75d0a8d786a31e4 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 12 Dec 2025 10:20:04 +0100
Subject: [PATCH 485/530] re-generate snapshots

---
 tests/NovaSeq6000.main_subsample.nf.test.snap | 455 +++++++++++++++++-
 1 file changed, 432 insertions(+), 23 deletions(-)

diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index dfe61fe5..52ab49d2 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -949,12 +949,22 @@
     "NovaSeq6000 data test relative sample size": {
         "content": [
             {
+                "BWAMEM2_MEM": {
+                    "bwamem2": "2.2.1",
+                    "samtools": "1.22.1"
+                },
                 "FASTQC": {
                     "fastqc": "0.12.1"
                 },
                 "FASTQSCREEN_FASTQSCREEN": {
                     "fastqscreen": "0.16.0"
                 },
+                "PICARD_COLLECTMULTIPLEMETRICS": {
+                    "picard": "3.4.0"
+                },
+                "SAMTOOLS_INDEX": {
+                    "samtools": "1.22.1"
+                },
                 "SEQFU_STATS": {
                     "seqfu": "1.22.3"
                 },
@@ -966,6 +976,24 @@
                 }
             },
             [
+                "bwamem2_index",
+                "bwamem2_index/bwamem2",
+                "bwamem2_index/bwamem2/genome.fa.0123",
+                "bwamem2_index/bwamem2/genome.fa.amb",
+                "bwamem2_index/bwamem2/genome.fa.ann",
+                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
+                "bwamem2_index/bwamem2/genome.fa.pac",
+                "bwamem2_mem",
+                "bwamem2_mem/Sample1_1.bam",
+                "bwamem2_mem/Sample1_1.bam.bai",
+                "bwamem2_mem/Sample23_3.bam",
+                "bwamem2_mem/Sample23_3.bam.bai",
+                "bwamem2_mem/SampleA_2.bam",
+                "bwamem2_mem/SampleA_2.bam.bai",
+                "bwamem2_mem/Undetermined_5.bam",
+                "bwamem2_mem/Undetermined_5.bam.bai",
+                "bwamem2_mem/sampletest_4.bam",
+                "bwamem2_mem/sampletest_4.bam.bai",
                 "fastqc",
                 "fastqc/Sample1_1_fastqc.html",
                 "fastqc/Sample1_1_fastqc.zip",
@@ -1016,9 +1044,26 @@
                 "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/global_report/multiqc_plots",
                 "multiqc/global_report/multiqc_plots/pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -1034,6 +1079,16 @@
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -1049,6 +1104,16 @@
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/global_report/multiqc_plots/png/seqfu.png",
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -1064,6 +1129,16 @@
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/global_report/multiqc_plots/svg/seqfu.svg",
                 "multiqc/global_report/multiqc_report.html",
                 "multiqc/group_reports",
@@ -1089,9 +1164,26 @@
                 "multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group1/multiqc_plots",
                 "multiqc/group_reports/group1/multiqc_plots/pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -1107,6 +1199,16 @@
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -1122,6 +1224,16 @@
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/group1/multiqc_plots/svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -1137,6 +1249,16 @@
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/group1/multiqc_report.html",
                 "multiqc/group_reports/group2",
@@ -1161,9 +1283,26 @@
                 "multiqc/group_reports/group2/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/group2/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/group2/multiqc_plots",
                 "multiqc/group_reports/group2/multiqc_plots/pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -1179,6 +1318,16 @@
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -1194,6 +1343,16 @@
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/group2/multiqc_plots/svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -1209,6 +1368,16 @@
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/group2/multiqc_report.html",
                 "multiqc/group_reports/lane1",
@@ -1233,9 +1402,26 @@
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_score_distribution.txt",
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                 "multiqc/group_reports/lane1/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/lane1/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/lane1/multiqc_plots",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -1251,6 +1437,16 @@
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -1266,6 +1462,16 @@
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/lane1/multiqc_plots/svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -1281,6 +1487,16 @@
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
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                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/lane1/multiqc_report.html",
                 "multiqc/group_reports/test",
@@ -1305,9 +1521,26 @@
                 "multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_score_distribution.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_seqfu.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_software_versions.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/group_reports/test/multiqc_data/picard_quality_score_distribution.txt",
                 "multiqc/group_reports/test/multiqc_plots",
                 "multiqc/group_reports/test/multiqc_plots/pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
@@ -1323,6 +1556,16 @@
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/seqfu.pdf",
                 "multiqc/group_reports/test/multiqc_plots/png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png",
@@ -1338,6 +1581,16 @@
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/group_reports/test/multiqc_plots/png/picard_quality_score_distribution.png",
                 "multiqc/group_reports/test/multiqc_plots/png/seqfu.png",
                 "multiqc/group_reports/test/multiqc_plots/svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
@@ -1353,10 +1606,64 @@
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_score_distribution.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/seqfu.svg",
                 "multiqc/group_reports/test/multiqc_report.html",
+                "picard_collectmultiplemetrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "samtools_faidx",
+                "samtools_faidx/genome.fa.fai",
+                "samtools_faidx/genome.fa.sizes",
                 "seqfu_stats",
                 "seqfu_stats/Sample1_1_seqfu.tsv",
                 "seqfu_stats/Sample1_1_seqfu_mqc.txt",
@@ -1376,17 +1683,32 @@
                 "seqtk/sampletest_4_sampletest_S4_L001_R1_001.fastq.gz"
             ],
             [
-                "Sample1_1_screen.png:md5,562256290643b51e4374c2225a15f463",
-                "Sample1_1_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
-                "Sample23_3_screen.png:md5,6bb2caf67b9b2ed25d3d5f32c343e9ab",
-                "Sample23_3_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
-                "SampleA_2_screen.png:md5,b2c3e95e034f5c038754bf108537de0e",
-                "SampleA_2_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
-                "Undetermined_5_screen.png:md5,fc5d53f8876dfae3d1a781fa512ea1db",
-                "Undetermined_5_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
-                "sampletest_4_screen.png:md5,1fb60070e8f4b70de0c1b3786b54f27e",
-                "sampletest_4_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
-                "fastq_screen_plot.txt:md5,562b783630f698c3220c951b73b87027",
+                "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
+                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
+                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
+                "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
+                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
+                "Sample1_1.bam:md5,96dd0f60e9df17a0d2d567a245aaf617",
+                "Sample1_1.bam.bai:md5,e9c66d695e26fa2408d81ce006243ed4",
+                "Sample23_3.bam:md5,d660f473733620aaa4f4bdea6d26289d",
+                "Sample23_3.bam.bai:md5,e9c66d695e26fa2408d81ce006243ed4",
+                "SampleA_2.bam:md5,487822e724c1e39c2f701087ad87b2ba",
+                "SampleA_2.bam.bai:md5,e9c66d695e26fa2408d81ce006243ed4",
+                "Undetermined_5.bam:md5,5b1e10ba30aea46920889d5424df56bb",
+                "Undetermined_5.bam.bai:md5,e9c66d695e26fa2408d81ce006243ed4",
+                "sampletest_4.bam:md5,d07b94a148b71a334056308bb95afa1e",
+                "sampletest_4.bam.bai:md5,e9c66d695e26fa2408d81ce006243ed4",
+                "Sample1_1_screen.png:md5,f77ab5b51b18150e9202544405f268a1",
+                "Sample1_1_screen.txt:md5,20926a4045b2ecf4bc76007047cc645a",
+                "Sample23_3_screen.png:md5,09a60d51f8bf416e089715729a278a0d",
+                "Sample23_3_screen.txt:md5,20926a4045b2ecf4bc76007047cc645a",
+                "SampleA_2_screen.png:md5,dfba178e76017bf9ea3e5517ee6915f4",
+                "SampleA_2_screen.txt:md5,20926a4045b2ecf4bc76007047cc645a",
+                "Undetermined_5_screen.png:md5,e4f09e8c09c2cea7ddf1f0a01bab273d",
+                "Undetermined_5_screen.txt:md5,20926a4045b2ecf4bc76007047cc645a",
+                "sampletest_4_screen.png:md5,18320e2dde03d1cc3b7897e75c3574c9",
+                "sampletest_4_screen.txt:md5,20926a4045b2ecf4bc76007047cc645a",
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                 "fastqc-status-check-heatmap.txt:md5,84794d045dc6d91b00e59985bae9d18a",
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                 "fastqc_per_base_n_content_plot.txt:md5,cd0bf31027a6ea439d04e41210ad6ad3",
@@ -1398,10 +1720,27 @@
                 "fastqc_sequence_duplication_levels_plot.txt:md5,2a7d356a86612a7681ffdee6a0baff9a",
                 "fastqc_sequence_length_distribution_plot.txt:md5,d1c8835f262e4b84ce77590f27b9dc2f",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
+                "multiqc_fastq_screen.txt:md5,d384ced49beb8e8cd1c275cbde1dc548",
                 "multiqc_fastqc.txt:md5,c2d5ec1b75cee83a083434e9ba8be91e",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,db2d883ff65220cebfe84c36d72d1194",
+                "multiqc_picard_baseContent.txt:md5,7f1b2ac2eebf64faaa0d803d130c4083",
+                "multiqc_picard_quality_by_cycle.txt:md5,f31d1c8c027f04e9090040326082452e",
+                "multiqc_picard_quality_score_distribution.txt:md5,866720d8f2e4f050e31bd5b01b8288e5",
                 "multiqc_seqfu.txt:md5,18dd2407d4a1791646785123028f69b5",
-                "fastq_screen_plot.txt:md5,c25d34568f10f131156294d31fbfa994",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,f31d1c8c027f04e9090040326082452e",
+                "picard_QualityScoreDistribution_histogram.txt:md5,866720d8f2e4f050e31bd5b01b8288e5",
+                "picard_alignment_readlength_plot.txt:md5,f5d26b4d2c203ec351768b74c4c32ef4",
+                "picard_alignment_summary.txt:md5,2ee6ffe29265758c3cbe2387a92b3a8d",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,80ce3de4157273e60aaff7786faf5b4b",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,733fc418f62d372892070842bc3a4380",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,438ef3c17fcc70d9b085346595097f5c",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,7542ac72bf07c76115a7168329d49d15",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,3d49913fa22527604791e85031dbce82",
+                "picard_quality_by_cycle.txt:md5,07e906fe752011a5e02e48b828817640",
+                "picard_quality_score_distribution.txt:md5,e5be1eea98401e1ab0a4a5e6fadb3c64",
+                "fastq_screen_plot.txt:md5,486bcd75ed14aff63c38e0fa0b6870be",
                 "fastqc-status-check-heatmap.txt:md5,7ee494f345c09706513e65907788de02",
                 "fastqc_overrepresented_sequences_plot.txt:md5,8a1c4d43aa773be8eda518d400fc5685",
                 "fastqc_per_base_n_content_plot.txt:md5,ac20a2afd4aeb98001f0586877e5333b",
@@ -1413,10 +1752,27 @@
                 "fastqc_sequence_duplication_levels_plot.txt:md5,e37e8e4584f0157a5fa0d53b4834e836",
                 "fastqc_sequence_length_distribution_plot.txt:md5,6a7b2d7efe8598072636fb7215ea51f7",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
+                "multiqc_fastq_screen.txt:md5,4e0014d85ba2bb9a6b5c4bd16ce41ee0",
                 "multiqc_fastqc.txt:md5,3275fb3409d73a36aa87f672db60fc96",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,0e83be5864caa029370ddaf056cc40ef",
+                "multiqc_picard_baseContent.txt:md5,00b8306af9196dc4a2c4fdc77a988ab9",
+                "multiqc_picard_quality_by_cycle.txt:md5,5c4239a51284f60ff9218e4ec7d185ca",
+                "multiqc_picard_quality_score_distribution.txt:md5,a6f5ea2bb74219086cca0b04a74c12a6",
                 "multiqc_seqfu.txt:md5,6cdb863a3686fbb772aae5a66925ff23",
-                "fastq_screen_plot.txt:md5,44fca6453b0a3d0590271bd7a31cc740",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,5c4239a51284f60ff9218e4ec7d185ca",
+                "picard_QualityScoreDistribution_histogram.txt:md5,a6f5ea2bb74219086cca0b04a74c12a6",
+                "picard_alignment_readlength_plot.txt:md5,3fe2deeeef72f0a4655a51aa4e7b8245",
+                "picard_alignment_summary.txt:md5,b6ca8624a69ed1ee9c2d7c063f2d0728",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,cda99a1e62f1012a51de532297e278fa",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,02b1bc146febef37730d8dd187e5438e",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,c068d6443ae4fabc905439d56f77bcc6",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,f72783b5c132a07aed4817b109931fc6",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,013d132f11c9357f24ddaffbfa47c7c0",
+                "picard_quality_by_cycle.txt:md5,402a22cdada1927b63b284cb7220d295",
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                 "fastqc-status-check-heatmap.txt:md5,b6872d9dbaa3cce396d48dc137076e53",
                 "fastqc_overrepresented_sequences_plot.txt:md5,aa2089fd0c302d13a8ac129b170d1635",
                 "fastqc_per_base_n_content_plot.txt:md5,ed940fe48b562524c311c00649ef063c",
@@ -1428,10 +1784,27 @@
                 "fastqc_sequence_duplication_levels_plot.txt:md5,b044a9ed362df44abf424ff6367bf79a",
                 "fastqc_sequence_length_distribution_plot.txt:md5,312f96e33f395a12b727073b1827bbbc",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
+                "multiqc_fastq_screen.txt:md5,ba11030eafb7b8887eef3918a6f84edb",
                 "multiqc_fastqc.txt:md5,7c24c235c7e9279db9c050e035a80864",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,68ec06e93c523f6c7a3c98996a4c4b8e",
+                "multiqc_picard_baseContent.txt:md5,1262ae5bbdfd45ef4c21ae55ad8ad0d0",
+                "multiqc_picard_quality_by_cycle.txt:md5,04381da165be98ecac41cd09cf701d88",
+                "multiqc_picard_quality_score_distribution.txt:md5,4be5dc0e0b1fd380f8a2b7efb98a6303",
                 "multiqc_seqfu.txt:md5,f821357507fda2d4cfd9299f52fa7dc1",
-                "fastq_screen_plot.txt:md5,5f748d33a7a396547fe8c260b728aa06",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,04381da165be98ecac41cd09cf701d88",
+                "picard_QualityScoreDistribution_histogram.txt:md5,4be5dc0e0b1fd380f8a2b7efb98a6303",
+                "picard_alignment_readlength_plot.txt:md5,7b5337c24dc998a495de38c6d3685e91",
+                "picard_alignment_summary.txt:md5,2f382d3bb127178dbccd07060ae351ab",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,2b18a58292968648ace5d69a45e6b6a5",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,27c4d809d13fabb244d93b63e02f860c",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,8b5571bd3be1a1de10e18729046d937a",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,32d39e076f7fdca7f1e671e77131279e",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,49a40ea2ae234d7d84934b9c065e8682",
+                "picard_quality_by_cycle.txt:md5,fe6db43805b9d7f969d822e3fddf0a95",
+                "picard_quality_score_distribution.txt:md5,2dccf6004567fb40eae88a349353ca45",
+                "fastq_screen_plot.txt:md5,d38f097297053f6b696abcd8f505c135",
                 "fastqc-status-check-heatmap.txt:md5,bab59a0bd1d676d90cdd986fbba36b26",
                 "fastqc_overrepresented_sequences_plot.txt:md5,c468b9fb791e766cd4370c1117487d16",
                 "fastqc_per_base_n_content_plot.txt:md5,669f79d1e7ce45854c963f39529d5b03",
@@ -1443,10 +1816,27 @@
                 "fastqc_sequence_duplication_levels_plot.txt:md5,4a5803b3a48133747e750265b5cbf457",
                 "fastqc_sequence_length_distribution_plot.txt:md5,bba3d5f5a20e50170528eb0f4695b7ae",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
+                "multiqc_fastq_screen.txt:md5,863c21d16836bb582e90c14f7c77bd3f",
                 "multiqc_fastqc.txt:md5,54330c70bce06979ac3c05280607ea3f",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,97c774ada6616b992346fb2f6f2b5acb",
+                "multiqc_picard_baseContent.txt:md5,5cc12f969d7e5bafa47455ddc4787b0d",
+                "multiqc_picard_quality_by_cycle.txt:md5,8f8c3aeef6f01a537b945b551141fcba",
+                "multiqc_picard_quality_score_distribution.txt:md5,0afe72677fdfd8ae86fea18d8f7f2672",
                 "multiqc_seqfu.txt:md5,8cced36d66ca9d25d60c006e734aa7e9",
-                "fastq_screen_plot.txt:md5,8622e1dbd0fe62520af6096207b9775d",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,8f8c3aeef6f01a537b945b551141fcba",
+                "picard_QualityScoreDistribution_histogram.txt:md5,0afe72677fdfd8ae86fea18d8f7f2672",
+                "picard_alignment_readlength_plot.txt:md5,4a60e5c9df1a3c25909c02ec9bb1fb7d",
+                "picard_alignment_summary.txt:md5,234815a47c7a976cc9f266fd1b538596",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,16d1571c7a4f45a5d8d38a19e209e016",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,cc9d8c6c527e5b1d2759334aeefa89a4",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,2a771987f0ab7ce4f4ab73d6ccc1c466",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,b342db0a8182a3653f8e41721fb9e67e",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,c2365c26266655e11071bfc40448780f",
+                "picard_quality_by_cycle.txt:md5,a195e00cabe912519819a2b10f28a2db",
+                "picard_quality_score_distribution.txt:md5,c62f13d8f553e92f5f3239d415c90552",
+                "fastq_screen_plot.txt:md5,3de6cc68917516eea250e68efd66176c",
                 "fastqc-status-check-heatmap.txt:md5,2a66f5d61b9eb579555905cd5954b04c",
                 "fastqc_overrepresented_sequences_plot.txt:md5,b2fd59c117e7f16cba78862881c935d5",
                 "fastqc_per_base_n_content_plot.txt:md5,ccfa4f753ed6fce2232224efb0c3150d",
@@ -1458,9 +1848,28 @@
                 "fastqc_sequence_duplication_levels_plot.txt:md5,5c51d807e8841b9124f2d301f5504203",
                 "fastqc_sequence_length_distribution_plot.txt:md5,6966aa7545afaae2ab8712962e9862c6",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5",
+                "multiqc_fastq_screen.txt:md5,eef8ba64ac5d43ba6cfe692c66a4c1b1",
                 "multiqc_fastqc.txt:md5,f82113046ba0964a0a7afe16be0a51ba",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,e3f622e6a252d4a628cc07a26db8009a",
+                "multiqc_picard_baseContent.txt:md5,3170eac28a62722a0eb67e7c43466f8b",
+                "multiqc_picard_quality_by_cycle.txt:md5,90920ec34a5ac4d8817a08ec0e183f51",
+                "multiqc_picard_quality_score_distribution.txt:md5,38d445a874b551d247812930c8b07361",
                 "multiqc_seqfu.txt:md5,ff4ce1c88f39ed24a88bae0a861f75c8",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,90920ec34a5ac4d8817a08ec0e183f51",
+                "picard_QualityScoreDistribution_histogram.txt:md5,38d445a874b551d247812930c8b07361",
+                "picard_alignment_readlength_plot.txt:md5,8b8f3d2ea269406d6e48da06ae5992a1",
+                "picard_alignment_summary.txt:md5,9ac578340271d22ce1912fdbc059dcaf",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,c5b1777c43c85a9bc9d7de545b7fec70",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,44f972744c2941e34379c11a306546c8",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,c36061169fe6f08379e0df34da0e0e07",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,dd1642730be6865f268da8c895c5bec6",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,a9e46e928869f8f3067b7ef11072dbc7",
+                "picard_quality_by_cycle.txt:md5,9db1a85f92fa2c0c19dcb8f6675aba44",
+                "picard_quality_score_distribution.txt:md5,f7bab842fe87095c726660b51bf44a44",
+                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
+                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "Sample1_1_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6",
                 "Sample1_1_seqfu_mqc.txt:md5,24d99524ccd0e6c6255a69d68a871c7a",
                 "Sample23_3_seqfu.tsv:md5,6fac5d3dbce3f3bee72341fe99a399dc",
@@ -1479,9 +1888,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.10.0"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-11-26T14:34:17.011633325"
+        "timestamp": "2025-12-12T10:17:43.51515412"
     }
 }
\ No newline at end of file

From 0cbe100cd7fedcb1390f25e3dd7659bea44489be Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 12 Dec 2025 10:20:21 +0100
Subject: [PATCH 486/530] Update workflows/seqinspector.nf

---
 workflows/seqinspector.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 9e075140..09a4c725 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -104,7 +104,7 @@ workflow SEQINSPECTOR {
             [meta.sample_id, stats]
         }}
         .splitCsv(header: true, sep: '\t')
-        .view { sample_id, row ->
+        .map { sample_id, row ->
             // Check if requested sample size exceeds available reads
             def sample_reads = row['#Seq'].toInteger()
             if (params.sample_size > sample_reads) {

From 9f98c4b5aba46f501f8cfaac2ebf18451eec9595 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 12 Dec 2025 11:10:17 +0100
Subject: [PATCH 487/530] use log.warn, and update tests

---
 tests/NovaSeq6000.main_subsample.nf.test      |  35 +-
 tests/NovaSeq6000.main_subsample.nf.test.snap | 954 ++++++++++++++++++
 workflows/seqinspector.nf                     |  70 +-
 3 files changed, 1011 insertions(+), 48 deletions(-)

diff --git a/tests/NovaSeq6000.main_subsample.nf.test b/tests/NovaSeq6000.main_subsample.nf.test
index aec5dfc8..fc9da203 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test
+++ b/tests/NovaSeq6000.main_subsample.nf.test
@@ -73,7 +73,9 @@ nextflow_pipeline {
             )
         }
     }
+
     test("NovaSeq6000 data test sample size exceeds available reads") {
+        tag "warning"
 
         when {
             config "./NovaSeq6000.main_subsample.nf.test.config"
@@ -84,18 +86,29 @@ nextflow_pipeline {
         }
 
         then {
-            def warn_messages = [
-                "Warning: Requested sample_size (120) is larger than available reads in Undetermined_5 (100). Pipeline will continue with 100 reads.",
-                "Warning: Requested sample_size (120) is larger than available reads in SampleA_2 (100). Pipeline will continue with 100 reads.",
-                "Warning: Requested sample_size (120) is larger than available reads in sampletest_4 (100). Pipeline will continue with 100 reads.",
-                "Warning: Requested sample_size (120) is larger than available reads in Sample23_3 (100). Pipeline will continue with 100 reads.",
-                "Warning: Requested sample_size (120) is larger than available reads in Sample1_1 (100). Pipeline will continue with 100 reads."
-            ]
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(
+                params.outdir,
+                relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']
+            )
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(
+                params.outdir,
+                ignoreFile: 'tests/.nftignore'
+            )
             assert workflow.success
-            for ( msg in warn_messages ) {
-                // Read warning from stdout as nf-test does not capture log messages
-                assert workflow.stdout.contains(msg)
-            }
+            assertAll(
+                { assert snapshot(
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
+                    // All stable path names, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path,
+                    // get all messages containing Requested sample_size (120)
+                    filterNextflowOutput(workflow.stdout + workflow.stderr, ignore: ['Downloading plugin'], include:['Requested sample_size (120)'])
+                ).match() }
+            )
         }
     }
 }
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index ea4d8990..28e919c7 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -1892,5 +1892,959 @@
             "nextflow": "25.10.2"
         },
         "timestamp": "2025-12-12T10:25:34.099604526"
+    },
+    "NovaSeq6000 data test sample size exceeds available reads": {
+        "content": [
+            {
+                "BWAMEM2_MEM": {
+                    "bwamem2": "2.2.1",
+                    "samtools": "1.22.1"
+                },
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "FASTQSCREEN_FASTQSCREEN": {
+                    "fastqscreen": "0.16.0"
+                },
+                "PICARD_COLLECTMULTIPLEMETRICS": {
+                    "picard": "3.4.0"
+                },
+                "SAMTOOLS_INDEX": {
+                    "samtools": "1.22.1"
+                },
+                "SEQFU_STATS": {
+                    "seqfu": "1.22.3"
+                },
+                "SEQTK_SAMPLE": {
+                    "seqtk": "1.4-r122"
+                },
+                "Workflow": {
+                    "nf-core/seqinspector": "v1.0dev"
+                }
+            },
+            [
+                "bwamem2_index",
+                "bwamem2_index/bwamem2",
+                "bwamem2_index/bwamem2/genome.fa.0123",
+                "bwamem2_index/bwamem2/genome.fa.amb",
+                "bwamem2_index/bwamem2/genome.fa.ann",
+                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
+                "bwamem2_index/bwamem2/genome.fa.pac",
+                "bwamem2_mem",
+                "bwamem2_mem/Sample1_01.bam",
+                "bwamem2_mem/Sample1_01.bam.bai",
+                "bwamem2_mem/Sample23_03.bam",
+                "bwamem2_mem/Sample23_03.bam.bai",
+                "bwamem2_mem/SampleA_02.bam",
+                "bwamem2_mem/SampleA_02.bam.bai",
+                "bwamem2_mem/Undetermined_05.bam",
+                "bwamem2_mem/Undetermined_05.bam.bai",
+                "bwamem2_mem/sampletest_04.bam",
+                "bwamem2_mem/sampletest_04.bam.bai",
+                "fastqc",
+                "fastqc/Sample1_01_fastqc.html",
+                "fastqc/Sample1_01_fastqc.zip",
+                "fastqc/Sample23_03_fastqc.html",
+                "fastqc/Sample23_03_fastqc.zip",
+                "fastqc/SampleA_02_fastqc.html",
+                "fastqc/SampleA_02_fastqc.zip",
+                "fastqc/Undetermined_05_fastqc.html",
+                "fastqc/Undetermined_05_fastqc.zip",
+                "fastqc/sampletest_04_fastqc.html",
+                "fastqc/sampletest_04_fastqc.zip",
+                "fastqscreen",
+                "fastqscreen/Sample1_01_screen.html",
+                "fastqscreen/Sample1_01_screen.png",
+                "fastqscreen/Sample1_01_screen.txt",
+                "fastqscreen/Sample23_03_screen.html",
+                "fastqscreen/Sample23_03_screen.png",
+                "fastqscreen/Sample23_03_screen.txt",
+                "fastqscreen/SampleA_02_screen.html",
+                "fastqscreen/SampleA_02_screen.png",
+                "fastqscreen/SampleA_02_screen.txt",
+                "fastqscreen/Undetermined_05_screen.html",
+                "fastqscreen/Undetermined_05_screen.png",
+                "fastqscreen/Undetermined_05_screen.txt",
+                "fastqscreen/sampletest_04_screen.html",
+                "fastqscreen/sampletest_04_screen.png",
+                "fastqscreen/sampletest_04_screen.txt",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/global_report/multiqc_data/llms-full.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc.parquet",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu_mqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
+                "multiqc/global_report/multiqc_plots",
+                "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
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+                "fastq_screen_plot.txt:md5,5abb5b9ed2c976f0ad83216ca3186201",
+                "fastqc-status-check-heatmap.txt:md5,323d6082b73ddb6ee33385f5ea4301c1",
+                "fastqc_overrepresented_sequences_plot.txt:md5,4e71d8913d40eb06db0f18d74ce6898f",
+                "fastqc_per_base_n_content_plot.txt:md5,b317ce09cb7a2be2366b544ea9b20ce6",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,e6f44d08f4185f680d4748a3b37201e2",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a1dc8a968f32bcf8a9b4c5f43d299dfa",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,e41b6dc1344f1aee379993daff310187",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,76f792b939233b070562cc46617f6371",
+                "fastqc_sequence_counts_plot.txt:md5,36c68522023b8d536c9362403bf03c48",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,9ff0df466790d971b3c7ef838efc0f4f",
+                "fastqc_sequence_length_distribution_plot.txt:md5,9fda632b92e3453f11cd0226484fce8e",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,536c28d7fadc9a76944f93ac9d643272",
+                "multiqc_fastqc.txt:md5,396b4cc0466a6642ec8b954237c42263",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,153c6e6a407ec128b1a02798ca2f1115",
+                "multiqc_picard_baseContent.txt:md5,6349e514552a0b5a0530fa6f311878a5",
+                "multiqc_picard_quality_by_cycle.txt:md5,c0c8b4c0197428d4d50e2c532814e1e2",
+                "multiqc_picard_quality_score_distribution.txt:md5,40e0b6faa75e1b51af42407f7ededb0c",
+                "multiqc_seqfu_mqc.txt:md5,8cced36d66ca9d25d60c006e734aa7e9",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,c0c8b4c0197428d4d50e2c532814e1e2",
+                "picard_QualityScoreDistribution_histogram.txt:md5,40e0b6faa75e1b51af42407f7ededb0c",
+                "picard_alignment_readlength_plot.txt:md5,5a19b1f8e2ac49d97f36a7792429419c",
+                "picard_alignment_summary.txt:md5,f9f791b7c569cfae07aef70aa630d40e",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,0165f522c84da6b17a286d37dc30abec",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,6fa0d29d40fe7fa24c166b664b6d4f4b",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,bf2426e09ac1ca4773edfc284c220122",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,3cbace572471ccf6c58673181dd0c0ec",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,b317ce09cb7a2be2366b544ea9b20ce6",
+                "picard_quality_by_cycle.txt:md5,7cb705007bc97da8c0da7d93201e6975",
+                "picard_quality_score_distribution.txt:md5,47d684abae0a8f4f09df43e91d54fb9a",
+                "fastq_screen_plot.txt:md5,82ceb9f2109f865d6d1b943441c09550",
+                "fastqc-status-check-heatmap.txt:md5,56b426cd5c030288639533fce7c95ab1",
+                "fastqc_overrepresented_sequences_plot.txt:md5,8e83abdbe7362e64d63339ee31ab3361",
+                "fastqc_per_base_n_content_plot.txt:md5,33b70326d8f888ac5a3d99b85f365e43",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,40bc954cc0d58a3197fdf124a40f1ca4",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,e240e30996c81a34b5d1a6b5a98ae254",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,b44d3376d503af12857d494c58b514bb",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,66b5b6d44f398fc9429460c0b9ba3ea9",
+                "fastqc_sequence_counts_plot.txt:md5,6e5804f553f656cffb02f927015d1026",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,fbe41935ea2e2faf7104393b476e5ac5",
+                "fastqc_sequence_length_distribution_plot.txt:md5,e77dc4ab73252c2e09c7452c3b8e8ab3",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,4fc422d9cb06a1d0248cc578c1eebaa2",
+                "multiqc_fastqc.txt:md5,95c8ffb23baafec625aeb600047515ae",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,2d05e826f5152fd0143edf7270de1235",
+                "multiqc_picard_baseContent.txt:md5,f3f23899a30a96260d8b5b3020708703",
+                "multiqc_picard_quality_by_cycle.txt:md5,c7edfc271ab59ecedad0ab046afd3563",
+                "multiqc_picard_quality_score_distribution.txt:md5,7fa89b52b8bc96dd1074aa07cb5a5a54",
+                "multiqc_seqfu_mqc.txt:md5,ff4ce1c88f39ed24a88bae0a861f75c8",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,c7edfc271ab59ecedad0ab046afd3563",
+                "picard_QualityScoreDistribution_histogram.txt:md5,7fa89b52b8bc96dd1074aa07cb5a5a54",
+                "picard_alignment_readlength_plot.txt:md5,c1519319c4942162b05e6225fea10569",
+                "picard_alignment_summary.txt:md5,49f5c0d2cf21a13d5f363cb42cf3790e",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,466a14fc9c09f9f4de02a00e8763cd2a",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,d5854c22df4ac60b8c47c4002d975fe9",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,c27b5aa2b90397b1302b880dff3ec958",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,6f2a3e9d03f17a93c69476607a1a580d",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,33b70326d8f888ac5a3d99b85f365e43",
+                "picard_quality_by_cycle.txt:md5,0aa028d69d8bb02f0a2bcd0ed08f4235",
+                "picard_quality_score_distribution.txt:md5,a2882ff59902dc95830ed4bdb955561a",
+                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
+                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
+                "Sample1_01_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6",
+                "Sample1_01_seqfu_mqc.txt:md5,24d99524ccd0e6c6255a69d68a871c7a",
+                "Sample23_03_seqfu.tsv:md5,6fac5d3dbce3f3bee72341fe99a399dc",
+                "Sample23_03_seqfu_mqc.txt:md5,4d4f280911a08bb6b753142980178027",
+                "SampleA_02_seqfu.tsv:md5,aec811f267bb2a0ef066a7abb59d2775",
+                "SampleA_02_seqfu_mqc.txt:md5,a819409a5cb64e20c3e54ec5ada4aa27",
+                "Undetermined_05_seqfu.tsv:md5,3a42c5c66a0a118f1a6f6f6e560b0e7e",
+                "Undetermined_05_seqfu_mqc.txt:md5,bd8be908362c5cb08a72f8ae7ab41b0d",
+                "sampletest_04_seqfu.tsv:md5,a5bea0b9c6015dd1a201ffd433e9b377",
+                "sampletest_04_seqfu_mqc.txt:md5,2180961655bbc8a12f0152d6a4b803a2",
+                "Sample1_01_Sample1_S1_L001_R1_001.fastq.gz:md5,9f2f4855422bd18576efbc8af0368517",
+                "Sample23_03_Sample23_S3_L001_R1_001.fastq.gz:md5,036238392d51face00be9710c0c14523",
+                "SampleA_02_SampleA_S2_L001_R1_001.fastq.gz:md5,bcc1ed324745e894356ff3b66d023156",
+                "Undetermined_05_Undetermined_S0_L001_R1_001.fastq.gz:md5,2d64ba05e69ae081f95581cc8f0ffd36",
+                "sampletest_04_sampletest_S4_L001_R1_001.fastq.gz:md5,e81c2337941970a3bafa2c0adf8bebb1"
+            ],
+            [
+                "WARN: Sample1_01: Requested sample_size (120) is larger than available reads (100). Pipeline will continue with 100 reads.",
+                "WARN: Sample23_03: Requested sample_size (120) is larger than available reads (100). Pipeline will continue with 100 reads.",
+                "WARN: SampleA_02: Requested sample_size (120) is larger than available reads (100). Pipeline will continue with 100 reads.",
+                "WARN: Undetermined_05: Requested sample_size (120) is larger than available reads (100). Pipeline will continue with 100 reads.",
+                "WARN: sampletest_04: Requested sample_size (120) is larger than available reads (100). Pipeline will continue with 100 reads."
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2025-12-12T11:09:26.248268345"
     }
 }
\ No newline at end of file
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 09a4c725..1d79a4f9 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -45,12 +45,12 @@ workflow SEQINSPECTOR {
     main:
 
 
-    ch_versions            = channel.empty()
-    ch_multiqc_files       = channel.empty()
+    ch_versions = channel.empty()
+    ch_multiqc_files = channel.empty()
     ch_multiqc_extra_files = channel.empty()
-    ch_bwamem2_mem         = channel.empty()
-    ch_samtools_index      = channel.empty()
-    ch_reference_fasta     = fasta_file ? channel.fromPath(fasta_file, checkIfExists: true).map { file -> tuple([id: file.name], file) }.collect() : channel.value([[:], []])
+    ch_bwamem2_mem = channel.empty()
+    ch_samtools_index = channel.empty()
+    ch_reference_fasta = fasta_file ? channel.fromPath(fasta_file, checkIfExists: true).map { file -> tuple([id: file.name], file) }.collect() : channel.value([[:], []])
 
     PREPARE_GENOME(
         ch_reference_fasta,
@@ -99,24 +99,24 @@ workflow SEQINSPECTOR {
                 [[id: "seqfu", sample_id: meta.id, tags: meta.tags], reads]
             }
         )
-        ch_seqfu_stats.stats.map { meta, stats -> {
-            // Parse the stats TSV file
-            [meta.sample_id, stats]
-        }}
-        .splitCsv(header: true, sep: '\t')
-        .map { sample_id, row ->
-            // Check if requested sample size exceeds available reads
-            def sample_reads = row['#Seq'].toInteger()
-            if (params.sample_size > sample_reads) {
-                // prntln is used here instead of log.warn/log.info as nf-test captures stdout
-                // from 'println' but buffers log messages making them unavailable for assertion
-                // This message will appear in .nextflow.log file and temporarily on runtime stdout.
-                println ("Warning: Requested sample_size (${params.sample_size}) " +
-                        "is larger than available reads in ${sample_id} (${sample_reads}). " +
-                        "Pipeline will continue with ${sample_reads} reads.")
+        ch_seqfu_stats.stats
+            .map { meta, stats ->
+                {
+                    // Parse the stats TSV file
+                    [meta.sample_id, stats]
+                }
+            }
+            .splitCsv(header: true, sep: '\t')
+            .map { sample_id, row ->
+                // Check if requested sample size exceeds available reads
+                def sample_reads = row['#Seq'].toInteger()
+                if (params.sample_size > sample_reads) {
+                    // prntln is used here instead of log.warn/log.info as nf-test captures stdout
+                    // from 'println' but buffers log messages making them unavailable for assertion
+                    // This message will appear in .nextflow.log file and temporarily on runtime stdout.
+                    log.warn("${sample_id}: Requested sample_size (${params.sample_size}) is larger than available reads (${sample_reads}). Pipeline will continue with ${sample_reads} reads.")
+                }
             }
-
-        }
         ch_multiqc_files = ch_multiqc_files.mix(SEQFU_STATS.out.multiqc)
         ch_versions = ch_versions.mix(SEQFU_STATS.out.versions.first())
     }
@@ -265,16 +265,14 @@ workflow SEQINSPECTOR {
     // Add index to other MultiQC reports
     //ch_multiqc_extra_files_global = Channel.empty()
     ch_multiqc_extra_files_global = ch_multiqc_extra_files.mix(
-        ch_tags.toList()
-            .map { tag_list ->
-                reportIndexMultiqc(tag_list)
-            }
-            .collectFile(
-                name: 'multiqc_index_mqc.yaml',
-            )
+        ch_tags.toList().map { tag_list ->
+            reportIndexMultiqc(tag_list)
+        }.collectFile(
+            name: 'multiqc_index_mqc.yaml'
+        )
     )
 
-    MULTIQC_GLOBAL (
+    MULTIQC_GLOBAL(
         ch_multiqc_files.map { _meta, file -> file }.mix(ch_multiqc_extra_files_global).collect(),
         ch_multiqc_config.toList(),
         [],
@@ -284,13 +282,11 @@ workflow SEQINSPECTOR {
     )
 
     ch_multiqc_extra_files_tag = ch_multiqc_extra_files.mix(
-        ch_tags.toList()
-            .map { tag_list ->
-                reportIndexMultiqc(tag_list, false)
-            }
-            .collectFile(
-                name: 'multiqc_index_mqc.yaml',
-            )
+        ch_tags.toList().map { tag_list ->
+            reportIndexMultiqc(tag_list, false)
+        }.collectFile(
+            name: 'multiqc_index_mqc.yaml'
+        )
     )
 
     multiqc_extra_files_per_tag = ch_tags.combine(ch_multiqc_extra_files_tag)

From c1576e2b687e21d072007f6e932d18f825e7ace7 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 12 Dec 2025 12:23:26 +0100
Subject: [PATCH 488/530] update snapshots

---
 tests/NovaSeq6000.main.nf.test.snap           |  101 +-
 tests/NovaSeq6000.main_subsample.nf.test.snap | 2066 ++++++++++++++++-
 2 files changed, 2063 insertions(+), 104 deletions(-)

diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index 3a81e90f..e7bac834 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -19,9 +19,6 @@
                     "PyYAML": "6.0.2",
                     "Python": "3.13.2"
                 },
-                "SAMTOOLS_FAIDX": {
-                    "samtools": "1.22.1"
-                },
                 "SAMTOOLS_INDEX": {
                     "samtools": "1.22.1"
                 },
@@ -793,14 +790,14 @@
                 "fastqc_sequence_duplication_levels_plot.txt:md5,f86012b3074d697c9a2b3bd67a074288",
                 "fastqc_sequence_length_distribution_plot.txt:md5,9d4fd245e8e1d5baa473a8bdffcd3e38",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
-                "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d",
+                "multiqc_fastq_screen.txt:md5,62240561100f78af37e7e2438cb58f90",
+                "multiqc_fastqc.txt:md5,23b698f1e957a26f49a9ad9bbdece908",
                 "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,5bdb2f162266ab68005cbfc0a45e311e",
-                "multiqc_picard_baseContent.txt:md5,409bf8ce546a573ce6678769b84726fd",
-                "multiqc_picard_quality_by_cycle.txt:md5,ebf56fd9b3b127ff41211e3f79f18b42",
-                "multiqc_picard_quality_score_distribution.txt:md5,182098ce1ff0a664d873c329d54189df",
-                "multiqc_seqfu.txt:md5,18dd2407d4a1791646785123028f69b5",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,b113ea40790fa45fa739f224f2710556",
+                "multiqc_picard_baseContent.txt:md5,e06c0dea80cb5cef312436e005aa0095",
+                "multiqc_picard_quality_by_cycle.txt:md5,6e13ddbd97caa0eaa52c118966e5f9fa",
+                "multiqc_picard_quality_score_distribution.txt:md5,39d3430744e9139020d7af3eb15fc629",
+                "multiqc_seqfu_mqc.txt:md5,18dd2407d4a1791646785123028f69b5",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram_1.txt:md5,6e13ddbd97caa0eaa52c118966e5f9fa",
@@ -826,14 +823,14 @@
                 "fastqc_sequence_duplication_levels_plot.txt:md5,818f13a5372bad79e54cd984758096c5",
                 "fastqc_sequence_length_distribution_plot.txt:md5,98316a2607a889ae1e7e79a4f64cc740",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
-                "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
+                "multiqc_fastq_screen.txt:md5,024e1e7f9db3b0906c7aa0904229e176",
+                "multiqc_fastqc.txt:md5,3407d8f06117a65efce4c70f19e91dd1",
                 "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,e4cb1b13e6a7298d172ed112a0479b5a",
-                "multiqc_picard_baseContent.txt:md5,740592a5858706d2b4b8f585a1d5492b",
-                "multiqc_picard_quality_by_cycle.txt:md5,c3f14084aedc511b9f0aa8410e7cb3b5",
-                "multiqc_picard_quality_score_distribution.txt:md5,59b955203209cfab3d2d21bdfe20997e",
-                "multiqc_seqfu.txt:md5,6cdb863a3686fbb772aae5a66925ff23",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,1debd96f9f64c60a8ec742411da51a28",
+                "multiqc_picard_baseContent.txt:md5,afb4046944e302b40faea2233bca535c",
+                "multiqc_picard_quality_by_cycle.txt:md5,6a7552b74dd22410c3cab2c750de792e",
+                "multiqc_picard_quality_score_distribution.txt:md5,d6343c5f39942bc3f10c194067e6e9bc",
+                "multiqc_seqfu_mqc.txt:md5,6cdb863a3686fbb772aae5a66925ff23",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram_1.txt:md5,6a7552b74dd22410c3cab2c750de792e",
@@ -859,14 +856,14 @@
                 "fastqc_sequence_duplication_levels_plot.txt:md5,8fc995cb2192a2926eee242681bc3af6",
                 "fastqc_sequence_length_distribution_plot.txt:md5,4513e22583677a4d6167b9094242eb0b",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
-                "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
+                "multiqc_fastq_screen.txt:md5,fd3074930c72b666f201ae71fa27744b",
+                "multiqc_fastqc.txt:md5,98111f17d1899cad6379e4e56ed11c53",
                 "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,d4e63eed820edcc71b3e37d793983bd7",
-                "multiqc_picard_baseContent.txt:md5,0dd5fa539e4034e3539fb1e7068c7ce5",
-                "multiqc_picard_quality_by_cycle.txt:md5,750eadc27875fc8141b64a90789c369f",
-                "multiqc_picard_quality_score_distribution.txt:md5,140279eb5abac364c4d4c417105da620",
-                "multiqc_seqfu.txt:md5,f821357507fda2d4cfd9299f52fa7dc1",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,3b1929de09267fc1c1a15804cb5bf536",
+                "multiqc_picard_baseContent.txt:md5,ff36be9e2642089aa711c637d3cdba29",
+                "multiqc_picard_quality_by_cycle.txt:md5,9521c83313eaf5f681ac9a75de83a4b7",
+                "multiqc_picard_quality_score_distribution.txt:md5,90b9e29f22fa16cf2b0c4d92caf2dbb0",
+                "multiqc_seqfu_mqc.txt:md5,f821357507fda2d4cfd9299f52fa7dc1",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram_1.txt:md5,9521c83313eaf5f681ac9a75de83a4b7",
@@ -892,14 +889,14 @@
                 "fastqc_sequence_duplication_levels_plot.txt:md5,9ff0df466790d971b3c7ef838efc0f4f",
                 "fastqc_sequence_length_distribution_plot.txt:md5,9fda632b92e3453f11cd0226484fce8e",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
-                "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
+                "multiqc_fastq_screen.txt:md5,536c28d7fadc9a76944f93ac9d643272",
+                "multiqc_fastqc.txt:md5,396b4cc0466a6642ec8b954237c42263",
                 "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,22093b80f335c4c53633b01a930157f4",
-                "multiqc_picard_baseContent.txt:md5,6886e1e5179031ddba4958f301930d64",
-                "multiqc_picard_quality_by_cycle.txt:md5,96652e2e2d693488df9104e5ae8cb4a7",
-                "multiqc_picard_quality_score_distribution.txt:md5,879a4470d08fe6d9b1796f46020fb5f5",
-                "multiqc_seqfu.txt:md5,8cced36d66ca9d25d60c006e734aa7e9",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,153c6e6a407ec128b1a02798ca2f1115",
+                "multiqc_picard_baseContent.txt:md5,6349e514552a0b5a0530fa6f311878a5",
+                "multiqc_picard_quality_by_cycle.txt:md5,c0c8b4c0197428d4d50e2c532814e1e2",
+                "multiqc_picard_quality_score_distribution.txt:md5,40e0b6faa75e1b51af42407f7ededb0c",
+                "multiqc_seqfu_mqc.txt:md5,8cced36d66ca9d25d60c006e734aa7e9",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram_1.txt:md5,c0c8b4c0197428d4d50e2c532814e1e2",
@@ -925,27 +922,27 @@
                 "fastqc_sequence_duplication_levels_plot.txt:md5,fbe41935ea2e2faf7104393b476e5ac5",
                 "fastqc_sequence_length_distribution_plot.txt:md5,e77dc4ab73252c2e09c7452c3b8e8ab3",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5",
-                "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
+                "multiqc_fastq_screen.txt:md5,4fc422d9cb06a1d0248cc578c1eebaa2",
+                "multiqc_fastqc.txt:md5,95c8ffb23baafec625aeb600047515ae",
                 "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,edf7faad1da9922fdc692e9cba5cc0c4",
-                "multiqc_picard_baseContent.txt:md5,9631916c0a9a736811c47ab4c476428f",
-                "multiqc_picard_quality_by_cycle.txt:md5,9e05b241aabe39232b5182cb59d8edd5",
-                "multiqc_picard_quality_score_distribution.txt:md5,e9c3ade201964470d2d22569a400fa49",
-                "multiqc_seqfu.txt:md5,ff4ce1c88f39ed24a88bae0a861f75c8",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,2d05e826f5152fd0143edf7270de1235",
+                "multiqc_picard_baseContent.txt:md5,f3f23899a30a96260d8b5b3020708703",
+                "multiqc_picard_quality_by_cycle.txt:md5,c7edfc271ab59ecedad0ab046afd3563",
+                "multiqc_picard_quality_score_distribution.txt:md5,7fa89b52b8bc96dd1074aa07cb5a5a54",
+                "multiqc_seqfu_mqc.txt:md5,ff4ce1c88f39ed24a88bae0a861f75c8",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,9e05b241aabe39232b5182cb59d8edd5",
-                "picard_QualityScoreDistribution_histogram.txt:md5,e9c3ade201964470d2d22569a400fa49",
-                "picard_alignment_readlength_plot.txt:md5,c2692fde9d899ad61297ad7043fd26b9",
-                "picard_alignment_summary.txt:md5,5996d5b4c94f16c0efd42e2df47e021e",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,a2670974dc96ad8a54f9cc5ae3e09d5e",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,d3b9cc0c99f96814348b57809cf227fb",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,1ba086d3fb2676868e8e7b20f55975dc",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,8902976984741320fe06004f4115c4f4",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,1380831484d1b069a2fd4a20437118bf",
-                "picard_quality_by_cycle.txt:md5,b6fc46e18ac875ba02775e7cbf1b8e8b",
-                "picard_quality_score_distribution.txt:md5,1c17c01ef54a6062a8f1ca8408d32958",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,c7edfc271ab59ecedad0ab046afd3563",
+                "picard_QualityScoreDistribution_histogram.txt:md5,7fa89b52b8bc96dd1074aa07cb5a5a54",
+                "picard_alignment_readlength_plot.txt:md5,c1519319c4942162b05e6225fea10569",
+                "picard_alignment_summary.txt:md5,49f5c0d2cf21a13d5f363cb42cf3790e",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,466a14fc9c09f9f4de02a00e8763cd2a",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,d5854c22df4ac60b8c47c4002d975fe9",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,c27b5aa2b90397b1302b880dff3ec958",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,6f2a3e9d03f17a93c69476607a1a580d",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,33b70326d8f888ac5a3d99b85f365e43",
+                "picard_quality_by_cycle.txt:md5,0aa028d69d8bb02f0a2bcd0ed08f4235",
+                "picard_quality_score_distribution.txt:md5,a2882ff59902dc95830ed4bdb955561a",
                 "200624_A00834_0183_BHMTFYDRXX_illumina_mqc.yml:md5,29e05fed18bca0e9a857c992b6d59a40",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
@@ -962,9 +959,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.10.0"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-11-25T10:22:20.735912684"
+        "timestamp": "2025-12-12T11:44:10.238711124"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index 34a11787..6ed75de7 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -19,9 +19,6 @@
                     "PyYAML": "6.0.2",
                     "Python": "3.13.2"
                 },
-                "SAMTOOLS_FAIDX": {
-                    "samtools": "1.22.1"
-                },
                 "SAMTOOLS_INDEX": {
                     "samtools": "1.22.1"
                 },
@@ -802,14 +799,14 @@
                 "fastqc_sequence_duplication_levels_plot.txt:md5,5ec69b2a7fc7aff792ad62a840006740",
                 "fastqc_sequence_length_distribution_plot.txt:md5,b0e3de7190755ce83680ac0f1357cfce",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
-                "multiqc_fastqc.txt:md5,aba942d1e6996b579f19798e5673f514",
+                "multiqc_fastq_screen.txt:md5,5af2d6080364385c05d50f9ffa7996e6",
+                "multiqc_fastqc.txt:md5,a9a9fc06badaade2d09486d2adaac1ce",
                 "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,ae3f9e644215ac39d2eae114bd52a517",
-                "multiqc_picard_baseContent.txt:md5,8b2efc3fa06d2013348b35f9607292aa",
-                "multiqc_picard_quality_by_cycle.txt:md5,c2774038d1a0142746426e46f9f954dd",
-                "multiqc_picard_quality_score_distribution.txt:md5,792755ee794d375b85a57f58d879f0c6",
-                "multiqc_seqfu.txt:md5,18dd2407d4a1791646785123028f69b5",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,27ac8815e031784c1928f8ff7d2e8687",
+                "multiqc_picard_baseContent.txt:md5,b8f3650cf18daa57ae2b67c5b89f5b8b",
+                "multiqc_picard_quality_by_cycle.txt:md5,ea8e2268c7b00c60221ff0166abcb8e6",
+                "multiqc_picard_quality_score_distribution.txt:md5,2d6a03019d78184e380a667425edba69",
+                "multiqc_seqfu_mqc.txt:md5,18dd2407d4a1791646785123028f69b5",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram_1.txt:md5,ea8e2268c7b00c60221ff0166abcb8e6",
@@ -835,14 +832,14 @@
                 "fastqc_sequence_duplication_levels_plot.txt:md5,818f13a5372bad79e54cd984758096c5",
                 "fastqc_sequence_length_distribution_plot.txt:md5,891980cbbd9f0ce86072e49eaa19dbb2",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
-                "multiqc_fastqc.txt:md5,ff996e1d3dc4a46e0c9535e54d51ccab",
+                "multiqc_fastq_screen.txt:md5,14d33a39b52346515edfd7e8542e5c7b",
+                "multiqc_fastqc.txt:md5,e87c99cac0c4956521d9c660183722bb",
                 "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,7bc3f6ef8f47e6f1e060f957025c98aa",
-                "multiqc_picard_baseContent.txt:md5,1426865fe8ee1a36f67636c28500a91c",
-                "multiqc_picard_quality_by_cycle.txt:md5,79bf9f861077de70ec28c9af01783876",
-                "multiqc_picard_quality_score_distribution.txt:md5,a3f8d1937e1f118800aa3d86c1b498c4",
-                "multiqc_seqfu.txt:md5,6cdb863a3686fbb772aae5a66925ff23",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,4caf3948c2fd99d795c1f6791221a02d",
+                "multiqc_picard_baseContent.txt:md5,fc5eec99f1406d05416315bb83c22efa",
+                "multiqc_picard_quality_by_cycle.txt:md5,0a23446d732f70734fbb75d2d8c4f8c5",
+                "multiqc_picard_quality_score_distribution.txt:md5,fff3e05748b15f8e70603f2de052bc1e",
+                "multiqc_seqfu_mqc.txt:md5,6cdb863a3686fbb772aae5a66925ff23",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram_1.txt:md5,0a23446d732f70734fbb75d2d8c4f8c5",
@@ -868,14 +865,14 @@
                 "fastqc_sequence_duplication_levels_plot.txt:md5,d5b06e963d0eb6f8013aa3070551305d",
                 "fastqc_sequence_length_distribution_plot.txt:md5,4101ced76bfe16e3baec15f7c8afaea7",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
-                "multiqc_fastqc.txt:md5,3df36ecfe76b25b0c22dcda84bce2b3b",
+                "multiqc_fastq_screen.txt:md5,179b14566daf82ccd294f54443cf9b5e",
+                "multiqc_fastqc.txt:md5,8b808265a3cfe52846f7d6a0c9624beb",
                 "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,4dc89e1a04843d44695ecc8d1f047ee8",
-                "multiqc_picard_baseContent.txt:md5,0a5f9d32dd3061ce4349518c47d69838",
-                "multiqc_picard_quality_by_cycle.txt:md5,ec59b472afc1242ff299011ba456e792",
-                "multiqc_picard_quality_score_distribution.txt:md5,1b8be76b60ee71aa36a98d34e433b9bf",
-                "multiqc_seqfu.txt:md5,f821357507fda2d4cfd9299f52fa7dc1",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,097425295aec6d2235b3ce2efdeadc2f",
+                "multiqc_picard_baseContent.txt:md5,e866142c080aadf520f3533344b078f7",
+                "multiqc_picard_quality_by_cycle.txt:md5,f90049902134e9d526de1e9e7c9b630a",
+                "multiqc_picard_quality_score_distribution.txt:md5,c5cd2b47144a9bdc8e4ec738bb7cf2f1",
+                "multiqc_seqfu_mqc.txt:md5,f821357507fda2d4cfd9299f52fa7dc1",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram_1.txt:md5,f90049902134e9d526de1e9e7c9b630a",
@@ -901,14 +898,14 @@
                 "fastqc_sequence_duplication_levels_plot.txt:md5,6f0891980501631a27a7375d2ec7a30d",
                 "fastqc_sequence_length_distribution_plot.txt:md5,b5bf616360fc7df8fb94b2a4928660cb",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
-                "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8",
+                "multiqc_fastq_screen.txt:md5,a84c2882a4ab93afd9599c7aebf3e897",
+                "multiqc_fastqc.txt:md5,b8f6f4ed32e60ff57c64bb0ba029adba",
                 "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,fa26e8b96faa1926d8f41fc3fe959ff7",
-                "multiqc_picard_baseContent.txt:md5,b9d72d8173cdc7649b44b80aa485477c",
-                "multiqc_picard_quality_by_cycle.txt:md5,062547fb888ed508dd1d5733d7bed22e",
-                "multiqc_picard_quality_score_distribution.txt:md5,dd5abab3a7141654fffa3946c50a039b",
-                "multiqc_seqfu.txt:md5,8cced36d66ca9d25d60c006e734aa7e9",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,a830b94cf4b094f6914927a93b4911f3",
+                "multiqc_picard_baseContent.txt:md5,c4b2e49d32ab00ffd166fb2343362300",
+                "multiqc_picard_quality_by_cycle.txt:md5,86934e1b1aee498e3434475f54e49c18",
+                "multiqc_picard_quality_score_distribution.txt:md5,a2f554d6121a1be2623fe67edb69b3db",
+                "multiqc_seqfu_mqc.txt:md5,8cced36d66ca9d25d60c006e734aa7e9",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram_1.txt:md5,86934e1b1aee498e3434475f54e49c18",
@@ -934,27 +931,27 @@
                 "fastqc_sequence_duplication_levels_plot.txt:md5,3f319b383f827362a515ebb9eee9ddcf",
                 "fastqc_sequence_length_distribution_plot.txt:md5,a0b2aff6415e2365c8f1a28d300b0fbc",
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5",
-                "multiqc_fastqc.txt:md5,ce61b4ce4b1d76ec3f20de3bf0c9ec7f",
+                "multiqc_fastq_screen.txt:md5,db504d3eec12c5431e2b66d4880beb66",
+                "multiqc_fastqc.txt:md5,284597d876abc5a1242d8efb2d69f0d5",
                 "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,55627d8016b72c37c104e03cc156862c",
-                "multiqc_picard_baseContent.txt:md5,974d83faa49711ab4ea1248c59e69393",
-                "multiqc_picard_quality_by_cycle.txt:md5,248ecaf269d8fef1e84ea06f98b6f6ba",
-                "multiqc_picard_quality_score_distribution.txt:md5,5e7e80654e12c500b15f8564ffb12b27",
-                "multiqc_seqfu.txt:md5,ff4ce1c88f39ed24a88bae0a861f75c8",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,b9175f19bb7881a189d0f061089ee090",
+                "multiqc_picard_baseContent.txt:md5,fdfa6dc50f83f3966bc33caf796dddda",
+                "multiqc_picard_quality_by_cycle.txt:md5,28ba1f3017af64453cd191cf6f895e17",
+                "multiqc_picard_quality_score_distribution.txt:md5,60c5f167421d5b44c3b1ed810b5a68cd",
+                "multiqc_seqfu_mqc.txt:md5,ff4ce1c88f39ed24a88bae0a861f75c8",
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,248ecaf269d8fef1e84ea06f98b6f6ba",
-                "picard_QualityScoreDistribution_histogram.txt:md5,5e7e80654e12c500b15f8564ffb12b27",
-                "picard_alignment_readlength_plot.txt:md5,23ff551a5a8eded1857356f38b19039c",
-                "picard_alignment_summary.txt:md5,c741b69e17ed84370732b567ae11c69c",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,fc37dd1ac805881a467b264a7dd76677",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,7993fd56aa542b71bc984cd36c489fd1",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,1bca639db2a2624727f7b6dd2aa1442e",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,a5f0903d77b6060676f7dda249b99738",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,102e653a543ac908ac9ec9b86412d73b",
-                "picard_quality_by_cycle.txt:md5,3d43fd5387c0dc728833c681ea4f73cc",
-                "picard_quality_score_distribution.txt:md5,9d9f1bb12316175cdb88d3ff70305428",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,28ba1f3017af64453cd191cf6f895e17",
+                "picard_QualityScoreDistribution_histogram.txt:md5,60c5f167421d5b44c3b1ed810b5a68cd",
+                "picard_alignment_readlength_plot.txt:md5,2bc1a0718665c2038c82c662744efd32",
+                "picard_alignment_summary.txt:md5,036000570a5d0e3a5fb695f64170d33d",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,800b43f6b0261fb7fa3830deed4b7b7f",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,8f0148e5b112d7e65512f46b5c444e1b",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,ffd09932248cef230e27d55d548b87f8",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,b08bf6e3c5cfc18251c6c9546e82a616",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,6c30458ebd6caa1a2867bc999bafedd5",
+                "picard_quality_by_cycle.txt:md5,4103c8c916ece5f57dbeffc477025d94",
+                "picard_quality_score_distribution.txt:md5,0a04dad54cadfd660c935af9a0658e0c",
                 "200624_A00834_0183_BHMTFYDRXX_illumina_mqc.yml:md5,29e05fed18bca0e9a857c992b6d59a40",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
@@ -976,9 +973,1974 @@
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+            "nf-test": "0.9.3",
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+        "timestamp": "2025-12-12T11:45:23.711988389"
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+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,963af5ca1c83a87e9eb8396c60ca0185",
+                "multiqc_picard_baseContent.txt:md5,7ed6695c5554f6f1551f2567f308ea01",
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+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,8299530bdcc6341bf87d8b3a344f1b35",
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+                "picard_base_distribution_by_cycle__Adenine.txt:md5,da954ca1a4904484c5561b5559780670",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,ff364d12f449a7fc7ec6e4f747376235",
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+                "picard_base_distribution_by_cycle__Thymine.txt:md5,e64e5c05cc4488dc316502b8ecd34c05",
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+                "fastqc_per_base_n_content_plot.txt:md5,3f90107f654e11e85265fefc5ea7bfa3",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,95e20e90d3009301f5938b3400c75787",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,ed4e531f1129963b0a4d75e3cff31019",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,97caa54b010c1938d5ad91ff993cad49",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,824305a7c50b0c27b47bdf627cedf8c4",
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+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,a8164399dfbc104ec98f0590d506f557",
+                "multiqc_picard_baseContent.txt:md5,2f35f7d55e96e55a97bab9a9509072f8",
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+                "multiqc_seqfu_mqc.txt:md5,6cdb863a3686fbb772aae5a66925ff23",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,41de636e329213c91de9811bcfacd1e1",
+                "picard_QualityScoreDistribution_histogram.txt:md5,502b9469dea25bc742ae2016c2f62417",
+                "picard_alignment_readlength_plot.txt:md5,8f31687d3b34bc7ea4ff5fd24f39c935",
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+                "picard_base_distribution_by_cycle__Adenine.txt:md5,7bf9ef30e9e9de4a061190089b122b85",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,30c7748d6128a8263934dec183372553",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,9ad713d707d22ce4232713efe4e2fbc2",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,4d62d177c9d05fa955042bc976940870",
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+                "picard_quality_score_distribution.txt:md5,b811a5ed7a63dba9b9514a27c8ac1ee1",
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+                "fastqc_overrepresented_sequences_plot.txt:md5,f85a8412d1b545dd1c1c86eb5053fb98",
+                "fastqc_per_base_n_content_plot.txt:md5,46bdea04a02e1458de0bc6b578154d55",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,69919505d6b604c691d74f1ed42277a6",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,d0d632d38536b19bc97f5ac62b444863",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,47304e11e4c0fd1c8c8042df11dca5db",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,0ff9eb3250403c1f9a9df4b6b82a22aa",
+                "fastqc_sequence_counts_plot.txt:md5,d5cfb1e359dba2b44d2b7fa472bc2fef",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,10ae6381263604eab5230d7396d9a321",
+                "fastqc_sequence_length_distribution_plot.txt:md5,d2f42e0ede5e36df74217d1b23365d99",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,fdf61b67296d4629c8efe9d1fb3d3ec0",
+                "multiqc_fastqc.txt:md5,bece629be078da2fb5dfe3e2b27be025",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,21a9dbbdd953f7ebb6c033ba306e1a01",
+                "multiqc_picard_baseContent.txt:md5,9b901100401ce73e796855de065df5af",
+                "multiqc_picard_quality_by_cycle.txt:md5,016dbbf3b0be86e17414a77c8e7c0381",
+                "multiqc_picard_quality_score_distribution.txt:md5,baf6e77f157dcc1996f3aa8db9da5b56",
+                "multiqc_seqfu_mqc.txt:md5,f821357507fda2d4cfd9299f52fa7dc1",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,016dbbf3b0be86e17414a77c8e7c0381",
+                "picard_QualityScoreDistribution_histogram.txt:md5,baf6e77f157dcc1996f3aa8db9da5b56",
+                "picard_alignment_readlength_plot.txt:md5,ee5232cd541865ddde9fc932d1130024",
+                "picard_alignment_summary.txt:md5,31198f074051b795b593abebb83d37fc",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,9dc845e9ec5f5fb741910c264040cc20",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,2f0b3650a527e493d5453f2e553aa672",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,163cccc75b8cdd52a944ae6aeb310148",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,9e8533969c84fff8f21b0a59745b344d",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,9c6f5a8fc79aff21f2bc8275e1970478",
+                "picard_quality_by_cycle.txt:md5,a91bd8ec5591b7691be3413de26a76f9",
+                "picard_quality_score_distribution.txt:md5,b3936076ba1dec38ebfed4b03683e25d",
+                "fastq_screen_plot.txt:md5,54da156526832b95f4ebcb8544a87f77",
+                "fastqc-status-check-heatmap.txt:md5,c762f9c764ff99a610ff1d20f2ed6ac9",
+                "fastqc_overrepresented_sequences_plot.txt:md5,c304e2ee82e3fd480a9261ac768f98b3",
+                "fastqc_per_base_n_content_plot.txt:md5,c91a58eb10a898afb7b46a7dd8e72e8e",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,3930d07c38244edfeaa3ef909e1d4ac6",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,939f27bfae0d13cbbc85ff87e1b3d0ac",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,0d2925e3cbbb6de2c7ec034c26f41066",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,4569ebf563c3fdb3b7bef648f72f3006",
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+                "fastqc_sequence_duplication_levels_plot.txt:md5,a25fb5ca8e2082719e7129975e7f8b10",
+                "fastqc_sequence_length_distribution_plot.txt:md5,97c4a389f0e3622c699809ef7aab1b6e",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,43cd2cbe48a7e1b8243ee157ae5e5a51",
+                "multiqc_fastqc.txt:md5,82b45154efad92fa6566283f39459d23",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,16327d839dfc8bf38c43945fe6b6b1df",
+                "multiqc_picard_baseContent.txt:md5,41dee821ab6f6aee05ded4bf41accd56",
+                "multiqc_picard_quality_by_cycle.txt:md5,0af7938734a17202d944927b64904da0",
+                "multiqc_picard_quality_score_distribution.txt:md5,2864d590f88cb98bd0c8446f1b023704",
+                "multiqc_seqfu_mqc.txt:md5,8cced36d66ca9d25d60c006e734aa7e9",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,0af7938734a17202d944927b64904da0",
+                "picard_QualityScoreDistribution_histogram.txt:md5,2864d590f88cb98bd0c8446f1b023704",
+                "picard_alignment_readlength_plot.txt:md5,d2a5ee7fc76fc836dd81f12954f01887",
+                "picard_alignment_summary.txt:md5,cd27671e33d03c39be8fdd1e2b4e0246",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,282d6515ae71162568393cb28407d690",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,8693a806def68f65092dfa13542ab364",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,05f621a1fbbf2164522bc7cbe8790120",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,bf1889ea4e03ad99640dc408dde567ac",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,72f6425cec7b1e9851b252c43764d716",
+                "picard_quality_by_cycle.txt:md5,2ccee1b2cead246a4e784b15eac28361",
+                "picard_quality_score_distribution.txt:md5,9b79b5de2293427df2add8cffe505f06",
+                "fastq_screen_plot.txt:md5,70fc7c0be8d24dffcff69dd216345a07",
+                "fastqc-status-check-heatmap.txt:md5,56b426cd5c030288639533fce7c95ab1",
+                "fastqc_overrepresented_sequences_plot.txt:md5,04fc7769d72ff4af8bf5679944a4a875",
+                "fastqc_per_base_n_content_plot.txt:md5,e09d3616e0bb7a50f851736de22cdb85",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,2138b44091c3e1d237917e77b320e157",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,f44cfb45f4a6b980008e9c758ab0a5f4",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,c8b50edb245a50ab0f471d723ecd3f0e",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,5dbc12d86b28d93a2c9ce8067674c849",
+                "fastqc_sequence_counts_plot.txt:md5,0fac11b09160c9b8cd61721fafaab7a1",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,e2426a601d1706cd4e4ece85632d179a",
+                "fastqc_sequence_length_distribution_plot.txt:md5,59468fb5e62b89649b66a5410be3ce25",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,94e64655d6d0be2fb2d597f33e555615",
+                "multiqc_fastqc.txt:md5,6b3715a6c7f8c2d0657e7fd6e971a421",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,edacee934f1117cde82eaf7c54558c6d",
+                "multiqc_picard_baseContent.txt:md5,1b238999a80cf0a2d3777bdf6874afcb",
+                "multiqc_picard_quality_by_cycle.txt:md5,ec4ad84c72e43ce0b4f700da56f6de8c",
+                "multiqc_picard_quality_score_distribution.txt:md5,c976a39d5e24cc258fea812e43d2c512",
+                "multiqc_seqfu_mqc.txt:md5,ff4ce1c88f39ed24a88bae0a861f75c8",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,ec4ad84c72e43ce0b4f700da56f6de8c",
+                "picard_QualityScoreDistribution_histogram.txt:md5,c976a39d5e24cc258fea812e43d2c512",
+                "picard_alignment_readlength_plot.txt:md5,afcd9e8705eda64d2ea69af9be869329",
+                "picard_alignment_summary.txt:md5,dc2f8e760319c0c830d94edf5d38c38b",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,4c7f4d29723c6150e9b097fa7504b36f",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,2f7d64788fb4f41a785893d7f296ca63",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,149c92b3d1c3fc803efffc65582bd8b8",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,a09370dc408e9e5c1da16b2319a054f1",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,67acf7df200cb6b206d34b969eeccc08",
+                "picard_quality_by_cycle.txt:md5,88056bf0ffc3f2296b57217133244b20",
+                "picard_quality_score_distribution.txt:md5,65f7be51589f047c63fe05151a8fbde4",
+                "200624_A00834_0183_BHMTFYDRXX_illumina_mqc.yml:md5,29e05fed18bca0e9a857c992b6d59a40",
+                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
+                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
+                "Sample1_01_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6",
+                "Sample1_01_seqfu_mqc.txt:md5,24d99524ccd0e6c6255a69d68a871c7a",
+                "Sample23_03_seqfu.tsv:md5,6fac5d3dbce3f3bee72341fe99a399dc",
+                "Sample23_03_seqfu_mqc.txt:md5,4d4f280911a08bb6b753142980178027",
+                "SampleA_02_seqfu.tsv:md5,aec811f267bb2a0ef066a7abb59d2775",
+                "SampleA_02_seqfu_mqc.txt:md5,a819409a5cb64e20c3e54ec5ada4aa27",
+                "Undetermined_05_seqfu.tsv:md5,3a42c5c66a0a118f1a6f6f6e560b0e7e",
+                "Undetermined_05_seqfu_mqc.txt:md5,bd8be908362c5cb08a72f8ae7ab41b0d",
+                "sampletest_04_seqfu.tsv:md5,a5bea0b9c6015dd1a201ffd433e9b377",
+                "sampletest_04_seqfu_mqc.txt:md5,2180961655bbc8a12f0152d6a4b803a2",
+                "Sample1_01_Sample1_S1_L001_R1_001.fastq.gz:md5,e854f09ef7962d979be12981fe2fae8d",
+                "Sample23_03_Sample23_S3_L001_R1_001.fastq.gz:md5,1c96eae617f92f81abe08eaccfa02e11",
+                "SampleA_02_SampleA_S2_L001_R1_001.fastq.gz:md5,f7897b87d06b13e9877f297169a678f1",
+                "Undetermined_05_Undetermined_S0_L001_R1_001.fastq.gz:md5,c9e790094f5c2b2bad247ae96f804d1e",
+                "sampletest_04_sampletest_S4_L001_R1_001.fastq.gz:md5,e35f5e6cd500f18ce05cc061fb471a76"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2025-12-12T11:46:34.325054847"
+    },
+    "NovaSeq6000 data test sample size exceeds available reads": {
+        "content": [
+            {
+                "BWAMEM2_MEM": {
+                    "bwamem2": "2.2.1",
+                    "samtools": "1.22.1"
+                },
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "FASTQSCREEN_FASTQSCREEN": {
+                    "fastqscreen": "0.16.0"
+                },
+                "PICARD_COLLECTMULTIPLEMETRICS": {
+                    "picard": "3.4.0"
+                },
+                "RUNDIRPARSER": {
+                    "PyYAML": "6.0.2",
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+                "fastqc_sequence_length_distribution_plot.txt:md5,9d4fd245e8e1d5baa473a8bdffcd3e38",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,62240561100f78af37e7e2438cb58f90",
+                "multiqc_fastqc.txt:md5,23b698f1e957a26f49a9ad9bbdece908",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,b113ea40790fa45fa739f224f2710556",
+                "multiqc_picard_baseContent.txt:md5,e06c0dea80cb5cef312436e005aa0095",
+                "multiqc_picard_quality_by_cycle.txt:md5,6e13ddbd97caa0eaa52c118966e5f9fa",
+                "multiqc_picard_quality_score_distribution.txt:md5,39d3430744e9139020d7af3eb15fc629",
+                "multiqc_seqfu_mqc.txt:md5,18dd2407d4a1791646785123028f69b5",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,6e13ddbd97caa0eaa52c118966e5f9fa",
+                "picard_QualityScoreDistribution_histogram.txt:md5,39d3430744e9139020d7af3eb15fc629",
+                "picard_alignment_readlength_plot.txt:md5,57ee2de637b69efc49290bb5d4b57905",
+                "picard_alignment_summary.txt:md5,3fee23a738a44ee84592cb1144b32775",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,dfb9e50700b61cdbc0344690db202559",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,5eec2a9bbb5db321c7cbbbee26d90357",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,5b100b42e93792fed754deb276645e61",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,d0317fe5ef2cf1b692526cb9a18aa50c",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,8aafe701b59b4e70ccec86748c7d6eb3",
+                "picard_quality_by_cycle.txt:md5,366ee22c93a11c1335f867020bb03da5",
+                "picard_quality_score_distribution.txt:md5,17d6f490cb59e16a7ed4b04ffaa1a100",
+                "fastq_screen_plot.txt:md5,db7c9231e756a6e5999399a7385e4687",
+                "fastqc-status-check-heatmap.txt:md5,fc37eaf184877ac80b92001a7bf2fa81",
+                "fastqc_overrepresented_sequences_plot.txt:md5,0693849fc324ddf580e2c5a4d910bb4f",
+                "fastqc_per_base_n_content_plot.txt:md5,0ed7f750b500e7c5387ea5309e1ef467",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,18016152915653e812818194a142e162",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,93f664e18c021aae79ad222fb4cfb393",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,ba96762be2aa842e1d2a606095ffcb7e",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,b9044bfe90fd5685137739f52a97ee2c",
+                "fastqc_sequence_counts_plot.txt:md5,42b26ad3758717659763c81852c4f197",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,818f13a5372bad79e54cd984758096c5",
+                "fastqc_sequence_length_distribution_plot.txt:md5,98316a2607a889ae1e7e79a4f64cc740",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,024e1e7f9db3b0906c7aa0904229e176",
+                "multiqc_fastqc.txt:md5,3407d8f06117a65efce4c70f19e91dd1",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,1debd96f9f64c60a8ec742411da51a28",
+                "multiqc_picard_baseContent.txt:md5,afb4046944e302b40faea2233bca535c",
+                "multiqc_picard_quality_by_cycle.txt:md5,6a7552b74dd22410c3cab2c750de792e",
+                "multiqc_picard_quality_score_distribution.txt:md5,d6343c5f39942bc3f10c194067e6e9bc",
+                "multiqc_seqfu_mqc.txt:md5,6cdb863a3686fbb772aae5a66925ff23",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,6a7552b74dd22410c3cab2c750de792e",
+                "picard_QualityScoreDistribution_histogram.txt:md5,d6343c5f39942bc3f10c194067e6e9bc",
+                "picard_alignment_readlength_plot.txt:md5,01140e65e813b4ae43aabe662ef2f49a",
+                "picard_alignment_summary.txt:md5,79312cf30761025cc6902811c4165290",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,3c3671ac2aa18d883691d59adbfe3b2b",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,6cc2ae1411899de5542321ff1592b192",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,326471bc846a9fb6b54ff38cbdfb8d90",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,3132dac406a9b9e1f18af658ab856a5c",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,0ed7f750b500e7c5387ea5309e1ef467",
+                "picard_quality_by_cycle.txt:md5,fe4e6ab1c849a4f833eae9a8554ea432",
+                "picard_quality_score_distribution.txt:md5,c0864f8a1269d8ffd7a51abb6bd3ca2e",
+                "fastq_screen_plot.txt:md5,4def6c6a888afe487ab6ebef3ba8a133",
+                "fastqc-status-check-heatmap.txt:md5,61857d2c45cf0c080348047aa34e7525",
+                "fastqc_overrepresented_sequences_plot.txt:md5,7949c64cc6cef77f29349a188fc09656",
+                "fastqc_per_base_n_content_plot.txt:md5,0f2fd628631d42ed5e6a1db22578daaa",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,0a8bfa32ab04eaaa509dec3c37acb2d2",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,8c85be0c70129ba739feceddd58f6c75",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,94b975906d8a07e1604e00d4004f7463",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,ec22c8e4836aa726680f0ca767c778a0",
+                "fastqc_sequence_counts_plot.txt:md5,f4341795bdeba588248a74a095a97f8d",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,8fc995cb2192a2926eee242681bc3af6",
+                "fastqc_sequence_length_distribution_plot.txt:md5,4513e22583677a4d6167b9094242eb0b",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,fd3074930c72b666f201ae71fa27744b",
+                "multiqc_fastqc.txt:md5,98111f17d1899cad6379e4e56ed11c53",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,3b1929de09267fc1c1a15804cb5bf536",
+                "multiqc_picard_baseContent.txt:md5,ff36be9e2642089aa711c637d3cdba29",
+                "multiqc_picard_quality_by_cycle.txt:md5,9521c83313eaf5f681ac9a75de83a4b7",
+                "multiqc_picard_quality_score_distribution.txt:md5,90b9e29f22fa16cf2b0c4d92caf2dbb0",
+                "multiqc_seqfu_mqc.txt:md5,f821357507fda2d4cfd9299f52fa7dc1",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,9521c83313eaf5f681ac9a75de83a4b7",
+                "picard_QualityScoreDistribution_histogram.txt:md5,90b9e29f22fa16cf2b0c4d92caf2dbb0",
+                "picard_alignment_readlength_plot.txt:md5,9c80659c5c9b2fe9926b789fb67ba6ac",
+                "picard_alignment_summary.txt:md5,27bbb1fcdeecd26641938e5622087c23",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,99c5e961a4d26754e68047c8eb983798",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,44981dd399013d8c06481958be338040",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,b6369a23d3926edb90ae9bfdc6d90526",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,b253d3fca7c07b6a6dfea91725c58102",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,0f2fd628631d42ed5e6a1db22578daaa",
+                "picard_quality_by_cycle.txt:md5,3c34ae2bd2442a816577b1a794add2d6",
+                "picard_quality_score_distribution.txt:md5,0d58c59eac2952e6f71cefc35d4c4477",
+                "fastq_screen_plot.txt:md5,5abb5b9ed2c976f0ad83216ca3186201",
+                "fastqc-status-check-heatmap.txt:md5,323d6082b73ddb6ee33385f5ea4301c1",
+                "fastqc_overrepresented_sequences_plot.txt:md5,4e71d8913d40eb06db0f18d74ce6898f",
+                "fastqc_per_base_n_content_plot.txt:md5,b317ce09cb7a2be2366b544ea9b20ce6",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,e6f44d08f4185f680d4748a3b37201e2",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a1dc8a968f32bcf8a9b4c5f43d299dfa",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,e41b6dc1344f1aee379993daff310187",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,76f792b939233b070562cc46617f6371",
+                "fastqc_sequence_counts_plot.txt:md5,36c68522023b8d536c9362403bf03c48",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,9ff0df466790d971b3c7ef838efc0f4f",
+                "fastqc_sequence_length_distribution_plot.txt:md5,9fda632b92e3453f11cd0226484fce8e",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,536c28d7fadc9a76944f93ac9d643272",
+                "multiqc_fastqc.txt:md5,396b4cc0466a6642ec8b954237c42263",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,153c6e6a407ec128b1a02798ca2f1115",
+                "multiqc_picard_baseContent.txt:md5,6349e514552a0b5a0530fa6f311878a5",
+                "multiqc_picard_quality_by_cycle.txt:md5,c0c8b4c0197428d4d50e2c532814e1e2",
+                "multiqc_picard_quality_score_distribution.txt:md5,40e0b6faa75e1b51af42407f7ededb0c",
+                "multiqc_seqfu_mqc.txt:md5,8cced36d66ca9d25d60c006e734aa7e9",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,c0c8b4c0197428d4d50e2c532814e1e2",
+                "picard_QualityScoreDistribution_histogram.txt:md5,40e0b6faa75e1b51af42407f7ededb0c",
+                "picard_alignment_readlength_plot.txt:md5,5a19b1f8e2ac49d97f36a7792429419c",
+                "picard_alignment_summary.txt:md5,f9f791b7c569cfae07aef70aa630d40e",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,0165f522c84da6b17a286d37dc30abec",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,6fa0d29d40fe7fa24c166b664b6d4f4b",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,bf2426e09ac1ca4773edfc284c220122",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,3cbace572471ccf6c58673181dd0c0ec",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,b317ce09cb7a2be2366b544ea9b20ce6",
+                "picard_quality_by_cycle.txt:md5,7cb705007bc97da8c0da7d93201e6975",
+                "picard_quality_score_distribution.txt:md5,47d684abae0a8f4f09df43e91d54fb9a",
+                "fastq_screen_plot.txt:md5,82ceb9f2109f865d6d1b943441c09550",
+                "fastqc-status-check-heatmap.txt:md5,56b426cd5c030288639533fce7c95ab1",
+                "fastqc_overrepresented_sequences_plot.txt:md5,8e83abdbe7362e64d63339ee31ab3361",
+                "fastqc_per_base_n_content_plot.txt:md5,33b70326d8f888ac5a3d99b85f365e43",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,40bc954cc0d58a3197fdf124a40f1ca4",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,e240e30996c81a34b5d1a6b5a98ae254",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,b44d3376d503af12857d494c58b514bb",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,66b5b6d44f398fc9429460c0b9ba3ea9",
+                "fastqc_sequence_counts_plot.txt:md5,6e5804f553f656cffb02f927015d1026",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,fbe41935ea2e2faf7104393b476e5ac5",
+                "fastqc_sequence_length_distribution_plot.txt:md5,e77dc4ab73252c2e09c7452c3b8e8ab3",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,4fc422d9cb06a1d0248cc578c1eebaa2",
+                "multiqc_fastqc.txt:md5,95c8ffb23baafec625aeb600047515ae",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,2d05e826f5152fd0143edf7270de1235",
+                "multiqc_picard_baseContent.txt:md5,f3f23899a30a96260d8b5b3020708703",
+                "multiqc_picard_quality_by_cycle.txt:md5,c7edfc271ab59ecedad0ab046afd3563",
+                "multiqc_picard_quality_score_distribution.txt:md5,7fa89b52b8bc96dd1074aa07cb5a5a54",
+                "multiqc_seqfu_mqc.txt:md5,ff4ce1c88f39ed24a88bae0a861f75c8",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,c7edfc271ab59ecedad0ab046afd3563",
+                "picard_QualityScoreDistribution_histogram.txt:md5,7fa89b52b8bc96dd1074aa07cb5a5a54",
+                "picard_alignment_readlength_plot.txt:md5,c1519319c4942162b05e6225fea10569",
+                "picard_alignment_summary.txt:md5,49f5c0d2cf21a13d5f363cb42cf3790e",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,466a14fc9c09f9f4de02a00e8763cd2a",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,d5854c22df4ac60b8c47c4002d975fe9",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,c27b5aa2b90397b1302b880dff3ec958",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,6f2a3e9d03f17a93c69476607a1a580d",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,33b70326d8f888ac5a3d99b85f365e43",
+                "picard_quality_by_cycle.txt:md5,0aa028d69d8bb02f0a2bcd0ed08f4235",
+                "picard_quality_score_distribution.txt:md5,a2882ff59902dc95830ed4bdb955561a",
+                "200624_A00834_0183_BHMTFYDRXX_illumina_mqc.yml:md5,29e05fed18bca0e9a857c992b6d59a40",
+                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
+                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
+                "Sample1_01_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6",
+                "Sample1_01_seqfu_mqc.txt:md5,24d99524ccd0e6c6255a69d68a871c7a",
+                "Sample23_03_seqfu.tsv:md5,6fac5d3dbce3f3bee72341fe99a399dc",
+                "Sample23_03_seqfu_mqc.txt:md5,4d4f280911a08bb6b753142980178027",
+                "SampleA_02_seqfu.tsv:md5,aec811f267bb2a0ef066a7abb59d2775",
+                "SampleA_02_seqfu_mqc.txt:md5,a819409a5cb64e20c3e54ec5ada4aa27",
+                "Undetermined_05_seqfu.tsv:md5,3a42c5c66a0a118f1a6f6f6e560b0e7e",
+                "Undetermined_05_seqfu_mqc.txt:md5,bd8be908362c5cb08a72f8ae7ab41b0d",
+                "sampletest_04_seqfu.tsv:md5,a5bea0b9c6015dd1a201ffd433e9b377",
+                "sampletest_04_seqfu_mqc.txt:md5,2180961655bbc8a12f0152d6a4b803a2",
+                "Sample1_01_Sample1_S1_L001_R1_001.fastq.gz:md5,9f2f4855422bd18576efbc8af0368517",
+                "Sample23_03_Sample23_S3_L001_R1_001.fastq.gz:md5,036238392d51face00be9710c0c14523",
+                "SampleA_02_SampleA_S2_L001_R1_001.fastq.gz:md5,bcc1ed324745e894356ff3b66d023156",
+                "Undetermined_05_Undetermined_S0_L001_R1_001.fastq.gz:md5,2d64ba05e69ae081f95581cc8f0ffd36",
+                "sampletest_04_sampletest_S4_L001_R1_001.fastq.gz:md5,e81c2337941970a3bafa2c0adf8bebb1"
+            ],
+            [
+                "WARN: Sample1_01: Requested sample_size (120) is larger than available reads (100). Pipeline will continue with 100 reads.",
+                "WARN: Sample23_03: Requested sample_size (120) is larger than available reads (100). Pipeline will continue with 100 reads.",
+                "WARN: SampleA_02: Requested sample_size (120) is larger than available reads (100). Pipeline will continue with 100 reads.",
+                "WARN: Undetermined_05: Requested sample_size (120) is larger than available reads (100). Pipeline will continue with 100 reads.",
+                "WARN: sampletest_04: Requested sample_size (120) is larger than available reads (100). Pipeline will continue with 100 reads."
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-11-25T10:31:07.07892869"
+        "timestamp": "2025-12-12T11:47:44.482972598"
     }
 }
\ No newline at end of file

From d4c530684097c259e2c1c780d3d840ddd8ee235d Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 12 Dec 2025 12:29:14 +0100
Subject: [PATCH 489/530] update module

---
 modules/nf-core/seqfu/stats/main.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/nf-core/seqfu/stats/main.nf b/modules/nf-core/seqfu/stats/main.nf
index 89cddc20..ced2451c 100644
--- a/modules/nf-core/seqfu/stats/main.nf
+++ b/modules/nf-core/seqfu/stats/main.nf
@@ -12,7 +12,6 @@ process SEQFU_STATS {
     tuple val(meta), path(files)
 
     output:
-
     tuple val(meta), path("*.tsv")    , emit: stats
     tuple val(meta), path("*_mqc.txt"), emit: multiqc
     path "versions.yml"               , emit: versions

From 54609e9312de5d1a755420f3a1662fc8d6f0c834 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 12 Dec 2025 13:31:01 +0100
Subject: [PATCH 490/530] code polish + topics

---
 modules/local/rundirparser/main.nf | 36 ++++++++++--------------------
 1 file changed, 12 insertions(+), 24 deletions(-)

diff --git a/modules/local/rundirparser/main.nf b/modules/local/rundirparser/main.nf
index 66c7aafc..23951235 100644
--- a/modules/local/rundirparser/main.nf
+++ b/modules/local/rundirparser/main.nf
@@ -1,18 +1,19 @@
 process RUNDIRPARSER {
-    tag "$rundir.simpleName"
+    tag "${rundir.simpleName}"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/41/412df2cdcf04e0a12971ba61b12cacaa5a49705442afe99ad96668bebbb8f880/data' :
-        'community.wave.seqera.io/library/pip_pyyaml_xmltodict:a4e48bd1ab4b6a53' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/41/412df2cdcf04e0a12971ba61b12cacaa5a49705442afe99ad96668bebbb8f880/data'
+        : 'community.wave.seqera.io/library/pip_pyyaml_xmltodict:a4e48bd1ab4b6a53'}"
 
     input:
     tuple val(dir_meta), path(rundir)
 
     output:
     tuple val(dir_meta), path("*_mqc.*"), emit: multiqc
-    path "versions.yml",                  emit: versions
+    tuple val("${task.process}"), val('Python'), eval("python --version |& sed '1!d ; s/Python //'"), emit: versions_python, topic: versions
+    tuple val("${task.process}"), val('PyYAML'), eval("python -c 'import yaml; print(yaml.__version__)'"), emit: versions_pyyaml, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -21,46 +22,33 @@ process RUNDIRPARSER {
     def input_tar = rundir.toString().endsWith(".tar.gz") ? true : false
     def input_dir = input_tar ? rundir.toString() - '.tar.gz' : rundir
     """
-
     if [ ! -d ${input_dir} ]; then
         mkdir -p ${input_dir}
     fi
 
     if ${input_tar}; then
         ## Ensures --strip-components only applied when top level of tar contents is a directory
-        ## If just files or multiple directories, place all in $input_dir
+        ## If just files or multiple directories, place all in ${input_dir}
 
         if [[ \$(tar -taf ${rundir} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then
             tar \\
-                -C $input_dir --strip-components 1 \\
+                -C ${input_dir} --strip-components 1 \\
                 -xavf \\
-                $rundir
+                ${rundir}
         else
             tar \\
-                -C $input_dir \\
+                -C ${input_dir} \\
                 -xavf \\
-                $rundir
+                ${rundir}
         fi
     fi
 
     # TODO: check what kind of seq platfrom to decide which script to use
     parse_illumina.py ${input_dir}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        Python: \$(python --version |& sed '1!d ; s/Python //')
-        PyYAML: \$(python -c "import yaml; print(yaml.__version__)")
-    END_VERSIONS
     """
 
     stub:
     """
-    touch rundir_mqc.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        Python: stub_version
-        PyYAML: stub_version
-    END_VERSIONS
+    touch ${rundir}_mqc.yml
     """
 }

From ea4b20c7e6bae1fe5c68528d6c22b2438a0d6286 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 12 Dec 2025 13:31:45 +0100
Subject: [PATCH 491/530] code polish

---
 workflows/seqinspector.nf | 22 ++++++++++------------
 1 file changed, 10 insertions(+), 12 deletions(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 14f92fc3..227fd292 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -14,7 +14,7 @@ include { PICARD_COLLECTMULTIPLEMETRICS } from '../modules/nf-core/picard/collec
 include { SAMTOOLS_FAIDX                } from '../modules/nf-core/samtools/faidx'
 include { SAMTOOLS_INDEX                } from '../modules/nf-core/samtools/index'
 include { SEQFU_STATS                   } from '../modules/nf-core/seqfu/stats'
-include { RUNDIRPARSER                  } from '../modules/local/rundirparser/main'
+include { RUNDIRPARSER                  } from '../modules/local/rundirparser'
 include { SEQTK_SAMPLE                  } from '../modules/nf-core/seqtk/sample'
 include { QC_BAM                        } from '../subworkflows/local/qc_bam'
 
@@ -44,8 +44,6 @@ workflow SEQINSPECTOR {
     bwamem2
 
     main:
-
-
     ch_versions = channel.empty()
     ch_multiqc_files = channel.empty()
     ch_multiqc_extra_files = channel.empty()
@@ -73,7 +71,7 @@ workflow SEQINSPECTOR {
             .groupTuple()
             .map { rundir, metas ->
                 // Collect all unique tags into a list
-                def all_tags = metas.collect { it.tags }.flatten().unique()
+                def all_tags = metas.collect { meta -> meta.tags }.flatten().unique()
                 // Create a new meta object whose attributes are...
                 //  1. tags: The list of merged tags, used for grouping MultiQC reports
                 //  2. dirname: The simple name of the rundir, used for setting unique output names in publishDir
@@ -83,11 +81,12 @@ workflow SEQINSPECTOR {
                 //  2. Mix with the ch_multiqc_files channel downstream
                 [dir_meta, rundir]
             }
+            .view()
 
         RUNDIRPARSER(ch_rundir)
 
         ch_multiqc_files = ch_multiqc_files.mix(RUNDIRPARSER.out.multiqc)
-        ch_versions = ch_versions.mix(RUNDIRPARSER.out.versions.first())
+        ch_versions = ch_versions.mix(RUNDIRPARSER.out.versions)
     }
 
     //
@@ -99,7 +98,7 @@ workflow SEQINSPECTOR {
                 [meta, reads, params.sample_size]
             }
         ).reads
-        ch_versions = ch_versions.mix(SEQTK_SAMPLE.out.versions.first())
+        ch_versions = ch_versions.mix(SEQTK_SAMPLE.out.versions)
     }
     else {
         // No subsampling
@@ -116,7 +115,7 @@ workflow SEQINSPECTOR {
             }
         )
         ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip)
-        ch_versions = ch_versions.mix(FASTQC.out.versions.first())
+        ch_versions = ch_versions.mix(FASTQC.out.versions)
     }
 
 
@@ -148,7 +147,7 @@ workflow SEQINSPECTOR {
                 }
             }
         ch_multiqc_files = ch_multiqc_files.mix(SEQFU_STATS.out.multiqc)
-        ch_versions = ch_versions.mix(SEQFU_STATS.out.versions.first())
+        ch_versions = ch_versions.mix(SEQFU_STATS.out.versions)
     }
 
     //
@@ -174,7 +173,7 @@ workflow SEQINSPECTOR {
             ch_fastqscreen_refs,
         )
         ch_multiqc_files = ch_multiqc_files.mix(FASTQSCREEN_FASTQSCREEN.out.txt)
-        ch_versions = ch_versions.mix(FASTQSCREEN_FASTQSCREEN.out.versions.first())
+        ch_versions = ch_versions.mix(FASTQSCREEN_FASTQSCREEN.out.versions)
     }
 
     // MODULE: Align reads with BWA-MEM2
@@ -223,8 +222,7 @@ workflow SEQINSPECTOR {
 
     // Collate and save software versions
     //
-    def topic_versions = Channel
-        .topic("versions")
+    def topic_versions = channel.topic("versions")
         .distinct()
         .branch { entry ->
             versions_file: entry instanceof Path
@@ -292,7 +290,7 @@ workflow SEQINSPECTOR {
         )
     )
     // Add index to other MultiQC reports
-    //ch_multiqc_extra_files_global = Channel.empty()
+    //ch_multiqc_extra_files_global = channel.empty()
     ch_multiqc_extra_files_global = ch_multiqc_extra_files.mix(
         ch_tags.toList().map { tag_list ->
             reportIndexMultiqc(tag_list)

From 16db84c98afdba932209342f542de7b4de7e901f Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 12 Dec 2025 13:33:56 +0100
Subject: [PATCH 492/530] fix tests

---
 modules/local/rundirparser/tests/main.nf.test | 43 +++++++--------
 .../rundirparser/tests/main.nf.test.snap      | 54 +++++++++++++++++--
 2 files changed, 68 insertions(+), 29 deletions(-)

diff --git a/modules/local/rundirparser/tests/main.nf.test b/modules/local/rundirparser/tests/main.nf.test
index b1899c72..894ead33 100644
--- a/modules/local/rundirparser/tests/main.nf.test
+++ b/modules/local/rundirparser/tests/main.nf.test
@@ -5,50 +5,45 @@ nextflow_process {
     process "RUNDIRPARSER"
     config "./nextflow.config"
 
-    test("Should run without failures") {
-
+    test("NovaSeq6000") {
 
         when {
             process {
                 """
-                input[0] = [[], file("$moduleDir/tests/data/test_rundir")]
+                input[0] = [[],
+                    file(params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz', checkIfExists: true)
+                ]
                 """
             }
-            params {
-                outdir = "results"
-            }
         }
-
         then {
             assert process.success
-            assert snapshot(process.out.yml).match()
-            assert process.out.versions.size() == 1
+            assert snapshot(
+                process.out.multiqc[0][1],
+                process.out.findAll { key, val -> key.startsWith("versions")}
+            ).match()
         }
-
-
     }
 
-    test("Should create correct yaml structure") {
+    test("NovaSeq6000 - stub") {
+
+        options "-stub"
 
         when {
             process {
                 """
-                input[0] = [[], file("$moduleDir/tests/data/test_rundir")]
+                input[0] = [[],
+                    file(params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz', checkIfExists: true)
+                ]
                 """
             }
-            params {
-                outdir = "results"
-            }
-
         }
-
         then {
-            def yamlcontent = path(process.out.yml[0]).yaml
-
-            assert yamlcontent.custom_data.my_data_type.data."Instrument type" == "NovaSeqXPlus"
-            assert snapshot(process.out.yml).match()
+            assert process.success
+            assert snapshot(
+                process.out.multiqc[0][1],
+                process.out.findAll { key, val -> key.startsWith("versions")}
+            ).match()
         }
-
     }
-
 }
diff --git a/modules/local/rundirparser/tests/main.nf.test.snap b/modules/local/rundirparser/tests/main.nf.test.snap
index 81e38dca..4031a773 100644
--- a/modules/local/rundirparser/tests/main.nf.test.snap
+++ b/modules/local/rundirparser/tests/main.nf.test.snap
@@ -1,10 +1,54 @@
 {
-    "Should run without failures": {
-        "content": null,
+    "NovaSeq6000": {
+        "content": [
+            "illumina_mqc.yml:md5,29e05fed18bca0e9a857c992b6d59a40",
+            {
+                "versions_python": [
+                    [
+                        "RUNDIRPARSER",
+                        "Python",
+                        "3.13.2"
+                    ]
+                ],
+                "versions_pyyaml": [
+                    [
+                        "RUNDIRPARSER",
+                        "PyYAML",
+                        "6.0.2"
+                    ]
+                ]
+            }
+        ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.10.0"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-11-25T13:44:30.894411279"
+        "timestamp": "2025-12-12T13:30:03.998435274"
+    },
+    "NovaSeq6000 - stub": {
+        "content": [
+            "200624_A00834_0183_BHMTFYDRXX.tar.gz_mqc.yml:md5,d41d8cd98f00b204e9800998ecf8427e",
+            {
+                "versions_python": [
+                    [
+                        "RUNDIRPARSER",
+                        "Python",
+                        "3.13.2"
+                    ]
+                ],
+                "versions_pyyaml": [
+                    [
+                        "RUNDIRPARSER",
+                        "PyYAML",
+                        "6.0.2"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2025-12-12T13:30:11.388290534"
     }
 }
\ No newline at end of file

From daf18b0d4d418dd230f97b3ed2a314432553b86a Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 12 Dec 2025 13:39:32 +0100
Subject: [PATCH 493/530] no need for view()

---
 tests/NovaSeq6000.main.nf.test.snap | 2 +-
 workflows/seqinspector.nf           | 2 --
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index e7bac834..d4b88720 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -962,6 +962,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-12T11:44:10.238711124"
+        "timestamp": "2025-12-12T13:39:06.915289541"
     }
 }
\ No newline at end of file
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 227fd292..ab2354c1 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -81,12 +81,10 @@ workflow SEQINSPECTOR {
                 //  2. Mix with the ch_multiqc_files channel downstream
                 [dir_meta, rundir]
             }
-            .view()
 
         RUNDIRPARSER(ch_rundir)
 
         ch_multiqc_files = ch_multiqc_files.mix(RUNDIRPARSER.out.multiqc)
-        ch_versions = ch_versions.mix(RUNDIRPARSER.out.versions)
     }
 
     //

From 70fdcf2425a6390e215df52da5c3b0354cfedf70 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 12 Dec 2025 13:53:14 +0100
Subject: [PATCH 494/530] simplify config

---
 conf/modules.config                           |  2 +-
 .../local/rundirparser/tests/nextflow.config  | 29 -------------------
 2 files changed, 1 insertion(+), 30 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 1b8cf8c2..d432c2b7 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -99,7 +99,7 @@ process {
             // The process _mqc.txt outputs should have identical names for the same sequencing platforms
             // in order to be grouped together in the MultiQC report, but here we need to enforce uniqueness
             // to avoid overwriting results in the publishDir.
-            saveAs: { filename -> filename.equals('versions.yml') ? null : "${dir_meta.dirname}_$filename" }
+            saveAs: { filename -> "${dir_meta.dirname}_$filename" }
         ]
     }
 
diff --git a/modules/local/rundirparser/tests/nextflow.config b/modules/local/rundirparser/tests/nextflow.config
index ff74e779..651f0b86 100644
--- a/modules/local/rundirparser/tests/nextflow.config
+++ b/modules/local/rundirparser/tests/nextflow.config
@@ -1,30 +1 @@
 nextflow.enable.moduleBinaries = true
-
-process {
-    withName: 'RUNDIRPARSER' {
-        publishDir = [
-            path: "$PWD",
-            //path: { "${params.outdir}/rundirparser" },
-            mode: "copy",
-            // The process _mqc.txt outputs should have identical names for the same sequencing platforms
-            // in order to be grouped together in the MultiQC report, but here we need to enforce uniqueness
-            // to avoid overwriting results in the publishDir.
-            saveAs: { filename -> filename.equals('versions.yml') ? null : "${dir_meta.dirname}_$filename" }
-        ]
-
-    }
-}
-
-
-timeline {
-    overwrite = true
-}
-report {
-    overwrite = true
-}
-trace {
-    overwrite = true
-}
-dag {
-    overwrite = true
-}

From 8766778292b71f77824ef853f19e0dc3cdf7c232 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 12 Dec 2025 13:57:01 +0100
Subject: [PATCH 495/530] dir_meta -> meta

---
 conf/modules.config                | 2 +-
 modules/local/rundirparser/main.nf | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index d432c2b7..c9b047d1 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -99,7 +99,7 @@ process {
             // The process _mqc.txt outputs should have identical names for the same sequencing platforms
             // in order to be grouped together in the MultiQC report, but here we need to enforce uniqueness
             // to avoid overwriting results in the publishDir.
-            saveAs: { filename -> "${dir_meta.dirname}_$filename" }
+            saveAs: { filename -> "${meta.dirname}_$filename" }
         ]
     }
 
diff --git a/modules/local/rundirparser/main.nf b/modules/local/rundirparser/main.nf
index 23951235..dd02b58c 100644
--- a/modules/local/rundirparser/main.nf
+++ b/modules/local/rundirparser/main.nf
@@ -8,10 +8,10 @@ process RUNDIRPARSER {
         : 'community.wave.seqera.io/library/pip_pyyaml_xmltodict:a4e48bd1ab4b6a53'}"
 
     input:
-    tuple val(dir_meta), path(rundir)
+    tuple val(meta), path(rundir)
 
     output:
-    tuple val(dir_meta), path("*_mqc.*"), emit: multiqc
+    tuple val(meta), path("*_mqc.*"), emit: multiqc
     tuple val("${task.process}"), val('Python'), eval("python --version |& sed '1!d ; s/Python //'"), emit: versions_python, topic: versions
     tuple val("${task.process}"), val('PyYAML'), eval("python -c 'import yaml; print(yaml.__version__)'"), emit: versions_pyyaml, topic: versions
 

From 4a5024cc436f5d014e552c7110521dee6618489d Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 12 Dec 2025 13:57:48 +0100
Subject: [PATCH 496/530] Delete modules/local/rundirparser/meta.yml

---
 modules/local/rundirparser/meta.yml | 68 -----------------------------
 1 file changed, 68 deletions(-)
 delete mode 100644 modules/local/rundirparser/meta.yml

diff --git a/modules/local/rundirparser/meta.yml b/modules/local/rundirparser/meta.yml
deleted file mode 100644
index 7027a80d..00000000
--- a/modules/local/rundirparser/meta.yml
+++ /dev/null
@@ -1,68 +0,0 @@
----
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
-name: "rundirparser"
-## TODO nf-core: Add a description of the module and list keywords
-description: write your description here
-keywords:
-  - sort
-  - example
-  - genomics
-tools:
-  - "rundirparser":
-      ## TODO nf-core: Add a description and other details for the software below
-      description: ""
-      homepage: ""
-      documentation: ""
-      tool_dev_url: ""
-      doi: ""
-      licence:
-      identifier:
-
-## TODO nf-core: Add a description of all of the variables used as input
-input:
-  # Only when we have meta
-  - - meta:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. `[ id:'sample1', single_end:false ]`
-
-    ## TODO nf-core: Delete / customise this example input
-    - bam:
-        type: file
-        description: Sorted BAM/CRAM/SAM file
-        pattern: "*.{bam,cram,sam}"
-        ontologies:
-          - edam: "http://edamontology.org/format_25722"
-          - edam: "http://edamontology.org/format_2573"
-          - edam: "http://edamontology.org/format_3462"
-
-## TODO nf-core: Add a description of all of the variables used as output
-output:
-  - bam:
-      #Only when we have meta
-      - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. `[ id:'sample1', single_end:false ]`
-      ## TODO nf-core: Delete / customise this example output
-      - "*.bam":
-          type: file
-          description: Sorted BAM/CRAM/SAM file
-          pattern: "*.{bam,cram,sam}"
-          ontologies:
-            - edam: "http://edamontology.org/format_25722"
-            - edam: "http://edamontology.org/format_2573"
-            - edam: "http://edamontology.org/format_3462"
-
-  - versions:
-      - "versions.yml":
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
-
-authors:
-  - "@kedhammar"
-maintainers:
-  - "@kedhammar"

From ff89c38fb46ebb73ed17fca66f03c6c91357e3b0 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 12 Dec 2025 13:58:49 +0100
Subject: [PATCH 497/530] Update tests/NovaSeq6000.main.nf.test.config

---
 tests/NovaSeq6000.main.nf.test.config | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/NovaSeq6000.main.nf.test.config b/tests/NovaSeq6000.main.nf.test.config
index dbdd5409..e9af36a7 100644
--- a/tests/NovaSeq6000.main.nf.test.config
+++ b/tests/NovaSeq6000.main.nf.test.config
@@ -8,5 +8,4 @@ params {
 
     // Genome references
     genome = 'R64-1-1'
-
 }

From dcd7c8a41ae8e3a68e947930a9cb7fe3467d2fff Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 12 Dec 2025 14:00:38 +0100
Subject: [PATCH 498/530] sort modules import

---
 workflows/seqinspector.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index ab2354c1..2b192820 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -11,12 +11,12 @@ include { BWAMEM2_MEM                   } from '../modules/nf-core/bwamem2/mem'
 include { FASTQC                        } from '../modules/nf-core/fastqc'
 include { FASTQSCREEN_FASTQSCREEN       } from '../modules/nf-core/fastqscreen/fastqscreen'
 include { PICARD_COLLECTMULTIPLEMETRICS } from '../modules/nf-core/picard/collectmultiplemetrics'
+include { QC_BAM                        } from '../subworkflows/local/qc_bam'
+include { RUNDIRPARSER                  } from '../modules/local/rundirparser'
 include { SAMTOOLS_FAIDX                } from '../modules/nf-core/samtools/faidx'
 include { SAMTOOLS_INDEX                } from '../modules/nf-core/samtools/index'
 include { SEQFU_STATS                   } from '../modules/nf-core/seqfu/stats'
-include { RUNDIRPARSER                  } from '../modules/local/rundirparser'
 include { SEQTK_SAMPLE                  } from '../modules/nf-core/seqtk/sample'
-include { QC_BAM                        } from '../subworkflows/local/qc_bam'
 
 include { MULTIQC as MULTIQC_GLOBAL     } from '../modules/nf-core/multiqc'
 include { MULTIQC as MULTIQC_PER_TAG    } from '../modules/nf-core/multiqc'

From f54f4c7b9c174a686b72a56f83bd178af164fdbd Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 12 Dec 2025 14:02:41 +0100
Subject: [PATCH 499/530] sort import

---
 workflows/seqinspector.nf | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 2b192820..cb556cbe 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -6,29 +6,29 @@ include { samplesheetToList             } from 'plugin/nf-schema'
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-// nf-core
+// modules
 include { BWAMEM2_MEM                   } from '../modules/nf-core/bwamem2/mem'
 include { FASTQC                        } from '../modules/nf-core/fastqc'
 include { FASTQSCREEN_FASTQSCREEN       } from '../modules/nf-core/fastqscreen/fastqscreen'
+include { MULTIQC as MULTIQC_GLOBAL     } from '../modules/nf-core/multiqc'
+include { MULTIQC as MULTIQC_PER_TAG    } from '../modules/nf-core/multiqc'
 include { PICARD_COLLECTMULTIPLEMETRICS } from '../modules/nf-core/picard/collectmultiplemetrics'
-include { QC_BAM                        } from '../subworkflows/local/qc_bam'
 include { RUNDIRPARSER                  } from '../modules/local/rundirparser'
 include { SAMTOOLS_FAIDX                } from '../modules/nf-core/samtools/faidx'
 include { SAMTOOLS_INDEX                } from '../modules/nf-core/samtools/index'
 include { SEQFU_STATS                   } from '../modules/nf-core/seqfu/stats'
 include { SEQTK_SAMPLE                  } from '../modules/nf-core/seqtk/sample'
 
-include { MULTIQC as MULTIQC_GLOBAL     } from '../modules/nf-core/multiqc'
-include { MULTIQC as MULTIQC_PER_TAG    } from '../modules/nf-core/multiqc'
+// subworkflow
+include { PREPARE_GENOME                } from '../subworkflows/local/prepare_genome'
+include { QC_BAM                        } from '../subworkflows/local/qc_bam'
 
+// functions
+include { methodsDescriptionText        } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline'
 include { paramsSummaryMap              } from 'plugin/nf-schema'
 include { paramsSummaryMultiqc          } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-include { softwareVersionsToYAML        } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-include { methodsDescriptionText        } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline'
 include { reportIndexMultiqc            } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline'
-
-// local
-include { PREPARE_GENOME                } from '../subworkflows/local/prepare_genome'
+include { softwareVersionsToYAML        } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

From 5d224a4f2af293137f29fe1e8b7f08dd0d145081 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 12 Dec 2025 14:07:02 +0100
Subject: [PATCH 500/530] Trigger Build


From 5f04718544d914d60fa6a167ec50fa98f856b010 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 12 Dec 2025 14:15:33 +0100
Subject: [PATCH 501/530] update snapshots

---
 tests/PromethION.main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/PromethION.main.nf.test b/tests/PromethION.main.nf.test
index e33288d6..8aef6770 100644
--- a/tests/PromethION.main.nf.test
+++ b/tests/PromethION.main.nf.test
@@ -11,7 +11,7 @@ nextflow_pipeline {
             config "./PromethION.main.nf.test.config"
             params {
                 outdir = "$outputDir"
-                skip_tools = "rundirparser"
+                skip_tools = "bwamem2_index,bwamem2_mem,rundirparser"
             }
         }
 

From e78578d92bfd77968bc161397ef3415cec0fec53 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 12 Dec 2025 15:35:16 +0100
Subject: [PATCH 502/530] rename test files and delete config

---
 tests/MiSeq.main.nf.test.config               |  7 -----
 tests/{MiSeq.main.nf.test => MiSeq.nf.test}   |  6 ++--
 ...q.main.nf.test.snap => MiSeq.nf.test.snap} |  0
 tests/MiSeq_PairedEnd.main.nf.test.config     | 31 -------------------
 ...d.main.nf.test => MiSeq_PairedEnd.nf.test} |  2 +-
 ...test.snap => MiSeq_PairedEnd.nf.test.snap} |  0
 tests/NovaSeq6000.main.nf.test.config         | 11 -------
 .../NovaSeq6000.main_subsample.nf.test.config |  8 -----
 ...q6000.main.nf.test => NovaSeq6000.nf.test} |  4 ++-
 ....nf.test.snap => NovaSeq6000.nf.test.snap} |  0
 ....nf.test => NovaSeq6000_subsample.nf.test} |  7 +++--
 ...nap => NovaSeq6000_subsample.nf.test.snap} |  0
 tests/PromethION.main.nf.test.config          | 10 ------
 ...ethION.main.nf.test => PromethION.nf.test} |  3 +-
 ...n.nf.test.snap => PromethION.nf.test.snap} |  0
 15 files changed, 13 insertions(+), 76 deletions(-)
 delete mode 100644 tests/MiSeq.main.nf.test.config
 rename tests/{MiSeq.main.nf.test => MiSeq.nf.test} (92%)
 rename tests/{MiSeq.main.nf.test.snap => MiSeq.nf.test.snap} (100%)
 delete mode 100644 tests/MiSeq_PairedEnd.main.nf.test.config
 rename tests/{MiSeq_PairedEnd.main.nf.test => MiSeq_PairedEnd.nf.test} (92%)
 rename tests/{MiSeq_PairedEnd.main.nf.test.snap => MiSeq_PairedEnd.nf.test.snap} (100%)
 delete mode 100644 tests/NovaSeq6000.main.nf.test.config
 delete mode 100644 tests/NovaSeq6000.main_subsample.nf.test.config
 rename tests/{NovaSeq6000.main.nf.test => NovaSeq6000.nf.test} (84%)
 rename tests/{NovaSeq6000.main.nf.test.snap => NovaSeq6000.nf.test.snap} (100%)
 rename tests/{NovaSeq6000.main_subsample.nf.test => NovaSeq6000_subsample.nf.test} (92%)
 rename tests/{NovaSeq6000.main_subsample.nf.test.snap => NovaSeq6000_subsample.nf.test.snap} (100%)
 delete mode 100644 tests/PromethION.main.nf.test.config
 rename tests/{PromethION.main.nf.test => PromethION.nf.test} (91%)
 rename tests/{PromethION.main.nf.test.snap => PromethION.nf.test.snap} (100%)

diff --git a/tests/MiSeq.main.nf.test.config b/tests/MiSeq.main.nf.test.config
deleted file mode 100644
index 073a9774..00000000
--- a/tests/MiSeq.main.nf.test.config
+++ /dev/null
@@ -1,7 +0,0 @@
-// Load the basic test config
-includeConfig 'nextflow.config'
-
-// Load the correct samplesheet for that test
-params {
-    input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/MiSeq/samplesheet.csv'
-}
diff --git a/tests/MiSeq.main.nf.test b/tests/MiSeq.nf.test
similarity index 92%
rename from tests/MiSeq.main.nf.test
rename to tests/MiSeq.nf.test
index f8f325b9..9d697085 100644
--- a/tests/MiSeq.main.nf.test
+++ b/tests/MiSeq.nf.test
@@ -8,8 +8,8 @@ nextflow_pipeline {
     test("MiSeq data test (single end reads)") {
 
         when {
-            config "./MiSeq.main.nf.test.config"
             params {
+                input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/MiSeq/samplesheet.csv'
                 outdir = "$outputDir"
                 skip_tools = "rundirparser"
             }
@@ -42,8 +42,8 @@ nextflow_pipeline {
 
     test("Miseq data test (skip fastqc)") {
         when {
-            config "./MiSeq.main.nf.test.config"
             params {
+                input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/MiSeq/samplesheet.csv'
                 outdir = "$outputDir"
                 skip_tools = "fastqc,rundirparser"
             }
@@ -76,8 +76,8 @@ nextflow_pipeline {
 
     test("Miseq data test (skip all tools)") {
         when {
-            config "./MiSeq.main.nf.test.config"
             params {
+                input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/MiSeq/samplesheet.csv'
                 outdir = "$outputDir"
                 skip_tools = "fastqc,fastqscreen,seqfu_stats,seqtk_sample,bwamem2_index,bwamem2_mem,rundirparser"
             }
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.nf.test.snap
similarity index 100%
rename from tests/MiSeq.main.nf.test.snap
rename to tests/MiSeq.nf.test.snap
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.config b/tests/MiSeq_PairedEnd.main.nf.test.config
deleted file mode 100644
index 35fe5d6d..00000000
--- a/tests/MiSeq_PairedEnd.main.nf.test.config
+++ /dev/null
@@ -1,31 +0,0 @@
-// Load the basic test config
-includeConfig 'nextflow.config'
-
-// Load the correct samplesheet for that test
-params {
-    input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/Miseq_PairedEnd/samplesheet.csv'
-}
-
-process {
-    resourceLimits = [
-        cpus: 4,
-        memory: '15.GB',
-        time: '1.h'
-    ]
-    withLabel: 'process_high' {
-        cpus = 4
-        memory = '15.GB'
-    }
-    withLabel: 'process_medium' {
-        cpus = 2
-        memory = '7.GB'
-    }
-    withLabel: 'process_low' {
-        cpus = 1
-        memory = '3.GB'
-    }
-    withLabel: 'process_single' {
-        cpus = 1
-        memory = '3.GB'
-    }
-}
diff --git a/tests/MiSeq_PairedEnd.main.nf.test b/tests/MiSeq_PairedEnd.nf.test
similarity index 92%
rename from tests/MiSeq_PairedEnd.main.nf.test
rename to tests/MiSeq_PairedEnd.nf.test
index 2a69711a..d650d94c 100644
--- a/tests/MiSeq_PairedEnd.main.nf.test
+++ b/tests/MiSeq_PairedEnd.nf.test
@@ -8,10 +8,10 @@ nextflow_pipeline {
     test("MiSeq data test (paired end reads)") {
 
         when {
-            config "./MiSeq_PairedEnd.main.nf.test.config"
             params {
                 outdir = "$outputDir"
                 skip_tools = "rundirparser"
+                input = params.pipelines_testdata_base_path + 'seqinspector/testdata/Miseq_PairedEnd/samplesheet.csv'
             }
         }
 
diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.nf.test.snap
similarity index 100%
rename from tests/MiSeq_PairedEnd.main.nf.test.snap
rename to tests/MiSeq_PairedEnd.nf.test.snap
diff --git a/tests/NovaSeq6000.main.nf.test.config b/tests/NovaSeq6000.main.nf.test.config
deleted file mode 100644
index e9af36a7..00000000
--- a/tests/NovaSeq6000.main.nf.test.config
+++ /dev/null
@@ -1,11 +0,0 @@
-// Load the basic test config
-includeConfig 'nextflow.config'
-
-// Load the correct samplesheet for that test
-params {
-    input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
-    fastq_screen_references = "${projectDir}/assets/example_fastq_screen_references.csv"
-
-    // Genome references
-    genome = 'R64-1-1'
-}
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.config b/tests/NovaSeq6000.main_subsample.nf.test.config
deleted file mode 100644
index acda74dd..00000000
--- a/tests/NovaSeq6000.main_subsample.nf.test.config
+++ /dev/null
@@ -1,8 +0,0 @@
-// Load the basic test config
-includeConfig 'nextflow.config'
-
-// Load the correct samplesheet for that test
-params {
-    input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
-    sample_size = 90
-}
diff --git a/tests/NovaSeq6000.main.nf.test b/tests/NovaSeq6000.nf.test
similarity index 84%
rename from tests/NovaSeq6000.main.nf.test
rename to tests/NovaSeq6000.nf.test
index 63dcc300..613f57cd 100644
--- a/tests/NovaSeq6000.main.nf.test
+++ b/tests/NovaSeq6000.nf.test
@@ -8,8 +8,10 @@ nextflow_pipeline {
     test("NovaSeq6000 data test") {
 
         when {
-            config "./NovaSeq6000.main.nf.test.config"
             params {
+                input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
+                fastq_screen_references = "${projectDir}/assets/example_fastq_screen_references.csv"
+                genome = 'R64-1-1'
                 outdir = "$outputDir"
             }
         }
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.nf.test.snap
similarity index 100%
rename from tests/NovaSeq6000.main.nf.test.snap
rename to tests/NovaSeq6000.nf.test.snap
diff --git a/tests/NovaSeq6000.main_subsample.nf.test b/tests/NovaSeq6000_subsample.nf.test
similarity index 92%
rename from tests/NovaSeq6000.main_subsample.nf.test
rename to tests/NovaSeq6000_subsample.nf.test
index fc9da203..14041788 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test
+++ b/tests/NovaSeq6000_subsample.nf.test
@@ -8,8 +8,9 @@ nextflow_pipeline {
     test("NovaSeq6000 data test sample size") {
 
         when {
-            config "./NovaSeq6000.main_subsample.nf.test.config"
             params {
+                input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
+                sample_size = 90
                 outdir = "$outputDir"
             }
         }
@@ -42,8 +43,8 @@ nextflow_pipeline {
     test("NovaSeq6000 data test relative sample size") {
 
         when {
-            config "./NovaSeq6000.main_subsample.nf.test.config"
             params {
+                input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
                 outdir = "$outputDir"
                 sample_size = 0.9
             }
@@ -78,8 +79,8 @@ nextflow_pipeline {
         tag "warning"
 
         when {
-            config "./NovaSeq6000.main_subsample.nf.test.config"
             params {
+                input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
                 outdir = "$outputDir"
                 sample_size = 120
             }
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000_subsample.nf.test.snap
similarity index 100%
rename from tests/NovaSeq6000.main_subsample.nf.test.snap
rename to tests/NovaSeq6000_subsample.nf.test.snap
diff --git a/tests/PromethION.main.nf.test.config b/tests/PromethION.main.nf.test.config
deleted file mode 100644
index 46e9c091..00000000
--- a/tests/PromethION.main.nf.test.config
+++ /dev/null
@@ -1,10 +0,0 @@
-// Load the basic test config
-includeConfig 'nextflow.config'
-
-// Load the correct samplesheet for that test
-params {
-    input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/PromethION/samplesheet.csv'
-    genome = 'EB1'
-    skip_tools = 'bwamem2_index,bwamem2_mem'
-
-}
diff --git a/tests/PromethION.main.nf.test b/tests/PromethION.nf.test
similarity index 91%
rename from tests/PromethION.main.nf.test
rename to tests/PromethION.nf.test
index 8aef6770..e74b4b6e 100644
--- a/tests/PromethION.main.nf.test
+++ b/tests/PromethION.nf.test
@@ -8,8 +8,9 @@ nextflow_pipeline {
     test("PromethION data test") {
 
         when {
-            config "./PromethION.main.nf.test.config"
             params {
+                input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/PromethION/samplesheet.csv'
+                genome = 'EB1'
                 outdir = "$outputDir"
                 skip_tools = "bwamem2_index,bwamem2_mem,rundirparser"
             }
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.nf.test.snap
similarity index 100%
rename from tests/PromethION.main.nf.test.snap
rename to tests/PromethION.nf.test.snap

From b3e6fedda2c2709712283ca971490d4c320ded5b Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 12 Dec 2025 15:55:17 +0100
Subject: [PATCH 503/530] need the params in the tests for now

---
 .nf-core.yml                        | 1 +
 tests/MiSeq.nf.test                 | 3 +++
 tests/MiSeq_PairedEnd.nf.test       | 1 +
 tests/NovaSeq6000.nf.test           | 1 -
 tests/NovaSeq6000_subsample.nf.test | 3 ---
 tests/PromethION.nf.test            | 5 +++--
 tests/nextflow.config               | 5 -----
 7 files changed, 8 insertions(+), 11 deletions(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index e935704e..df59962a 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -10,6 +10,7 @@ lint:
   nextflow_config:
     - config_defaults:
         - params.fastq_screen_references
+  nf_test_content: false
 nf_core_version: 3.5.1
 repository_type: pipeline
 template:
diff --git a/tests/MiSeq.nf.test b/tests/MiSeq.nf.test
index 9d697085..6e7efecf 100644
--- a/tests/MiSeq.nf.test
+++ b/tests/MiSeq.nf.test
@@ -9,6 +9,7 @@ nextflow_pipeline {
 
         when {
             params {
+                pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
                 input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/MiSeq/samplesheet.csv'
                 outdir = "$outputDir"
                 skip_tools = "rundirparser"
@@ -43,6 +44,7 @@ nextflow_pipeline {
     test("Miseq data test (skip fastqc)") {
         when {
             params {
+                pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
                 input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/MiSeq/samplesheet.csv'
                 outdir = "$outputDir"
                 skip_tools = "fastqc,rundirparser"
@@ -77,6 +79,7 @@ nextflow_pipeline {
     test("Miseq data test (skip all tools)") {
         when {
             params {
+                pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
                 input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/MiSeq/samplesheet.csv'
                 outdir = "$outputDir"
                 skip_tools = "fastqc,fastqscreen,seqfu_stats,seqtk_sample,bwamem2_index,bwamem2_mem,rundirparser"
diff --git a/tests/MiSeq_PairedEnd.nf.test b/tests/MiSeq_PairedEnd.nf.test
index d650d94c..b35dfd07 100644
--- a/tests/MiSeq_PairedEnd.nf.test
+++ b/tests/MiSeq_PairedEnd.nf.test
@@ -9,6 +9,7 @@ nextflow_pipeline {
 
         when {
             params {
+                pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
                 outdir = "$outputDir"
                 skip_tools = "rundirparser"
                 input = params.pipelines_testdata_base_path + 'seqinspector/testdata/Miseq_PairedEnd/samplesheet.csv'
diff --git a/tests/NovaSeq6000.nf.test b/tests/NovaSeq6000.nf.test
index 613f57cd..fa4b1670 100644
--- a/tests/NovaSeq6000.nf.test
+++ b/tests/NovaSeq6000.nf.test
@@ -9,7 +9,6 @@ nextflow_pipeline {
 
         when {
             params {
-                input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
                 fastq_screen_references = "${projectDir}/assets/example_fastq_screen_references.csv"
                 genome = 'R64-1-1'
                 outdir = "$outputDir"
diff --git a/tests/NovaSeq6000_subsample.nf.test b/tests/NovaSeq6000_subsample.nf.test
index 14041788..232cd040 100644
--- a/tests/NovaSeq6000_subsample.nf.test
+++ b/tests/NovaSeq6000_subsample.nf.test
@@ -9,7 +9,6 @@ nextflow_pipeline {
 
         when {
             params {
-                input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
                 sample_size = 90
                 outdir = "$outputDir"
             }
@@ -44,7 +43,6 @@ nextflow_pipeline {
 
         when {
             params {
-                input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
                 outdir = "$outputDir"
                 sample_size = 0.9
             }
@@ -80,7 +78,6 @@ nextflow_pipeline {
 
         when {
             params {
-                input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
                 outdir = "$outputDir"
                 sample_size = 120
             }
diff --git a/tests/PromethION.nf.test b/tests/PromethION.nf.test
index e74b4b6e..1af31ddd 100644
--- a/tests/PromethION.nf.test
+++ b/tests/PromethION.nf.test
@@ -9,8 +9,9 @@ nextflow_pipeline {
 
         when {
             params {
-                input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/PromethION/samplesheet.csv'
+                pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
                 genome = 'EB1'
+                input  = params.pipelines_testdata_base_path + '/seqinspector/testdata/PromethION/samplesheet.csv'
                 outdir = "$outputDir"
                 skip_tools = "bwamem2_index,bwamem2_mem,rundirparser"
             }
@@ -27,8 +28,8 @@ nextflow_pipeline {
                 params.outdir,
                 ignoreFile: 'tests/.nftignore'
             )
+            assert workflow.success
             assertAll(
-                { assert workflow.success},
                 { assert snapshot(
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
diff --git a/tests/nextflow.config b/tests/nextflow.config
index f1daba3a..5d979d45 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -4,9 +4,4 @@
 ========================================================================================
 */
 
-params {
-    modules_testdata_base_path     = 's3://ngi-igenomes/testdata/nf-core/modules/'
-    pipelines_testdata_base_path   = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
-}
-
 aws.client.anonymous = true // fixes S3 access issues on self-hosted runners

From dbe8114d6ffb4bad72b28fd7d472081f21250b41 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 12 Dec 2025 15:57:17 +0100
Subject: [PATCH 504/530] early failure for test for smaller diff

---
 tests/MiSeq.nf.test                 | 6 +++---
 tests/MiSeq_PairedEnd.nf.test       | 2 +-
 tests/NovaSeq6000.nf.test           | 2 +-
 tests/NovaSeq6000_subsample.nf.test | 4 ++--
 4 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/tests/MiSeq.nf.test b/tests/MiSeq.nf.test
index 6e7efecf..ec406936 100644
--- a/tests/MiSeq.nf.test
+++ b/tests/MiSeq.nf.test
@@ -27,8 +27,8 @@ nextflow_pipeline {
                 params.outdir,
                 ignoreFile: 'tests/.nftignore'
             )
+            assert workflow.success
             assertAll(
-                { assert workflow.success},
                 { assert snapshot(
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
@@ -62,8 +62,8 @@ nextflow_pipeline {
                 params.outdir,
                 ignoreFile: 'tests/.nftignore'
             )
+            assert workflow.success
             assertAll(
-                { assert workflow.success},
                 { assert snapshot(
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
@@ -97,8 +97,8 @@ nextflow_pipeline {
                 params.outdir,
                 ignoreFile: 'tests/.nftignore'
             )
+            assert workflow.success
             assertAll(
-                { assert workflow.success},
                 { assert snapshot(
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
diff --git a/tests/MiSeq_PairedEnd.nf.test b/tests/MiSeq_PairedEnd.nf.test
index b35dfd07..20a8c0f0 100644
--- a/tests/MiSeq_PairedEnd.nf.test
+++ b/tests/MiSeq_PairedEnd.nf.test
@@ -27,8 +27,8 @@ nextflow_pipeline {
                 params.outdir,
                 ignoreFile: 'tests/.nftignore'
             )
+            assert workflow.success
             assertAll(
-                { assert workflow.success},
                 { assert snapshot(
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
diff --git a/tests/NovaSeq6000.nf.test b/tests/NovaSeq6000.nf.test
index fa4b1670..68b47344 100644
--- a/tests/NovaSeq6000.nf.test
+++ b/tests/NovaSeq6000.nf.test
@@ -26,8 +26,8 @@ nextflow_pipeline {
                 params.outdir,
                 ignoreFile: 'tests/.nftignore'
             )
+            assert workflow.success
             assertAll(
-                { assert workflow.success},
                 { assert snapshot(
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
diff --git a/tests/NovaSeq6000_subsample.nf.test b/tests/NovaSeq6000_subsample.nf.test
index 232cd040..8ea215c2 100644
--- a/tests/NovaSeq6000_subsample.nf.test
+++ b/tests/NovaSeq6000_subsample.nf.test
@@ -25,8 +25,8 @@ nextflow_pipeline {
                 params.outdir,
                 ignoreFile: 'tests/.nftignore'
             )
+            assert workflow.success
             assertAll(
-                { assert workflow.success},
                 { assert snapshot(
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
@@ -59,8 +59,8 @@ nextflow_pipeline {
                 params.outdir,
                 ignoreFile: 'tests/.nftignore'
             )
+            assert workflow.success
             assertAll(
-                { assert workflow.success},
                 { assert snapshot(
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),

From e09b1667d44f2e462175e51ba3966db2341fc148 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 12 Dec 2025 16:11:46 +0100
Subject: [PATCH 505/530] simplify tests

---
 .../local/prepare_genome/tests/main.nf.test   |  92 +++------
 .../prepare_genome/tests/main.nf.test.snap    | 184 +++++++++++++-----
 .../prepare_genome/tests/nextflow.config      |   7 -
 3 files changed, 157 insertions(+), 126 deletions(-)
 delete mode 100644 subworkflows/local/prepare_genome/tests/nextflow.config

diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test b/subworkflows/local/prepare_genome/tests/main.nf.test
index c0fff4e5..acca322d 100644
--- a/subworkflows/local/prepare_genome/tests/main.nf.test
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test
@@ -9,7 +9,6 @@ nextflow_workflow {
     test("Test without bwamem2 index file path and with run_picard_collecthsmetrics=false") {
 
         when {
-            config "./nextflow.config"
             params {
                 outdir = "$outputDir"
                 run_picard_collecthsmetrics = true
@@ -17,7 +16,7 @@ nextflow_workflow {
             }
             workflow {
                 """
-                input[0]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta', checkIfExists: true)).collect()
+                input[0]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/modules/data/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)).collect()
                 input[1]  = null
                 input[2]  = ''
                 input[3]  = false
@@ -27,34 +26,19 @@ nextflow_workflow {
         }
 
         then {
-            // All files + folders produced by BWAMEM2_INDEX
-            def bwamem2_index_files = getAllFilesFromDir(
-                params.outdir + '/bwamem2_index',
-                relative: true, includeDir: true
-            )
-            // All files + folders produced by SAMTOOLS_FAIDX
-            def samtools_faidx_files = getAllFilesFromDir(
-                params.outdir + '/samtools_faidx',
-                relative: true, includeDir: true
-            )
-
             assert workflow.success
-
-            assert snapshot(
-                    bwamem2_index_files,
-                    samtools_faidx_files
-                ).match()
-
-            // BWAMEM2_INDEX and SAMTOOLS_FAIDX should run
-            assert workflow.out.versions.size() == 2
+            assert snapshot(sanitizeOutput(workflow.out).collectEntries { key, val ->
+                if (key == "versions") {
+                    return [key, val.collect { path(it).yaml }]
+                }
+                return [key, val]
+            }).match()
         }
-
     }
 
     test("Test without bwamem2 index file path, with run_picard_collecthsmetrics=true and with ref_dict") {
 
         when {
-            config "./nextflow.config"
             params {
                 outdir = "$outputDir"
                 run_picard_collecthsmetrics = true
@@ -62,42 +46,29 @@ nextflow_workflow {
             }
             workflow {
                 """
-                input[0]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta', checkIfExists: true)).collect()
+                input[0]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/modules/data/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)).collect()
                 input[1]  = null
                 input[2]  = ''
                 input[3]  = true
-                input[4]  = params.pipelines_testdata_base_path + '/reference/reference.dict'
+                input[4]  = params.pipelines_testdata_base_path + '/modules/data/genomics/homo_sapiens/genome/genome.dict'
                 """
             }
         }
 
         then {
-            // All files + folders produced by BWAMEM2_INDEX
-            def bwamem2_index_files = getAllFilesFromDir(
-                params.outdir + '/bwamem2_index',
-                relative: true, includeDir: true
-            )
-            // All files + folders produced by SAMTOOLS_FAIDX
-            def samtools_faidx_files = getAllFilesFromDir(
-                params.outdir + '/samtools_faidx',
-                relative: true, includeDir: true
-            )
-
             assert workflow.success
-            assert snapshot(
-                    bwamem2_index_files,
-                    samtools_faidx_files
-                ).match()
-            // BWAMEM2_INDEX and SAMTOOLS_FAIDX should run
-            assert workflow.out.versions.size() == 2
+            assert snapshot(sanitizeOutput(workflow.out).collectEntries { key, val ->
+                if (key == "versions") {
+                    return [key, val.collect { path(it).yaml }]
+                }
+                return [key, val]
+            }).match()
         }
-
     }
 
     test("Test without bwamem2 index file path, with run_picard_collecthsmetrics=true and without ref_dict") {
 
         when {
-            config "./nextflow.config"
             params {
                 outdir = "$outputDir"
                 run_picard_collecthsmetrics = true
@@ -105,7 +76,7 @@ nextflow_workflow {
             }
             workflow {
                 """
-                input[0]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/reference.fasta', checkIfExists: true)).collect()
+                input[0]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/modules/data/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)).collect()
                 input[1]  = null
                 input[2]  = ''
                 input[3]  = true
@@ -115,32 +86,13 @@ nextflow_workflow {
         }
 
         then {
-            // All files + folders produced by BWAMEM2_INDEX
-            def bwamem2_index_files = getAllFilesFromDir(
-                params.outdir + '/bwamem2_index',
-                relative: true, includeDir: true
-            )
-            // All files + folders produced by SAMTOOLS_FAIDX
-            def samtools_faidx_files = getAllFilesFromDir(
-                params.outdir + '/samtools_faidx',
-                relative: true, includeDir: true
-            )
-            // All files + folders produced by PICARD_CREATESEQUENCEDICTIONARY
-            def picard_createsequencedictionary_files = getAllFilesFromDir(
-                params.outdir + '/picard_createsequencedictionary',
-                relative: true, includeDir: true
-            )
-
             assert workflow.success
-            assert snapshot(
-                    bwamem2_index_files,
-                    samtools_faidx_files,
-                    picard_createsequencedictionary_files
-                ).match()
-            // BWAMEM2_INDEX, SAMTOOLS_FAIDX and PICARD_CREATESEQUENCEDICTIONARY should run
-            assert workflow.out.versions.size() == 3
+            assert snapshot(sanitizeOutput(workflow.out).collectEntries { key, val ->
+                if (key == "versions") {
+                    return [key, val.collect { path(it).yaml }]
+                }
+                return [key, val]
+            }).match()
         }
-
     }
-
 }
diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test.snap b/subworkflows/local/prepare_genome/tests/main.nf.test.snap
index 69aaba82..59526cc9 100644
--- a/subworkflows/local/prepare_genome/tests/main.nf.test.snap
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test.snap
@@ -1,75 +1,161 @@
 {
     "Test without bwamem2 index file path, with run_picard_collecthsmetrics=true and without ref_dict": {
         "content": [
-            [
-                "",
-                "bwamem2",
-                "bwamem2/reference.fasta.0123",
-                "bwamem2/reference.fasta.amb",
-                "bwamem2/reference.fasta.ann",
-                "bwamem2/reference.fasta.bwt.2bit.64",
-                "bwamem2/reference.fasta.pac"
-            ],
-            [
-                "",
-                "reference.fasta.fai",
-                "reference.fasta.sizes"
-            ],
-            [
-                "",
-                "genome.dict"
-            ]
+            {
+                "bwamem2_index": [
+                    [
+                        {
+                            "id": "genome"
+                        },
+                        [
+                            "genome.fasta.0123:md5,d73300d44f733bcdb7c988fc3ff3e3e9",
+                            "genome.fasta.amb:md5,1891c1de381b3a96d4e72f590fde20c1",
+                            "genome.fasta.ann:md5,2df4aa2d7580639fa0fcdbcad5e2e969",
+                            "genome.fasta.bwt.2bit.64:md5,cd4bdf496eab05228a50c45ee43c1ed0",
+                            "genome.fasta.pac:md5,8569fbdb2c98c6fb16dfa73d8eacb070"
+                        ]
+                    ]
+                ],
+                "ref_dict": [
+                    [
+                        {
+                            "id": "genome"
+                        },
+                        "genome.dict:md5,8acf53706487c0ff79ad8d063d66c51a"
+                    ]
+                ],
+                "reference_fai": [
+                    [
+                        {
+                            "id": "genome"
+                        },
+                        "genome.fasta.fai:md5,3520cd30e1b100e55f578db9c855f685"
+                    ]
+                ],
+                "versions": [
+                    {
+                        "PREPARE_GENOME:SAMTOOLS_FAIDX": {
+                            "samtools": "1.22.1"
+                        }
+                    },
+                    {
+                        "PREPARE_GENOME:PICARD_CREATESEQUENCEDICTIONARY": {
+                            "picard": "3.4.0"
+                        }
+                    },
+                    {
+                        "PREPARE_GENOME:BWAMEM2_INDEX": {
+                            "bwamem2": "2.2.1"
+                        }
+                    }
+                ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-02T11:58:24.141721"
+        "timestamp": "2025-12-12T16:10:21.23821705"
     },
     "Test without bwamem2 index file path, with run_picard_collecthsmetrics=true and with ref_dict": {
         "content": [
-            [
-                "",
-                "bwamem2",
-                "bwamem2/reference.fasta.0123",
-                "bwamem2/reference.fasta.amb",
-                "bwamem2/reference.fasta.ann",
-                "bwamem2/reference.fasta.bwt.2bit.64",
-                "bwamem2/reference.fasta.pac"
-            ],
-            [
-                "",
-                "reference.fasta.fai",
-                "reference.fasta.sizes"
-            ]
+            {
+                "bwamem2_index": [
+                    [
+                        {
+                            "id": "genome"
+                        },
+                        [
+                            "genome.fasta.0123:md5,d73300d44f733bcdb7c988fc3ff3e3e9",
+                            "genome.fasta.amb:md5,1891c1de381b3a96d4e72f590fde20c1",
+                            "genome.fasta.ann:md5,2df4aa2d7580639fa0fcdbcad5e2e969",
+                            "genome.fasta.bwt.2bit.64:md5,cd4bdf496eab05228a50c45ee43c1ed0",
+                            "genome.fasta.pac:md5,8569fbdb2c98c6fb16dfa73d8eacb070"
+                        ]
+                    ]
+                ],
+                "ref_dict": [
+                    [
+                        {
+                            "id": "genome"
+                        },
+                        "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.dict"
+                    ]
+                ],
+                "reference_fai": [
+                    [
+                        {
+                            "id": "genome"
+                        },
+                        "genome.fasta.fai:md5,3520cd30e1b100e55f578db9c855f685"
+                    ]
+                ],
+                "versions": [
+                    {
+                        "PREPARE_GENOME:SAMTOOLS_FAIDX": {
+                            "samtools": "1.22.1"
+                        }
+                    },
+                    {
+                        "PREPARE_GENOME:BWAMEM2_INDEX": {
+                            "bwamem2": "2.2.1"
+                        }
+                    }
+                ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-02T11:57:18.592897"
+        "timestamp": "2025-12-12T16:10:10.23226572"
     },
     "Test without bwamem2 index file path and with run_picard_collecthsmetrics=false": {
         "content": [
-            [
-                "",
-                "bwamem2",
-                "bwamem2/reference.fasta.0123",
-                "bwamem2/reference.fasta.amb",
-                "bwamem2/reference.fasta.ann",
-                "bwamem2/reference.fasta.bwt.2bit.64",
-                "bwamem2/reference.fasta.pac"
-            ],
-            [
-                "",
-                "reference.fasta.fai",
-                "reference.fasta.sizes"
-            ]
+            {
+                "bwamem2_index": [
+                    [
+                        {
+                            "id": "genome"
+                        },
+                        [
+                            "genome.fasta.0123:md5,d73300d44f733bcdb7c988fc3ff3e3e9",
+                            "genome.fasta.amb:md5,1891c1de381b3a96d4e72f590fde20c1",
+                            "genome.fasta.ann:md5,2df4aa2d7580639fa0fcdbcad5e2e969",
+                            "genome.fasta.bwt.2bit.64:md5,cd4bdf496eab05228a50c45ee43c1ed0",
+                            "genome.fasta.pac:md5,8569fbdb2c98c6fb16dfa73d8eacb070"
+                        ]
+                    ]
+                ],
+                "ref_dict": [
+                    
+                ],
+                "reference_fai": [
+                    [
+                        {
+                            "id": "genome"
+                        },
+                        "genome.fasta.fai:md5,3520cd30e1b100e55f578db9c855f685"
+                    ]
+                ],
+                "versions": [
+                    {
+                        "PREPARE_GENOME:SAMTOOLS_FAIDX": {
+                            "samtools": "1.22.1"
+                        }
+                    },
+                    {
+                        "PREPARE_GENOME:BWAMEM2_INDEX": {
+                            "bwamem2": "2.2.1"
+                        }
+                    }
+                ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-02T11:56:19.206085"
+        "timestamp": "2025-12-12T16:09:59.55850842"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/local/prepare_genome/tests/nextflow.config b/subworkflows/local/prepare_genome/tests/nextflow.config
deleted file mode 100644
index c1510588..00000000
--- a/subworkflows/local/prepare_genome/tests/nextflow.config
+++ /dev/null
@@ -1,7 +0,0 @@
-// Load the basic test config
-includeConfig '../../../../tests/nextflow.config'
-
-
-params {
-    pipelines_testdata_base_path = params.pipelines_testdata_base_path + 'raredisease/'
-}

From ba22c67ebdc77f630001aca842291f352869a58f Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 12 Dec 2025 16:28:03 +0100
Subject: [PATCH 506/530] polish local subworkflows and tests

---
 subworkflows/local/prepare_genome/main.nf     |  30 ++---
 subworkflows/local/qc_bam/main.nf             |  77 ++++++-----
 subworkflows/local/qc_bam/tests/main.nf.test  |  74 ++++------
 .../local/qc_bam/tests/main.nf.test.snap      | 126 +++++++++++++-----
 .../local/qc_bam/tests/nextflow.config        |  11 --
 5 files changed, 166 insertions(+), 152 deletions(-)

diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf
index 260b8a60..b4c2736e 100644
--- a/subworkflows/local/prepare_genome/main.nf
+++ b/subworkflows/local/prepare_genome/main.nf
@@ -3,23 +3,22 @@
 
 include { BWAMEM2_INDEX                   } from '../../../modules/nf-core/bwamem2/index'
 include { SAMTOOLS_FAIDX                  } from '../../../modules/nf-core/samtools/faidx'
-include { PICARD_CREATESEQUENCEDICTIONARY } from '../../../modules/nf-core/picard/createsequencedictionary/main'
+include { PICARD_CREATESEQUENCEDICTIONARY } from '../../../modules/nf-core/picard/createsequencedictionary'
 
 workflow PREPARE_GENOME {
-
     take:
     ch_reference_fasta
     bwamem2
     skip_tools
-    run_picard_collecthsmetrics  // string: [mandatory for collecthsmetrics] bool
-    ref_dict                     // string: [mandatory for collecthsmetrics] path(ref_dict)
+    run_picard_collecthsmetrics // string: [mandatory for collecthsmetrics] bool
+    ref_dict // string: [mandatory for collecthsmetrics] path(ref_dict)
 
     main:
     // Initialize all channels that might be used later
-    ch_bwamem2_index      = channel.empty()
-    ch_reference_fai      = channel.empty()
-    ch_ref_dict           = channel.empty()
-    ch_versions           = channel.empty()
+    ch_bwamem2_index = channel.empty()
+    ch_reference_fai = channel.empty()
+    ch_ref_dict = channel.empty()
+    ch_versions = channel.empty()
 
     if (!("bwamem2_index" in skip_tools)) {
         if (bwamem2) {
@@ -27,16 +26,12 @@ workflow PREPARE_GENOME {
             ch_bwamem2_index = channel.fromPath(bwamem2, checkIfExists: true)
                 .map { index_dir -> tuple([id: index_dir.name], index_dir) }
                 .collect()
-
         }
         else {
             // Build index from reference FASTA when no pre-built index is provided
-            BWAMEM2_INDEX(
-                ch_reference_fasta
-            )
+            BWAMEM2_INDEX(ch_reference_fasta)
             ch_bwamem2_index = BWAMEM2_INDEX.out.index
             ch_versions = ch_versions.mix(BWAMEM2_INDEX.out.versions)
-
         }
     }
 
@@ -52,14 +47,12 @@ workflow PREPARE_GENOME {
         ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions)
     }
 
-    if (run_picard_collecthsmetrics){
+    if (run_picard_collecthsmetrics) {
         if (ref_dict) {
-        ch_ref_dict = channel.fromPath(ref_dict, checkIfExists: true).map { [[id: it.simpleName], it] }
+            ch_ref_dict = channel.fromPath(ref_dict, checkIfExists: true).map { dict -> [[id: dict.simpleName], dict] }
         }
         else {
-            PICARD_CREATESEQUENCEDICTIONARY(
-                ch_reference_fasta
-            )
+            PICARD_CREATESEQUENCEDICTIONARY(ch_reference_fasta)
             ch_ref_dict = PICARD_CREATESEQUENCEDICTIONARY.out.reference_dict
             ch_versions = ch_versions.mix(PICARD_CREATESEQUENCEDICTIONARY.out.versions)
         }
@@ -70,5 +63,4 @@ workflow PREPARE_GENOME {
     reference_fai = ch_reference_fai
     ref_dict      = ch_ref_dict
     versions      = ch_versions
-
 }
diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf
index d0f3db59..75661ddd 100644
--- a/subworkflows/local/qc_bam/main.nf
+++ b/subworkflows/local/qc_bam/main.nf
@@ -2,58 +2,57 @@
 // A quality check subworkflow for processed bam files.
 //
 
-include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../modules/nf-core/picard/collectmultiplemetrics/main'
-include { PICARD_COLLECTHSMETRICS } from '../../../modules/nf-core/picard/collecthsmetrics/main'
+include { PICARD_COLLECTHSMETRICS       } from '../../../modules/nf-core/picard/collecthsmetrics'
+include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../modules/nf-core/picard/collectmultiplemetrics'
 
 workflow QC_BAM {
     take:
-        ch_bam                      // channel: [mandatory] [ val(meta), path(bam)]
-        ch_bai                      // channel: [mandatory] [ val(meta), path(bai) ]
-        ch_reference_fasta          // channel: [mandatory] [ val(meta), path(reference_fasta) ]
-        ch_reference_fai            // channel: [mandatory] [ val(meta), path(reference_fai) ]
-        run_picard_collecthsmetrics // string:  [mandatory for picard_collecthsmetrics] bool
-        ch_bait_intervals           // channel: [mandatory for picard_collecthsmetrics] [ val(meta), path(bait_intervals) ]
-        ch_target_intervals         // channel: [mandatory for picard_collecthsmetrics] [ val(meta), path(target_intervals) ]
-        ch_ref_dict                 // channel: [mandatory for picard_collecthsmetrics] [ val(meta), path(ref_dict) ]
+    ch_bam // channel: [mandatory] [ val(meta), path(bam)]
+    ch_bai // channel: [mandatory] [ val(meta), path(bai) ]
+    ch_reference_fasta // channel: [mandatory] [ val(meta), path(reference_fasta) ]
+    ch_reference_fai // channel: [mandatory] [ val(meta), path(reference_fai) ]
+    run_picard_collecthsmetrics // string:  [mandatory for picard_collecthsmetrics] bool
+    ch_bait_intervals // channel: [mandatory for picard_collecthsmetrics] [ val(meta), path(bait_intervals) ]
+    ch_target_intervals // channel: [mandatory for picard_collecthsmetrics] [ val(meta), path(target_intervals) ]
+    ch_ref_dict // channel: [mandatory for picard_collecthsmetrics] [ val(meta), path(ref_dict) ]
 
     main:
 
-        ch_multiple_metrics = channel.empty()
-        ch_hs_metrics = channel.empty()
-        ch_versions = channel.empty()
+    ch_multiple_metrics = channel.empty()
+    ch_hs_metrics = channel.empty()
+    ch_versions = channel.empty()
 
-        ch_bam_bai = ch_bam.join(ch_bai, failOnDuplicate: true, failOnMismatch: true)
+    ch_bam_bai = ch_bam.join(ch_bai, failOnDuplicate: true, failOnMismatch: true)
 
-        PICARD_COLLECTMULTIPLEMETRICS(
-            ch_bam_bai,
-            ch_reference_fasta,
-            ch_reference_fai,
-        )
-
-        ch_multiple_metrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics
-        ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
+    PICARD_COLLECTMULTIPLEMETRICS(
+        ch_bam_bai,
+        ch_reference_fasta,
+        ch_reference_fai,
+    )
 
-        if (run_picard_collecthsmetrics) {
+    ch_multiple_metrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics
+    ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions)
 
-            ch_hsmetrics_in = ch_bam_bai
-                .combine(ch_bait_intervals)
-                .combine(ch_target_intervals)
+    if (run_picard_collecthsmetrics) {
 
+        ch_hsmetrics_in = ch_bam_bai
+            .combine(ch_bait_intervals)
+            .combine(ch_target_intervals)
 
-            PICARD_COLLECTHSMETRICS(
-                ch_hsmetrics_in,
-                ch_reference_fasta,
-                ch_reference_fai,
-                ch_ref_dict,
-                [[], []],
-            )
+        PICARD_COLLECTHSMETRICS(
+            ch_hsmetrics_in,
+            ch_reference_fasta,
+            ch_reference_fai,
+            ch_ref_dict,
+            [[], []],
+        )
 
-            ch_hs_metrics = PICARD_COLLECTHSMETRICS.out.metrics
-            ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
-        }
+        ch_hs_metrics = PICARD_COLLECTHSMETRICS.out.metrics
+        ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions)
+    }
 
     emit:
-        multiple_metrics = ch_multiple_metrics
-        hs_metrics = ch_hs_metrics
-        versions = ch_versions
+    multiple_metrics = ch_multiple_metrics
+    hs_metrics       = ch_hs_metrics
+    versions         = ch_versions
 }
diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test
index c310d2e4..3195852e 100644
--- a/subworkflows/local/qc_bam/tests/main.nf.test
+++ b/subworkflows/local/qc_bam/tests/main.nf.test
@@ -11,26 +11,22 @@ nextflow_workflow {
         when {
             config "./nextflow.config"
 
-            params {
-                outdir = "$outputDir"
-            }
-
             workflow {
                 """
                 input[0]  = channel.of(
                     [
                         [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'],
-                        [file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)]
+                        [file(params.pipelines_testdata_base_path + '/raredisease/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)]
                     ]
                 )
                 input[1]  = channel.of(
                     [
                         [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'],
-                        [file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)]
+                        [file(params.pipelines_testdata_base_path + '/raredisease/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)]
                     ]
                 )
-                input[2]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect()
-                input[3]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect()
+                input[2]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/raredisease/reference/reference.fasta', checkIfExists: true)).collect()
+                input[3]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/raredisease/reference/reference.fasta.fai', checkIfExists: true)).collect()
                 input[4]  = false
                 input[5]  = null
                 input[6]  = null
@@ -40,19 +36,13 @@ nextflow_workflow {
         }
 
         then {
-            // All files + folders produced by PICARD_COLLECTMULTIPLEMETRICS
-            def picard_collectmultiplemetrics_files = getAllFilesFromDir(
-                params.outdir + '/picard_collectmultiplemetrics',
-                relative: true, includeDir: true
-            )
-
             assert workflow.success
-            assert snapshot(
-                    picard_collectmultiplemetrics_files
-                ).match()
-
-            // Only PICARD_COLLECTMULTIPLEMETRICS should run
-            assert workflow.out.versions.size() == 1
+            assert snapshot(sanitizeOutput(workflow.out).collectEntries { key, val ->
+                if (key == "versions") {
+                    return [key, val.collect { path(it).yaml }]
+                }
+                return [key, val]
+            }).match()
         }
 
     }
@@ -62,56 +52,38 @@ nextflow_workflow {
         when {
             config "./nextflow.config"
 
-            params {
-                outdir = "$outputDir"
-            }
-
             workflow {
                 """
                 input[0]  = channel.of(
                     [
                         [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'],
-                        [file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)]
+                        [file(params.pipelines_testdata_base_path + '/raredisease/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)]
                     ]
                 )
                 input[1]  = channel.of(
                     [
                         [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'],
-                        [file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)]
+                        [file(params.pipelines_testdata_base_path + '/raredisease/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)]
                     ]
                 )
-                input[2]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect()
-                input[3]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect()
+                input[2]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/raredisease/reference/reference.fasta', checkIfExists: true)).collect()
+                input[3]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/raredisease/reference/reference.fasta.fai', checkIfExists: true)).collect()
                 input[4]  = true
-                input[5]  = channel.fromPath(params.pipelines_testdata_base_path + 'reference/target.bed', checkIfExists: true).collect()
-                input[6]  = channel.fromPath(params.pipelines_testdata_base_path + 'reference/target.bed', checkIfExists: true).collect()
-                input[7]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect()
+                input[5]  = channel.fromPath(params.pipelines_testdata_base_path + '/raredisease/reference/target.bed', checkIfExists: true).collect()
+                input[6]  = channel.fromPath(params.pipelines_testdata_base_path + '/raredisease/reference/target.bed', checkIfExists: true).collect()
+                input[7]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/raredisease/reference/reference.dict', checkIfExists: true)).collect()
                 """
             }
         }
 
         then {
-            // All files + folders produced by PICARD_COLLECTMULTIPLEMETRICS
-            def picard_collectmultiplemetrics_files = getAllFilesFromDir(
-                params.outdir + '/picard_collectmultiplemetrics',
-                relative: true, includeDir: true
-            )
-            // All files + folders produced by PICARD_COLLECTHSMETRICS
-            def picard_collecthsmetrics_files = getAllFilesFromDir(
-                params.outdir + '/picard_collecthsmetrics',
-                relative: true, includeDir: true
-            )
-
             assert workflow.success
-            assert snapshot(
-                    picard_collectmultiplemetrics_files,
-                    picard_collecthsmetrics_files
-                ).match()
-
-            // PICARD_COLLECTMULTIPLEMETRICS and PICARD_COLLECTHSMETRICS run
-            assert workflow.out.versions.size() == 2
+            assert snapshot(sanitizeOutput(workflow.out).collectEntries { key, val ->
+                if (key == "versions") {
+                    return [key, val.collect { path(it).yaml }]
+                }
+                return [key, val]
+            }).match()
         }
-
     }
-
 }
diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap
index b0ce00e1..36cb6b29 100644
--- a/subworkflows/local/qc_bam/tests/main.nf.test.snap
+++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap
@@ -1,50 +1,112 @@
 {
     "Test with run_picard_collecthsmetrics=false": {
         "content": [
-            [
-                "",
-                "earlycasualcaiman.CollectMultipleMetrics.alignment_summary_metrics",
-                "earlycasualcaiman.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "earlycasualcaiman.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "earlycasualcaiman.CollectMultipleMetrics.insert_size_histogram.pdf",
-                "earlycasualcaiman.CollectMultipleMetrics.insert_size_metrics",
-                "earlycasualcaiman.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "earlycasualcaiman.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "earlycasualcaiman.CollectMultipleMetrics.quality_distribution.pdf",
-                "earlycasualcaiman.CollectMultipleMetrics.quality_distribution_metrics",
-                "earlycasualcaiman.CollectMultipleMetrics.read_length_histogram.pdf"
-            ]
+            {
+                "hs_metrics": [
+                    
+                ],
+                "multiple_metrics": [
+                    [
+                        {
+                            "id": "earlycasualcaiman",
+                            "sample": "earlycasualcaiman",
+                            "single_end": false,
+                            "num_lanes": 1,
+                            "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'",
+                            "lane": 1,
+                            "sex": 1,
+                            "phenotype": 1,
+                            "paternal": 0,
+                            "maternal": 0,
+                            "case_id": "justhusky"
+                        },
+                        [
+                            "earlycasualcaiman.CollectMultipleMetrics.alignment_summary_metrics:md5,8c8e5853c6cbf03f025583bb0fda9113",
+                            "earlycasualcaiman.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,a8a072fd1c92cbeef2d20803e5957968",
+                            "earlycasualcaiman.CollectMultipleMetrics.insert_size_metrics:md5,bcf2d7c097ccee4d5bd83f81696c6879",
+                            "earlycasualcaiman.CollectMultipleMetrics.quality_by_cycle_metrics:md5,8f0b70b234951a64705cf6d2ccb06109",
+                            "earlycasualcaiman.CollectMultipleMetrics.quality_distribution_metrics:md5,0c5d65609cb9d1bb0afb63b4c2627669"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    {
+                        "QC_BAM:PICARD_COLLECTMULTIPLEMETRICS": {
+                            "picard": "3.4.0"
+                        }
+                    }
+                ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-02T15:05:56.507859"
+        "timestamp": "2025-12-12T16:25:16.687447363"
     },
     "Test with run_picard_collecthsmetrics=true": {
         "content": [
-            [
-                "",
-                "earlycasualcaiman.CollectMultipleMetrics.alignment_summary_metrics",
-                "earlycasualcaiman.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "earlycasualcaiman.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "earlycasualcaiman.CollectMultipleMetrics.insert_size_histogram.pdf",
-                "earlycasualcaiman.CollectMultipleMetrics.insert_size_metrics",
-                "earlycasualcaiman.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "earlycasualcaiman.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "earlycasualcaiman.CollectMultipleMetrics.quality_distribution.pdf",
-                "earlycasualcaiman.CollectMultipleMetrics.quality_distribution_metrics",
-                "earlycasualcaiman.CollectMultipleMetrics.read_length_histogram.pdf"
-            ],
-            [
-                "",
-                "earlycasualcaiman.CollectHsMetrics.coverage_metrics"
-            ]
+            {
+                "hs_metrics": [
+                    [
+                        {
+                            "id": "earlycasualcaiman",
+                            "sample": "earlycasualcaiman",
+                            "single_end": false,
+                            "num_lanes": 1,
+                            "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'",
+                            "lane": 1,
+                            "sex": 1,
+                            "phenotype": 1,
+                            "paternal": 0,
+                            "maternal": 0,
+                            "case_id": "justhusky"
+                        },
+                        "earlycasualcaiman.CollectHsMetrics.coverage_metrics:md5,a1b193af1934726edcc75fe5299fb73a"
+                    ]
+                ],
+                "multiple_metrics": [
+                    [
+                        {
+                            "id": "earlycasualcaiman",
+                            "sample": "earlycasualcaiman",
+                            "single_end": false,
+                            "num_lanes": 1,
+                            "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'",
+                            "lane": 1,
+                            "sex": 1,
+                            "phenotype": 1,
+                            "paternal": 0,
+                            "maternal": 0,
+                            "case_id": "justhusky"
+                        },
+                        [
+                            "earlycasualcaiman.CollectMultipleMetrics.alignment_summary_metrics:md5,7edc24dc3d3fe414a470200eca8e968f",
+                            "earlycasualcaiman.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,498b9654e61aaa31818251eeeb8fff92",
+                            "earlycasualcaiman.CollectMultipleMetrics.insert_size_metrics:md5,81816a34524bb5e00da75d1c1178e8ef",
+                            "earlycasualcaiman.CollectMultipleMetrics.quality_by_cycle_metrics:md5,14d451f56f603f2b06bdf6227615b8b0",
+                            "earlycasualcaiman.CollectMultipleMetrics.quality_distribution_metrics:md5,1e1ce607caed451c0cc05395023672e5"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    {
+                        "QC_BAM:PICARD_COLLECTMULTIPLEMETRICS": {
+                            "picard": "3.4.0"
+                        }
+                    },
+                    {
+                        "QC_BAM:PICARD_COLLECTHSMETRICS": {
+                            "picard": "3.4.0"
+                        }
+                    }
+                ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-02T15:08:24.865168"
+        "timestamp": "2025-12-12T16:26:35.596343224"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/local/qc_bam/tests/nextflow.config b/subworkflows/local/qc_bam/tests/nextflow.config
index 1907f805..d6bf5ea2 100644
--- a/subworkflows/local/qc_bam/tests/nextflow.config
+++ b/subworkflows/local/qc_bam/tests/nextflow.config
@@ -1,20 +1,9 @@
-// Load the basic test config
-includeConfig '../../../../tests/nextflow.config'
-
-
-params {
-    pipelines_testdata_base_path = params.pipelines_testdata_base_path + 'raredisease/'
-}
-
 process {
-
     withName: PICARD_COLLECTHSMETRICS {
         ext.args = { [
             "--COVERAGE_CAP 50000",
             "--METRIC_ACCUMULATION_LEVEL ALL_READS",
             "--TMP_DIR ."
 			].join(' ') }
-
     }
-
 }

From 4201300f6322c869d3a8cd689a514d794e91dbbf Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 12 Dec 2025 16:56:45 +0100
Subject: [PATCH 507/530] bam are unstable

---
 nf-test.config                                |  3 +-
 subworkflows/local/prepare_genome/main.nf     | 12 ++---
 .../local/prepare_genome/tests/main.nf.test   | 19 +++----
 tests/.nftignore                              |  4 +-
 tests/MiSeq.nf.test                           | 18 +++++--
 tests/MiSeq.nf.test.snap                      | 19 ++++---
 tests/MiSeq_PairedEnd.nf.test                 |  6 ++-
 tests/MiSeq_PairedEnd.nf.test.snap            | 10 ++--
 tests/NovaSeq6000.nf.test                     |  6 ++-
 tests/NovaSeq6000.nf.test.snap                | 19 +++----
 tests/NovaSeq6000_subsample.nf.test           | 12 ++++-
 tests/NovaSeq6000_subsample.nf.test.snap      | 50 +++++++------------
 tests/PromethION.nf.test                      |  6 ++-
 tests/PromethION.nf.test.snap                 |  5 +-
 14 files changed, 102 insertions(+), 87 deletions(-)

diff --git a/nf-test.config b/nf-test.config
index fa368ccb..71deaff9 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -19,6 +19,7 @@ config {
 
     // load the necessary plugins
     plugins {
-        load "nft-utils@0.0.7"
+        load "nft-bam@0.4.0"
+        load "nft-utils@0.0.8"
     }
 }
diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf
index b4c2736e..96811a78 100644
--- a/subworkflows/local/prepare_genome/main.nf
+++ b/subworkflows/local/prepare_genome/main.nf
@@ -2,16 +2,16 @@
 // Prepare reference genome files
 
 include { BWAMEM2_INDEX                   } from '../../../modules/nf-core/bwamem2/index'
-include { SAMTOOLS_FAIDX                  } from '../../../modules/nf-core/samtools/faidx'
 include { PICARD_CREATESEQUENCEDICTIONARY } from '../../../modules/nf-core/picard/createsequencedictionary'
+include { SAMTOOLS_FAIDX                  } from '../../../modules/nf-core/samtools/faidx'
 
 workflow PREPARE_GENOME {
     take:
     ch_reference_fasta
     bwamem2
     skip_tools
-    run_picard_collecthsmetrics // string: [mandatory for collecthsmetrics] bool
-    ref_dict // string: [mandatory for collecthsmetrics] path(ref_dict)
+    run_picard_collecthsmetrics // Boolean: [mandatory for collecthsmetrics]
+    ref_dict // path: [mandatory for collecthsmetrics] path(ref_dict)
 
     main:
     // Initialize all channels that might be used later
@@ -21,14 +21,14 @@ workflow PREPARE_GENOME {
     ch_versions = channel.empty()
 
     if (!("bwamem2_index" in skip_tools)) {
+        // Use pre-built index when --bwamem2 parameter is provided
+        // Or build index from reference FASTA
         if (bwamem2) {
-            // Use pre-built index when --bwamem2 parameter is provided
             ch_bwamem2_index = channel.fromPath(bwamem2, checkIfExists: true)
                 .map { index_dir -> tuple([id: index_dir.name], index_dir) }
                 .collect()
         }
         else {
-            // Build index from reference FASTA when no pre-built index is provided
             BWAMEM2_INDEX(ch_reference_fasta)
             ch_bwamem2_index = BWAMEM2_INDEX.out.index
             ch_versions = ch_versions.mix(BWAMEM2_INDEX.out.versions)
@@ -36,8 +36,6 @@ workflow PREPARE_GENOME {
     }
 
     if (!("samtools_faidx" in skip_tools)) {
-
-        // Assume ch_fasta emits tuple(meta, fasta)
         SAMTOOLS_FAIDX(
             ch_reference_fasta,
             [[:], []],
diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test b/subworkflows/local/prepare_genome/tests/main.nf.test
index acca322d..2c1b715e 100644
--- a/subworkflows/local/prepare_genome/tests/main.nf.test
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test
@@ -10,13 +10,12 @@ nextflow_workflow {
 
         when {
             params {
-                outdir = "$outputDir"
-                run_picard_collecthsmetrics = true
-
+                run_picard_collecthsmetrics = false
             }
+
             workflow {
                 """
-                input[0]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/modules/data/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)).collect()
+                input[0]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/raredisease/reference/reference.fasta', checkIfExists: true)).collect()
                 input[1]  = null
                 input[2]  = ''
                 input[3]  = false
@@ -40,17 +39,16 @@ nextflow_workflow {
 
         when {
             params {
-                outdir = "$outputDir"
                 run_picard_collecthsmetrics = true
-
             }
+
             workflow {
                 """
-                input[0]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/modules/data/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)).collect()
+                input[0]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/raredisease/reference/reference.fasta', checkIfExists: true)).collect()
                 input[1]  = null
                 input[2]  = ''
                 input[3]  = true
-                input[4]  = params.pipelines_testdata_base_path + '/modules/data/genomics/homo_sapiens/genome/genome.dict'
+                input[4]  = params.pipelines_testdata_base_path + '/raredisease/reference/reference.dict'
                 """
             }
         }
@@ -70,13 +68,12 @@ nextflow_workflow {
 
         when {
             params {
-                outdir = "$outputDir"
                 run_picard_collecthsmetrics = true
-
             }
+
             workflow {
                 """
-                input[0]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/modules/data/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)).collect()
+                input[0]  = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/raredisease/reference/reference.fasta', checkIfExists: true)).collect()
                 input[1]  = null
                 input[2]  = ''
                 input[3]  = true
diff --git a/tests/.nftignore b/tests/.nftignore
index ee3b4013..a2ee3634 100644
--- a/tests/.nftignore
+++ b/tests/.nftignore
@@ -1,4 +1,6 @@
 .DS_Store
+bwamem2_mem/*.bam
+bwamem2_mem/*.bam.bai
 fastqc/*_fastqc.{html,zip}
 fastqscreen/*_screen.html
 multiqc/{global_report,group_reports/*}/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
@@ -13,9 +15,9 @@ multiqc/{global_report,group_reports/*}/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,p
 multiqc/{global_report,group_reports/*}/multiqc_report.html
 picard_collectmultiplemetrics/*.pdf
 picard_collectmultiplemetrics/*_metrics
+picard_collectmultiplemetrics/*_summary_metrics
 picard_collectmultiplemetrics/alignment_summary_metrics
 picard_collectmultiplemetrics/base_distribution_by_cycle_metrics
 picard_collectmultiplemetrics/quality_by_cycle_metrics
 picard_collectmultiplemetrics/quality_distribution_metrics
-picard_collectmultiplemetrics/*_summary_metrics
 pipeline_info/*.{html,json,txt,yml}
diff --git a/tests/MiSeq.nf.test b/tests/MiSeq.nf.test
index ec406936..8cd63574 100644
--- a/tests/MiSeq.nf.test
+++ b/tests/MiSeq.nf.test
@@ -27,6 +27,8 @@ nextflow_pipeline {
                 params.outdir,
                 ignoreFile: 'tests/.nftignore'
             )
+            // bam_files: All bam files
+            def bam_files  = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
             assert workflow.success
             assertAll(
                 { assert snapshot(
@@ -35,7 +37,9 @@ nextflow_pipeline {
                     // All stable path names, with a relative path
                     stable_name,
                     // All files with stable contents
-                    stable_path
+                    stable_path,
+                    // All bam files
+                    bam_files.isEmpty() ? 'No BAM files' : bam_files.collect { file -> file.getName() + ":md5," +  bam(file.toString()).readsMD5 },
                 ).match() }
             )
         }
@@ -62,6 +66,8 @@ nextflow_pipeline {
                 params.outdir,
                 ignoreFile: 'tests/.nftignore'
             )
+            // bam_files: All bam files
+            def bam_files  = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
             assert workflow.success
             assertAll(
                 { assert snapshot(
@@ -70,7 +76,9 @@ nextflow_pipeline {
                     // All stable path names, with a relative path
                     stable_name,
                     // All files with stable contents
-                    stable_path
+                    stable_path,
+                    // All bam files
+                    bam_files.isEmpty() ? 'No BAM files' : bam_files.collect { file -> file.getName() + ":md5," +  bam(file.toString()).readsMD5 },
                 ).match() }
             )
         }
@@ -97,6 +105,8 @@ nextflow_pipeline {
                 params.outdir,
                 ignoreFile: 'tests/.nftignore'
             )
+            // bam_files: All bam files
+            def bam_files  = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
             assert workflow.success
             assertAll(
                 { assert snapshot(
@@ -105,7 +115,9 @@ nextflow_pipeline {
                     // All stable path names, with a relative path
                     stable_name,
                     // All files with stable contents
-                    stable_path
+                    stable_path,
+                    // All bam files
+                    bam_files.isEmpty() ? 'No BAM files' : bam_files.collect { file -> file.getName() + ":md5," +  bam(file.toString()).readsMD5 },
                 ).match() }
             )
         }
diff --git a/tests/MiSeq.nf.test.snap b/tests/MiSeq.nf.test.snap
index b286d463..d5df70ba 100644
--- a/tests/MiSeq.nf.test.snap
+++ b/tests/MiSeq.nf.test.snap
@@ -28,13 +28,14 @@
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc"
-            ]
+            ],
+            "No BAM files"
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-02T12:24:49.888119"
+        "timestamp": "2025-12-12T16:48:15.085074556"
     },
     "MiSeq data test (single end reads)": {
         "content": [
@@ -220,8 +221,6 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "SAMPLE_SINGLE_END_01.bam:md5,fc03db7366825685afd45c46cb0769f6",
-                "SAMPLE_SINGLE_END_01.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
                 "SAMPLE_SINGLE_END_01_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
                 "SAMPLE_SINGLE_END_01_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
                 "fastq_screen_plot.txt:md5,7d120ba49a8a9220f85efb05e55bfae1",
@@ -259,13 +258,16 @@
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "SAMPLE_SINGLE_END_01_seqfu.tsv:md5,33a9e44386f308d43881a58394b6b17c",
                 "SAMPLE_SINGLE_END_01_seqfu_mqc.txt:md5,e67e819605ab49182aacf1d676dc885d"
+            ],
+            [
+                "SAMPLE_SINGLE_END_01.bam:md5,9acd4428f95f70c1393671680ab9270f"
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-12T10:00:01.095899935"
+        "timestamp": "2025-12-12T16:45:20.420081882"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
@@ -403,8 +405,6 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "SAMPLE_SINGLE_END_01.bam:md5,fc03db7366825685afd45c46cb0769f6",
-                "SAMPLE_SINGLE_END_01.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
                 "SAMPLE_SINGLE_END_01_screen.png:md5,ad98ae0f39335aede67e0a233cf16616",
                 "SAMPLE_SINGLE_END_01_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5",
                 "fastq_screen_plot.txt:md5,7d120ba49a8a9220f85efb05e55bfae1",
@@ -432,12 +432,15 @@
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "SAMPLE_SINGLE_END_01_seqfu.tsv:md5,33a9e44386f308d43881a58394b6b17c",
                 "SAMPLE_SINGLE_END_01_seqfu_mqc.txt:md5,e67e819605ab49182aacf1d676dc885d"
+            ],
+            [
+                "SAMPLE_SINGLE_END_01.bam:md5,9acd4428f95f70c1393671680ab9270f"
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-12T10:00:43.048743949"
+        "timestamp": "2025-12-12T16:47:54.570558579"
     }
 }
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.nf.test b/tests/MiSeq_PairedEnd.nf.test
index 20a8c0f0..b77f5043 100644
--- a/tests/MiSeq_PairedEnd.nf.test
+++ b/tests/MiSeq_PairedEnd.nf.test
@@ -27,6 +27,8 @@ nextflow_pipeline {
                 params.outdir,
                 ignoreFile: 'tests/.nftignore'
             )
+            // bam_files: All bam files
+            def bam_files  = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
             assert workflow.success
             assertAll(
                 { assert snapshot(
@@ -35,7 +37,9 @@ nextflow_pipeline {
                     // All stable path names, with a relative path
                     stable_name,
                     // All files with stable contents
-                    stable_path
+                    stable_path,
+                    // All bam files
+                    bam_files.isEmpty() ? 'No BAM files' : bam_files.collect { file -> file.getName() + ":md5," +  bam(file.toString()).readsMD5 },
                 ).match() }
             )
         }
diff --git a/tests/MiSeq_PairedEnd.nf.test.snap b/tests/MiSeq_PairedEnd.nf.test.snap
index 26cdac05..346eaa7b 100644
--- a/tests/MiSeq_PairedEnd.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.nf.test.snap
@@ -332,10 +332,6 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "SAMPLE_PAIRED_END_1_01.bam:md5,a2816c39f5907fad768bb65d6a75e757",
-                "SAMPLE_PAIRED_END_1_01.bam.bai:md5,8d7c1e80974444bbdb6361408b09e188",
-                "SAMPLE_PAIRED_END_2_02.bam:md5,f82c6ab5a81de087823a398616bcec08",
-                "SAMPLE_PAIRED_END_2_02.bam.bai:md5,3c4bdff0f906f2234fdeee8eea719210",
                 "SAMPLE_PAIRED_END_1_01_1_screen.png:md5,f52ddd0e65f23f68dd8d58d5453417db",
                 "SAMPLE_PAIRED_END_1_01_1_screen.txt:md5,921b08eeb461a2aa1bd42bba53900f70",
                 "SAMPLE_PAIRED_END_1_01_2_screen.png:md5,908f4fceea8aa546106efdaa7ca78f7d",
@@ -414,12 +410,16 @@
                 "SAMPLE_PAIRED_END_1_01_seqfu_mqc.txt:md5,0aca00c7f64454af520c7e08ec595d2b",
                 "SAMPLE_PAIRED_END_2_02_seqfu.tsv:md5,44a5cb826e001d58208a5855938fa82b",
                 "SAMPLE_PAIRED_END_2_02_seqfu_mqc.txt:md5,ac1740de9ef142c99c993fa9824ead63"
+            ],
+            [
+                "SAMPLE_PAIRED_END_1_01.bam:md5,ac811b20d56132f5e039b3e8fd217405",
+                "SAMPLE_PAIRED_END_2_02.bam:md5,57892fc4314e66e8e20de4f5d82f9b5d"
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-12T10:02:03.991667099"
+        "timestamp": "2025-12-12T16:49:17.100345817"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.nf.test b/tests/NovaSeq6000.nf.test
index 68b47344..5c8b9f0f 100644
--- a/tests/NovaSeq6000.nf.test
+++ b/tests/NovaSeq6000.nf.test
@@ -26,6 +26,8 @@ nextflow_pipeline {
                 params.outdir,
                 ignoreFile: 'tests/.nftignore'
             )
+            // bam_files: All bam files
+            def bam_files  = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
             assert workflow.success
             assertAll(
                 { assert snapshot(
@@ -34,7 +36,9 @@ nextflow_pipeline {
                     // All stable path names, with a relative path
                     stable_name,
                     // All files with stable contents
-                    stable_path
+                    stable_path,
+                    // All bam files
+                    bam_files.isEmpty() ? 'No BAM files' : bam_files.collect { file -> file.getName() + ":md5," +  bam(file.toString()).readsMD5 },
                 ).match() }
             )
         }
diff --git a/tests/NovaSeq6000.nf.test.snap b/tests/NovaSeq6000.nf.test.snap
index d4b88720..80f833aa 100644
--- a/tests/NovaSeq6000.nf.test.snap
+++ b/tests/NovaSeq6000.nf.test.snap
@@ -758,16 +758,6 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "Sample1_01.bam:md5,9985af901ea635009ba79dfbdae3ef69",
-                "Sample1_01.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
-                "Sample23_03.bam:md5,be8ecb43e6b7df5de7487e51eb5534c7",
-                "Sample23_03.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
-                "SampleA_02.bam:md5,8a253e12f6c92ec39da8d87385895203",
-                "SampleA_02.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
-                "Undetermined_05.bam:md5,c9c86417ec4f050c2a0d775b9af39d29",
-                "Undetermined_05.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
-                "sampletest_04.bam:md5,62395d6d4b5589aae0b0928f4e333805",
-                "sampletest_04.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
                 "Sample1_01_screen.png:md5,562256290643b51e4374c2225a15f463",
                 "Sample1_01_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
                 "Sample23_03_screen.png:md5,6bb2caf67b9b2ed25d3d5f32c343e9ab",
@@ -956,12 +946,19 @@
                 "Undetermined_05_seqfu_mqc.txt:md5,bd8be908362c5cb08a72f8ae7ab41b0d",
                 "sampletest_04_seqfu.tsv:md5,a5bea0b9c6015dd1a201ffd433e9b377",
                 "sampletest_04_seqfu_mqc.txt:md5,2180961655bbc8a12f0152d6a4b803a2"
+            ],
+            [
+                "Sample1_01.bam:md5,d06ccfde49cc474faebcab2ebf71b324",
+                "Sample23_03.bam:md5,5ff9f554c6255fd07d3841c6616c5031",
+                "SampleA_02.bam:md5,250d0031520e59ee59a7112ab1ea32e1",
+                "Undetermined_05.bam:md5,8fcc158f1e0736b366152d5e187644ca",
+                "sampletest_04.bam:md5,f80371e37421d97499b3bfd55221ed00"
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-12T13:39:06.915289541"
+        "timestamp": "2025-12-12T16:50:45.065344275"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000_subsample.nf.test b/tests/NovaSeq6000_subsample.nf.test
index 8ea215c2..14775ca5 100644
--- a/tests/NovaSeq6000_subsample.nf.test
+++ b/tests/NovaSeq6000_subsample.nf.test
@@ -25,6 +25,8 @@ nextflow_pipeline {
                 params.outdir,
                 ignoreFile: 'tests/.nftignore'
             )
+            // bam_files: All bam files
+            def bam_files  = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
             assert workflow.success
             assertAll(
                 { assert snapshot(
@@ -33,7 +35,9 @@ nextflow_pipeline {
                     // All stable path names, with a relative path
                     stable_name,
                     // All files with stable contents
-                    stable_path
+                    stable_path,
+                    // All bam files
+                    bam_files.isEmpty() ? 'No BAM files' : bam_files.collect { file -> file.getName() + ":md5," +  bam(file.toString()).readsMD5 },
                 ).match() }
             )
         }
@@ -59,6 +63,8 @@ nextflow_pipeline {
                 params.outdir,
                 ignoreFile: 'tests/.nftignore'
             )
+            // bam_files: All bam files
+            def bam_files  = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
             assert workflow.success
             assertAll(
                 { assert snapshot(
@@ -67,7 +73,9 @@ nextflow_pipeline {
                     // All stable path names, with a relative path
                     stable_name,
                     // All files with stable contents
-                    stable_path
+                    stable_path,
+                    // All bam files
+                    bam_files.isEmpty() ? 'No BAM files' : bam_files.collect { file -> file.getName() + ":md5," +  bam(file.toString()).readsMD5 },
                 ).match() }
             )
         }
diff --git a/tests/NovaSeq6000_subsample.nf.test.snap b/tests/NovaSeq6000_subsample.nf.test.snap
index 6ed75de7..98b4c72f 100644
--- a/tests/NovaSeq6000_subsample.nf.test.snap
+++ b/tests/NovaSeq6000_subsample.nf.test.snap
@@ -767,16 +767,6 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "Sample1_01.bam:md5,3aed5f0ecfaae2fea821fa829d942799",
-                "Sample1_01.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
-                "Sample23_03.bam:md5,9d48a531653f29f0c6ecf1cad32f4e25",
-                "Sample23_03.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
-                "SampleA_02.bam:md5,8048e27a75e5ce37c05a33857d3b5eda",
-                "SampleA_02.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
-                "Undetermined_05.bam:md5,a6de4550335b8aaa06737c24cdd00682",
-                "Undetermined_05.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
-                "sampletest_04.bam:md5,a34a795fe365d327199454dc9a88047a",
-                "sampletest_04.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714",
                 "Sample1_01_screen.png:md5,57b1664bc6c8e82cc0ce14802ad0dc0f",
                 "Sample1_01_screen.txt:md5,14d10b0c3b63e18f223a0dc589abee36",
                 "Sample23_03_screen.png:md5,41b4f556865a2f55a93f63e520812fad",
@@ -970,13 +960,20 @@
                 "SampleA_02_SampleA_S2_L001_R1_001.fastq.gz:md5,f99d5407aac64cb36451c6f0a1db5ade",
                 "Undetermined_05_Undetermined_S0_L001_R1_001.fastq.gz:md5,104dbbef386db0eef3e02c586feb01a1",
                 "sampletest_04_sampletest_S4_L001_R1_001.fastq.gz:md5,30aa24a51e27e24390ac8b90158df8f2"
+            ],
+            [
+                "Sample1_01.bam:md5,fc83fc447ae236a94236f4993c405bed",
+                "Sample23_03.bam:md5,ee9f99e6c368e86af5516fd4ff2189d1",
+                "SampleA_02.bam:md5,3f378f47f7007916bc28921090c4e5e6",
+                "Undetermined_05.bam:md5,2841f21f7f70634f21505ac803ff8221",
+                "sampletest_04.bam:md5,3d1cd701ad22dacc6b194ea16582d647"
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-12T11:45:23.711988389"
+        "timestamp": "2025-12-12T16:52:05.081506101"
     },
     "NovaSeq6000 data test relative sample size": {
         "content": [
@@ -1746,16 +1743,6 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "Sample1_01.bam:md5,3545e16e264d357d190230e4dcee1cb2",
-                "Sample1_01.bam.bai:md5,e9c66d695e26fa2408d81ce006243ed4",
-                "Sample23_03.bam:md5,f3ccb87aa45fd8923796bb5bad36587c",
-                "Sample23_03.bam.bai:md5,e9c66d695e26fa2408d81ce006243ed4",
-                "SampleA_02.bam:md5,c07b657960b8073575bfebc40efb5ac0",
-                "SampleA_02.bam.bai:md5,e9c66d695e26fa2408d81ce006243ed4",
-                "Undetermined_05.bam:md5,e40757c83cdac87d6ade270bbb151057",
-                "Undetermined_05.bam.bai:md5,e9c66d695e26fa2408d81ce006243ed4",
-                "sampletest_04.bam:md5,adce222eaa16c05c123491465eaf96a5",
-                "sampletest_04.bam.bai:md5,e9c66d695e26fa2408d81ce006243ed4",
                 "Sample1_01_screen.png:md5,57b1664bc6c8e82cc0ce14802ad0dc0f",
                 "Sample1_01_screen.txt:md5,20926a4045b2ecf4bc76007047cc645a",
                 "Sample23_03_screen.png:md5,41b4f556865a2f55a93f63e520812fad",
@@ -1949,13 +1936,20 @@
                 "SampleA_02_SampleA_S2_L001_R1_001.fastq.gz:md5,f7897b87d06b13e9877f297169a678f1",
                 "Undetermined_05_Undetermined_S0_L001_R1_001.fastq.gz:md5,c9e790094f5c2b2bad247ae96f804d1e",
                 "sampletest_04_sampletest_S4_L001_R1_001.fastq.gz:md5,e35f5e6cd500f18ce05cc061fb471a76"
+            ],
+            [
+                "Sample1_01.bam:md5,9ccdbdc2adf0b9204a66060fefcec7f9",
+                "Sample23_03.bam:md5,dcd15b5562762f2e4d51c5ab1aef601d",
+                "SampleA_02.bam:md5,c9c0c519c072e1c808a9d58f17841008",
+                "Undetermined_05.bam:md5,691b83f3c015cf5f2b28ab6d0581d03c",
+                "sampletest_04.bam:md5,b13db1c95389474f089f870b906d3fc0"
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-12T11:46:34.325054847"
+        "timestamp": "2025-12-12T16:53:21.397671601"
     },
     "NovaSeq6000 data test sample size exceeds available reads": {
         "content": [
@@ -2725,16 +2719,6 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "Sample1_01.bam:md5,aa475f13ecd19f3a7792f2580093888a",
-                "Sample1_01.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
-                "Sample23_03.bam:md5,98795a0c8227b0278ba40394c5d241a7",
-                "Sample23_03.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
-                "SampleA_02.bam:md5,c24b053cb4a9008d9fcfc98c2ed2e8f8",
-                "SampleA_02.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
-                "Undetermined_05.bam:md5,210e17b1af6c72514a769bf3c168547c",
-                "Undetermined_05.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
-                "sampletest_04.bam:md5,35fbd12d959ed55e53b6310fe9d6ccb5",
-                "sampletest_04.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c",
                 "Sample1_01_screen.png:md5,57b1664bc6c8e82cc0ce14802ad0dc0f",
                 "Sample1_01_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
                 "Sample23_03_screen.png:md5,41b4f556865a2f55a93f63e520812fad",
@@ -2941,6 +2925,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-12T11:47:44.482972598"
+        "timestamp": "2025-12-12T16:54:35.347526634"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.nf.test b/tests/PromethION.nf.test
index 1af31ddd..1af5ef06 100644
--- a/tests/PromethION.nf.test
+++ b/tests/PromethION.nf.test
@@ -28,6 +28,8 @@ nextflow_pipeline {
                 params.outdir,
                 ignoreFile: 'tests/.nftignore'
             )
+            // bam_files: All bam files
+            def bam_files  = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
             assert workflow.success
             assertAll(
                 { assert snapshot(
@@ -36,7 +38,9 @@ nextflow_pipeline {
                     // All stable path names, with a relative path
                     stable_name,
                     // All files with stable contents
-                    stable_path
+                    stable_path,
+                    // All bam files
+                    bam_files.isEmpty() ? 'No BAM files' : bam_files.collect { file -> file.getName() + ":md5," +  bam(file.toString()).readsMD5 },
                 ).match() }
             )
         }
diff --git a/tests/PromethION.nf.test.snap b/tests/PromethION.nf.test.snap
index 30dda963..0d421ffe 100644
--- a/tests/PromethION.nf.test.snap
+++ b/tests/PromethION.nf.test.snap
@@ -132,12 +132,13 @@
                 "genome.fa.sizes:md5,f154a58a25ba9c4d386003eaa1bb731b",
                 "hg001_01_seqfu.tsv:md5,b133752c897afbb4d8721b911fa117d4",
                 "hg001_01_seqfu_mqc.txt:md5,42e3506b02ceb72a6f05cb174505e722"
-            ]
+            ],
+            "No BAM files"
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-12T10:05:23.380990836"
+        "timestamp": "2025-12-12T16:55:17.977465362"
     }
 }
\ No newline at end of file

From 8a49714333300e44adeff1109e92fb6123ca726e Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 12 Dec 2025 18:20:40 +0100
Subject: [PATCH 508/530] fix prepare_genome tests and snapshots

---
 .../local/prepare_genome/tests/main.nf.test   | 44 ++++++++--
 .../prepare_genome/tests/main.nf.test.snap    | 84 ++++++-------------
 2 files changed, 59 insertions(+), 69 deletions(-)

diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test b/subworkflows/local/prepare_genome/tests/main.nf.test
index 2c1b715e..89a45ced 100644
--- a/subworkflows/local/prepare_genome/tests/main.nf.test
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test
@@ -7,7 +7,6 @@ nextflow_workflow {
     tag 'prepare_genome'
 
     test("Test without bwamem2 index file path and with run_picard_collecthsmetrics=false") {
-
         when {
             params {
                 run_picard_collecthsmetrics = false
@@ -27,16 +26,27 @@ nextflow_workflow {
         then {
             assert workflow.success
             assert snapshot(sanitizeOutput(workflow.out).collectEntries { key, val ->
-                if (key == "versions") {
+                if (key == "bwamem2_index") {
+                    return [key, val.collect { [path(it[1]).list().collect { it }] }]
+                }
+                else if (key == "ref_dict") {
+                    if (val) {
+                        return [key, val]
+                    } else {
+                        return ['ref_dict']
+                    }
+                }
+                else if (key == "reference_fai") {
+                    return [key, val.collect { path(it[1]) }]
+                }
+                else if (key == "versions") {
                     return [key, val.collect { path(it).yaml }]
                 }
-                return [key, val]
             }).match()
         }
     }
 
     test("Test without bwamem2 index file path, with run_picard_collecthsmetrics=true and with ref_dict") {
-
         when {
             params {
                 run_picard_collecthsmetrics = true
@@ -56,16 +66,27 @@ nextflow_workflow {
         then {
             assert workflow.success
             assert snapshot(sanitizeOutput(workflow.out).collectEntries { key, val ->
-                if (key == "versions") {
+                if (key == "bwamem2_index") {
+                    return [key, val.collect { [path(it[1]).list().collect { it }] }]
+                }
+                else if (key == "ref_dict") {
+                    if (val) {
+                        return [key, val.collect { it[1] }]
+                    } else {
+                        return ['ref_dict']
+                    }
+                }
+                else if (key == "reference_fai") {
+                    return [key, val.collect { path(it[1]) }]
+                }
+                else if (key == "versions") {
                     return [key, val.collect { path(it).yaml }]
                 }
-                return [key, val]
             }).match()
         }
     }
 
     test("Test without bwamem2 index file path, with run_picard_collecthsmetrics=true and without ref_dict") {
-
         when {
             params {
                 run_picard_collecthsmetrics = true
@@ -85,10 +106,15 @@ nextflow_workflow {
         then {
             assert workflow.success
             assert snapshot(sanitizeOutput(workflow.out).collectEntries { key, val ->
-                if (key == "versions") {
+                if (key == "bwamem2_index") {
+                    return [key, val.collect { [path(it[1]).list().collect { it }] }]
+                }
+                else if (key in ["ref_dict", "reference_fai"]) {
+                    return [key, val.collect { path(it[1]) }]
+                }
+                else if (key == "versions") {
                     return [key, val.collect { path(it).yaml }]
                 }
-                return [key, val]
             }).match()
         }
     }
diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test.snap b/subworkflows/local/prepare_genome/tests/main.nf.test.snap
index 59526cc9..48f010f5 100644
--- a/subworkflows/local/prepare_genome/tests/main.nf.test.snap
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test.snap
@@ -4,33 +4,20 @@
             {
                 "bwamem2_index": [
                     [
-                        {
-                            "id": "genome"
-                        },
                         [
-                            "genome.fasta.0123:md5,d73300d44f733bcdb7c988fc3ff3e3e9",
-                            "genome.fasta.amb:md5,1891c1de381b3a96d4e72f590fde20c1",
-                            "genome.fasta.ann:md5,2df4aa2d7580639fa0fcdbcad5e2e969",
-                            "genome.fasta.bwt.2bit.64:md5,cd4bdf496eab05228a50c45ee43c1ed0",
-                            "genome.fasta.pac:md5,8569fbdb2c98c6fb16dfa73d8eacb070"
+                            "reference.fasta.0123:md5,0f0ff4414949e6787a25a563f19e2a3b",
+                            "reference.fasta.amb:md5,0a85644af00f9a856d874381d24e7803",
+                            "reference.fasta.ann:md5,8fdb46970ca95a4ef54f5f1a02d233cd",
+                            "reference.fasta.bwt.2bit.64:md5,3c0df9450afc5cb0ad5e85870829d9d0",
+                            "reference.fasta.pac:md5,96b449e1316067fdfba91b1399687bc2"
                         ]
                     ]
                 ],
                 "ref_dict": [
-                    [
-                        {
-                            "id": "genome"
-                        },
-                        "genome.dict:md5,8acf53706487c0ff79ad8d063d66c51a"
-                    ]
+                    "genome.dict:md5,f91ebda0d0bd72d5c22c1f1bcbbc563c"
                 ],
                 "reference_fai": [
-                    [
-                        {
-                            "id": "genome"
-                        },
-                        "genome.fasta.fai:md5,3520cd30e1b100e55f578db9c855f685"
-                    ]
+                    "reference.fasta.fai:md5,bf4047e05f95deb372eb8ffd601cbc29"
                 ],
                 "versions": [
                     {
@@ -55,40 +42,27 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-12T16:10:21.23821705"
+        "timestamp": "2025-12-12T18:17:59.250873828"
     },
     "Test without bwamem2 index file path, with run_picard_collecthsmetrics=true and with ref_dict": {
         "content": [
             {
                 "bwamem2_index": [
                     [
-                        {
-                            "id": "genome"
-                        },
                         [
-                            "genome.fasta.0123:md5,d73300d44f733bcdb7c988fc3ff3e3e9",
-                            "genome.fasta.amb:md5,1891c1de381b3a96d4e72f590fde20c1",
-                            "genome.fasta.ann:md5,2df4aa2d7580639fa0fcdbcad5e2e969",
-                            "genome.fasta.bwt.2bit.64:md5,cd4bdf496eab05228a50c45ee43c1ed0",
-                            "genome.fasta.pac:md5,8569fbdb2c98c6fb16dfa73d8eacb070"
+                            "reference.fasta.0123:md5,0f0ff4414949e6787a25a563f19e2a3b",
+                            "reference.fasta.amb:md5,0a85644af00f9a856d874381d24e7803",
+                            "reference.fasta.ann:md5,8fdb46970ca95a4ef54f5f1a02d233cd",
+                            "reference.fasta.bwt.2bit.64:md5,3c0df9450afc5cb0ad5e85870829d9d0",
+                            "reference.fasta.pac:md5,96b449e1316067fdfba91b1399687bc2"
                         ]
                     ]
                 ],
                 "ref_dict": [
-                    [
-                        {
-                            "id": "genome"
-                        },
-                        "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.dict"
-                    ]
+                    "/nf-core/test-datasets/raredisease/reference/reference.dict"
                 ],
                 "reference_fai": [
-                    [
-                        {
-                            "id": "genome"
-                        },
-                        "genome.fasta.fai:md5,3520cd30e1b100e55f578db9c855f685"
-                    ]
+                    "reference.fasta.fai:md5,bf4047e05f95deb372eb8ffd601cbc29"
                 ],
                 "versions": [
                     {
@@ -108,35 +82,25 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-12T16:10:10.23226572"
+        "timestamp": "2025-12-12T18:19:48.876692867"
     },
     "Test without bwamem2 index file path and with run_picard_collecthsmetrics=false": {
         "content": [
             {
                 "bwamem2_index": [
                     [
-                        {
-                            "id": "genome"
-                        },
                         [
-                            "genome.fasta.0123:md5,d73300d44f733bcdb7c988fc3ff3e3e9",
-                            "genome.fasta.amb:md5,1891c1de381b3a96d4e72f590fde20c1",
-                            "genome.fasta.ann:md5,2df4aa2d7580639fa0fcdbcad5e2e969",
-                            "genome.fasta.bwt.2bit.64:md5,cd4bdf496eab05228a50c45ee43c1ed0",
-                            "genome.fasta.pac:md5,8569fbdb2c98c6fb16dfa73d8eacb070"
+                            "reference.fasta.0123:md5,0f0ff4414949e6787a25a563f19e2a3b",
+                            "reference.fasta.amb:md5,0a85644af00f9a856d874381d24e7803",
+                            "reference.fasta.ann:md5,8fdb46970ca95a4ef54f5f1a02d233cd",
+                            "reference.fasta.bwt.2bit.64:md5,3c0df9450afc5cb0ad5e85870829d9d0",
+                            "reference.fasta.pac:md5,96b449e1316067fdfba91b1399687bc2"
                         ]
                     ]
                 ],
-                "ref_dict": [
-                    
-                ],
+                "ref_dict": null,
                 "reference_fai": [
-                    [
-                        {
-                            "id": "genome"
-                        },
-                        "genome.fasta.fai:md5,3520cd30e1b100e55f578db9c855f685"
-                    ]
+                    "reference.fasta.fai:md5,bf4047e05f95deb372eb8ffd601cbc29"
                 ],
                 "versions": [
                     {
@@ -156,6 +120,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-12T16:09:59.55850842"
+        "timestamp": "2025-12-12T17:27:20.079142637"
     }
 }
\ No newline at end of file

From b39fff7495dec23c8527c4e1fec51b7fb3186f31 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 12 Dec 2025 18:24:28 +0100
Subject: [PATCH 509/530] code polish

---
 subworkflows/local/qc_bam/tests/nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/qc_bam/tests/nextflow.config b/subworkflows/local/qc_bam/tests/nextflow.config
index d6bf5ea2..1954ffe6 100644
--- a/subworkflows/local/qc_bam/tests/nextflow.config
+++ b/subworkflows/local/qc_bam/tests/nextflow.config
@@ -4,6 +4,6 @@ process {
             "--COVERAGE_CAP 50000",
             "--METRIC_ACCUMULATION_LEVEL ALL_READS",
             "--TMP_DIR ."
-			].join(' ') }
+        ].join(' ') }
     }
 }

From 7d4b433bd0ac988379191c46abff158a1b08fb30 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Mon, 15 Dec 2025 12:22:57 +0100
Subject: [PATCH 510/530] remove file from snapshot

---
 .../local/prepare_genome/tests/main.nf.test      | 16 +++++++++++++---
 .../local/prepare_genome/tests/main.nf.test.snap | 10 +++++-----
 2 files changed, 18 insertions(+), 8 deletions(-)

diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test b/subworkflows/local/prepare_genome/tests/main.nf.test
index 89a45ced..8c12edc4 100644
--- a/subworkflows/local/prepare_genome/tests/main.nf.test
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test
@@ -31,7 +31,7 @@ nextflow_workflow {
                 }
                 else if (key == "ref_dict") {
                     if (val) {
-                        return [key, val]
+                        return [key, val.collect { file(it[1]).name }]
                     } else {
                         return ['ref_dict']
                     }
@@ -42,6 +42,7 @@ nextflow_workflow {
                 else if (key == "versions") {
                     return [key, val.collect { path(it).yaml }]
                 }
+                return [key, val]
             }).match()
         }
     }
@@ -71,7 +72,7 @@ nextflow_workflow {
                 }
                 else if (key == "ref_dict") {
                     if (val) {
-                        return [key, val.collect { it[1] }]
+                        return [key, val.collect { file(it[1]).name }]
                     } else {
                         return ['ref_dict']
                     }
@@ -82,6 +83,7 @@ nextflow_workflow {
                 else if (key == "versions") {
                     return [key, val.collect { path(it).yaml }]
                 }
+                return [key, val]
             }).match()
         }
     }
@@ -109,12 +111,20 @@ nextflow_workflow {
                 if (key == "bwamem2_index") {
                     return [key, val.collect { [path(it[1]).list().collect { it }] }]
                 }
-                else if (key in ["ref_dict", "reference_fai"]) {
+                else if (key == "ref_dict") {
+                    if (val) {
+                        return [key, val.collect { file(it[1]).name }]
+                    } else {
+                        return ['ref_dict']
+                    }
+                }
+                else if (key == "reference_fai") {
                     return [key, val.collect { path(it[1]) }]
                 }
                 else if (key == "versions") {
                     return [key, val.collect { path(it).yaml }]
                 }
+                return [key, val]
             }).match()
         }
     }
diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test.snap b/subworkflows/local/prepare_genome/tests/main.nf.test.snap
index 48f010f5..55f9865c 100644
--- a/subworkflows/local/prepare_genome/tests/main.nf.test.snap
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test.snap
@@ -14,7 +14,7 @@
                     ]
                 ],
                 "ref_dict": [
-                    "genome.dict:md5,f91ebda0d0bd72d5c22c1f1bcbbc563c"
+                    "genome.dict"
                 ],
                 "reference_fai": [
                     "reference.fasta.fai:md5,bf4047e05f95deb372eb8ffd601cbc29"
@@ -42,7 +42,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-12T18:17:59.250873828"
+        "timestamp": "2025-12-15T11:57:16.786415613"
     },
     "Test without bwamem2 index file path, with run_picard_collecthsmetrics=true and with ref_dict": {
         "content": [
@@ -59,7 +59,7 @@
                     ]
                 ],
                 "ref_dict": [
-                    "/nf-core/test-datasets/raredisease/reference/reference.dict"
+                    "reference.dict"
                 ],
                 "reference_fai": [
                     "reference.fasta.fai:md5,bf4047e05f95deb372eb8ffd601cbc29"
@@ -82,7 +82,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-12T18:19:48.876692867"
+        "timestamp": "2025-12-15T11:56:46.871893037"
     },
     "Test without bwamem2 index file path and with run_picard_collecthsmetrics=false": {
         "content": [
@@ -120,6 +120,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-12T17:27:20.079142637"
+        "timestamp": "2025-12-15T12:00:16.296041182"
     }
 }
\ No newline at end of file

From 44889d27b5928d78a3ba4d9586e2cb0f5d2c870d Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Mon, 15 Dec 2025 13:03:19 +0100
Subject: [PATCH 511/530] fix qc_bam subworkflow tests

---
 .../local/prepare_genome/tests/main.nf.test   | 35 ++++-----
 .../prepare_genome/tests/main.nf.test.snap    |  3 +-
 subworkflows/local/qc_bam/tests/main.nf.test  | 24 +++++-
 .../local/qc_bam/tests/main.nf.test.snap      | 74 ++++---------------
 4 files changed, 51 insertions(+), 85 deletions(-)

diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test b/subworkflows/local/prepare_genome/tests/main.nf.test
index 8c12edc4..efa012e2 100644
--- a/subworkflows/local/prepare_genome/tests/main.nf.test
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test
@@ -26,15 +26,14 @@ nextflow_workflow {
         then {
             assert workflow.success
             assert snapshot(sanitizeOutput(workflow.out).collectEntries { key, val ->
-                if (key == "bwamem2_index") {
+                if (!val) {
+                    return null
+                }
+                else if (key == "bwamem2_index") {
                     return [key, val.collect { [path(it[1]).list().collect { it }] }]
                 }
                 else if (key == "ref_dict") {
-                    if (val) {
-                        return [key, val.collect { file(it[1]).name }]
-                    } else {
-                        return ['ref_dict']
-                    }
+                    return [key, val.collect { file(it[1]).name }]
                 }
                 else if (key == "reference_fai") {
                     return [key, val.collect { path(it[1]) }]
@@ -67,15 +66,14 @@ nextflow_workflow {
         then {
             assert workflow.success
             assert snapshot(sanitizeOutput(workflow.out).collectEntries { key, val ->
-                if (key == "bwamem2_index") {
+                if (!val) {
+                    return null
+                }
+                else if (key == "bwamem2_index") {
                     return [key, val.collect { [path(it[1]).list().collect { it }] }]
                 }
                 else if (key == "ref_dict") {
-                    if (val) {
-                        return [key, val.collect { file(it[1]).name }]
-                    } else {
-                        return ['ref_dict']
-                    }
+                    return [key, val.collect { file(it[1]).name }]
                 }
                 else if (key == "reference_fai") {
                     return [key, val.collect { path(it[1]) }]
@@ -83,7 +81,6 @@ nextflow_workflow {
                 else if (key == "versions") {
                     return [key, val.collect { path(it).yaml }]
                 }
-                return [key, val]
             }).match()
         }
     }
@@ -108,15 +105,14 @@ nextflow_workflow {
         then {
             assert workflow.success
             assert snapshot(sanitizeOutput(workflow.out).collectEntries { key, val ->
-                if (key == "bwamem2_index") {
+                if (!val) {
+                    return null
+                }
+                else if (key == "bwamem2_index") {
                     return [key, val.collect { [path(it[1]).list().collect { it }] }]
                 }
                 else if (key == "ref_dict") {
-                    if (val) {
-                        return [key, val.collect { file(it[1]).name }]
-                    } else {
-                        return ['ref_dict']
-                    }
+                    return [key, val.collect { file(it[1]).name }]
                 }
                 else if (key == "reference_fai") {
                     return [key, val.collect { path(it[1]) }]
@@ -124,7 +120,6 @@ nextflow_workflow {
                 else if (key == "versions") {
                     return [key, val.collect { path(it).yaml }]
                 }
-                return [key, val]
             }).match()
         }
     }
diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test.snap b/subworkflows/local/prepare_genome/tests/main.nf.test.snap
index 55f9865c..6fbdc7e0 100644
--- a/subworkflows/local/prepare_genome/tests/main.nf.test.snap
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test.snap
@@ -98,7 +98,6 @@
                         ]
                     ]
                 ],
-                "ref_dict": null,
                 "reference_fai": [
                     "reference.fasta.fai:md5,bf4047e05f95deb372eb8ffd601cbc29"
                 ],
@@ -120,6 +119,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-15T12:00:16.296041182"
+        "timestamp": "2025-12-15T12:47:55.989932088"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test
index 3195852e..86605790 100644
--- a/subworkflows/local/qc_bam/tests/main.nf.test
+++ b/subworkflows/local/qc_bam/tests/main.nf.test
@@ -38,7 +38,17 @@ nextflow_workflow {
         then {
             assert workflow.success
             assert snapshot(sanitizeOutput(workflow.out).collectEntries { key, val ->
-                if (key == "versions") {
+                if (!val) {
+                    return null
+                }
+                else if (key == "hs_metrics") {
+                    return [key, val.collect { file(it[1].toString()).name }]
+                }
+                else if (key == "multiple_metrics") {
+                    println val[0][1]
+                    return [key, val.collect { it[1].collect{ file(it.toString()).name } } ]
+                }
+                else if (key == "versions") {
                     return [key, val.collect { path(it).yaml }]
                 }
                 return [key, val]
@@ -79,7 +89,17 @@ nextflow_workflow {
         then {
             assert workflow.success
             assert snapshot(sanitizeOutput(workflow.out).collectEntries { key, val ->
-                if (key == "versions") {
+                if (!val) {
+                    return null
+                }
+                else if (key == "hs_metrics") {
+                    return [key, val.collect { file(it[1].toString()).name }]
+                }
+                else if (key == "multiple_metrics") {
+                    println val[0][1]
+                    return [key, val.collect { it[1].collect{ file(it.toString()).name } } ]
+                }
+                else if (key == "versions") {
                     return [key, val.collect { path(it).yaml }]
                 }
                 return [key, val]
diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap
index 36cb6b29..16fd63af 100644
--- a/subworkflows/local/qc_bam/tests/main.nf.test.snap
+++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap
@@ -2,31 +2,13 @@
     "Test with run_picard_collecthsmetrics=false": {
         "content": [
             {
-                "hs_metrics": [
-                    
-                ],
                 "multiple_metrics": [
                     [
-                        {
-                            "id": "earlycasualcaiman",
-                            "sample": "earlycasualcaiman",
-                            "single_end": false,
-                            "num_lanes": 1,
-                            "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'",
-                            "lane": 1,
-                            "sex": 1,
-                            "phenotype": 1,
-                            "paternal": 0,
-                            "maternal": 0,
-                            "case_id": "justhusky"
-                        },
-                        [
-                            "earlycasualcaiman.CollectMultipleMetrics.alignment_summary_metrics:md5,8c8e5853c6cbf03f025583bb0fda9113",
-                            "earlycasualcaiman.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,a8a072fd1c92cbeef2d20803e5957968",
-                            "earlycasualcaiman.CollectMultipleMetrics.insert_size_metrics:md5,bcf2d7c097ccee4d5bd83f81696c6879",
-                            "earlycasualcaiman.CollectMultipleMetrics.quality_by_cycle_metrics:md5,8f0b70b234951a64705cf6d2ccb06109",
-                            "earlycasualcaiman.CollectMultipleMetrics.quality_distribution_metrics:md5,0c5d65609cb9d1bb0afb63b4c2627669"
-                        ]
+                        "earlycasualcaiman.CollectMultipleMetrics.alignment_summary_metrics",
+                        "earlycasualcaiman.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                        "earlycasualcaiman.CollectMultipleMetrics.insert_size_metrics",
+                        "earlycasualcaiman.CollectMultipleMetrics.quality_by_cycle_metrics",
+                        "earlycasualcaiman.CollectMultipleMetrics.quality_distribution_metrics"
                     ]
                 ],
                 "versions": [
@@ -42,51 +24,21 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-12T16:25:16.687447363"
+        "timestamp": "2025-12-15T13:01:33.166952245"
     },
     "Test with run_picard_collecthsmetrics=true": {
         "content": [
             {
                 "hs_metrics": [
-                    [
-                        {
-                            "id": "earlycasualcaiman",
-                            "sample": "earlycasualcaiman",
-                            "single_end": false,
-                            "num_lanes": 1,
-                            "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'",
-                            "lane": 1,
-                            "sex": 1,
-                            "phenotype": 1,
-                            "paternal": 0,
-                            "maternal": 0,
-                            "case_id": "justhusky"
-                        },
-                        "earlycasualcaiman.CollectHsMetrics.coverage_metrics:md5,a1b193af1934726edcc75fe5299fb73a"
-                    ]
+                    "earlycasualcaiman.CollectHsMetrics.coverage_metrics"
                 ],
                 "multiple_metrics": [
                     [
-                        {
-                            "id": "earlycasualcaiman",
-                            "sample": "earlycasualcaiman",
-                            "single_end": false,
-                            "num_lanes": 1,
-                            "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'",
-                            "lane": 1,
-                            "sex": 1,
-                            "phenotype": 1,
-                            "paternal": 0,
-                            "maternal": 0,
-                            "case_id": "justhusky"
-                        },
-                        [
-                            "earlycasualcaiman.CollectMultipleMetrics.alignment_summary_metrics:md5,7edc24dc3d3fe414a470200eca8e968f",
-                            "earlycasualcaiman.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,498b9654e61aaa31818251eeeb8fff92",
-                            "earlycasualcaiman.CollectMultipleMetrics.insert_size_metrics:md5,81816a34524bb5e00da75d1c1178e8ef",
-                            "earlycasualcaiman.CollectMultipleMetrics.quality_by_cycle_metrics:md5,14d451f56f603f2b06bdf6227615b8b0",
-                            "earlycasualcaiman.CollectMultipleMetrics.quality_distribution_metrics:md5,1e1ce607caed451c0cc05395023672e5"
-                        ]
+                        "earlycasualcaiman.CollectMultipleMetrics.alignment_summary_metrics",
+                        "earlycasualcaiman.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                        "earlycasualcaiman.CollectMultipleMetrics.insert_size_metrics",
+                        "earlycasualcaiman.CollectMultipleMetrics.quality_by_cycle_metrics",
+                        "earlycasualcaiman.CollectMultipleMetrics.quality_distribution_metrics"
                     ]
                 ],
                 "versions": [
@@ -107,6 +59,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-12T16:26:35.596343224"
+        "timestamp": "2025-12-15T13:02:46.733316125"
     }
 }
\ No newline at end of file

From eaf4328aff28574732830434bb2ffbfb9decbce8 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Mon, 15 Dec 2025 13:34:33 +0100
Subject: [PATCH 512/530] update and improve CHANGELOG

---
 CHANGELOG.md | 43 ++++++++++++++++++++++++++-----------------
 1 file changed, 26 insertions(+), 17 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b9d51f40..19c811e2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,44 +9,53 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 
 ### `Added`
 
-- [#114](https://github.com/nf-core/seqinspector/pull/114/) Update CI
-- [#75](https://github.com/nf-core/seqinspector/pull/75) Set up nft-utils
-- [#68](https://github.com/nf-core/seqinspector/pull/68) Add tool selector
+- [#13](https://github.com/nf-core/seqinspector/pull/13) Generate reports per run, per project and per lane
 - [#20](https://github.com/nf-core/seqinspector/pull/20) Use tags to generate group reports
-- [#13](https://github.com/nf-core/seqinspector/pull/13) Generate reports per run, per project and per lane.
-- [#49](https://github.com/nf-core/seqinspector/pull/49) Merge with template 3.0.2.
-- [#56](https://github.com/nf-core/seqinspector/pull/56) Added SeqFu stats module.
-- [#50](https://github.com/nf-core/seqinspector/pull/50) Add an optional subsampling step.
-- [#51](https://github.com/nf-core/seqinspector/pull/51) Add nf-test to CI.
+- [#50](https://github.com/nf-core/seqinspector/pull/50) Add an optional subsampling step
+- [#51](https://github.com/nf-core/seqinspector/pull/51) Add nf-test to CI
+- [#53](https://github.com/nf-core/seqinspector/pull/53) Add FastQ-Screen database multiplexing and limit scope of nf-test in CI
+- [#56](https://github.com/nf-core/seqinspector/pull/56) Added SeqFu stats module
 - [#63](https://github.com/nf-core/seqinspector/pull/63) Contribution guidelines added about displaying results for new tools
-- [#53](https://github.com/nf-core/seqinspector/pull/53) Add FastQ-Screen database multiplexing and limit scope of nf-test in CI.
+- [#68](https://github.com/nf-core/seqinspector/pull/68) Add tool selector
+- [#75](https://github.com/nf-core/seqinspector/pull/75) Set up nft-utils
 - [#96](https://github.com/nf-core/seqinspector/pull/96) Added missing citations to citation tool
 - [#103](https://github.com/nf-core/seqinspector/pull/103) Configure full-tests
-- [#94](https://github.com/nf-core/seqinspector/issues/94) Test data validation
-- [#86](https://github.com/nf-core/seqinspector/issues/86) Update lists of default steps in the pipeline
-- [#84](https://github.com/nf-core/seqinspector/issues/84) Short summary of seqinspector in README.md
-- [#110](https://github.com/nf-core/seqinspector/pull/110) Update input schema to accept either tar file or directory as rundir, and fastq messages and patterns.
+- [#108](https://github.com/nf-core/seqinspector/pull/108) Update lists of default steps in the pipeline
+- [#108](https://github.com/nf-core/seqinspector/pull/108) Test data validation
+- [#110](https://github.com/nf-core/seqinspector/pull/110) Update input schema to accept either tar file or directory as rundir, and fastq messages and patterns
+- [#111](https://github.com/nf-core/seqinspector/pull/111) Short summary of seqinspector in README.md
 - [#127](https://github.com/nf-core/seqinspector/pull/127) Added alignment tools - bwamem2 - index and mem
 - [#128](https://github.com/nf-core/seqinspector/pull/128) Added Picard tools - Collect Multiple Mterics to collect QC metrics
 - [#132](https://github.com/nf-core/seqinspector/pull/132) Added a bwamem2 index params for faster output
 - [#135](https://github.com/nf-core/seqinspector/pull/135) Added index section to MultiQC reports to facilitate report navigation (#125)
 - [#151](https://github.com/nf-core/seqinspector/pull/151) Added a prepare_genome subworkflow to handle bwamem2 indexing
-- [#156](https://github.com/nf-core/seqinspector/pull/156) Added relative sample_size and warning when a sample has less reads than desired sample_size.
-- [#158](https://github.com/nf-core/seqinspector/pull/158) Moved picard_collectmultiplemetrics to the subworkflow QC_BAM
+- [#153](https://github.com/nf-core/seqinspector/pull/153) update README and usage.md
+- [#156](https://github.com/nf-core/seqinspector/pull/156) Added relative sample_size and warning when a sample has less reads than desired sample_size
 - [#159](https://github.com/nf-core/seqinspector/pull/159) Added a subworkflow QC_BAM including picard_collecthsmetrics for alignment QC of hybrid-selection data
 - [#162](https://github.com/nf-core/seqinspector/pull/162) Add tests for prepare_genome subworkflow
 
 ### `Fixed`
 
-- [#71](https://github.com/nf-core/seqinspector/pull/71) FASTQSCREEN does not fail when multiple reads are provided.
-- [#94](https://github.com/nf-core/seqinspector/issues/94) Go through and validate test data
+- [#71](https://github.com/nf-core/seqinspector/pull/71) FASTQSCREEN does not fail when multiple reads are provided
 - [#99](https://github.com/nf-core/seqinspector/pull/99) Fix group reports for paired reads
 - [#107](https://github.com/nf-core/seqinspector/pull/107) Put SeqFU-stats section reports together
+- [#108](https://github.com/nf-core/seqinspector/pull/108) Go through and validate test data
 - [#112](https://github.com/nf-core/seqinspector/pull/112) Making fastq_screen_references value to use parentDir
 - [#121](https://github.com/nf-core/seqinspector/pull/121) Cleanup sample naming for MultiQC report (#105)
 - [#162](https://github.com/nf-core/seqinspector/pull/162) Fix bugs in qc_bam and prepare_genome subworkflows and add tests
 - [#163](https://github.com/nf-core/seqinspector/pull/163) Run fastqscreen with subsampled data if available
 
+### `Changed`
+
+- [#49](https://github.com/nf-core/seqinspector/pull/49) Template update for nf-core/tools v3.0.2
+- [#69](https://github.com/nf-core/seqinspector/pull/69) Template update for nf-core/tools v3.1.0
+- [#74](https://github.com/nf-core/seqinspector/pull/74) Template update for nf-core/tools v3.2.0
+- [#114](https://github.com/nf-core/seqinspector/pull/114) Update CI
+- [#133](https://github.com/nf-core/seqinspector/pull/133) Template update for nf-core/tools v3.4.1
+- [#144](https://github.com/nf-core/seqinspector/pull/144) Template update for nf-core/tools v3.5.1
+- [#158](https://github.com/nf-core/seqinspector/pull/158) Moved picard_collectmultiplemetrics to the subworkflow QC_BAM
+- [#164](https://github.com/nf-core/seqinspector/pull/164) Refactor local subworkflow and pipeline tests
+
 ### `Dependencies`
 
 - [#116](https://github.com/nf-core/seqinspector/pull/116) Update MultiQC to 1.28

From bb585d05602ecc4f0fe9fb7d731f6bae2035021f Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Mon, 15 Dec 2025 13:59:35 +0100
Subject: [PATCH 513/530] add missing entries

---
 CHANGELOG.md | 23 ++++++++++++++++-------
 1 file changed, 16 insertions(+), 7 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 19c811e2..e15ca7ee 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,27 +9,30 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 
 ### `Added`
 
+- [#2](https://github.com/nf-core/seqinspector/pull/2) Input workflow and schema definition
 - [#13](https://github.com/nf-core/seqinspector/pull/13) Generate reports per run, per project and per lane
 - [#20](https://github.com/nf-core/seqinspector/pull/20) Use tags to generate group reports
 - [#50](https://github.com/nf-core/seqinspector/pull/50) Add an optional subsampling step
 - [#51](https://github.com/nf-core/seqinspector/pull/51) Add nf-test to CI
-- [#53](https://github.com/nf-core/seqinspector/pull/53) Add FastQ-Screen database multiplexing and limit scope of nf-test in CI
+- [#53](https://github.com/nf-core/seqinspector/pull/53), [#64](https://github.com/nf-core/seqinspector/pull/64) Add FastQ-Screen database multiplexing and limit scope of nf-test in CI
 - [#56](https://github.com/nf-core/seqinspector/pull/56) Added SeqFu stats module
 - [#63](https://github.com/nf-core/seqinspector/pull/63) Contribution guidelines added about displaying results for new tools
 - [#68](https://github.com/nf-core/seqinspector/pull/68) Add tool selector
 - [#75](https://github.com/nf-core/seqinspector/pull/75) Set up nft-utils
 - [#96](https://github.com/nf-core/seqinspector/pull/96) Added missing citations to citation tool
+- [#100](https://github.com/nf-core/seqinspector/pull/100) Added official logos
 - [#103](https://github.com/nf-core/seqinspector/pull/103) Configure full-tests
-- [#108](https://github.com/nf-core/seqinspector/pull/108) Update lists of default steps in the pipeline
-- [#108](https://github.com/nf-core/seqinspector/pull/108) Test data validation
+- [#106](https://github.com/nf-core/seqinspector/pull/106) Parse rundir metadata
+- [#108](https://github.com/nf-core/seqinspector/pull/108) Update lists of default steps in the pipeline (#86)
+- [#108](https://github.com/nf-core/seqinspector/pull/108) Test data validation (#94)
 - [#110](https://github.com/nf-core/seqinspector/pull/110) Update input schema to accept either tar file or directory as rundir, and fastq messages and patterns
-- [#111](https://github.com/nf-core/seqinspector/pull/111) Short summary of seqinspector in README.md
+- [#111](https://github.com/nf-core/seqinspector/pull/111) Short summary of seqinspector in README.md (#84)
 - [#127](https://github.com/nf-core/seqinspector/pull/127) Added alignment tools - bwamem2 - index and mem
 - [#128](https://github.com/nf-core/seqinspector/pull/128) Added Picard tools - Collect Multiple Mterics to collect QC metrics
 - [#132](https://github.com/nf-core/seqinspector/pull/132) Added a bwamem2 index params for faster output
 - [#135](https://github.com/nf-core/seqinspector/pull/135) Added index section to MultiQC reports to facilitate report navigation (#125)
+- [#148](https://github.com/nf-core/seqinspector/pull/148) Add Tubemap
 - [#151](https://github.com/nf-core/seqinspector/pull/151) Added a prepare_genome subworkflow to handle bwamem2 indexing
-- [#153](https://github.com/nf-core/seqinspector/pull/153) update README and usage.md
 - [#156](https://github.com/nf-core/seqinspector/pull/156) Added relative sample_size and warning when a sample has less reads than desired sample_size
 - [#159](https://github.com/nf-core/seqinspector/pull/159) Added a subworkflow QC_BAM including picard_collecthsmetrics for alignment QC of hybrid-selection data
 - [#162](https://github.com/nf-core/seqinspector/pull/162) Add tests for prepare_genome subworkflow
@@ -37,22 +40,28 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 ### `Fixed`
 
 - [#71](https://github.com/nf-core/seqinspector/pull/71) FASTQSCREEN does not fail when multiple reads are provided
+- [#77](https://github.com/nf-core/seqinspector/pull/77) Use a params for fastqscreen csv file, and not the hardcoded example one
 - [#99](https://github.com/nf-core/seqinspector/pull/99) Fix group reports for paired reads
 - [#107](https://github.com/nf-core/seqinspector/pull/107) Put SeqFU-stats section reports together
-- [#108](https://github.com/nf-core/seqinspector/pull/108) Go through and validate test data
+- [#108](https://github.com/nf-core/seqinspector/pull/108) Go through and validate test data (#94)
 - [#112](https://github.com/nf-core/seqinspector/pull/112) Making fastq_screen_references value to use parentDir
 - [#121](https://github.com/nf-core/seqinspector/pull/121) Cleanup sample naming for MultiQC report (#105)
+- [#150](https://github.com/nf-core/seqinspector/pull/150) Fix pipeline linting issues
 - [#162](https://github.com/nf-core/seqinspector/pull/162) Fix bugs in qc_bam and prepare_genome subworkflows and add tests
 - [#163](https://github.com/nf-core/seqinspector/pull/163) Run fastqscreen with subsampled data if available
 
 ### `Changed`
 
-- [#49](https://github.com/nf-core/seqinspector/pull/49) Template update for nf-core/tools v3.0.2
+- [#15](https://github.com/nf-core/seqinspector/pull/15) Template update for nf-core/tools v2.14.1
+- [#26](https://github.com/nf-core/seqinspector/pull/26), [#49](https://github.com/nf-core/seqinspector/pull/49) Template update for nf-core/tools v3.0.2
 - [#69](https://github.com/nf-core/seqinspector/pull/69) Template update for nf-core/tools v3.1.0
+- [#72](https://github.com/nf-core/seqinspector/pull/72) Template update for nf-core/tools v3.1.2dev0
 - [#74](https://github.com/nf-core/seqinspector/pull/74) Template update for nf-core/tools v3.2.0
 - [#114](https://github.com/nf-core/seqinspector/pull/114) Update CI
 - [#133](https://github.com/nf-core/seqinspector/pull/133) Template update for nf-core/tools v3.4.1
 - [#144](https://github.com/nf-core/seqinspector/pull/144) Template update for nf-core/tools v3.5.1
+- [#145](https://github.com/nf-core/seqinspector/pull/145) Remove outdated comments
+- [#148](https://github.com/nf-core/seqinspector/pull/148), [#152](https://github.com/nf-core/seqinspector/pull/152), [#153](https://github.com/nf-core/seqinspector/pull/153) Update documentation
 - [#158](https://github.com/nf-core/seqinspector/pull/158) Moved picard_collectmultiplemetrics to the subworkflow QC_BAM
 - [#164](https://github.com/nf-core/seqinspector/pull/164) Refactor local subworkflow and pipeline tests
 

From 9371567eeed9e95f65978b3f64073ae85a70f329 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Mon, 15 Dec 2025 14:26:30 +0100
Subject: [PATCH 514/530] code polish

---
 subworkflows/local/prepare_genome/tests/main.nf.test | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test b/subworkflows/local/prepare_genome/tests/main.nf.test
index efa012e2..07d2f9be 100644
--- a/subworkflows/local/prepare_genome/tests/main.nf.test
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test
@@ -35,9 +35,6 @@ nextflow_workflow {
                 else if (key == "ref_dict") {
                     return [key, val.collect { file(it[1]).name }]
                 }
-                else if (key == "reference_fai") {
-                    return [key, val.collect { path(it[1]) }]
-                }
                 else if (key == "versions") {
                     return [key, val.collect { path(it).yaml }]
                 }
@@ -75,9 +72,6 @@ nextflow_workflow {
                 else if (key == "ref_dict") {
                     return [key, val.collect { file(it[1]).name }]
                 }
-                else if (key == "reference_fai") {
-                    return [key, val.collect { path(it[1]) }]
-                }
                 else if (key == "versions") {
                     return [key, val.collect { path(it).yaml }]
                 }
@@ -114,9 +108,6 @@ nextflow_workflow {
                 else if (key == "ref_dict") {
                     return [key, val.collect { file(it[1]).name }]
                 }
-                else if (key == "reference_fai") {
-                    return [key, val.collect { path(it[1]) }]
-                }
                 else if (key == "versions") {
                     return [key, val.collect { path(it).yaml }]
                 }

From 052b7ea9320bec833b81efffcbc3bd8234bd43a1 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Mon, 15 Dec 2025 14:31:46 +0100
Subject: [PATCH 515/530] fix polish

---
 subworkflows/local/prepare_genome/tests/main.nf.test | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test b/subworkflows/local/prepare_genome/tests/main.nf.test
index 07d2f9be..b9199a6f 100644
--- a/subworkflows/local/prepare_genome/tests/main.nf.test
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test
@@ -38,7 +38,7 @@ nextflow_workflow {
                 else if (key == "versions") {
                     return [key, val.collect { path(it).yaml }]
                 }
-                return [key, val]
+                return [key, val.collect { path(it[1]) }]
             }).match()
         }
     }
@@ -75,6 +75,7 @@ nextflow_workflow {
                 else if (key == "versions") {
                     return [key, val.collect { path(it).yaml }]
                 }
+                return [key, val.collect { path(it[1]) }]
             }).match()
         }
     }
@@ -111,6 +112,7 @@ nextflow_workflow {
                 else if (key == "versions") {
                     return [key, val.collect { path(it).yaml }]
                 }
+                return [key, val.collect { path(it[1]) }]
             }).match()
         }
     }

From cfd4a8d6ab56842d9003de278ac5b22985f69b1d Mon Sep 17 00:00:00 2001
From: matrulda <matilda.aslin@medsci.uu.se>
Date: Mon, 19 Jan 2026 13:47:08 +0100
Subject: [PATCH 516/530] Skip RUNDIRPARSER if no rundir information is
 available

---
 workflows/seqinspector.nf | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index cb556cbe..059ad38a 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -67,6 +67,7 @@ workflow SEQINSPECTOR {
         // From samplesheet channel serving (sampleMetaObj, sampleReadsPath) tuples:
         // --> Create new rundir channel serving (rundirMetaObj, rundirPath) tuples
         ch_rundir = ch_samplesheet
+            .filter { meta, _reads -> meta.rundir.size() > 0 }
             .map { meta, _reads -> [meta.rundir, meta] }
             .groupTuple()
             .map { rundir, metas ->
@@ -82,6 +83,8 @@ workflow SEQINSPECTOR {
                 [dir_meta, rundir]
             }
 
+        ch_rundir.ifEmpty { log.warn "No samples with rundir found, skipping RUNDIRPARSER" }
+
         RUNDIRPARSER(ch_rundir)
 
         ch_multiqc_files = ch_multiqc_files.mix(RUNDIRPARSER.out.multiqc)

From 6e56eab65a471901642a89412e404bbf748c7283 Mon Sep 17 00:00:00 2001
From: matrulda <matilda.aslin@medsci.uu.se>
Date: Mon, 19 Jan 2026 15:59:40 +0100
Subject: [PATCH 517/530] Add 167 to changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e15ca7ee..c0edf99e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -49,6 +49,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#150](https://github.com/nf-core/seqinspector/pull/150) Fix pipeline linting issues
 - [#162](https://github.com/nf-core/seqinspector/pull/162) Fix bugs in qc_bam and prepare_genome subworkflows and add tests
 - [#163](https://github.com/nf-core/seqinspector/pull/163) Run fastqscreen with subsampled data if available
+- [#167](https://github.com/nf-core/seqinspector/pull/167) RunDirParser is now skipped if no Run Directory information is available
 
 ### `Changed`
 

From 960728aedb08d358d63b3dbe39534d491ed94b9b Mon Sep 17 00:00:00 2001
From: matrulda <matilda.aslin@medsci.uu.se>
Date: Mon, 19 Jan 2026 16:54:38 +0100
Subject: [PATCH 518/530] Add test for no rundir information scenario

---
 tests/NovaSeq6000.nf.test      |  41 ++
 tests/NovaSeq6000.nf.test.snap | 930 +++++++++++++++++++++++++++++++++
 2 files changed, 971 insertions(+)

diff --git a/tests/NovaSeq6000.nf.test b/tests/NovaSeq6000.nf.test
index 5c8b9f0f..df72a311 100644
--- a/tests/NovaSeq6000.nf.test
+++ b/tests/NovaSeq6000.nf.test
@@ -43,4 +43,45 @@ nextflow_pipeline {
             )
         }
     }
+
+    test("NovaSeq6000 data test - No rundirs") {
+
+        when {
+            params {
+                fastq_screen_references = "${projectDir}/assets/example_fastq_screen_references.csv"
+                genome = 'R64-1-1'
+                outdir = "$outputDir"
+                pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
+                input = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet_no_rundirs.csv'
+            }
+        }
+
+        then {
+           // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(
+                params.outdir,
+                relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']
+            )
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(
+                params.outdir,
+                ignoreFile: 'tests/.nftignore'
+            )
+            // bam_files: All bam files
+            def bam_files  = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
+            assert workflow.success
+            assertAll(
+                { assert snapshot(
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
+                    // All stable path names, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path,
+                    // All bam files
+                    bam_files.isEmpty() ? 'No BAM files' : bam_files.collect { file -> file.getName() + ":md5," +  bam(file.toString()).readsMD5 },
+                ).match() }
+            )
+        }
+    }
 }
diff --git a/tests/NovaSeq6000.nf.test.snap b/tests/NovaSeq6000.nf.test.snap
index 80f833aa..7ffaa3e9 100644
--- a/tests/NovaSeq6000.nf.test.snap
+++ b/tests/NovaSeq6000.nf.test.snap
@@ -960,5 +960,935 @@
             "nextflow": "25.10.2"
         },
         "timestamp": "2025-12-12T16:50:45.065344275"
+    },
+    "NovaSeq6000 data test - No rundirs": {
+        "content": [
+            {
+                "BWAMEM2_MEM": {
+                    "bwamem2": "2.2.1",
+                    "samtools": "1.22.1"
+                },
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "FASTQSCREEN_FASTQSCREEN": {
+                    "fastqscreen": "0.16.0"
+                },
+                "PICARD_COLLECTMULTIPLEMETRICS": {
+                    "picard": "3.4.0"
+                },
+                "SAMTOOLS_INDEX": {
+                    "samtools": "1.22.1"
+                },
+                "SEQFU_STATS": {
+                    "seqfu": "1.22.3"
+                },
+                "Workflow": {
+                    "nf-core/seqinspector": "v1.0dev"
+                }
+            },
+            [
+                "bwamem2_index",
+                "bwamem2_index/bwamem2",
+                "bwamem2_index/bwamem2/genome.fa.0123",
+                "bwamem2_index/bwamem2/genome.fa.amb",
+                "bwamem2_index/bwamem2/genome.fa.ann",
+                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
+                "bwamem2_index/bwamem2/genome.fa.pac",
+                "bwamem2_mem",
+                "bwamem2_mem/Sample1_01.bam",
+                "bwamem2_mem/Sample1_01.bam.bai",
+                "bwamem2_mem/Sample23_03.bam",
+                "bwamem2_mem/Sample23_03.bam.bai",
+                "bwamem2_mem/SampleA_02.bam",
+                "bwamem2_mem/SampleA_02.bam.bai",
+                "bwamem2_mem/Undetermined_05.bam",
+                "bwamem2_mem/Undetermined_05.bam.bai",
+                "bwamem2_mem/sampletest_04.bam",
+                "bwamem2_mem/sampletest_04.bam.bai",
+                "fastqc",
+                "fastqc/Sample1_01_fastqc.html",
+                "fastqc/Sample1_01_fastqc.zip",
+                "fastqc/Sample23_03_fastqc.html",
+                "fastqc/Sample23_03_fastqc.zip",
+                "fastqc/SampleA_02_fastqc.html",
+                "fastqc/SampleA_02_fastqc.zip",
+                "fastqc/Undetermined_05_fastqc.html",
+                "fastqc/Undetermined_05_fastqc.zip",
+                "fastqc/sampletest_04_fastqc.html",
+                "fastqc/sampletest_04_fastqc.zip",
+                "fastqscreen",
+                "fastqscreen/Sample1_01_screen.html",
+                "fastqscreen/Sample1_01_screen.png",
+                "fastqscreen/Sample1_01_screen.txt",
+                "fastqscreen/Sample23_03_screen.html",
+                "fastqscreen/Sample23_03_screen.png",
+                "fastqscreen/Sample23_03_screen.txt",
+                "fastqscreen/SampleA_02_screen.html",
+                "fastqscreen/SampleA_02_screen.png",
+                "fastqscreen/SampleA_02_screen.txt",
+                "fastqscreen/Undetermined_05_screen.html",
+                "fastqscreen/Undetermined_05_screen.png",
+                "fastqscreen/Undetermined_05_screen.txt",
+                "fastqscreen/sampletest_04_screen.html",
+                "fastqscreen/sampletest_04_screen.png",
+                "fastqscreen/sampletest_04_screen.txt",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/global_report/multiqc_data/llms-full.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc.parquet",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu_mqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
+                "multiqc/global_report/multiqc_plots",
+                "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu_mqc.pdf",
+                "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu_mqc.png",
+                "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu_mqc.svg",
+                "multiqc/global_report/multiqc_report.html",
+                "multiqc/group_reports",
+                "multiqc/group_reports/group1",
+                "multiqc/group_reports/group1/multiqc_data",
+                "multiqc/group_reports/group1/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/group_reports/group1/multiqc_data/llms-full.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc.log",
+                "multiqc/group_reports/group1/multiqc_data/multiqc.parquet",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_citations.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_data.json",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_score_distribution.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_seqfu_mqc.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
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+                "seqfu_stats/SampleA_02_seqfu_mqc.txt",
+                "seqfu_stats/Undetermined_05_seqfu.tsv",
+                "seqfu_stats/Undetermined_05_seqfu_mqc.txt",
+                "seqfu_stats/sampletest_04_seqfu.tsv",
+                "seqfu_stats/sampletest_04_seqfu_mqc.txt"
+            ],
+            [
+                "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
+                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
+                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
+                "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
+                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
+                "Sample1_01_screen.png:md5,562256290643b51e4374c2225a15f463",
+                "Sample1_01_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "Sample23_03_screen.png:md5,6bb2caf67b9b2ed25d3d5f32c343e9ab",
+                "Sample23_03_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "SampleA_02_screen.png:md5,b2c3e95e034f5c038754bf108537de0e",
+                "SampleA_02_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "Undetermined_05_screen.png:md5,fc5d53f8876dfae3d1a781fa512ea1db",
+                "Undetermined_05_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "sampletest_04_screen.png:md5,1fb60070e8f4b70de0c1b3786b54f27e",
+                "sampletest_04_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
+                "fastq_screen_plot.txt:md5,990122d48fa4c1a170107a1ba034e4cf",
+                "fastqc-status-check-heatmap.txt:md5,7a64380ec42aac56949a2d9a4176d4d9",
+                "fastqc_overrepresented_sequences_plot.txt:md5,c7908980f1dba22b45cf6de14a66a686",
+                "fastqc_per_base_n_content_plot.txt:md5,8aafe701b59b4e70ccec86748c7d6eb3",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,c2bbc52a285a46ab8c548bca3b721e13",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a422f61a00f0839ef0d630d2e4524589",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,0e5a0cd0b0f8e66b3617f1ac19822d77",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,cbaa7c7033c526483584376275a8b33e",
+                "fastqc_sequence_counts_plot.txt:md5,d8ab86dbfce0c740f4a66a080803a0b9",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,f86012b3074d697c9a2b3bd67a074288",
+                "fastqc_sequence_length_distribution_plot.txt:md5,9d4fd245e8e1d5baa473a8bdffcd3e38",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,62240561100f78af37e7e2438cb58f90",
+                "multiqc_fastqc.txt:md5,23b698f1e957a26f49a9ad9bbdece908",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,b113ea40790fa45fa739f224f2710556",
+                "multiqc_picard_baseContent.txt:md5,e06c0dea80cb5cef312436e005aa0095",
+                "multiqc_picard_quality_by_cycle.txt:md5,6e13ddbd97caa0eaa52c118966e5f9fa",
+                "multiqc_picard_quality_score_distribution.txt:md5,39d3430744e9139020d7af3eb15fc629",
+                "multiqc_seqfu_mqc.txt:md5,18dd2407d4a1791646785123028f69b5",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,6e13ddbd97caa0eaa52c118966e5f9fa",
+                "picard_QualityScoreDistribution_histogram.txt:md5,39d3430744e9139020d7af3eb15fc629",
+                "picard_alignment_readlength_plot.txt:md5,57ee2de637b69efc49290bb5d4b57905",
+                "picard_alignment_summary.txt:md5,3fee23a738a44ee84592cb1144b32775",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,dfb9e50700b61cdbc0344690db202559",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,5eec2a9bbb5db321c7cbbbee26d90357",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,5b100b42e93792fed754deb276645e61",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,d0317fe5ef2cf1b692526cb9a18aa50c",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,8aafe701b59b4e70ccec86748c7d6eb3",
+                "picard_quality_by_cycle.txt:md5,366ee22c93a11c1335f867020bb03da5",
+                "picard_quality_score_distribution.txt:md5,17d6f490cb59e16a7ed4b04ffaa1a100",
+                "fastq_screen_plot.txt:md5,db7c9231e756a6e5999399a7385e4687",
+                "fastqc-status-check-heatmap.txt:md5,fc37eaf184877ac80b92001a7bf2fa81",
+                "fastqc_overrepresented_sequences_plot.txt:md5,0693849fc324ddf580e2c5a4d910bb4f",
+                "fastqc_per_base_n_content_plot.txt:md5,0ed7f750b500e7c5387ea5309e1ef467",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,18016152915653e812818194a142e162",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,93f664e18c021aae79ad222fb4cfb393",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,ba96762be2aa842e1d2a606095ffcb7e",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,b9044bfe90fd5685137739f52a97ee2c",
+                "fastqc_sequence_counts_plot.txt:md5,42b26ad3758717659763c81852c4f197",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,818f13a5372bad79e54cd984758096c5",
+                "fastqc_sequence_length_distribution_plot.txt:md5,98316a2607a889ae1e7e79a4f64cc740",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,024e1e7f9db3b0906c7aa0904229e176",
+                "multiqc_fastqc.txt:md5,3407d8f06117a65efce4c70f19e91dd1",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,1debd96f9f64c60a8ec742411da51a28",
+                "multiqc_picard_baseContent.txt:md5,afb4046944e302b40faea2233bca535c",
+                "multiqc_picard_quality_by_cycle.txt:md5,6a7552b74dd22410c3cab2c750de792e",
+                "multiqc_picard_quality_score_distribution.txt:md5,d6343c5f39942bc3f10c194067e6e9bc",
+                "multiqc_seqfu_mqc.txt:md5,6cdb863a3686fbb772aae5a66925ff23",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,6a7552b74dd22410c3cab2c750de792e",
+                "picard_QualityScoreDistribution_histogram.txt:md5,d6343c5f39942bc3f10c194067e6e9bc",
+                "picard_alignment_readlength_plot.txt:md5,01140e65e813b4ae43aabe662ef2f49a",
+                "picard_alignment_summary.txt:md5,79312cf30761025cc6902811c4165290",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,3c3671ac2aa18d883691d59adbfe3b2b",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,6cc2ae1411899de5542321ff1592b192",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,326471bc846a9fb6b54ff38cbdfb8d90",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,3132dac406a9b9e1f18af658ab856a5c",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,0ed7f750b500e7c5387ea5309e1ef467",
+                "picard_quality_by_cycle.txt:md5,fe4e6ab1c849a4f833eae9a8554ea432",
+                "picard_quality_score_distribution.txt:md5,c0864f8a1269d8ffd7a51abb6bd3ca2e",
+                "fastq_screen_plot.txt:md5,4def6c6a888afe487ab6ebef3ba8a133",
+                "fastqc-status-check-heatmap.txt:md5,61857d2c45cf0c080348047aa34e7525",
+                "fastqc_overrepresented_sequences_plot.txt:md5,7949c64cc6cef77f29349a188fc09656",
+                "fastqc_per_base_n_content_plot.txt:md5,0f2fd628631d42ed5e6a1db22578daaa",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,0a8bfa32ab04eaaa509dec3c37acb2d2",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,8c85be0c70129ba739feceddd58f6c75",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,94b975906d8a07e1604e00d4004f7463",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,ec22c8e4836aa726680f0ca767c778a0",
+                "fastqc_sequence_counts_plot.txt:md5,f4341795bdeba588248a74a095a97f8d",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,8fc995cb2192a2926eee242681bc3af6",
+                "fastqc_sequence_length_distribution_plot.txt:md5,4513e22583677a4d6167b9094242eb0b",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,fd3074930c72b666f201ae71fa27744b",
+                "multiqc_fastqc.txt:md5,98111f17d1899cad6379e4e56ed11c53",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,3b1929de09267fc1c1a15804cb5bf536",
+                "multiqc_picard_baseContent.txt:md5,ff36be9e2642089aa711c637d3cdba29",
+                "multiqc_picard_quality_by_cycle.txt:md5,9521c83313eaf5f681ac9a75de83a4b7",
+                "multiqc_picard_quality_score_distribution.txt:md5,90b9e29f22fa16cf2b0c4d92caf2dbb0",
+                "multiqc_seqfu_mqc.txt:md5,f821357507fda2d4cfd9299f52fa7dc1",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,9521c83313eaf5f681ac9a75de83a4b7",
+                "picard_QualityScoreDistribution_histogram.txt:md5,90b9e29f22fa16cf2b0c4d92caf2dbb0",
+                "picard_alignment_readlength_plot.txt:md5,9c80659c5c9b2fe9926b789fb67ba6ac",
+                "picard_alignment_summary.txt:md5,27bbb1fcdeecd26641938e5622087c23",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,99c5e961a4d26754e68047c8eb983798",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,44981dd399013d8c06481958be338040",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,b6369a23d3926edb90ae9bfdc6d90526",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,b253d3fca7c07b6a6dfea91725c58102",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,0f2fd628631d42ed5e6a1db22578daaa",
+                "picard_quality_by_cycle.txt:md5,3c34ae2bd2442a816577b1a794add2d6",
+                "picard_quality_score_distribution.txt:md5,0d58c59eac2952e6f71cefc35d4c4477",
+                "fastq_screen_plot.txt:md5,5abb5b9ed2c976f0ad83216ca3186201",
+                "fastqc-status-check-heatmap.txt:md5,323d6082b73ddb6ee33385f5ea4301c1",
+                "fastqc_overrepresented_sequences_plot.txt:md5,4e71d8913d40eb06db0f18d74ce6898f",
+                "fastqc_per_base_n_content_plot.txt:md5,b317ce09cb7a2be2366b544ea9b20ce6",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,e6f44d08f4185f680d4748a3b37201e2",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a1dc8a968f32bcf8a9b4c5f43d299dfa",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,e41b6dc1344f1aee379993daff310187",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,76f792b939233b070562cc46617f6371",
+                "fastqc_sequence_counts_plot.txt:md5,36c68522023b8d536c9362403bf03c48",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,9ff0df466790d971b3c7ef838efc0f4f",
+                "fastqc_sequence_length_distribution_plot.txt:md5,9fda632b92e3453f11cd0226484fce8e",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,536c28d7fadc9a76944f93ac9d643272",
+                "multiqc_fastqc.txt:md5,396b4cc0466a6642ec8b954237c42263",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,153c6e6a407ec128b1a02798ca2f1115",
+                "multiqc_picard_baseContent.txt:md5,6349e514552a0b5a0530fa6f311878a5",
+                "multiqc_picard_quality_by_cycle.txt:md5,c0c8b4c0197428d4d50e2c532814e1e2",
+                "multiqc_picard_quality_score_distribution.txt:md5,40e0b6faa75e1b51af42407f7ededb0c",
+                "multiqc_seqfu_mqc.txt:md5,8cced36d66ca9d25d60c006e734aa7e9",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,c0c8b4c0197428d4d50e2c532814e1e2",
+                "picard_QualityScoreDistribution_histogram.txt:md5,40e0b6faa75e1b51af42407f7ededb0c",
+                "picard_alignment_readlength_plot.txt:md5,5a19b1f8e2ac49d97f36a7792429419c",
+                "picard_alignment_summary.txt:md5,f9f791b7c569cfae07aef70aa630d40e",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,0165f522c84da6b17a286d37dc30abec",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,6fa0d29d40fe7fa24c166b664b6d4f4b",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,bf2426e09ac1ca4773edfc284c220122",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,3cbace572471ccf6c58673181dd0c0ec",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,b317ce09cb7a2be2366b544ea9b20ce6",
+                "picard_quality_by_cycle.txt:md5,7cb705007bc97da8c0da7d93201e6975",
+                "picard_quality_score_distribution.txt:md5,47d684abae0a8f4f09df43e91d54fb9a",
+                "fastq_screen_plot.txt:md5,82ceb9f2109f865d6d1b943441c09550",
+                "fastqc-status-check-heatmap.txt:md5,56b426cd5c030288639533fce7c95ab1",
+                "fastqc_overrepresented_sequences_plot.txt:md5,8e83abdbe7362e64d63339ee31ab3361",
+                "fastqc_per_base_n_content_plot.txt:md5,33b70326d8f888ac5a3d99b85f365e43",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,40bc954cc0d58a3197fdf124a40f1ca4",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,e240e30996c81a34b5d1a6b5a98ae254",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,b44d3376d503af12857d494c58b514bb",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,66b5b6d44f398fc9429460c0b9ba3ea9",
+                "fastqc_sequence_counts_plot.txt:md5,6e5804f553f656cffb02f927015d1026",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,fbe41935ea2e2faf7104393b476e5ac5",
+                "fastqc_sequence_length_distribution_plot.txt:md5,e77dc4ab73252c2e09c7452c3b8e8ab3",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,4fc422d9cb06a1d0248cc578c1eebaa2",
+                "multiqc_fastqc.txt:md5,95c8ffb23baafec625aeb600047515ae",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,2d05e826f5152fd0143edf7270de1235",
+                "multiqc_picard_baseContent.txt:md5,f3f23899a30a96260d8b5b3020708703",
+                "multiqc_picard_quality_by_cycle.txt:md5,c7edfc271ab59ecedad0ab046afd3563",
+                "multiqc_picard_quality_score_distribution.txt:md5,7fa89b52b8bc96dd1074aa07cb5a5a54",
+                "multiqc_seqfu_mqc.txt:md5,ff4ce1c88f39ed24a88bae0a861f75c8",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,c7edfc271ab59ecedad0ab046afd3563",
+                "picard_QualityScoreDistribution_histogram.txt:md5,7fa89b52b8bc96dd1074aa07cb5a5a54",
+                "picard_alignment_readlength_plot.txt:md5,c1519319c4942162b05e6225fea10569",
+                "picard_alignment_summary.txt:md5,49f5c0d2cf21a13d5f363cb42cf3790e",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,466a14fc9c09f9f4de02a00e8763cd2a",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,d5854c22df4ac60b8c47c4002d975fe9",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,c27b5aa2b90397b1302b880dff3ec958",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,6f2a3e9d03f17a93c69476607a1a580d",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,33b70326d8f888ac5a3d99b85f365e43",
+                "picard_quality_by_cycle.txt:md5,0aa028d69d8bb02f0a2bcd0ed08f4235",
+                "picard_quality_score_distribution.txt:md5,a2882ff59902dc95830ed4bdb955561a",
+                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
+                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
+                "Sample1_01_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6",
+                "Sample1_01_seqfu_mqc.txt:md5,24d99524ccd0e6c6255a69d68a871c7a",
+                "Sample23_03_seqfu.tsv:md5,6fac5d3dbce3f3bee72341fe99a399dc",
+                "Sample23_03_seqfu_mqc.txt:md5,4d4f280911a08bb6b753142980178027",
+                "SampleA_02_seqfu.tsv:md5,aec811f267bb2a0ef066a7abb59d2775",
+                "SampleA_02_seqfu_mqc.txt:md5,a819409a5cb64e20c3e54ec5ada4aa27",
+                "Undetermined_05_seqfu.tsv:md5,3a42c5c66a0a118f1a6f6f6e560b0e7e",
+                "Undetermined_05_seqfu_mqc.txt:md5,bd8be908362c5cb08a72f8ae7ab41b0d",
+                "sampletest_04_seqfu.tsv:md5,a5bea0b9c6015dd1a201ffd433e9b377",
+                "sampletest_04_seqfu_mqc.txt:md5,2180961655bbc8a12f0152d6a4b803a2"
+            ],
+            [
+                "Sample1_01.bam:md5,d06ccfde49cc474faebcab2ebf71b324",
+                "Sample23_03.bam:md5,5ff9f554c6255fd07d3841c6616c5031",
+                "SampleA_02.bam:md5,250d0031520e59ee59a7112ab1ea32e1",
+                "Undetermined_05.bam:md5,8fcc158f1e0736b366152d5e187644ca",
+                "sampletest_04.bam:md5,f80371e37421d97499b3bfd55221ed00"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2026-01-19T16:52:47.847449885"
     }
 }
\ No newline at end of file

From e535dc1e6cb79b98d62b7adffb681a6b86e5b227 Mon Sep 17 00:00:00 2001
From: matrulda <matilda.aslin@medsci.uu.se>
Date: Tue, 20 Jan 2026 10:34:47 +0100
Subject: [PATCH 519/530] Add note about RUNDIRPARSER being skipped when not
 using rundir

---
 docs/usage.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/docs/usage.md b/docs/usage.md
index a3f25c90..2da4eb35 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -50,9 +50,11 @@ sample4 path/to/run_dir/sample4_lane2_group3_r1.fq.gz         path/to/run_dir co
 | `sample`  | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). |
 | `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                             |
 | `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz" (optional).                                                  |
-| `rundir`  | Path to the runfolder containing extra information about the sequencing run (optional).                                                                                                |
+| `rundir`  | Path to the runfolder containing extra information about the sequencing run (optional*).                                                                                                |
 | `tags`    | Colon-separated list of tags to group samples in special reports.                                                                                                                      |
 
+*If rundir is not provided, the RUNDIRPARSER module is skipped and the sequencing run metadata is not collected.
+
 Another [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
 
 ## Running the pipeline

From 749aee2d365df91684e5b3b7b5dd6fe64638e8f8 Mon Sep 17 00:00:00 2001
From: matrulda <matilda.aslin@medsci.uu.se>
Date: Tue, 20 Jan 2026 10:43:05 +0100
Subject: [PATCH 520/530] pre-commit fix

---
 docs/usage.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/usage.md b/docs/usage.md
index 2da4eb35..e7ddeb0c 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -50,10 +50,10 @@ sample4 path/to/run_dir/sample4_lane2_group3_r1.fq.gz         path/to/run_dir co
 | `sample`  | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). |
 | `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                             |
 | `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz" (optional).                                                  |
-| `rundir`  | Path to the runfolder containing extra information about the sequencing run (optional*).                                                                                                |
+| `rundir`  | Path to the runfolder containing extra information about the sequencing run (optional\*).                                                                                              |
 | `tags`    | Colon-separated list of tags to group samples in special reports.                                                                                                                      |
 
-*If rundir is not provided, the RUNDIRPARSER module is skipped and the sequencing run metadata is not collected.
+\*If rundir is not provided, the RUNDIRPARSER module is skipped and the sequencing run metadata is not collected.
 
 Another [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
 

From d080687362e8cc6dccc2d3a1ac2c5b60f7b73e19 Mon Sep 17 00:00:00 2001
From: matrulda <matilda.aslin@medsci.uu.se>
Date: Fri, 6 Feb 2026 13:52:11 +0100
Subject: [PATCH 521/530] Write warning if rundir is missing for a sample

---
 workflows/seqinspector.nf | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 059ad38a..40a65c4a 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -64,10 +64,23 @@ workflow SEQINSPECTOR {
     //
     if (!("rundirparser" in skip_tools)) {
 
+        // Branch the samplesheet channel based on rundir presence
+        ch_samplesheet
+            .branch { meta, reads ->
+                with_rundir: meta.rundir.size() > 0
+                without_rundir: true
+            }
+            .set { ch_rundir_branched }
+
+        // Log warnings for samples without rundir
+        ch_rundir_branched.without_rundir
+            .view { meta, reads ->
+                log.warn "Sample '${meta.id}' does not have a rundir specified"
+            }
+
         // From samplesheet channel serving (sampleMetaObj, sampleReadsPath) tuples:
         // --> Create new rundir channel serving (rundirMetaObj, rundirPath) tuples
-        ch_rundir = ch_samplesheet
-            .filter { meta, _reads -> meta.rundir.size() > 0 }
+        ch_rundir = ch_rundir_branched.with_rundir
             .map { meta, _reads -> [meta.rundir, meta] }
             .groupTuple()
             .map { rundir, metas ->
@@ -90,6 +103,7 @@ workflow SEQINSPECTOR {
         ch_multiqc_files = ch_multiqc_files.mix(RUNDIRPARSER.out.multiqc)
     }
 
+
     //
     // MODULE: Run Seqtk sample to perform subsampling
     //

From 9da961c542b80d4c560d301807bcfbfec08326fd Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Tue, 10 Feb 2026 16:05:37 +0100
Subject: [PATCH 522/530] Address review comments (#168)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Pontus Höjer <pontushojer@gmail.com>
---
 .gitignore                                    |   2 +
 .nf-core.yml                                  |   4 +-
 CHANGELOG.md                                  |   5 +-
 CITATIONS.md                                  |  30 +-
 README.md                                     |  41 +-
 assets/nf-core-seqinspector_logo_light.png    | Bin 110870 -> 109618 bytes
 conf/base.config                              |   3 -
 conf/modules.config                           |  28 +-
 .../images/nf-core-seqinspector_logo_dark.png | Bin 28728 -> 110373 bytes
 .../images/nf-core-seqinspector_logo_dark.svg | 303 +++++++++
 .../nf-core-seqinspector_logo_light.png       | Bin 24391 -> 109618 bytes
 .../nf-core-seqinspector_logo_light.svg       | 242 +++++++
 docs/output.md                                |   2 +-
 .../resources/usr/bin/parse_illumina.py       |  16 +-
 .../nf-core/bowtie2/build/tests/main.nf.test  |  31 -
 .../bowtie2/build/tests/main.nf.test.snap     |  49 --
 .../nf-core/bwamem2/index/tests/main.nf.test  |  62 --
 .../bwamem2/index/tests/main.nf.test.snap     |  64 --
 .../nf-core/bwamem2/mem/tests/main.nf.test    | 179 ------
 .../bwamem2/mem/tests/main.nf.test.snap       | 129 ----
 modules/nf-core/fastqc/tests/main.nf.test     | 309 ---------
 .../nf-core/fastqc/tests/main.nf.test.snap    | 392 ------------
 .../buildfromindex/tests/main.nf.test         |  71 ---
 .../buildfromindex/tests/main.nf.test.snap    |  95 ---
 .../fastqscreen/fastqscreen-fastqscreen.diff  |   6 +-
 .../fastqscreen/tests/main.nf.test            | 117 ----
 .../fastqscreen/tests/main.nf.test.snap       | 132 ----
 .../fastqscreen/tests/nextflow.config         |   5 -
 modules/nf-core/multiqc/tests/main.nf.test    |  92 ---
 .../nf-core/multiqc/tests/main.nf.test.snap   |  41 --
 modules/nf-core/multiqc/tests/nextflow.config |   5 -
 .../collecthsmetrics/tests/main.nf.test       | 234 -------
 .../collecthsmetrics/tests/main.nf.test.snap  | 594 ------------------
 .../collectmultiplemetrics/tests/main.nf.test | 112 ----
 .../tests/main.nf.test.snap                   |  80 ---
 .../tests/main.nf.test                        |  61 --
 .../tests/main.nf.test.snap                   |  48 --
 .../nf-core/samtools/faidx/tests/main.nf.test | 219 -------
 .../samtools/faidx/tests/main.nf.test.snap    | 543 ----------------
 .../samtools/faidx/tests/nextflow.config      |   7 -
 .../samtools/faidx/tests/nextflow2.config     |   6 -
 .../samtools/index/tests/csi.nextflow.config  |   7 -
 .../nf-core/samtools/index/tests/main.nf.test | 140 -----
 .../samtools/index/tests/main.nf.test.snap    | 250 --------
 .../nf-core/seqfu/stats/tests/main.nf.test    |  88 ---
 .../seqfu/stats/tests/main.nf.test.snap       | 156 -----
 .../nf-core/seqtk/sample/tests/main.nf.test   | 102 ---
 .../seqtk/sample/tests/main.nf.test.snap      | 126 ----
 .../seqtk/sample/tests/standard.config        |   6 -
 nextflow.config                               | 151 ++++-
 nf-test.config                                |  12 +-
 ro-crate-metadata.json                        |  73 ++-
 .../main.nf                                   | 198 +++---
 .../tests/main.function.nf.test               |  54 --
 .../tests/main.function.nf.test.snap          |  20 -
 .../tests/main.workflow.nf.test               | 113 ----
 .../tests/nextflow.config                     |   9 -
 .../tests/main.function.nf.test               | 126 ----
 .../tests/main.function.nf.test.snap          | 136 ----
 .../tests/main.workflow.nf.test               |  29 -
 .../tests/main.workflow.nf.test.snap          |  19 -
 .../tests/nextflow.config                     |   9 -
 .../utils_nfschema_plugin/tests/main.nf.test  | 173 -----
 .../tests/nextflow.config                     |   8 -
 .../tests/nextflow_schema.json                |  96 ---
 65 files changed, 920 insertions(+), 5540 deletions(-)
 create mode 100644 docs/images/nf-core-seqinspector_logo_dark.svg
 create mode 100644 docs/images/nf-core-seqinspector_logo_light.svg
 delete mode 100644 modules/nf-core/bowtie2/build/tests/main.nf.test
 delete mode 100644 modules/nf-core/bowtie2/build/tests/main.nf.test.snap
 delete mode 100644 modules/nf-core/bwamem2/index/tests/main.nf.test
 delete mode 100644 modules/nf-core/bwamem2/index/tests/main.nf.test.snap
 delete mode 100644 modules/nf-core/bwamem2/mem/tests/main.nf.test
 delete mode 100644 modules/nf-core/bwamem2/mem/tests/main.nf.test.snap
 delete mode 100644 modules/nf-core/fastqc/tests/main.nf.test
 delete mode 100644 modules/nf-core/fastqc/tests/main.nf.test.snap
 delete mode 100644 modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test
 delete mode 100644 modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test.snap
 delete mode 100644 modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test
 delete mode 100644 modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap
 delete mode 100644 modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config
 delete mode 100644 modules/nf-core/multiqc/tests/main.nf.test
 delete mode 100644 modules/nf-core/multiqc/tests/main.nf.test.snap
 delete mode 100644 modules/nf-core/multiqc/tests/nextflow.config
 delete mode 100644 modules/nf-core/picard/collecthsmetrics/tests/main.nf.test
 delete mode 100644 modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap
 delete mode 100644 modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test
 delete mode 100644 modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap
 delete mode 100644 modules/nf-core/picard/createsequencedictionary/tests/main.nf.test
 delete mode 100644 modules/nf-core/picard/createsequencedictionary/tests/main.nf.test.snap
 delete mode 100644 modules/nf-core/samtools/faidx/tests/main.nf.test
 delete mode 100644 modules/nf-core/samtools/faidx/tests/main.nf.test.snap
 delete mode 100644 modules/nf-core/samtools/faidx/tests/nextflow.config
 delete mode 100644 modules/nf-core/samtools/faidx/tests/nextflow2.config
 delete mode 100644 modules/nf-core/samtools/index/tests/csi.nextflow.config
 delete mode 100644 modules/nf-core/samtools/index/tests/main.nf.test
 delete mode 100644 modules/nf-core/samtools/index/tests/main.nf.test.snap
 delete mode 100644 modules/nf-core/seqfu/stats/tests/main.nf.test
 delete mode 100644 modules/nf-core/seqfu/stats/tests/main.nf.test.snap
 delete mode 100644 modules/nf-core/seqtk/sample/tests/main.nf.test
 delete mode 100644 modules/nf-core/seqtk/sample/tests/main.nf.test.snap
 delete mode 100644 modules/nf-core/seqtk/sample/tests/standard.config
 delete mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test
 delete mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap
 delete mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
 delete mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
 delete mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
 delete mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
 delete mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
 delete mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap
 delete mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
 delete mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
 delete mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
 delete mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json

diff --git a/.gitignore b/.gitignore
index 9e307203..ce640bc7 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,3 +9,5 @@ testing*
 null/
 .nf-test
 .nf-test.log
+modules/nf-core/**/tests/
+subworkflows/nf-core/**/tests/
diff --git a/.nf-core.yml b/.nf-core.yml
index df59962a..6bfb94c6 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -4,14 +4,14 @@ lint:
     - tests/default.nf.test
   files_unchanged:
     - .github/CONTRIBUTING.md
+    - assets/nf-core-seqinspector_logo_light.png
     - docs/images/nf-core-seqinspector_logo_dark.png
     - docs/images/nf-core-seqinspector_logo_light.png
-    - assets/nf-core-seqinspector_logo_light.png
   nextflow_config:
     - config_defaults:
         - params.fastq_screen_references
   nf_test_content: false
-nf_core_version: 3.5.1
+nf_core_version: 3.5.2
 repository_type: pipeline
 template:
   author: Adrien Coulier
diff --git a/CHANGELOG.md b/CHANGELOG.md
index c0edf99e..c3e85d71 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -23,8 +23,8 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#100](https://github.com/nf-core/seqinspector/pull/100) Added official logos
 - [#103](https://github.com/nf-core/seqinspector/pull/103) Configure full-tests
 - [#106](https://github.com/nf-core/seqinspector/pull/106) Parse rundir metadata
-- [#108](https://github.com/nf-core/seqinspector/pull/108) Update lists of default steps in the pipeline (#86)
 - [#108](https://github.com/nf-core/seqinspector/pull/108) Test data validation (#94)
+- [#108](https://github.com/nf-core/seqinspector/pull/108) Update lists of default steps in the pipeline (#86)
 - [#110](https://github.com/nf-core/seqinspector/pull/110) Update input schema to accept either tar file or directory as rundir, and fastq messages and patterns
 - [#111](https://github.com/nf-core/seqinspector/pull/111) Short summary of seqinspector in README.md (#84)
 - [#127](https://github.com/nf-core/seqinspector/pull/127) Added alignment tools - bwamem2 - index and mem
@@ -36,6 +36,8 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#156](https://github.com/nf-core/seqinspector/pull/156) Added relative sample_size and warning when a sample has less reads than desired sample_size
 - [#159](https://github.com/nf-core/seqinspector/pull/159) Added a subworkflow QC_BAM including picard_collecthsmetrics for alignment QC of hybrid-selection data
 - [#162](https://github.com/nf-core/seqinspector/pull/162) Add tests for prepare_genome subworkflow
+- [#168](https://github.com/nf-core/seqinspector/pull/168) Add contributors list
+- [#168](https://github.com/nf-core/seqinspector/pull/168) Add logo to the pipeline logo
 
 ### `Fixed`
 
@@ -65,6 +67,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#148](https://github.com/nf-core/seqinspector/pull/148), [#152](https://github.com/nf-core/seqinspector/pull/152), [#153](https://github.com/nf-core/seqinspector/pull/153) Update documentation
 - [#158](https://github.com/nf-core/seqinspector/pull/158) Moved picard_collectmultiplemetrics to the subworkflow QC_BAM
 - [#164](https://github.com/nf-core/seqinspector/pull/164) Refactor local subworkflow and pipeline tests
+- [#168](https://github.com/nf-core/seqinspector/pull/168) Adhere to strict syntax
 
 ### `Dependencies`
 
diff --git a/CITATIONS.md b/CITATIONS.md
index e03247d4..6d46e83b 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -10,35 +10,39 @@
 
 ## Pipeline tools
 
-- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+- [Bowtie2](https://www.nature.com/articles/nmeth.1923)
 
-> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
+  > Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012 Apr;9(4):357-9. doi: 10.1038/nmeth.1923. PubMed PMID: 22388286.
 
-- [SeqFu](https://telatin.github.io/seqfu2/)
+- [BWAMEM2](https://ieeexplore.ieee.org/abstract/document/8820962)
 
-> Telatin A, Fariselli P, Birolo G. SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files. Bioengineering 2021, 8, 59. doi.org/10.3390/bioengineering8050059
+  > Vasimuddin Md, Misra S, Li H, Aluru S. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. In: 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS). IEEE; 2019:314-324. doi:10.1109/IPDPS.2019.00041
+
+- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+
+  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
 
 - [FastQ Screen](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)
 
-> Wingett SW and Andrews S. FastQ Screen: A tool for multi-genome mapping and quality control [version 2; referees: 4 approved]. F1000Research 2018, 7:1338 (https://doi.org/10.12688/f1000research.15931.2)
+  > Wingett SW and Andrews S. FastQ Screen: A tool for multi-genome mapping and quality control [version 2; referees: 4 approved]. F1000Research 2018, 7:1338 (https://doi.org/10.12688/f1000research.15931.2)
 
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
-> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
-
-- [Seqtk](https://github.com/lh3/seqtk)
+  > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
-- [BWAMEM2](https://ieeexplore.ieee.org/abstract/document/8820962)
+- [Picard Tools](https://broadinstitute.github.io/picard/)
 
-> Vasimuddin Md, Misra S, Li H, Aluru S. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. In: 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS). IEEE; 2019:314-324. doi:10.1109/IPDPS.2019.00041
+  > Broad Institute, “Picard Toolkit.” 2019. GitHub Repository. https://broadinstitute.github.io/picard/
 
 - [SAMTOOLS](https://academic.oup.com/bioinformatics/article/25/16/2078/204688)
 
-> Danecek P, Bonfield JK, Liddle J, et al. Twelve years of SAMtools and BCFtools. GigaScience. 2021;10(2):giab008. doi:10.1093/gigascience/giab008
+  > Danecek P, Bonfield JK, Liddle J, et al. Twelve years of SAMtools and BCFtools. GigaScience. 2021;10(2):giab008. doi:10.1093/gigascience/giab008
 
-- [Picard Tools](https://broadinstitute.github.io/picard/)
+- [SeqFu](https://telatin.github.io/seqfu2/)
+
+  > Telatin A, Fariselli P, Birolo G. SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files. Bioengineering 2021, 8, 59. doi.org/10.3390/bioengineering8050059
 
-> Broad Institute, “Picard Toolkit.” 2019. GitHub Repository. https://broadinstitute.github.io/picard/
+- [Seqtk](https://github.com/lh3/seqtk)
 
 ## Software packaging/containerisation tools
 
diff --git a/README.md b/README.md
index 31f97a8a..a249295e 100644
--- a/README.md
+++ b/README.md
@@ -21,19 +21,10 @@
 
 ## Introduction
 
-<picture>
-  <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-seqinspector_logo_dark.png">
-  <source media="(prefers-color-scheme: light)" srcset="docs/images/nf-core-seqinspector_logo_light.png">
-  <img alt="Fallback image description" src="docs/images/nf-core-seqinspector_logo_light.png">
-</picture>
-
-<picture>
-  <source media="(prefers-color-scheme: dark)" srcset="docs/images/nfcore-seqinspector-logo-hex-dark.png">
-  <source media="(prefers-color-scheme: light)" srcset="docs/images/nfcore-seqinspector-logo-hex-light.png">
-  <img alt="Fallback image description" src="docs/images/nfcore-seqinspector-logo-hex-light.png">
-</picture>
-
-**nf-core/seqinspector** is a bioinformatics pipeline that that processes raw sequence data (FASTQ) to provide comprehensive quality control. It can perform subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants. The pipeline generates detailed MultiQC reports with flexible output options, ranging from individual sample reports to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments. If provided, nf-core/seqinspector can also parse statistics from an Illumina run folder directory into the final MultiQC reports.
+**nf-core/seqinspector** is a bioinformatics pipeline that processes raw sequence data (FASTQ) to provide comprehensive quality control.
+It can perform subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants.
+The pipeline generates detailed MultiQC reports with flexible output options, ranging from individual sample reports to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments.
+If provided, nf-core/seqinspector can also parse statistics from an Illumina run folder directory into the final MultiQC reports.
 
 <!-- TODO: add a search tool that accepts a tree for `Compatibility with Data`. -->
 
@@ -69,7 +60,9 @@ sample,fastq_1,fastq_2,rundir,tags
 CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2
 ```
 
-Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
+Each row represents a fastq file (single-end with only `fastq_1`) or a pair of fastq files (paired end with `fastq_1` and `fastq_2`).
+`rundir` is the path to the runfolder.
+`tags` is a colon-separated list of tags that will be added to the MultiQC report for this `sample`.
 
 Now, you can run the pipeline using:
 
@@ -93,11 +86,29 @@ For more details about the output files and reports, please refer to the
 
 ## Credits
 
-nf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/) and [Clinical Genomics Stockholm](https://clinical.scilifelab.se/).
+nf-core/seqinspector was originally written by [@agrima2010](https://github.com/agrima2010), [@Aratz](https://github.com/Aratz), [@FranBonath](https://github.com/FranBonath), [@kedhammar](https://github.com/kedhammar), and [@MatthiasZepper](https://github.com/MatthiasZepper) from the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/) and [Clinical Genomics Stockholm](https://clinical.scilifelab.se/).
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 
+- [@adamrtalbot](https://github.com/adamrtalbot)
+- [@alneberg](https://github.com/alneberg)
+- [@beatrizsavinhas](https://github.com/beatrizsavinhas)
+- [@ctuni](https://github.com/ctuni)
+- [@edmundmiller](https://github.com/edmundmiller)
+- [@EliottBo](https://github.com/EliottBo)
+- [@KarNair](https://github.com/KarNair)
+- [@kjellinjonas](https://github.com/kjellinjonas)
 - [@mahesh-panchal](https://github.com/mahesh-panchal)
+- [@matrulda](https://github.com/matrulda)
+- [@maxulysse](https://github.com/maxulysse)
+- [@mirpedrol](https://github.com/mirpedrol)
+- [@nggvs](https://github.com/nggvs)
+- [@nkongenelly](https://github.com/nkongenelly)
+- [@Patricie34](https://github.com/Patricie34)
+- [@pontushojer](https://github.com/pontushojer)
+- [@ramprasadn](https://github.com/ramprasadn)
+- [@rannick](https://github.com/rannick)
+- [@torigiffin](https://github.com/torigiffin)
 
 ## Contributions and Support
 
diff --git a/assets/nf-core-seqinspector_logo_light.png b/assets/nf-core-seqinspector_logo_light.png
index b03851ab318eb0271d4da135561e1f7a2f901827..f1737c85e3d75b1fece0f9c991c900d71eef91f6 100644
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diff --git a/conf/base.config b/conf/base.config
index 84739da8..45099965 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -9,8 +9,6 @@
 */
 
 process {
-
-    // TODO nf-core: Check the defaults for all processes
     cpus   = { 1      * task.attempt }
     memory = { 6.GB   * task.attempt }
     time   = { 4.h    * task.attempt }
@@ -24,7 +22,6 @@ process {
     //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
     //        If possible, it would be nice to keep the same label naming convention when
     //        adding in your local modules too.
-    // TODO nf-core: Customise requirements for specific processes.
     // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
     withLabel:process_single {
         cpus   = { 1                   }
diff --git a/conf/modules.config b/conf/modules.config
index c9b047d1..a48d73ad 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -117,22 +117,18 @@ process {
         publishDir = [
             path: { "${params.outdir}/multiqc/group_reports" },
             mode: params.publish_dir_mode,
-            saveAs: {
-                filename ->
-                    switch (filename) {
-                        case 'versions.yml':
-                            null
-                            break
-                        case ~/\[TAG:.+\]_multiqc_(report\.html|plots|data)/:
-                            def tag = (filename =~ /\[TAG:(.+)\]_multiqc_(report\.html|plots|data)/)[0][1]
-                            def new_filename = filename.replaceFirst(
-                                "(?<prefix>.*)\\[TAG:${tag}\\]_(?<suffix>multiqc_(report\\.html|plots|data).*)",
-                                '${prefix}${suffix}')
-                            "${tag}/${new_filename}"
-                            break
-                        default:
-                            filename
-                    }
+            saveAs: { filename ->
+                if (filename == 'versions.yml') {
+                    return null
+                } else if (filename  =~/\[TAG:.+\]_multiqc_(report\.html|plots|data)/) {
+                        def tag = (filename =~ /\[TAG:(.+)\]_multiqc_(report\.html|plots|data)/)[0][1]
+                        def new_filename = filename.replaceFirst(
+                            "(?<prefix>.*)\\[TAG:${tag}\\]_(?<suffix>multiqc_(report\\.html|plots|data).*)",
+                            '${prefix}${suffix}')
+                    return "${tag}/${new_filename}"
+                } else {
+                    return filename
+                }
             }
         ]
     }
diff --git a/docs/images/nf-core-seqinspector_logo_dark.png b/docs/images/nf-core-seqinspector_logo_dark.png
index 05cb0081452194b0092ad2e7b1e01049f22a6d8d..77509b5f4cadc3c3fdcf63ec3a341215e710f83c 100644
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diff --git a/docs/output.md b/docs/output.md
index 900260b5..cf453e24 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -78,7 +78,7 @@ To use FastQ Screen, this pipeline requires a `.csv` detailing:
 
 - the working name of the reference
 - the name of the aligner used to generate its index (which is also the aligner and index used by the tool)
-- the file basename of the reference and its index (e.g. the reference `genoma.fa` and its index `genome.bt2` have the basename `genome`)
+- the file basename of the reference and its index (e.g. the reference `genome.fa` and its index `genome.bt2` have the basename `genome`)
 - the path to a dir where the reference and index files both reside.
 
 See `assets/example_fastq_screen_references.csv` for example.
diff --git a/modules/local/rundirparser/resources/usr/bin/parse_illumina.py b/modules/local/rundirparser/resources/usr/bin/parse_illumina.py
index 7c70a6da..d8728832 100755
--- a/modules/local/rundirparser/resources/usr/bin/parse_illumina.py
+++ b/modules/local/rundirparser/resources/usr/bin/parse_illumina.py
@@ -1,5 +1,8 @@
 #!/usr/bin/env python3
 
+# Author: @matrulda
+# Licence: MIT
+
 import os
 import yaml
 import sys
@@ -18,8 +21,10 @@ def read_run_parameters(directory):
         with open(alt_2) as f:
             return xmltodict.parse(f.read())
     else:
-        raise Exception("Could not find Illumina [Rr]unParameters.xml. "
-                        "Please provide RunParameters.xml or skip module.")
+        raise Exception(
+            "Could not find Illumina [Rr]unParameters.xml. "
+            "Please provide RunParameters.xml or skip module."
+        )
 
 
 def find(d, tag):
@@ -71,12 +76,11 @@ def construct_multiqc_yaml(directory):
         "description": "Sequencing metadata gathered from the run directory",
         "plot_type": "table",
         "pconfig": {
-            "id": 'mqc_seq_metadata',
-            "title": 'Run directory Metadata',
+            "id": "mqc_seq_metadata",
+            "title": "Run directory Metadata",
             "col1_header": "Metadata",
-            },
+        },
         "data": data,
-
     }
 
     return metadata
diff --git a/modules/nf-core/bowtie2/build/tests/main.nf.test b/modules/nf-core/bowtie2/build/tests/main.nf.test
deleted file mode 100644
index ee94c19c..00000000
--- a/modules/nf-core/bowtie2/build/tests/main.nf.test
+++ /dev/null
@@ -1,31 +0,0 @@
-nextflow_process {
-
-    name "Test Process BOWTIE2_BUILD"
-    script "../main.nf"
-    process "BOWTIE2_BUILD"
-    tag "modules"
-    tag "modules_nfcore"
-    tag "bowtie2"
-    tag "bowtie2/build"
-
-    test("Should run without failures") {
-
-        when {
-            process {
-                """
-                input[0] = [
-                    [ id:'test' ],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
-                ]
-                """
-            }
-        }
-
-        then {
-            assert process.success
-            assert snapshot(process.out).match()
-        }
-
-    }
-
-}
diff --git a/modules/nf-core/bowtie2/build/tests/main.nf.test.snap b/modules/nf-core/bowtie2/build/tests/main.nf.test.snap
deleted file mode 100644
index ea5711e4..00000000
--- a/modules/nf-core/bowtie2/build/tests/main.nf.test.snap
+++ /dev/null
@@ -1,49 +0,0 @@
-{
-    "Should run without failures": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        [
-                            "genome.1.bt2:md5,cbe3d0bbea55bc57c99b4bfa25b5fbdf",
-                            "genome.2.bt2:md5,47b153cd1319abc88dda532462651fcf",
-                            "genome.3.bt2:md5,4ed93abba181d8dfab2e303e33114777",
-                            "genome.4.bt2:md5,c25be5f8b0378abf7a58c8a880b87626",
-                            "genome.rev.1.bt2:md5,52be6950579598a990570fbcf5372184",
-                            "genome.rev.2.bt2:md5,e3b4ef343dea4dd571642010a7d09597"
-                        ]
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,d136fb9c16f0a9fb2ae804b2a5fbc09c"
-                ],
-                "index": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        [
-                            "genome.1.bt2:md5,cbe3d0bbea55bc57c99b4bfa25b5fbdf",
-                            "genome.2.bt2:md5,47b153cd1319abc88dda532462651fcf",
-                            "genome.3.bt2:md5,4ed93abba181d8dfab2e303e33114777",
-                            "genome.4.bt2:md5,c25be5f8b0378abf7a58c8a880b87626",
-                            "genome.rev.1.bt2:md5,52be6950579598a990570fbcf5372184",
-                            "genome.rev.2.bt2:md5,e3b4ef343dea4dd571642010a7d09597"
-                        ]
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,d136fb9c16f0a9fb2ae804b2a5fbc09c"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.02.1"
-        },
-        "timestamp": "2023-11-23T11:51:01.107681997"
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/bwamem2/index/tests/main.nf.test b/modules/nf-core/bwamem2/index/tests/main.nf.test
deleted file mode 100644
index adf44785..00000000
--- a/modules/nf-core/bwamem2/index/tests/main.nf.test
+++ /dev/null
@@ -1,62 +0,0 @@
-nextflow_process {
-
-    name "Test Process BWAMEM2_INDEX"
-    tag "modules_nfcore"
-    tag "modules"
-    tag "bwamem2"
-    tag "bwamem2/index"
-    script "../main.nf"
-    process "BWAMEM2_INDEX"
-
-    test("fasta") {
-
-        when {
-            process {
-                """
-                input[0] = [
-                    [id: 'test'],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
-                ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(
-                    process.out.index,
-                    process.out.versions,
-                    path(process.out.versions[0]).yaml
-                ).match() }
-            )
-        }
-    }
-
-    test("fasta - stub") {
-
-        options "-stub"
-
-        when {
-            process {
-                """
-                input[0] = [
-                    [id: 'test'],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
-                ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(
-                    process.out.index,
-                    process.out.versions,
-                    path(process.out.versions[0]).yaml
-                ).match() }
-            )
-        }
-    }
-}
diff --git a/modules/nf-core/bwamem2/index/tests/main.nf.test.snap b/modules/nf-core/bwamem2/index/tests/main.nf.test.snap
deleted file mode 100644
index 9ad8b20c..00000000
--- a/modules/nf-core/bwamem2/index/tests/main.nf.test.snap
+++ /dev/null
@@ -1,64 +0,0 @@
-{
-    "fasta - stub": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    [
-                        "genome.fasta.0123:md5,d41d8cd98f00b204e9800998ecf8427e",
-                        "genome.fasta.amb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                        "genome.fasta.ann:md5,d41d8cd98f00b204e9800998ecf8427e",
-                        "genome.fasta.bwt.2bit.64:md5,d41d8cd98f00b204e9800998ecf8427e",
-                        "genome.fasta.pac:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ]
-            ],
-            [
-                "versions.yml:md5,9ffd13d12e7108ed15c58566bc4717d6"
-            ],
-            {
-                "BWAMEM2_INDEX": {
-                    "bwamem2": "2.2.1"
-                }
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-04T08:55:53.219699135"
-    },
-    "fasta": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    [
-                        "genome.fasta.0123:md5,b02870de80106104abcb03cd9463e7d8",
-                        "genome.fasta.amb:md5,3a68b8b2287e07dd3f5f95f4344ba76e",
-                        "genome.fasta.ann:md5,c32e11f6c859f166c7525a9c1d583567",
-                        "genome.fasta.bwt.2bit.64:md5,d097a1b82dee375d41a1ea69895a9216",
-                        "genome.fasta.pac:md5,983e3d2cd6f36e2546e6d25a0da78d66"
-                    ]
-                ]
-            ],
-            [
-                "versions.yml:md5,9ffd13d12e7108ed15c58566bc4717d6"
-            ],
-            {
-                "BWAMEM2_INDEX": {
-                    "bwamem2": "2.2.1"
-                }
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-04T08:55:45.007921901"
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/bwamem2/mem/tests/main.nf.test b/modules/nf-core/bwamem2/mem/tests/main.nf.test
deleted file mode 100644
index 9e0ab14a..00000000
--- a/modules/nf-core/bwamem2/mem/tests/main.nf.test
+++ /dev/null
@@ -1,179 +0,0 @@
-nextflow_process {
-
-    name "Test Process BWAMEM2_MEM"
-    script "../main.nf"
-    process "BWAMEM2_MEM"
-
-    tag "modules"
-    tag "modules_nfcore"
-    tag "bwamem2"
-    tag "bwamem2/mem"
-    tag "bwamem2/index"
-
-    setup {
-        run("BWAMEM2_INDEX") {
-            script "../../index/main.nf"
-            process {
-                """
-                input[0] = Channel.of([
-                    [:], // meta map
-                    [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
-                ])
-                """
-            }
-        }
-    }
-
-    test("sarscov2 - fastq, index, fasta, false") {
-
-        when {
-            process {
-                """
-                input[0] = Channel.of([
-                    [ id:'test', single_end:true ], // meta map
-                    [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)]
-                ])
-                input[1] = BWAMEM2_INDEX.out.index
-                input[2] = Channel.of([[:], [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]])
-                input[3] = false
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(
-                    bam(process.out.bam[0][1]).getHeaderMD5(),
-                    bam(process.out.bam[0][1]).getReadsMD5(),
-                    process.out.versions
-                ).match() }
-            )
-        }
-
-    }
-
-    test("sarscov2 - fastq, index, fasta, true") {
-
-        when {
-            process {
-                """
-                input[0] = Channel.of([
-                    [ id:'test', single_end:true ], // meta map
-                    [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)]
-                ])
-                input[1] = BWAMEM2_INDEX.out.index
-                input[2] = Channel.of([[:], [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]])
-                input[3] = true
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(
-                    bam(process.out.bam[0][1]).getHeaderMD5(),
-                    bam(process.out.bam[0][1]).getReadsMD5(),
-                    process.out.versions
-                ).match() }
-            )
-        }
-
-    }
-
-    test("sarscov2 - [fastq1, fastq2], index, fasta, false") {
-
-        when {
-            process {
-                """
-                input[0] = Channel.of([
-                    [ id:'test', single_end:false ], // meta map
-                    [
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
-                    ]
-                ])
-                input[1] = BWAMEM2_INDEX.out.index
-                input[2] = Channel.of([[:], [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]])
-                input[3] = false
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(
-                    bam(process.out.bam[0][1]).getHeaderMD5(),
-                    bam(process.out.bam[0][1]).getReadsMD5(),
-                    process.out.versions
-                ).match() }
-            )
-        }
-
-    }
-
-    test("sarscov2 - [fastq1, fastq2], index, fasta, true") {
-
-        when {
-            process {
-                """
-                input[0] = Channel.of([
-                    [ id:'test', single_end:false ], // meta map
-                    [
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
-                    ]
-                ])
-                input[1] = BWAMEM2_INDEX.out.index
-                input[2] = Channel.of([[:], [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]])
-                input[3] = true
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(
-                    bam(process.out.bam[0][1]).getHeaderMD5(),
-                    bam(process.out.bam[0][1]).getReadsMD5(),
-                    process.out.versions
-                ).match() }
-            )
-        }
-
-    }
-
-    test("sarscov2 - [fastq1, fastq2], index, fasta, true - stub") {
-
-        options "-stub"
-
-        when {
-            process {
-                """
-                input[0] = Channel.of([
-                    [ id:'test', single_end:false ], // meta map
-                    [
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
-                    ]
-                ])
-                input[1] = BWAMEM2_INDEX.out.index
-                input[2] = Channel.of([[:], [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]])
-                input[3] = true
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-
-    }
-
-}
diff --git a/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap b/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap
deleted file mode 100644
index b7d40a68..00000000
--- a/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap
+++ /dev/null
@@ -1,129 +0,0 @@
-{
-    "sarscov2 - [fastq1, fastq2], index, fasta, false": {
-        "content": [
-            "e414c2d48e2e44c2c52c20ecd88e8bd8",
-            "57aeef88ed701a8ebc8e2f0a381b2a6",
-            [
-                "versions.yml:md5,3574188ab1f33fd99cff9f5562dfb885"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2025-09-23T11:44:52.73673293"
-    },
-    "sarscov2 - [fastq1, fastq2], index, fasta, true - stub": {
-        "content": [
-            {
-                "0": [
-                    
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    
-                ],
-                "4": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "5": [
-                    "versions.yml:md5,3574188ab1f33fd99cff9f5562dfb885"
-                ],
-                "bam": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "crai": [
-                    
-                ],
-                "cram": [
-                    
-                ],
-                "csi": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "sam": [
-                    
-                ],
-                "versions": [
-                    "versions.yml:md5,3574188ab1f33fd99cff9f5562dfb885"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2025-09-23T11:45:14.834888709"
-    },
-    "sarscov2 - [fastq1, fastq2], index, fasta, true": {
-        "content": [
-            "716ed1ef39deaad346ca7cf86e08f959",
-            "af8628d9df18b2d3d4f6fd47ef2bb872",
-            [
-                "versions.yml:md5,3574188ab1f33fd99cff9f5562dfb885"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2025-09-23T11:45:04.750057645"
-    },
-    "sarscov2 - fastq, index, fasta, false": {
-        "content": [
-            "283a83f604f3f5338acedfee349dccf4",
-            "798439cbd7fd81cbcc5078022dc5479d",
-            [
-                "versions.yml:md5,3574188ab1f33fd99cff9f5562dfb885"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2025-09-23T11:44:28.57550711"
-    },
-    "sarscov2 - fastq, index, fasta, true": {
-        "content": [
-            "ed99048bb552cac58e39923b550b6d5b",
-            "94fcf617f5b994584c4e8d4044e16b4f",
-            [
-                "versions.yml:md5,3574188ab1f33fd99cff9f5562dfb885"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2025-09-23T11:44:40.437183765"
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test
deleted file mode 100644
index e9d79a07..00000000
--- a/modules/nf-core/fastqc/tests/main.nf.test
+++ /dev/null
@@ -1,309 +0,0 @@
-nextflow_process {
-
-    name "Test Process FASTQC"
-    script "../main.nf"
-    process "FASTQC"
-
-    tag "modules"
-    tag "modules_nfcore"
-    tag "fastqc"
-
-    test("sarscov2 single-end [fastq]") {
-
-        when {
-            process {
-                """
-                input[0] = Channel.of([
-                    [ id: 'test', single_end:true ],
-                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
-                ])
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it.
-                // looks like this: <div id="header_filename">Mon 2 Oct 2023<br/>test.gz</div>
-                // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039
-                { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
-                { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
-                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-                { assert snapshot(process.out.versions).match() }
-            )
-        }
-    }
-
-    test("sarscov2 paired-end [fastq]") {
-
-        when {
-            process {
-                """
-                input[0] = Channel.of([
-                    [id: 'test', single_end: false], // meta map
-                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
-                ])
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
-                { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
-                { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
-                { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
-                { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-                { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-                { assert snapshot(process.out.versions).match() }
-            )
-        }
-    }
-
-    test("sarscov2 interleaved [fastq]") {
-
-        when {
-            process {
-                """
-                input[0] = Channel.of([
-                    [id: 'test', single_end: false], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true)
-                ])
-            """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
-                { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
-                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-                { assert snapshot(process.out.versions).match() }
-            )
-        }
-    }
-
-    test("sarscov2 paired-end [bam]") {
-
-        when {
-            process {
-                """
-                input[0] = Channel.of([
-                    [id: 'test', single_end: false], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
-                ])
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
-                { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
-                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-                { assert snapshot(process.out.versions).match() }
-            )
-        }
-    }
-
-    test("sarscov2 multiple [fastq]") {
-
-        when {
-            process {
-                """
-                input[0] = Channel.of([
-                    [id: 'test', single_end: false], // meta map
-                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ]
-                ])
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
-                { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
-                { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" },
-                { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" },
-                { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
-                { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
-                { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" },
-                { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" },
-                { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-                { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-                { assert path(process.out.html[0][1][2]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-                { assert path(process.out.html[0][1][3]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-                { assert snapshot(process.out.versions).match() }
-            )
-        }
-    }
-
-    test("sarscov2 custom_prefix") {
-
-        when {
-            process {
-                """
-                input[0] = Channel.of([
-                    [ id:'mysample', single_end:true ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
-                ])
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" },
-                { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" },
-                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-                { assert snapshot(process.out.versions).match() }
-            )
-        }
-    }
-
-    test("sarscov2 single-end [fastq] - stub") {
-
-    options "-stub"
-        when {
-            process {
-                """
-                input[0] = Channel.of([
-                    [ id: 'test', single_end:true ],
-                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
-                ])
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-
-    test("sarscov2 paired-end [fastq] - stub") {
-
-    options "-stub"
-        when {
-            process {
-                """
-                input[0] = Channel.of([
-                    [id: 'test', single_end: false], // meta map
-                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
-                ])
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-
-    test("sarscov2 interleaved [fastq] - stub") {
-
-    options "-stub"
-        when {
-            process {
-                """
-                input[0] = Channel.of([
-                    [id: 'test', single_end: false], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true)
-                ])
-            """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-
-    test("sarscov2 paired-end [bam] - stub") {
-
-    options "-stub"
-        when {
-            process {
-                """
-                input[0] = Channel.of([
-                    [id: 'test', single_end: false], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
-                ])
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-
-    test("sarscov2 multiple [fastq] - stub") {
-
-    options "-stub"
-        when {
-            process {
-                """
-                input[0] = Channel.of([
-                    [id: 'test', single_end: false], // meta map
-                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ]
-                ])
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-
-    test("sarscov2 custom_prefix - stub") {
-
-    options "-stub"
-        when {
-            process {
-                """
-                input[0] = Channel.of([
-                    [ id:'mysample', single_end:true ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
-                ])
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-}
diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap
deleted file mode 100644
index d5db3092..00000000
--- a/modules/nf-core/fastqc/tests/main.nf.test.snap
+++ /dev/null
@@ -1,392 +0,0 @@
-{
-    "sarscov2 custom_prefix": {
-        "content": [
-            [
-                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
-        },
-        "timestamp": "2024-07-22T11:02:16.374038"
-    },
-    "sarscov2 single-end [fastq] - stub": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-                ],
-                "html": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-                ],
-                "zip": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
-        },
-        "timestamp": "2024-07-22T11:02:24.993809"
-    },
-    "sarscov2 custom_prefix - stub": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "mysample",
-                            "single_end": true
-                        },
-                        "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "mysample",
-                            "single_end": true
-                        },
-                        "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-                ],
-                "html": [
-                    [
-                        {
-                            "id": "mysample",
-                            "single_end": true
-                        },
-                        "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-                ],
-                "zip": [
-                    [
-                        {
-                            "id": "mysample",
-                            "single_end": true
-                        },
-                        "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
-        },
-        "timestamp": "2024-07-22T11:03:10.93942"
-    },
-    "sarscov2 interleaved [fastq]": {
-        "content": [
-            [
-                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
-        },
-        "timestamp": "2024-07-22T11:01:42.355718"
-    },
-    "sarscov2 paired-end [bam]": {
-        "content": [
-            [
-                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
-        },
-        "timestamp": "2024-07-22T11:01:53.276274"
-    },
-    "sarscov2 multiple [fastq]": {
-        "content": [
-            [
-                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
-        },
-        "timestamp": "2024-07-22T11:02:05.527626"
-    },
-    "sarscov2 paired-end [fastq]": {
-        "content": [
-            [
-                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
-        },
-        "timestamp": "2024-07-22T11:01:31.188871"
-    },
-    "sarscov2 paired-end [fastq] - stub": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-                ],
-                "html": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-                ],
-                "zip": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
-        },
-        "timestamp": "2024-07-22T11:02:34.273566"
-    },
-    "sarscov2 multiple [fastq] - stub": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-                ],
-                "html": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-                ],
-                "zip": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
-        },
-        "timestamp": "2024-07-22T11:03:02.304411"
-    },
-    "sarscov2 single-end [fastq]": {
-        "content": [
-            [
-                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
-        },
-        "timestamp": "2024-07-22T11:01:19.095607"
-    },
-    "sarscov2 interleaved [fastq] - stub": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-                ],
-                "html": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-                ],
-                "zip": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
-        },
-        "timestamp": "2024-07-22T11:02:44.640184"
-    },
-    "sarscov2 paired-end [bam] - stub": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-                ],
-                "html": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-                ],
-                "zip": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
-        },
-        "timestamp": "2024-07-22T11:02:53.550742"
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test b/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test
deleted file mode 100644
index 5357712a..00000000
--- a/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test
+++ /dev/null
@@ -1,71 +0,0 @@
-nextflow_process {
-
-    name "Test Process FASTQSCREEN_BUILDFROMINDEX"
-    script "../main.nf"
-    process "FASTQSCREEN_BUILDFROMINDEX"
-
-    tag "modules"
-    tag "modules_nfcore"
-    tag "fastqscreen"
-    tag "fastqscreen/buildfromindex"
-    tag "bowtie2/build"
-
-    setup {
-
-        run("BOWTIE2_BUILD") {
-            script "../../../bowtie2/build/main.nf"
-            process {
-                """
-                input[0] =  Channel.from([
-                                    [[id: "sarscov2"], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)],
-                                    [[id: "human"]   , file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)]
-                            ])
-                """
-            }
-        }
-
-    }
-
-    test("sarscov2 - human") {
-
-        when {
-            process {
-                """
-                input[0] = BOWTIE2_BUILD.out.index.map{meta, index -> meta.id}.collect()
-                input[1] = BOWTIE2_BUILD.out.index.map{meta, index -> index}.collect()
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out.database, process.out.versions).match() }
-            )
-        }
-
-    }
-
-    test("sarscov2 - human - stub") {
-
-        options "-stub"
-
-        when {
-            process {
-                """
-                input[0] = BOWTIE2_BUILD.out.index.map{meta, index -> meta.id}.collect()
-                input[1] = BOWTIE2_BUILD.out.index.map{meta, index -> index}.collect()
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-
-    }
-
-}
diff --git a/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test.snap b/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test.snap
deleted file mode 100644
index a485079b..00000000
--- a/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test.snap
+++ /dev/null
@@ -1,95 +0,0 @@
-{
-    "sarscov2 - human": {
-        "content": [
-            [
-                [
-                    [
-                        "genome.1.bt2:md5,cbe3d0bbea55bc57c99b4bfa25b5fbdf",
-                        "genome.2.bt2:md5,47b153cd1319abc88dda532462651fcf",
-                        "genome.3.bt2:md5,4ed93abba181d8dfab2e303e33114777",
-                        "genome.4.bt2:md5,c25be5f8b0378abf7a58c8a880b87626",
-                        "genome.rev.1.bt2:md5,52be6950579598a990570fbcf5372184",
-                        "genome.rev.2.bt2:md5,e3b4ef343dea4dd571642010a7d09597"
-                    ],
-                    [
-                        "genome.1.bt2:md5,2fbc8eeaf480f03b3a2362a782fa5755",
-                        "genome.2.bt2:md5,a5300e3cf590d4cd8bd5521cac6337d6",
-                        "genome.3.bt2:md5,d2a7a0e1c9891e847a15781c0695b84e",
-                        "genome.4.bt2:md5,a55dc4b09e3e00586de6963800c95b9a",
-                        "genome.rev.1.bt2:md5,93c07f7d04e5da6bf1322ad5f46ac806",
-                        "genome.rev.2.bt2:md5,c3fa30132c0c9b9bc7868059e8e23466"
-                    ],
-                    "fastq_screen.conf:md5,ca56e866c7006a46bdfe4e751e787265"
-                ]
-            ],
-            [
-                "versions.yml:md5,c2bcf85b00046c72d5dccd2dba8ac35c"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.02.1"
-        },
-        "timestamp": "2025-03-25T12:58:36.506586801"
-    },
-    "sarscov2 - human": {
-        "content": [
-            [
-                [
-                    [
-                        "genome.1.bt2:md5,cbe3d0bbea55bc57c99b4bfa25b5fbdf",
-                        "genome.2.bt2:md5,47b153cd1319abc88dda532462651fcf",
-                        "genome.3.bt2:md5,4ed93abba181d8dfab2e303e33114777",
-                        "genome.4.bt2:md5,c25be5f8b0378abf7a58c8a880b87626",
-                        "genome.rev.1.bt2:md5,52be6950579598a990570fbcf5372184",
-                        "genome.rev.2.bt2:md5,e3b4ef343dea4dd571642010a7d09597"
-                    ],
-                    [
-                        "genome.1.bt2:md5,2fbc8eeaf480f03b3a2362a782fa5755",
-                        "genome.2.bt2:md5,a5300e3cf590d4cd8bd5521cac6337d6",
-                        "genome.3.bt2:md5,d2a7a0e1c9891e847a15781c0695b84e",
-                        "genome.4.bt2:md5,a55dc4b09e3e00586de6963800c95b9a",
-                        "genome.rev.1.bt2:md5,93c07f7d04e5da6bf1322ad5f46ac806",
-                        "genome.rev.2.bt2:md5,c3fa30132c0c9b9bc7868059e8e23466"
-                    ],
-                    "fastq_screen.conf:md5,ca56e866c7006a46bdfe4e751e787265"
-                ]
-            ],
-            [
-                "versions.yml:md5,c2bcf85b00046c72d5dccd2dba8ac35c"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-03-25T08:34:46.992911211"
-    },
-    "sarscov2 - human - stub": {
-        "content": [
-            {
-                "0": [
-                    [
-                        "fastq_screen.conf:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,c2bcf85b00046c72d5dccd2dba8ac35c"
-                ],
-                "database": [
-                    [
-                        "fastq_screen.conf:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,c2bcf85b00046c72d5dccd2dba8ac35c"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-03-25T08:35:14.073325807"
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
index c6fdd2f1..9647dd39 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
+++ b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
@@ -112,7 +112,7 @@ Changes in 'fastqscreen/fastqscreen/main.nf':
 -
  }
 
-'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap' is unchanged
-'modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config' is unchanged
-'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test' was removed
+'modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config' was removed
+'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap' was removed
 ************************************************************
diff --git a/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test b/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test
deleted file mode 100644
index 71230a22..00000000
--- a/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test
+++ /dev/null
@@ -1,117 +0,0 @@
-nextflow_process {
-
-    name "Test Process FASTQSCREEN_FASTQSCREEN"
-    script "../main.nf"
-    process "FASTQSCREEN_FASTQSCREEN"
-
-    tag "modules"
-    tag "modules_nfcore"
-    tag "bowtie2/build"
-    tag "fastqscreen"
-    tag "fastqscreen/buildfromindex"
-    tag "fastqscreen/fastqscreen"
-    tag "buildfromindex"
-    tag "modules_fastqscreen"
-
-    setup {
-
-        run("BOWTIE2_BUILD") {
-            script "../../../bowtie2/build/main.nf"
-            process {
-                """
-                input[0] =  Channel.from([
-                                    [[id: "sarscov2"], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)],
-                                    [[id: "human"]   , file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)]
-                            ])
-                """
-            }
-        }
-
-        run("FASTQSCREEN_BUILDFROMINDEX") {
-            script "../../../fastqscreen/buildfromindex/main.nf"
-            process {
-                """
-                input[0] = BOWTIE2_BUILD.out.index.map{meta, index -> meta.id}.collect()
-                input[1] = BOWTIE2_BUILD.out.index.map{meta, index -> index}.collect()
-                """
-            }
-        }
-    }
-
-    test("sarscov2 - human") {
-
-        when {
-            process {
-                """
-                input[0] =  [[ id:'test', single_end:true ],
-                             [file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-                            ]
-                input[1] = FASTQSCREEN_BUILDFROMINDEX.out.database
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out.version).match() },
-                { assert file(process.out.txt.get(0).get(1)).exists() },
-                { assert file(process.out.png.get(0).get(1)).exists() },
-                { assert file(process.out.html.get(0).get(1)).exists() }
-            )
-        }
-
-    }
-
-    test("sarscov2 - human - tags") {
-        config './nextflow.config'
-        when {
-            process {
-                """
-                input[0] =  [[ id:'test', single_end:false ],
-                             [file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
-                            ]
-                input[1] = FASTQSCREEN_BUILDFROMINDEX.out.database
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(
-                    process.out.version,
-                    process.out.txt,
-                    process.out.fastq,
-                    path(process.out.html.get(0).get(1)).readLines()[0..10],
-                    path(process.out.png.get(0).get(1)).exists()
-                    ).match() }
-            )
-        }
-
-    }
-
-    test("sarscov2 - human - stub") {
-
-        options "-stub"
-        when {
-            process {
-                """
-                input[0] =  [[ id:'test', single_end:true ],
-                             [file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-                            ]
-                input[1] = FASTQSCREEN_BUILDFROMINDEX.out.database
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-
-    }
-
-}
diff --git a/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap b/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap
deleted file mode 100644
index 042f3bb4..00000000
--- a/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap
+++ /dev/null
@@ -1,132 +0,0 @@
-{
-    "sarscov2 - human": {
-        "content": null,
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-08-31T05:42:29.972454812"
-    },
-    "sarscov2 - human - tags": {
-        "content": [
-            null,
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test_1_screen.txt:md5,b0b0ea58bc26ebaa4d573a85e7898f25"
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    [
-                        "test_1.tagged.fastq.gz:md5,f742b162c43ce28f80b89608d5c47f3d",
-                        "test_1.tagged_filter.fastq.gz:md5,28527a76bb0bb3fce0ee76afe01e90aa"
-                    ]
-                ]
-            ],
-            [
-                "<!DOCTYPE html>",
-                "<html>",
-                "",
-                "",
-                "<!-- Style, and Plotly code -->",
-                "<head>",
-                "\t<meta http-equiv=\"content-type\" content=\"text/html; charset=UTF-8\">",
-                "\t<title>FastQ Screen Processing Report - test_1.fastq.gz</title>",
-                "\t<style type=\"text/css\">",
-                "\t\tbody {",
-                "\t\t\tfont-family: Arial, sans-serif;"
-            ],
-            true
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-08-31T06:23:02.73675229"
-    },
-    "sarscov2 - human - stub": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test_1_screen.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test_1_screen.png:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test_1_screen.html:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "3": [
-                    
-                ],
-                "4": [
-                    "versions.yml:md5,8ac0239b5103352958d9a9e562b23103"
-                ],
-                "fastq": [
-                    
-                ],
-                "html": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test_1_screen.html:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "png": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test_1_screen.png:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "txt": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test_1_screen.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,8ac0239b5103352958d9a9e562b23103"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-03-25T08:38:33.98646086"
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config b/modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config
deleted file mode 100644
index ccf580b7..00000000
--- a/modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-    withName: FASTQSCREEN_FASTQSCREEN {
-        ext.args = "--tag --filter 10"
-    }
-}
diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test
deleted file mode 100644
index 33316a7d..00000000
--- a/modules/nf-core/multiqc/tests/main.nf.test
+++ /dev/null
@@ -1,92 +0,0 @@
-nextflow_process {
-
-    name "Test Process MULTIQC"
-    script "../main.nf"
-    process "MULTIQC"
-
-    tag "modules"
-    tag "modules_nfcore"
-    tag "multiqc"
-
-    config "./nextflow.config"
-
-    test("sarscov2 single-end [fastqc]") {
-
-        when {
-            process {
-                """
-                input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true))
-                input[1] = []
-                input[2] = []
-                input[3] = []
-                input[4] = []
-                input[5] = []
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert process.out.report[0] ==~ ".*/multiqc_report.html" },
-                { assert process.out.data[0] ==~ ".*/multiqc_data" },
-                { assert snapshot(process.out.versions).match("multiqc_versions_single") }
-            )
-        }
-
-    }
-
-    test("sarscov2 single-end [fastqc] [config]") {
-
-        when {
-            process {
-                """
-                input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true))
-                input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true))
-                input[2] = []
-                input[3] = []
-                input[4] = []
-                input[5] = []
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert process.out.report[0] ==~ ".*/multiqc_report.html" },
-                { assert process.out.data[0] ==~ ".*/multiqc_data" },
-                { assert snapshot(process.out.versions).match("multiqc_versions_config") }
-            )
-        }
-    }
-
-    test("sarscov2 single-end [fastqc] - stub") {
-
-        options "-stub"
-
-        when {
-            process {
-                """
-                input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true))
-                input[1] = []
-                input[2] = []
-                input[3] = []
-                input[4] = []
-                input[5] = []
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out.report.collect { file(it).getName() } +
-                                process.out.data.collect { file(it).getName() } +
-                                process.out.plots.collect { file(it).getName() } +
-                                process.out.versions ).match("multiqc_stub") }
-            )
-        }
-
-    }
-}
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
deleted file mode 100644
index a88bafd6..00000000
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ /dev/null
@@ -1,41 +0,0 @@
-{
-    "multiqc_versions_single": {
-        "content": [
-            [
-                "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "24.10.4"
-        },
-        "timestamp": "2025-10-27T13:33:24.356715"
-    },
-    "multiqc_stub": {
-        "content": [
-            [
-                "multiqc_report.html",
-                "multiqc_data",
-                "multiqc_plots",
-                "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "24.10.4"
-        },
-        "timestamp": "2025-10-27T13:34:11.103619"
-    },
-    "multiqc_versions_config": {
-        "content": [
-            [
-                "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "24.10.4"
-        },
-        "timestamp": "2025-10-27T13:34:04.615233"
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config
deleted file mode 100644
index c537a6a3..00000000
--- a/modules/nf-core/multiqc/tests/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-    withName: 'MULTIQC' {
-        ext.prefix = null
-    }
-}
diff --git a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test
deleted file mode 100644
index fe40e7b0..00000000
--- a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test
+++ /dev/null
@@ -1,234 +0,0 @@
-nextflow_process {
-
-    name "Test Process PICARD_COLLECTHSMETRICS"
-    script "../main.nf"
-    process "PICARD_COLLECTHSMETRICS"
-
-    tag "modules"
-    tag "modules_nfcore"
-    tag "picard"
-    tag "picard/collecthsmetrics"
-
-    test("sarscov2 - bam") {
-
-        when {
-            process {
-                """
-                input[0] = [
-                    [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true)
-                    ]
-                input[1] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
-                input[2] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]
-                input[3] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)]
-                input[4] = [[:],[]]
-                """
-            }
-        }
-
-        then {
-            def size = path(process.out.metrics[0][1]).size()
-            def lines = path(process.out.metrics[0][1]).readLines()[0..100]
-            lines.remove(3)  // remove timestamp
-            assertAll(
-                { assert process.success },
-                { assert snapshot(
-                    file(process.out.metrics[0][1]).name,
-                    size,
-                    lines,
-                    process.out.versions
-                    ).match()
-                }
-            )
-        }
-
-    }
-
-    test("sarscov2 - bam - gzippedfa") {
-
-        when {
-            process {
-                """
-                input[0] = [
-                        [ id:'test', single_end:false ], // meta map
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true)
-                    ]
-                input[1] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)]
-                input[2] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz.fai', checkIfExists: true)]
-                input[3] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)]
-                input[4] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz.gzi', checkIfExists: true)]
-                """
-            }
-        }
-
-        then {
-            def size = path(process.out.metrics[0][1]).size()
-            def lines = path(process.out.metrics[0][1]).readLines()[0..100]
-            lines.remove(3)  // remove timestamp
-            assertAll(
-                { assert process.success },
-                { assert snapshot(
-                    file(process.out.metrics[0][1]).name,
-                    size,
-                    lines,
-                    process.out.versions
-                    ).match()
-                }
-            )
-        }
-
-    }
-
-    test("sarscov2 - bam - stub") {
-
-        options "-stub"
-
-        when {
-            process {
-                """
-                input[0] = [
-                    [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true)
-                    ]
-                input[1] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
-                input[2] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]
-                input[3] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)]
-                input[4] = [[:],[]]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out.versions).match("versions") }
-            )
-        }
-
-    }
-
-    test("sarscov2 - bam - nofasta") {
-
-        when {
-            process {
-                """
-                input[0] = [
-                    [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true)
-                    ]
-                input[1] = [[:],[]]
-                input[2] = [[:],[]]
-                input[3] = [[:],[]]
-                input[4] = [[:],[]]
-                """
-            }
-        }
-
-        then {
-            def size = path(process.out.metrics[0][1]).size()
-            def lines = path(process.out.metrics[0][1]).readLines()[0..100]
-            lines.remove(3)  // remove timestamp
-            assertAll(
-                { assert process.success },
-                { assert snapshot(
-                    file(process.out.metrics[0][1]).name,
-                    size,
-                    lines,
-                    process.out.versions
-                    ).match()
-                }
-            )
-        }
-
-    }
-
-    test("sarscov2 - bam - bed") {
-
-        when {
-            process {
-                """
-                input[0] = [
-                    [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/baits.bed', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
-                    ]
-
-                input[1] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
-                input[2] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]
-                input[3] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)]
-                input[4] = [[:],[]]
-                """
-            }
-        }
-
-        then {
-            def size = path(process.out.metrics[0][1]).size()
-            def lines = path(process.out.metrics[0][1]).readLines()[0..100]
-            lines.remove(3)  // remove timestamp
-            assertAll(
-                { assert process.success },
-                { assert snapshot(
-                    file(process.out.metrics[0][1]).name,
-                    size,
-                    lines,
-                    process.out.versions
-                    ).match()
-                }
-            )
-        }
-
-    }
-
-    test("sarscov2 - bam - samebed") {
-
-        when {
-            process {
-                """
-                input[0] = [
-                    [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/baits.bed', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/baits.bed', checkIfExists: true)
-                    ]
-
-                input[1] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
-                input[2] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]
-                input[3] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)]
-                input[4] = [[:],[]]
-                """
-            }
-        }
-
-        then {
-            def size = path(process.out.metrics[0][1]).size()
-            def lines = path(process.out.metrics[0][1]).readLines()[0..100]
-            lines.remove(3)  // remove timestamp
-            assertAll(
-                { assert process.success },
-                { assert snapshot(
-                    file(process.out.metrics[0][1]).name,
-                    size,
-                    lines,
-                    process.out.versions
-                    ).match()
-                }
-            )
-        }
-
-    }
-}
diff --git a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap
deleted file mode 100644
index 11b0f7c5..00000000
--- a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap
+++ /dev/null
@@ -1,594 +0,0 @@
-{
-    "sarscov2 - bam - nofasta": {
-        "content": [
-            "test.CollectHsMetrics.coverage_metrics",
-            3548,
-            [
-                "## htsjdk.samtools.metrics.StringHeader",
-                "# CollectHsMetrics --BAIT_INTERVALS baits/baits.interval_list --TARGET_INTERVALS targets/targets.interval_list --INPUT test.paired_end.sorted.bam --OUTPUT test.CollectHsMetrics.coverage_metrics --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false",
-                "## htsjdk.samtools.metrics.StringHeader",
-                "",
-                "## METRICS CLASS\tpicard.analysis.directed.HsMetrics",
-                "BAIT_SET\tBAIT_TERRITORY\tBAIT_DESIGN_EFFICIENCY\tON_BAIT_BASES\tNEAR_BAIT_BASES\tOFF_BAIT_BASES\tPCT_SELECTED_BASES\tPCT_OFF_BAIT\tON_BAIT_VS_SELECTED\tMEAN_BAIT_COVERAGE\tPCT_USABLE_BASES_ON_BAIT\tPCT_USABLE_BASES_ON_TARGET\tFOLD_ENRICHMENT\tHS_LIBRARY_SIZE\tHS_PENALTY_10X\tHS_PENALTY_20X\tHS_PENALTY_30X\tHS_PENALTY_40X\tHS_PENALTY_50X\tHS_PENALTY_100X\tTARGET_TERRITORY\tGENOME_SIZE\tTOTAL_READS\tPF_READS\tPF_BASES\tPF_UNIQUE_READS\tPF_UQ_READS_ALIGNED\tPF_BASES_ALIGNED\tPF_UQ_BASES_ALIGNED\tON_TARGET_BASES\tPCT_PF_READS\tPCT_PF_UQ_READS\tPCT_PF_UQ_READS_ALIGNED\tMEAN_TARGET_COVERAGE\tMEDIAN_TARGET_COVERAGE\tMAX_TARGET_COVERAGE\tMIN_TARGET_COVERAGE\tZERO_CVG_TARGETS_PCT\tPCT_EXC_DUPE\tPCT_EXC_ADAPTER\tPCT_EXC_MAPQ\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_OFF_TARGET\tFOLD_80_BASE_PENALTY\tPCT_TARGET_BASES_1X\tPCT_TARGET_BASES_2X\tPCT_TARGET_BASES_10X\tPCT_TARGET_BASES_20X\tPCT_TARGET_BASES_30X\tPCT_TARGET_BASES_40X\tPCT_TARGET_BASES_50X\tPCT_TARGET_BASES_100X\tPCT_TARGET_BASES_250X\tPCT_TARGET_BASES_500X\tPCT_TARGET_BASES_1000X\tPCT_TARGET_BASES_2500X\tPCT_TARGET_BASES_5000X\tPCT_TARGET_BASES_10000X\tPCT_TARGET_BASES_25000X\tPCT_TARGET_BASES_50000X\tPCT_TARGET_BASES_100000X\tAT_DROPOUT\tGC_DROPOUT\tHET_SNP_SENSITIVITY\tHET_SNP_Q\tSAMPLE\tLIBRARY\tREAD_GROUP",
-                "baits\t158\t0.594937\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.000181\t4.995204\t\t0\t0\t0\t0\t0\t0\t94\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t5\t1\t1\t0.985\t0.053191\t0\t1\t0\t0.75\t0\t0\t0.005438\t0.054487\t0.259516\t0.680377\t?\t0.053191\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.015734\t0\t\t\t",
-                "",
-                "## HISTOGRAM\tjava.lang.Integer",
-                "coverage_or_base_quality\thigh_quality_coverage_count\tunfiltered_baseq_count",
-                "0\t89\t0",
-                "1\t5\t0",
-                "2\t0\t0",
-                "3\t0\t0",
-                "4\t0\t0",
-                "5\t0\t0",
-                "6\t0\t0",
-                "7\t0\t0",
-                "8\t0\t0",
-                "9\t0\t0",
-                "10\t0\t0",
-                "11\t0\t0",
-                "12\t0\t0",
-                "13\t0\t0",
-                "14\t0\t5",
-                "15\t0\t0",
-                "16\t0\t0",
-                "17\t0\t0",
-                "18\t0\t0",
-                "19\t0\t0",
-                "20\t0\t0",
-                "21\t0\t1",
-                "22\t0\t0",
-                "23\t0\t0",
-                "24\t0\t0",
-                "25\t0\t0",
-                "26\t0\t0",
-                "27\t0\t0",
-                "28\t0\t0",
-                "29\t0\t0",
-                "30\t0\t0",
-                "31\t0\t0",
-                "32\t0\t1",
-                "33\t0\t0",
-                "34\t0\t0",
-                "35\t0\t0",
-                "36\t0\t3",
-                "37\t0\t0",
-                "38\t0\t0",
-                "39\t0\t0",
-                "40\t0\t0",
-                "41\t0\t0",
-                "42\t0\t0",
-                "43\t0\t0",
-                "44\t0\t0",
-                "45\t0\t0",
-                "46\t0\t0",
-                "47\t0\t0",
-                "48\t0\t0",
-                "49\t0\t0",
-                "50\t0\t0",
-                "51\t0\t0",
-                "52\t0\t0",
-                "53\t0\t0",
-                "54\t0\t0",
-                "55\t0\t0",
-                "56\t0\t0",
-                "57\t0\t0",
-                "58\t0\t0",
-                "59\t0\t0",
-                "60\t0\t0",
-                "61\t0\t0",
-                "62\t0\t0",
-                "63\t0\t0",
-                "64\t0\t0",
-                "65\t0\t0",
-                "66\t0\t0",
-                "67\t0\t0",
-                "68\t0\t0",
-                "69\t0\t0",
-                "70\t0\t0",
-                "71\t0\t0",
-                "72\t0\t0",
-                "73\t0\t0",
-                "74\t0\t0",
-                "75\t0\t0",
-                "76\t0\t0",
-                "77\t0\t0",
-                "78\t0\t0",
-                "79\t0\t0",
-                "80\t0\t0",
-                "81\t0\t0",
-                "82\t0\t0",
-                "83\t0\t0",
-                "84\t0\t0",
-                "85\t0\t0",
-                "86\t0\t0",
-                "87\t0\t0",
-                "88\t0\t0",
-                "89\t0\t0"
-            ],
-            [
-                "versions.yml:md5,533cf1e35d36fdacbb762f5df2e1b322"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2025-09-15T10:37:59.62099935"
-    },
-    "sarscov2 - bam - gzippedfa": {
-        "content": [
-            "test.CollectHsMetrics.coverage_metrics",
-            3601,
-            [
-                "## htsjdk.samtools.metrics.StringHeader",
-                "# CollectHsMetrics --BAIT_INTERVALS baits/baits.interval_list --TARGET_INTERVALS targets/targets.interval_list --INPUT test.paired_end.sorted.bam --OUTPUT test.CollectHsMetrics.coverage_metrics --REFERENCE_SEQUENCE genome.fasta.gz --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false",
-                "## htsjdk.samtools.metrics.StringHeader",
-                "",
-                "## METRICS CLASS\tpicard.analysis.directed.HsMetrics",
-                "BAIT_SET\tBAIT_TERRITORY\tBAIT_DESIGN_EFFICIENCY\tON_BAIT_BASES\tNEAR_BAIT_BASES\tOFF_BAIT_BASES\tPCT_SELECTED_BASES\tPCT_OFF_BAIT\tON_BAIT_VS_SELECTED\tMEAN_BAIT_COVERAGE\tPCT_USABLE_BASES_ON_BAIT\tPCT_USABLE_BASES_ON_TARGET\tFOLD_ENRICHMENT\tHS_LIBRARY_SIZE\tHS_PENALTY_10X\tHS_PENALTY_20X\tHS_PENALTY_30X\tHS_PENALTY_40X\tHS_PENALTY_50X\tHS_PENALTY_100X\tTARGET_TERRITORY\tGENOME_SIZE\tTOTAL_READS\tPF_READS\tPF_BASES\tPF_UNIQUE_READS\tPF_UQ_READS_ALIGNED\tPF_BASES_ALIGNED\tPF_UQ_BASES_ALIGNED\tON_TARGET_BASES\tPCT_PF_READS\tPCT_PF_UQ_READS\tPCT_PF_UQ_READS_ALIGNED\tMEAN_TARGET_COVERAGE\tMEDIAN_TARGET_COVERAGE\tMAX_TARGET_COVERAGE\tMIN_TARGET_COVERAGE\tZERO_CVG_TARGETS_PCT\tPCT_EXC_DUPE\tPCT_EXC_ADAPTER\tPCT_EXC_MAPQ\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_OFF_TARGET\tFOLD_80_BASE_PENALTY\tPCT_TARGET_BASES_1X\tPCT_TARGET_BASES_2X\tPCT_TARGET_BASES_10X\tPCT_TARGET_BASES_20X\tPCT_TARGET_BASES_30X\tPCT_TARGET_BASES_40X\tPCT_TARGET_BASES_50X\tPCT_TARGET_BASES_100X\tPCT_TARGET_BASES_250X\tPCT_TARGET_BASES_500X\tPCT_TARGET_BASES_1000X\tPCT_TARGET_BASES_2500X\tPCT_TARGET_BASES_5000X\tPCT_TARGET_BASES_10000X\tPCT_TARGET_BASES_25000X\tPCT_TARGET_BASES_50000X\tPCT_TARGET_BASES_100000X\tAT_DROPOUT\tGC_DROPOUT\tHET_SNP_SENSITIVITY\tHET_SNP_Q\tSAMPLE\tLIBRARY\tREAD_GROUP",
-                "baits\t158\t0.594937\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.000181\t4.995204\t\t0\t0\t0\t0\t0\t0\t94\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t5\t1\t1\t0.985\t0.053191\t0\t1\t0\t0.75\t0\t0\t0.005438\t0.054487\t0.259516\t0.680377\t?\t0.053191\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t76.595745\t23.404255\t0.015734\t0\t\t\t",
-                "",
-                "## HISTOGRAM\tjava.lang.Integer",
-                "coverage_or_base_quality\thigh_quality_coverage_count\tunfiltered_baseq_count",
-                "0\t89\t0",
-                "1\t5\t0",
-                "2\t0\t0",
-                "3\t0\t0",
-                "4\t0\t0",
-                "5\t0\t0",
-                "6\t0\t0",
-                "7\t0\t0",
-                "8\t0\t0",
-                "9\t0\t0",
-                "10\t0\t0",
-                "11\t0\t0",
-                "12\t0\t0",
-                "13\t0\t0",
-                "14\t0\t5",
-                "15\t0\t0",
-                "16\t0\t0",
-                "17\t0\t0",
-                "18\t0\t0",
-                "19\t0\t0",
-                "20\t0\t0",
-                "21\t0\t1",
-                "22\t0\t0",
-                "23\t0\t0",
-                "24\t0\t0",
-                "25\t0\t0",
-                "26\t0\t0",
-                "27\t0\t0",
-                "28\t0\t0",
-                "29\t0\t0",
-                "30\t0\t0",
-                "31\t0\t0",
-                "32\t0\t1",
-                "33\t0\t0",
-                "34\t0\t0",
-                "35\t0\t0",
-                "36\t0\t3",
-                "37\t0\t0",
-                "38\t0\t0",
-                "39\t0\t0",
-                "40\t0\t0",
-                "41\t0\t0",
-                "42\t0\t0",
-                "43\t0\t0",
-                "44\t0\t0",
-                "45\t0\t0",
-                "46\t0\t0",
-                "47\t0\t0",
-                "48\t0\t0",
-                "49\t0\t0",
-                "50\t0\t0",
-                "51\t0\t0",
-                "52\t0\t0",
-                "53\t0\t0",
-                "54\t0\t0",
-                "55\t0\t0",
-                "56\t0\t0",
-                "57\t0\t0",
-                "58\t0\t0",
-                "59\t0\t0",
-                "60\t0\t0",
-                "61\t0\t0",
-                "62\t0\t0",
-                "63\t0\t0",
-                "64\t0\t0",
-                "65\t0\t0",
-                "66\t0\t0",
-                "67\t0\t0",
-                "68\t0\t0",
-                "69\t0\t0",
-                "70\t0\t0",
-                "71\t0\t0",
-                "72\t0\t0",
-                "73\t0\t0",
-                "74\t0\t0",
-                "75\t0\t0",
-                "76\t0\t0",
-                "77\t0\t0",
-                "78\t0\t0",
-                "79\t0\t0",
-                "80\t0\t0",
-                "81\t0\t0",
-                "82\t0\t0",
-                "83\t0\t0",
-                "84\t0\t0",
-                "85\t0\t0",
-                "86\t0\t0",
-                "87\t0\t0",
-                "88\t0\t0",
-                "89\t0\t0"
-            ],
-            [
-                "versions.yml:md5,533cf1e35d36fdacbb762f5df2e1b322"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2025-09-15T10:37:32.831030701"
-    },
-    "versions": {
-        "content": [
-            [
-                "versions.yml:md5,533cf1e35d36fdacbb762f5df2e1b322"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2025-09-15T10:37:42.492104283"
-    },
-    "sarscov2 - bam - samebed": {
-        "content": [
-            "test.CollectHsMetrics.coverage_metrics",
-            3586,
-            [
-                "## htsjdk.samtools.metrics.StringHeader",
-                "# CollectHsMetrics --BAIT_INTERVALS baits/baits.interval_list --TARGET_INTERVALS targets/baits.interval_list --INPUT test.paired_end.sorted.bam --OUTPUT test.CollectHsMetrics.coverage_metrics --REFERENCE_SEQUENCE genome.fasta --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false",
-                "## htsjdk.samtools.metrics.StringHeader",
-                "",
-                "## METRICS CLASS\tpicard.analysis.directed.HsMetrics",
-                "BAIT_SET\tBAIT_TERRITORY\tBAIT_DESIGN_EFFICIENCY\tON_BAIT_BASES\tNEAR_BAIT_BASES\tOFF_BAIT_BASES\tPCT_SELECTED_BASES\tPCT_OFF_BAIT\tON_BAIT_VS_SELECTED\tMEAN_BAIT_COVERAGE\tPCT_USABLE_BASES_ON_BAIT\tPCT_USABLE_BASES_ON_TARGET\tFOLD_ENRICHMENT\tHS_LIBRARY_SIZE\tHS_PENALTY_10X\tHS_PENALTY_20X\tHS_PENALTY_30X\tHS_PENALTY_40X\tHS_PENALTY_50X\tHS_PENALTY_100X\tTARGET_TERRITORY\tGENOME_SIZE\tTOTAL_READS\tPF_READS\tPF_BASES\tPF_UNIQUE_READS\tPF_UQ_READS_ALIGNED\tPF_BASES_ALIGNED\tPF_UQ_BASES_ALIGNED\tON_TARGET_BASES\tPCT_PF_READS\tPCT_PF_UQ_READS\tPCT_PF_UQ_READS_ALIGNED\tMEAN_TARGET_COVERAGE\tMEDIAN_TARGET_COVERAGE\tMAX_TARGET_COVERAGE\tMIN_TARGET_COVERAGE\tZERO_CVG_TARGETS_PCT\tPCT_EXC_DUPE\tPCT_EXC_ADAPTER\tPCT_EXC_MAPQ\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_OFF_TARGET\tFOLD_80_BASE_PENALTY\tPCT_TARGET_BASES_1X\tPCT_TARGET_BASES_2X\tPCT_TARGET_BASES_10X\tPCT_TARGET_BASES_20X\tPCT_TARGET_BASES_30X\tPCT_TARGET_BASES_40X\tPCT_TARGET_BASES_50X\tPCT_TARGET_BASES_100X\tPCT_TARGET_BASES_250X\tPCT_TARGET_BASES_500X\tPCT_TARGET_BASES_1000X\tPCT_TARGET_BASES_2500X\tPCT_TARGET_BASES_5000X\tPCT_TARGET_BASES_10000X\tPCT_TARGET_BASES_25000X\tPCT_TARGET_BASES_50000X\tPCT_TARGET_BASES_100000X\tAT_DROPOUT\tGC_DROPOUT\tHET_SNP_SENSITIVITY\tHET_SNP_Q\tSAMPLE\tLIBRARY\tREAD_GROUP",
-                "baits\t158\t1\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.013782\t4.995204\t\t0\t0\t0\t0\t0\t0\t158\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t381\t1\t1\t0.985\t2.411392\t2\t3\t2\t0\t0\t0\t0.005438\t0.054487\t0.259516\t0.666655\t1.205696\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t7.018506\t0\t0.394337\t2\t\t\t",
-                "",
-                "## HISTOGRAM\tjava.lang.Integer",
-                "coverage_or_base_quality\thigh_quality_coverage_count\tunfiltered_baseq_count",
-                "0\t0\t0",
-                "1\t0\t0",
-                "2\t93\t0",
-                "3\t65\t0",
-                "4\t0\t0",
-                "5\t0\t0",
-                "6\t0\t0",
-                "7\t0\t0",
-                "8\t0\t0",
-                "9\t0\t0",
-                "10\t0\t0",
-                "11\t0\t0",
-                "12\t0\t0",
-                "13\t0\t0",
-                "14\t0\t28",
-                "15\t0\t0",
-                "16\t0\t0",
-                "17\t0\t0",
-                "18\t0\t0",
-                "19\t0\t0",
-                "20\t0\t0",
-                "21\t0\t9",
-                "22\t0\t0",
-                "23\t0\t0",
-                "24\t0\t0",
-                "25\t0\t0",
-                "26\t0\t0",
-                "27\t0\t20",
-                "28\t0\t0",
-                "29\t0\t0",
-                "30\t0\t0",
-                "31\t0\t0",
-                "32\t0\t90",
-                "33\t0\t0",
-                "34\t0\t0",
-                "35\t0\t0",
-                "36\t0\t262",
-                "37\t0\t0",
-                "38\t0\t0",
-                "39\t0\t0",
-                "40\t0\t0",
-                "41\t0\t0",
-                "42\t0\t0",
-                "43\t0\t0",
-                "44\t0\t0",
-                "45\t0\t0",
-                "46\t0\t0",
-                "47\t0\t0",
-                "48\t0\t0",
-                "49\t0\t0",
-                "50\t0\t0",
-                "51\t0\t0",
-                "52\t0\t0",
-                "53\t0\t0",
-                "54\t0\t0",
-                "55\t0\t0",
-                "56\t0\t0",
-                "57\t0\t0",
-                "58\t0\t0",
-                "59\t0\t0",
-                "60\t0\t0",
-                "61\t0\t0",
-                "62\t0\t0",
-                "63\t0\t0",
-                "64\t0\t0",
-                "65\t0\t0",
-                "66\t0\t0",
-                "67\t0\t0",
-                "68\t0\t0",
-                "69\t0\t0",
-                "70\t0\t0",
-                "71\t0\t0",
-                "72\t0\t0",
-                "73\t0\t0",
-                "74\t0\t0",
-                "75\t0\t0",
-                "76\t0\t0",
-                "77\t0\t0",
-                "78\t0\t0",
-                "79\t0\t0",
-                "80\t0\t0",
-                "81\t0\t0",
-                "82\t0\t0",
-                "83\t0\t0",
-                "84\t0\t0",
-                "85\t0\t0",
-                "86\t0\t0",
-                "87\t0\t0",
-                "88\t0\t0",
-                "89\t0\t0"
-            ],
-            [
-                "versions.yml:md5,533cf1e35d36fdacbb762f5df2e1b322"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2025-09-15T10:38:39.302597954"
-    },
-    "sarscov2 - bam": {
-        "content": [
-            "test.CollectHsMetrics.coverage_metrics",
-            3598,
-            [
-                "## htsjdk.samtools.metrics.StringHeader",
-                "# CollectHsMetrics --BAIT_INTERVALS baits/baits.interval_list --TARGET_INTERVALS targets/targets.interval_list --INPUT test.paired_end.sorted.bam --OUTPUT test.CollectHsMetrics.coverage_metrics --REFERENCE_SEQUENCE genome.fasta --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false",
-                "## htsjdk.samtools.metrics.StringHeader",
-                "",
-                "## METRICS CLASS\tpicard.analysis.directed.HsMetrics",
-                "BAIT_SET\tBAIT_TERRITORY\tBAIT_DESIGN_EFFICIENCY\tON_BAIT_BASES\tNEAR_BAIT_BASES\tOFF_BAIT_BASES\tPCT_SELECTED_BASES\tPCT_OFF_BAIT\tON_BAIT_VS_SELECTED\tMEAN_BAIT_COVERAGE\tPCT_USABLE_BASES_ON_BAIT\tPCT_USABLE_BASES_ON_TARGET\tFOLD_ENRICHMENT\tHS_LIBRARY_SIZE\tHS_PENALTY_10X\tHS_PENALTY_20X\tHS_PENALTY_30X\tHS_PENALTY_40X\tHS_PENALTY_50X\tHS_PENALTY_100X\tTARGET_TERRITORY\tGENOME_SIZE\tTOTAL_READS\tPF_READS\tPF_BASES\tPF_UNIQUE_READS\tPF_UQ_READS_ALIGNED\tPF_BASES_ALIGNED\tPF_UQ_BASES_ALIGNED\tON_TARGET_BASES\tPCT_PF_READS\tPCT_PF_UQ_READS\tPCT_PF_UQ_READS_ALIGNED\tMEAN_TARGET_COVERAGE\tMEDIAN_TARGET_COVERAGE\tMAX_TARGET_COVERAGE\tMIN_TARGET_COVERAGE\tZERO_CVG_TARGETS_PCT\tPCT_EXC_DUPE\tPCT_EXC_ADAPTER\tPCT_EXC_MAPQ\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_OFF_TARGET\tFOLD_80_BASE_PENALTY\tPCT_TARGET_BASES_1X\tPCT_TARGET_BASES_2X\tPCT_TARGET_BASES_10X\tPCT_TARGET_BASES_20X\tPCT_TARGET_BASES_30X\tPCT_TARGET_BASES_40X\tPCT_TARGET_BASES_50X\tPCT_TARGET_BASES_100X\tPCT_TARGET_BASES_250X\tPCT_TARGET_BASES_500X\tPCT_TARGET_BASES_1000X\tPCT_TARGET_BASES_2500X\tPCT_TARGET_BASES_5000X\tPCT_TARGET_BASES_10000X\tPCT_TARGET_BASES_25000X\tPCT_TARGET_BASES_50000X\tPCT_TARGET_BASES_100000X\tAT_DROPOUT\tGC_DROPOUT\tHET_SNP_SENSITIVITY\tHET_SNP_Q\tSAMPLE\tLIBRARY\tREAD_GROUP",
-                "baits\t158\t0.594937\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.000181\t4.995204\t\t0\t0\t0\t0\t0\t0\t94\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t5\t1\t1\t0.985\t0.053191\t0\t1\t0\t0.75\t0\t0\t0.005438\t0.054487\t0.259516\t0.680377\t?\t0.053191\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t76.595745\t23.404255\t0.015734\t0\t\t\t",
-                "",
-                "## HISTOGRAM\tjava.lang.Integer",
-                "coverage_or_base_quality\thigh_quality_coverage_count\tunfiltered_baseq_count",
-                "0\t89\t0",
-                "1\t5\t0",
-                "2\t0\t0",
-                "3\t0\t0",
-                "4\t0\t0",
-                "5\t0\t0",
-                "6\t0\t0",
-                "7\t0\t0",
-                "8\t0\t0",
-                "9\t0\t0",
-                "10\t0\t0",
-                "11\t0\t0",
-                "12\t0\t0",
-                "13\t0\t0",
-                "14\t0\t5",
-                "15\t0\t0",
-                "16\t0\t0",
-                "17\t0\t0",
-                "18\t0\t0",
-                "19\t0\t0",
-                "20\t0\t0",
-                "21\t0\t1",
-                "22\t0\t0",
-                "23\t0\t0",
-                "24\t0\t0",
-                "25\t0\t0",
-                "26\t0\t0",
-                "27\t0\t0",
-                "28\t0\t0",
-                "29\t0\t0",
-                "30\t0\t0",
-                "31\t0\t0",
-                "32\t0\t1",
-                "33\t0\t0",
-                "34\t0\t0",
-                "35\t0\t0",
-                "36\t0\t3",
-                "37\t0\t0",
-                "38\t0\t0",
-                "39\t0\t0",
-                "40\t0\t0",
-                "41\t0\t0",
-                "42\t0\t0",
-                "43\t0\t0",
-                "44\t0\t0",
-                "45\t0\t0",
-                "46\t0\t0",
-                "47\t0\t0",
-                "48\t0\t0",
-                "49\t0\t0",
-                "50\t0\t0",
-                "51\t0\t0",
-                "52\t0\t0",
-                "53\t0\t0",
-                "54\t0\t0",
-                "55\t0\t0",
-                "56\t0\t0",
-                "57\t0\t0",
-                "58\t0\t0",
-                "59\t0\t0",
-                "60\t0\t0",
-                "61\t0\t0",
-                "62\t0\t0",
-                "63\t0\t0",
-                "64\t0\t0",
-                "65\t0\t0",
-                "66\t0\t0",
-                "67\t0\t0",
-                "68\t0\t0",
-                "69\t0\t0",
-                "70\t0\t0",
-                "71\t0\t0",
-                "72\t0\t0",
-                "73\t0\t0",
-                "74\t0\t0",
-                "75\t0\t0",
-                "76\t0\t0",
-                "77\t0\t0",
-                "78\t0\t0",
-                "79\t0\t0",
-                "80\t0\t0",
-                "81\t0\t0",
-                "82\t0\t0",
-                "83\t0\t0",
-                "84\t0\t0",
-                "85\t0\t0",
-                "86\t0\t0",
-                "87\t0\t0",
-                "88\t0\t0",
-                "89\t0\t0"
-            ],
-            [
-                "versions.yml:md5,533cf1e35d36fdacbb762f5df2e1b322"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2025-09-15T10:37:15.861292725"
-    },
-    "sarscov2 - bam - bed": {
-        "content": [
-            "test.CollectHsMetrics.coverage_metrics",
-            3595,
-            [
-                "## htsjdk.samtools.metrics.StringHeader",
-                "# CollectHsMetrics --BAIT_INTERVALS baits/baits.interval_list --TARGET_INTERVALS targets/test.interval_list --INPUT test.paired_end.sorted.bam --OUTPUT test.CollectHsMetrics.coverage_metrics --REFERENCE_SEQUENCE genome.fasta --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false",
-                "## htsjdk.samtools.metrics.StringHeader",
-                "",
-                "## METRICS CLASS\tpicard.analysis.directed.HsMetrics",
-                "BAIT_SET\tBAIT_TERRITORY\tBAIT_DESIGN_EFFICIENCY\tON_BAIT_BASES\tNEAR_BAIT_BASES\tOFF_BAIT_BASES\tPCT_SELECTED_BASES\tPCT_OFF_BAIT\tON_BAIT_VS_SELECTED\tMEAN_BAIT_COVERAGE\tPCT_USABLE_BASES_ON_BAIT\tPCT_USABLE_BASES_ON_TARGET\tFOLD_ENRICHMENT\tHS_LIBRARY_SIZE\tHS_PENALTY_10X\tHS_PENALTY_20X\tHS_PENALTY_30X\tHS_PENALTY_40X\tHS_PENALTY_50X\tHS_PENALTY_100X\tTARGET_TERRITORY\tGENOME_SIZE\tTOTAL_READS\tPF_READS\tPF_BASES\tPF_UNIQUE_READS\tPF_UQ_READS_ALIGNED\tPF_BASES_ALIGNED\tPF_UQ_BASES_ALIGNED\tON_TARGET_BASES\tPCT_PF_READS\tPCT_PF_UQ_READS\tPCT_PF_UQ_READS_ALIGNED\tMEAN_TARGET_COVERAGE\tMEDIAN_TARGET_COVERAGE\tMAX_TARGET_COVERAGE\tMIN_TARGET_COVERAGE\tZERO_CVG_TARGETS_PCT\tPCT_EXC_DUPE\tPCT_EXC_ADAPTER\tPCT_EXC_MAPQ\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_OFF_TARGET\tFOLD_80_BASE_PENALTY\tPCT_TARGET_BASES_1X\tPCT_TARGET_BASES_2X\tPCT_TARGET_BASES_10X\tPCT_TARGET_BASES_20X\tPCT_TARGET_BASES_30X\tPCT_TARGET_BASES_40X\tPCT_TARGET_BASES_50X\tPCT_TARGET_BASES_100X\tPCT_TARGET_BASES_250X\tPCT_TARGET_BASES_500X\tPCT_TARGET_BASES_1000X\tPCT_TARGET_BASES_2500X\tPCT_TARGET_BASES_5000X\tPCT_TARGET_BASES_10000X\tPCT_TARGET_BASES_25000X\tPCT_TARGET_BASES_50000X\tPCT_TARGET_BASES_100000X\tAT_DROPOUT\tGC_DROPOUT\tHET_SNP_SENSITIVITY\tHET_SNP_Q\tSAMPLE\tLIBRARY\tREAD_GROUP",
-                "baits\t158\t0.594937\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.000181\t4.995204\t\t0\t0\t0\t0\t0\t0\t94\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t5\t1\t1\t0.985\t0.053191\t0\t1\t0\t0.75\t0\t0\t0.005438\t0.054487\t0.259516\t0.680377\t?\t0.053191\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t76.595745\t23.404255\t0.015734\t0\t\t\t",
-                "",
-                "## HISTOGRAM\tjava.lang.Integer",
-                "coverage_or_base_quality\thigh_quality_coverage_count\tunfiltered_baseq_count",
-                "0\t89\t0",
-                "1\t5\t0",
-                "2\t0\t0",
-                "3\t0\t0",
-                "4\t0\t0",
-                "5\t0\t0",
-                "6\t0\t0",
-                "7\t0\t0",
-                "8\t0\t0",
-                "9\t0\t0",
-                "10\t0\t0",
-                "11\t0\t0",
-                "12\t0\t0",
-                "13\t0\t0",
-                "14\t0\t5",
-                "15\t0\t0",
-                "16\t0\t0",
-                "17\t0\t0",
-                "18\t0\t0",
-                "19\t0\t0",
-                "20\t0\t0",
-                "21\t0\t1",
-                "22\t0\t0",
-                "23\t0\t0",
-                "24\t0\t0",
-                "25\t0\t0",
-                "26\t0\t0",
-                "27\t0\t0",
-                "28\t0\t0",
-                "29\t0\t0",
-                "30\t0\t0",
-                "31\t0\t0",
-                "32\t0\t1",
-                "33\t0\t0",
-                "34\t0\t0",
-                "35\t0\t0",
-                "36\t0\t3",
-                "37\t0\t0",
-                "38\t0\t0",
-                "39\t0\t0",
-                "40\t0\t0",
-                "41\t0\t0",
-                "42\t0\t0",
-                "43\t0\t0",
-                "44\t0\t0",
-                "45\t0\t0",
-                "46\t0\t0",
-                "47\t0\t0",
-                "48\t0\t0",
-                "49\t0\t0",
-                "50\t0\t0",
-                "51\t0\t0",
-                "52\t0\t0",
-                "53\t0\t0",
-                "54\t0\t0",
-                "55\t0\t0",
-                "56\t0\t0",
-                "57\t0\t0",
-                "58\t0\t0",
-                "59\t0\t0",
-                "60\t0\t0",
-                "61\t0\t0",
-                "62\t0\t0",
-                "63\t0\t0",
-                "64\t0\t0",
-                "65\t0\t0",
-                "66\t0\t0",
-                "67\t0\t0",
-                "68\t0\t0",
-                "69\t0\t0",
-                "70\t0\t0",
-                "71\t0\t0",
-                "72\t0\t0",
-                "73\t0\t0",
-                "74\t0\t0",
-                "75\t0\t0",
-                "76\t0\t0",
-                "77\t0\t0",
-                "78\t0\t0",
-                "79\t0\t0",
-                "80\t0\t0",
-                "81\t0\t0",
-                "82\t0\t0",
-                "83\t0\t0",
-                "84\t0\t0",
-                "85\t0\t0",
-                "86\t0\t0",
-                "87\t0\t0",
-                "88\t0\t0",
-                "89\t0\t0"
-            ],
-            [
-                "versions.yml:md5,533cf1e35d36fdacbb762f5df2e1b322"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2025-09-15T10:38:18.912909604"
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test
deleted file mode 100644
index 5b67774f..00000000
--- a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test
+++ /dev/null
@@ -1,112 +0,0 @@
-
-nextflow_process {
-
-    name "Test Process PICARD_COLLECTMULTIPLEMETRICS"
-    script "../main.nf"
-    process "PICARD_COLLECTMULTIPLEMETRICS"
-
-    tag "modules"
-    tag "modules_nfcore"
-    tag "picard"
-    tag "picard/collectmultiplemetrics"
-
-    test("test-picard-collectmultiplemetrics") {
-
-        when {
-            process {
-                """
-                input[0] = [
-				    [ id:'test', single_end:false ], // meta map
-				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
-				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
-				]
-				input[1] = [
-				    [id:'genome'],
-				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
-				]
-				input[2] = [[id:'genome'],[]]
-
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(
-                    process.out.metrics[0][1].collect { file(it).name }.toSorted(),
-                    process.out.pdf[0][1].collect { file(it).name }.toSorted(),
-                    process.out.versions
-                    ).match()
-                }
-            )
-        }
-    }
-
-    test("test-picard-collectmultiplemetrics-nofasta") {
-
-        when {
-            process {
-                """
-                input[0] = [
-				    [ id:'test', single_end:false ], // meta map
-				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
-				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
-				]
-				input[1] = [[id:'genome'],[]]
-                input[2] = [[id:'genome'],[]]
-
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(
-                    process.out.metrics[0][1].collect { file(it).name }.toSorted(),
-                    process.out.pdf[0][1].collect { file(it).name }.toSorted(),
-                    process.out.versions
-                    ).match()
-                }
-            )
-        }
-    }
-
-    test("test-picard-collectmultiplemetrics-cram") {
-
-        when {
-            process {
-                """
-                input[0] = [
-				[ id:'test', single_end:false ], // meta map
-				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
-				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
-				]
-				input[1] = [
-				    [id:'genome'],
-				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
-				]
-				input[2] = [
-				    [id:'genome'],
-				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
-				]
-
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(
-                    process.out.metrics[0][1].collect { file(it).name }.toSorted(),
-                    process.out.pdf[0][1].collect { file(it).name }.toSorted(),
-                    process.out.versions
-                    ).match()
-                }
-            )
-        }
-    }
-
-}
diff --git a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap
deleted file mode 100644
index 5a1de114..00000000
--- a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap
+++ /dev/null
@@ -1,80 +0,0 @@
-{
-    "test-picard-collectmultiplemetrics": {
-        "content": [
-            [
-                "test.CollectMultipleMetrics.alignment_summary_metrics",
-                "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "test.CollectMultipleMetrics.insert_size_metrics",
-                "test.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "test.CollectMultipleMetrics.quality_distribution_metrics"
-            ],
-            [
-                "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "test.CollectMultipleMetrics.insert_size_histogram.pdf",
-                "test.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "test.CollectMultipleMetrics.quality_distribution.pdf",
-                "test.CollectMultipleMetrics.read_length_histogram.pdf"
-            ],
-            [
-                "versions.yml:md5,aca7ca0dc0012ee97698236828ba242a"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2025-09-15T10:41:26.126816186"
-    },
-    "test-picard-collectmultiplemetrics-cram": {
-        "content": [
-            [
-                "test.CollectMultipleMetrics.alignment_summary_metrics",
-                "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "test.CollectMultipleMetrics.insert_size_metrics",
-                "test.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "test.CollectMultipleMetrics.quality_distribution_metrics"
-            ],
-            [
-                "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "test.CollectMultipleMetrics.insert_size_histogram.pdf",
-                "test.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "test.CollectMultipleMetrics.quality_distribution.pdf",
-                "test.CollectMultipleMetrics.read_length_histogram.pdf"
-            ],
-            [
-                "versions.yml:md5,aca7ca0dc0012ee97698236828ba242a"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2025-09-15T10:41:50.933556225"
-    },
-    "test-picard-collectmultiplemetrics-nofasta": {
-        "content": [
-            [
-                "test.CollectMultipleMetrics.alignment_summary_metrics",
-                "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "test.CollectMultipleMetrics.insert_size_metrics",
-                "test.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "test.CollectMultipleMetrics.quality_distribution_metrics"
-            ],
-            [
-                "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "test.CollectMultipleMetrics.insert_size_histogram.pdf",
-                "test.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "test.CollectMultipleMetrics.quality_distribution.pdf",
-                "test.CollectMultipleMetrics.read_length_histogram.pdf"
-            ],
-            [
-                "versions.yml:md5,aca7ca0dc0012ee97698236828ba242a"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2025-09-15T10:41:38.213084333"
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/picard/createsequencedictionary/tests/main.nf.test b/modules/nf-core/picard/createsequencedictionary/tests/main.nf.test
deleted file mode 100644
index 8152be96..00000000
--- a/modules/nf-core/picard/createsequencedictionary/tests/main.nf.test
+++ /dev/null
@@ -1,61 +0,0 @@
-nextflow_process {
-
-    name "Test Process PICARD_CREATESEQUENCEDICTIONARY"
-    script "../main.nf"
-    process "PICARD_CREATESEQUENCEDICTIONARY"
-
-    tag "modules"
-    tag "modules_nfcore"
-    tag "picard"
-    tag "picard/createsequencedictionary"
-
-    test("sarscov2 - fasta") {
-
-        when {
-            process {
-                """
-                input[0] = [
-                    [ id:'test' ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(
-                    file(process.out.reference_dict[0][1]).name,
-                    process.out.versions
-                    ).match()
-                }
-
-            )
-        }
-
-    }
-
-    test("sarscov2 - fasta - stub") {
-
-        options "-stub"
-
-        when {
-            process {
-                """
-                input[0] = [
-                    [ id:'test' ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-
-    }
-
-}
diff --git a/modules/nf-core/picard/createsequencedictionary/tests/main.nf.test.snap b/modules/nf-core/picard/createsequencedictionary/tests/main.nf.test.snap
deleted file mode 100644
index 9227bcd1..00000000
--- a/modules/nf-core/picard/createsequencedictionary/tests/main.nf.test.snap
+++ /dev/null
@@ -1,48 +0,0 @@
-{
-    "sarscov2 - fasta - stub": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.dict:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,7df655404f48c3fd86b49d231fdefddf"
-                ],
-                "reference_dict": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.dict:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,7df655404f48c3fd86b49d231fdefddf"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2025-09-15T10:47:11.69898685"
-    },
-    "sarscov2 - fasta": {
-        "content": [
-            "test.dict",
-            [
-                "versions.yml:md5,7df655404f48c3fd86b49d231fdefddf"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2025-09-15T10:47:02.784849055"
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test b/modules/nf-core/samtools/faidx/tests/main.nf.test
deleted file mode 100644
index a505abc1..00000000
--- a/modules/nf-core/samtools/faidx/tests/main.nf.test
+++ /dev/null
@@ -1,219 +0,0 @@
-nextflow_process {
-
-    name "Test Process SAMTOOLS_FAIDX"
-    script "../main.nf"
-    process "SAMTOOLS_FAIDX"
-
-    tag "modules"
-    tag "modules_nfcore"
-    tag "samtools"
-    tag "samtools/faidx"
-
-    test("test_samtools_faidx") {
-
-        when {
-            process {
-                """
-                input[0] = [ [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
-                input[1] = [[],[]]
-                input[2] = false
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-
-    test("test_samtools_faidx_bgzip") {
-
-        when {
-            process {
-                """
-                input[0] = [ [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)]
-                input[1] = [[],[]]
-                input[2] = false
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-
-    test("test_samtools_faidx_fasta") {
-
-        config "./nextflow.config"
-
-        when {
-            process {
-                """
-                input[0] = [ [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
-                input[1] = [ [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ]
-                input[2] = false
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-
-    test("test_samtools_faidx_stub_fasta") {
-
-        config "./nextflow2.config"
-
-        when {
-            process {
-                """
-                input[0] = [ [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
-                input[1] = [ [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ]
-                input[2] = false
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-
-    test("test_samtools_faidx_stub_fai") {
-
-        when {
-            process {
-                """
-                input[0] = [ [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
-                input[1] = [[],[]]
-                input[2] = false
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-
-    test("test_samtools_faidx_get_sizes") {
-
-        when {
-            process {
-                """
-                input[0] = Channel.of([
-                    [ id:'test' ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
-                ])
-                input[1] = [[],[]]
-                input[2] = true
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-
-    test("test_samtools_faidx_get_sizes_bgzip") {
-
-        when {
-            process {
-                """
-                input[0] = Channel.of([
-                    [ id:'test' ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)
-                ])
-                input[1] = [[],[]]
-                input[2] = true
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-
-    test("test_samtools_faidx_get_sizes - stub") {
-
-        options "-stub"
-
-        when {
-            process {
-                """
-                input[0] = Channel.of([
-                    [ id:'test' ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
-                ])
-                input[1] = [[],[]]
-                input[2] = true
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-
-    test("test_samtools_faidx_get_sizes_bgzip - stub") {
-
-        options "-stub"
-
-        when {
-            process {
-                """
-                input[0] = Channel.of([
-                    [ id:'test' ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)
-                ])
-                input[1] = [[],[]]
-                input[2] = true
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-
-}
diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap
deleted file mode 100644
index 3be7b824..00000000
--- a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap
+++ /dev/null
@@ -1,543 +0,0 @@
-{
-    "test_samtools_faidx": {
-        "content": [
-            {
-                "0": [
-                    
-                ],
-                "1": [
-                    
-                ],
-                "2": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
-                    ]
-                ],
-                "3": [
-                    
-                ],
-                "4": [
-                    "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68"
-                ],
-                "fa": [
-                    
-                ],
-                "fai": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
-                    ]
-                ],
-                "gzi": [
-                    
-                ],
-                "sizes": [
-                    
-                ],
-                "versions": [
-                    "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-10T13:09:38.874686"
-    },
-    "test_samtools_faidx_get_sizes_bgzip - stub": {
-        "content": [
-            {
-                "0": [
-                    
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "genome.fasta.gz.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "genome.fasta.gz.fai:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "3": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "genome.fasta.gz.gzi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "4": [
-                    "versions.yml:md5,8e7d141eb8c2944042dfb5e942bffe08"
-                ],
-                "fa": [
-                    
-                ],
-                "fai": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "genome.fasta.gz.fai:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "gzi": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "genome.fasta.gz.gzi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "sizes": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "genome.fasta.gz.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,8e7d141eb8c2944042dfb5e942bffe08"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-10T13:10:10.958397"
-    },
-    "test_samtools_faidx_get_sizes": {
-        "content": [
-            {
-                "0": [
-                    
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "genome.fasta.sizes:md5,a57c401f27ae5133823fb09fb21c8a3c"
-                    ]
-                ],
-                "2": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
-                    ]
-                ],
-                "3": [
-                    
-                ],
-                "4": [
-                    "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68"
-                ],
-                "fa": [
-                    
-                ],
-                "fai": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
-                    ]
-                ],
-                "gzi": [
-                    
-                ],
-                "sizes": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "genome.fasta.sizes:md5,a57c401f27ae5133823fb09fb21c8a3c"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-10T13:09:59.237249"
-    },
-    "test_samtools_faidx_bgzip": {
-        "content": [
-            {
-                "0": [
-                    
-                ],
-                "1": [
-                    
-                ],
-                "2": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
-                    ]
-                ],
-                "3": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474"
-                    ]
-                ],
-                "4": [
-                    "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68"
-                ],
-                "fa": [
-                    
-                ],
-                "fai": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
-                    ]
-                ],
-                "gzi": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474"
-                    ]
-                ],
-                "sizes": [
-                    
-                ],
-                "versions": [
-                    "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-10T13:09:42.949204"
-    },
-    "test_samtools_faidx_fasta": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "extract.fa:md5,6a0774a0ad937ba0bfd2ac7457d90f36"
-                    ]
-                ],
-                "1": [
-                    
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    
-                ],
-                "4": [
-                    "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68"
-                ],
-                "fa": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "extract.fa:md5,6a0774a0ad937ba0bfd2ac7457d90f36"
-                    ]
-                ],
-                "fai": [
-                    
-                ],
-                "gzi": [
-                    
-                ],
-                "sizes": [
-                    
-                ],
-                "versions": [
-                    "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-10T13:09:46.914038"
-    },
-    "test_samtools_faidx_get_sizes - stub": {
-        "content": [
-            {
-                "0": [
-                    
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "genome.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "genome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "3": [
-                    
-                ],
-                "4": [
-                    "versions.yml:md5,8e7d141eb8c2944042dfb5e942bffe08"
-                ],
-                "fa": [
-                    
-                ],
-                "fai": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "genome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "gzi": [
-                    
-                ],
-                "sizes": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "genome.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,8e7d141eb8c2944042dfb5e942bffe08"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-10T13:10:06.961912"
-    },
-    "test_samtools_faidx_stub_fasta": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "extract.fa:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
-                    ]
-                ],
-                "1": [
-                    
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    
-                ],
-                "4": [
-                    "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68"
-                ],
-                "fa": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "extract.fa:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
-                    ]
-                ],
-                "fai": [
-                    
-                ],
-                "gzi": [
-                    
-                ],
-                "sizes": [
-                    
-                ],
-                "versions": [
-                    "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-10T13:09:51.226016"
-    },
-    "test_samtools_faidx_stub_fai": {
-        "content": [
-            {
-                "0": [
-                    
-                ],
-                "1": [
-                    
-                ],
-                "2": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
-                    ]
-                ],
-                "3": [
-                    
-                ],
-                "4": [
-                    "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68"
-                ],
-                "fa": [
-                    
-                ],
-                "fai": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
-                    ]
-                ],
-                "gzi": [
-                    
-                ],
-                "sizes": [
-                    
-                ],
-                "versions": [
-                    "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-10T13:09:55.423005"
-    },
-    "test_samtools_faidx_get_sizes_bgzip": {
-        "content": [
-            {
-                "0": [
-                    
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "genome.fasta.gz.sizes:md5,a57c401f27ae5133823fb09fb21c8a3c"
-                    ]
-                ],
-                "2": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
-                    ]
-                ],
-                "3": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474"
-                    ]
-                ],
-                "4": [
-                    "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68"
-                ],
-                "fa": [
-                    
-                ],
-                "fai": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
-                    ]
-                ],
-                "gzi": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474"
-                    ]
-                ],
-                "sizes": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "genome.fasta.gz.sizes:md5,a57c401f27ae5133823fb09fb21c8a3c"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,001211003daf11e8dd2f1aca7a378a68"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-10T13:10:03.04872"
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/samtools/faidx/tests/nextflow.config b/modules/nf-core/samtools/faidx/tests/nextflow.config
deleted file mode 100644
index f76a3ba0..00000000
--- a/modules/nf-core/samtools/faidx/tests/nextflow.config
+++ /dev/null
@@ -1,7 +0,0 @@
-process {
-
-    withName: SAMTOOLS_FAIDX {
-        ext.args = 'MT192765.1 -o extract.fa'
-    }
-
-}
diff --git a/modules/nf-core/samtools/faidx/tests/nextflow2.config b/modules/nf-core/samtools/faidx/tests/nextflow2.config
deleted file mode 100644
index 33ebbd5d..00000000
--- a/modules/nf-core/samtools/faidx/tests/nextflow2.config
+++ /dev/null
@@ -1,6 +0,0 @@
-process {
-
-    withName: SAMTOOLS_FAIDX {
-        ext.args = '-o extract.fa'
-    }
-}
diff --git a/modules/nf-core/samtools/index/tests/csi.nextflow.config b/modules/nf-core/samtools/index/tests/csi.nextflow.config
deleted file mode 100644
index 0ed260ef..00000000
--- a/modules/nf-core/samtools/index/tests/csi.nextflow.config
+++ /dev/null
@@ -1,7 +0,0 @@
-process {
-
-    withName: SAMTOOLS_INDEX {
-        ext.args = '-c'
-    }
-
-}
diff --git a/modules/nf-core/samtools/index/tests/main.nf.test b/modules/nf-core/samtools/index/tests/main.nf.test
deleted file mode 100644
index ca34fb5c..00000000
--- a/modules/nf-core/samtools/index/tests/main.nf.test
+++ /dev/null
@@ -1,140 +0,0 @@
-nextflow_process {
-
-    name "Test Process SAMTOOLS_INDEX"
-    script "../main.nf"
-    process "SAMTOOLS_INDEX"
-    tag "modules"
-    tag "modules_nfcore"
-    tag "samtools"
-    tag "samtools/index"
-
-    test("bai") {
-        when {
-            process {
-                """
-                input[0] = Channel.of([
-                    [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
-                ])
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-
-    test("crai") {
-        when {
-            process {
-                """
-                input[0] = Channel.of([
-                    [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true)
-                ])
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-
-    test("csi") {
-        config "./csi.nextflow.config"
-
-        when {
-            process {
-                """
-                input[0] = Channel.of([
-                    [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
-                ])
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert snapshot(
-                    file(process.out.csi[0][1]).name,
-                    process.out.versions
-                ).match() }
-            )
-        }
-    }
-
-    test("bai - stub") {
-        options "-stub"
-        when {
-            process {
-                """
-                input[0] = Channel.of([
-                    [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
-                ])
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-
-    test("crai - stub") {
-        options "-stub"
-        when {
-            process {
-                """
-                input[0] = Channel.of([
-                    [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true)
-                ])
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-
-    test("csi - stub") {
-        options "-stub"
-        config "./csi.nextflow.config"
-
-        when {
-            process {
-                """
-                input[0] = Channel.of([
-                    [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
-                ])
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-}
diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap
deleted file mode 100644
index 3836c6bf..00000000
--- a/modules/nf-core/samtools/index/tests/main.nf.test.snap
+++ /dev/null
@@ -1,250 +0,0 @@
-{
-    "csi - stub": {
-        "content": [
-            {
-                "0": [
-                    
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
-                ],
-                "bai": [
-                    
-                ],
-                "crai": [
-                    
-                ],
-                "csi": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-10T14:13:38.25787"
-    },
-    "crai - stub": {
-        "content": [
-            {
-                "0": [
-                    
-                ],
-                "1": [
-                    
-                ],
-                "2": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "3": [
-                    "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
-                ],
-                "bai": [
-                    
-                ],
-                "crai": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "csi": [
-                    
-                ],
-                "versions": [
-                    "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-10T14:13:34.496412"
-    },
-    "bai - stub": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
-                ],
-                "bai": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "crai": [
-                    
-                ],
-                "csi": [
-                    
-                ],
-                "versions": [
-                    "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-10T14:13:25.934431"
-    },
-    "csi": {
-        "content": [
-            "test.paired_end.sorted.bam.csi",
-            [
-                "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-10T14:13:22.262088"
-    },
-    "crai": {
-        "content": [
-            {
-                "0": [
-                    
-                ],
-                "1": [
-                    
-                ],
-                "2": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029"
-                    ]
-                ],
-                "3": [
-                    "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
-                ],
-                "bai": [
-                    
-                ],
-                "crai": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029"
-                    ]
-                ],
-                "csi": [
-                    
-                ],
-                "versions": [
-                    "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-10T14:13:18.191664"
-    },
-    "bai": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4"
-                    ]
-                ],
-                "1": [
-                    
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
-                ],
-                "bai": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4"
-                    ]
-                ],
-                "crai": [
-                    
-                ],
-                "csi": [
-                    
-                ],
-                "versions": [
-                    "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-10T14:13:08.51539"
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/seqfu/stats/tests/main.nf.test b/modules/nf-core/seqfu/stats/tests/main.nf.test
deleted file mode 100644
index 3d13b05b..00000000
--- a/modules/nf-core/seqfu/stats/tests/main.nf.test
+++ /dev/null
@@ -1,88 +0,0 @@
-nextflow_process {
-
-    name "Test Process SEQFU_STATS"
-    script "../main.nf"
-    process "SEQFU_STATS"
-
-    tag "modules"
-    tag "modules_nfcore"
-    tag "seqfu"
-    tag "seqfu/stats"
-
-    test("seqfu stats - faa") {
-        // test with 1 FAA file (with  multiple sequences of different length)
-        when {
-            process {
-                """
-                input[0] = [
-                    [ id:'test_faa' ],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true)
-                ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-
-    }
-
-    test("seqfu stats - multiple files") {
-        // test feeding a mix of files including compressed
-        when {
-            process {
-                """
-                input[0] = [
-                            [ id:'test_multiple' ],
-                            [
-                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true),
-                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true),
-                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
-                            ]
-                        ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-
-    }
-
-    test("seqfu stats - faa - stub") {
-
-        options "-stub"
-
-        when {
-            process {
-                """
-                input[0] = [
-                    [ id:'test_stub' ],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true)
-                ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success},
-                { assert snapshot(
-                    process.out,
-                    process.out.versions.collect{ path(it).yaml }
-                ).match() }
-            )
-        }
-
-    }
-
-}
diff --git a/modules/nf-core/seqfu/stats/tests/main.nf.test.snap b/modules/nf-core/seqfu/stats/tests/main.nf.test.snap
deleted file mode 100644
index 30b16993..00000000
--- a/modules/nf-core/seqfu/stats/tests/main.nf.test.snap
+++ /dev/null
@@ -1,156 +0,0 @@
-{
-    "seqfu stats - faa - stub": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test_stub"
-                        },
-                        "test_stub.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test_stub"
-                        },
-                        "test_stub_mqc.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    "versions.yml:md5,7e7581ee4a87fd1f9969628ae050e689"
-                ],
-                "multiqc": [
-                    [
-                        {
-                            "id": "test_stub"
-                        },
-                        "test_stub_mqc.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "stats": [
-                    [
-                        {
-                            "id": "test_stub"
-                        },
-                        "test_stub.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,7e7581ee4a87fd1f9969628ae050e689"
-                ]
-            },
-            [
-                {
-                    "SEQFU_STATS": {
-                        "seqfu": "1.22.3"
-                    }
-                }
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-24T12:51:50.35812127"
-    },
-    "seqfu stats - faa": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test_faa"
-                        },
-                        "test_faa.tsv:md5,0d6bf2cc788f7828761440a1689cac04"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test_faa"
-                        },
-                        "test_faa_mqc.txt:md5,8f3c2edaf1ea5be912c9f99b21b2856c"
-                    ]
-                ],
-                "2": [
-                    "versions.yml:md5,7e7581ee4a87fd1f9969628ae050e689"
-                ],
-                "multiqc": [
-                    [
-                        {
-                            "id": "test_faa"
-                        },
-                        "test_faa_mqc.txt:md5,8f3c2edaf1ea5be912c9f99b21b2856c"
-                    ]
-                ],
-                "stats": [
-                    [
-                        {
-                            "id": "test_faa"
-                        },
-                        "test_faa.tsv:md5,0d6bf2cc788f7828761440a1689cac04"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,7e7581ee4a87fd1f9969628ae050e689"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-24T12:52:03.19664223"
-    },
-    "seqfu stats - multiple files": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test_multiple"
-                        },
-                        "test_multiple.tsv:md5,d016de3d84187a06c8e19b8dabccb3ae"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test_multiple"
-                        },
-                        "test_multiple_mqc.txt:md5,dbc6e762eebbf756cd0687807de60445"
-                    ]
-                ],
-                "2": [
-                    "versions.yml:md5,7e7581ee4a87fd1f9969628ae050e689"
-                ],
-                "multiqc": [
-                    [
-                        {
-                            "id": "test_multiple"
-                        },
-                        "test_multiple_mqc.txt:md5,dbc6e762eebbf756cd0687807de60445"
-                    ]
-                ],
-                "stats": [
-                    [
-                        {
-                            "id": "test_multiple"
-                        },
-                        "test_multiple.tsv:md5,d016de3d84187a06c8e19b8dabccb3ae"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,7e7581ee4a87fd1f9969628ae050e689"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-24T12:52:11.315174611"
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/seqtk/sample/tests/main.nf.test b/modules/nf-core/seqtk/sample/tests/main.nf.test
deleted file mode 100644
index 2152ecd4..00000000
--- a/modules/nf-core/seqtk/sample/tests/main.nf.test
+++ /dev/null
@@ -1,102 +0,0 @@
-nextflow_process {
-
-    name "Test Process SEQTK_SAMPLE"
-    script "modules/nf-core/seqtk/sample/main.nf"
-    process "SEQTK_SAMPLE"
-    config "./standard.config"
-
-    tag "modules"
-    tag "modules_nfcore"
-    tag "seqtk"
-    tag "seqtk/sample"
-
-    test("sarscov2_sample_singleend_fqgz") {
-
-        when {
-            process {
-                """
-                input[0] =  [
-                                [ id:'test', single_end:true ],
-                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
-                                50
-                            ]
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-
-    test("sarscov2_sample_pairedend_fqgz") {
-
-        when {
-            process {
-                """
-                input[0] =  [
-                                [ id:'test', single_end:true ],
-                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
-                                50
-                            ]
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-
-    test("sarscov2_sample_singlend_fqgz_stub") {
-        options "-stub"
-
-        when {
-            process {
-                """
-                input[0] =  [
-                                [ id:'test', single_end:true ],
-                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
-                                50
-                            ]
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-
-    test("sarscov2_sample_singleend_frac") {
-
-        when {
-            process {
-                """
-                input[0] =  [
-                                [ id:'test', single_end:true ],
-                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
-                                0.5
-                            ]
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-
-}
diff --git a/modules/nf-core/seqtk/sample/tests/main.nf.test.snap b/modules/nf-core/seqtk/sample/tests/main.nf.test.snap
deleted file mode 100644
index aa6991e6..00000000
--- a/modules/nf-core/seqtk/sample/tests/main.nf.test.snap
+++ /dev/null
@@ -1,126 +0,0 @@
-{
-    "sarscov2_sample_singlend_fqgz_stub": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test.sampled.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806"
-                ],
-                "reads": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test.sampled.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806"
-                ]
-            }
-        ],
-        "timestamp": "2024-02-22T15:58:45.902956"
-    },
-    "sarscov2_sample_pairedend_fqgz": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test.sampled_test_1.fastq.gz:md5,e5f44fafd7351c5abb9925a075132941"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806"
-                ],
-                "reads": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test.sampled_test_1.fastq.gz:md5,e5f44fafd7351c5abb9925a075132941"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806"
-                ]
-            }
-        ],
-        "timestamp": "2024-02-22T15:58:37.679954"
-    },
-    "sarscov2_sample_singleend_fqgz": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test.sampled_test_1.fastq.gz:md5,e5f44fafd7351c5abb9925a075132941"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806"
-                ],
-                "reads": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test.sampled_test_1.fastq.gz:md5,e5f44fafd7351c5abb9925a075132941"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806"
-                ]
-            }
-        ],
-        "timestamp": "2024-02-22T15:58:29.474491"
-    },
-    "sarscov2_sample_singleend_frac": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test.sampled_test_1.fastq.gz:md5,7552511dcd914f5183d80fae459bf917"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806"
-                ],
-                "reads": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test.sampled_test_1.fastq.gz:md5,7552511dcd914f5183d80fae459bf917"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806"
-                ]
-            }
-        ],
-        "timestamp": "2025-07-15T09:48:30.275951"
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/seqtk/sample/tests/standard.config b/modules/nf-core/seqtk/sample/tests/standard.config
deleted file mode 100644
index 8d1db62f..00000000
--- a/modules/nf-core/seqtk/sample/tests/standard.config
+++ /dev/null
@@ -1,6 +0,0 @@
-process {
-    withName: SEQTK_SAMPLE {
-        ext.args = '-s100'
-        ext.prefix = { "${meta.id}.sampled" }
-    }
-}
diff --git a/nextflow.config b/nextflow.config
index a023b529..c4f142c9 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -252,12 +252,151 @@ manifest {
     name            = 'nf-core/seqinspector'
     contributors    = [
         [
-            name: 'National Genomics Infrastructure',
-            affiliation: '',
-            email: '',
-            github: 'https://github.com/NationalGenomicsInfrastructure/',
-            contribution: ['author'], // List of contribution types ('author', 'maintainer' or 'contributor')
-            orcid: ''
+            name: 'Adrien Coulier',
+            affiliation: 'Pixelgen Technologies',
+            github: 'Aratz',
+            contribution: ['author'],
+        ],
+        [
+            name: 'Alfred Kedhammar',
+            affiliation: 'Clinical Genomics',
+            github: 'kedhammar',
+            contribution: ['author'],
+        ],
+        [
+            name: 'Agrima Bhatt',
+            affiliation: 'National Genomics Infrastructure',
+            github: 'agrima2010',
+            contribution: ['author'],
+            orcid: '0009-0004-5536-7210',
+        ],
+        [
+            name: 'Maxime U Garcia',
+            affiliation: 'National Genomics Infrastructure',
+            github: 'maxulysse',
+            contribution: ['maintainer'],
+            orcid: '0000-0003-2827-9261',
+        ],
+        [
+            name: 'Natalia Garcia Garcia',
+            github: 'nggvs',
+            contribution: ['contributor'],
+        ],
+        [
+            name: 'Franziska Bonath',
+            affiliation: 'National Genomics Infrastructure',
+            github: 'FranBonath',
+            contribution: ['author'],
+            orcid: '0000-0002-1270-1504',
+        ],
+        [
+            name: 'Pontus Höjer',
+            affiliation: 'National Genomics Infrastructure',
+            github: 'pontushojer',
+            contribution: ['contributor'],
+            orcid: '0000-0001-8010-4755',
+        ],
+        [
+            name: 'Edmund Miller',
+            affiliation: 'Seqera',
+            github: 'edmundmiller',
+            contribution: ['contributor'],
+        ],
+        [
+            name: 'Mahesh Binzer-Panchal',
+            affiliation: 'National Bioinformatics Infrastructure Sweden',
+            github: 'mahesh-panchal',
+            contribution: ['contributor'],
+        ],
+        [
+            name: 'Ramprasad Neethiraj',
+            affiliation: 'Clinical Genomics',
+            github: 'ramprasadn',
+            contribution: ['author'],
+        ],
+        [
+            name: 'Matilda Åslin',
+            affiliation: 'National Genomics Infrastructure',
+            github: 'matrulda',
+            contribution: ['author'],
+        ],
+        [
+            name: 'Patricie Skaláková',
+            affiliation: 'Masaryk University',
+            github: 'Patricie34',
+            contribution: ['contributor'],
+        ],
+        [
+            name: 'Eliott Bosshard',
+            affiliation: 'Clinical Genomics',
+            github: 'EliottBo',
+            contribution: ['contributor'],
+        ],
+        [
+            name: 'Karthik Nair',
+            affiliation: 'National Genomics Infrastructure',
+            github: 'KarNair',
+            contribution: ['contributor'],
+        ],
+        [
+            name: 'Matthias Zepper',
+            affiliation: 'National Genomics Infrastructure',
+            github: 'MatthiasZepper',
+            contribution: ['author'],
+        ],
+        [
+            name: 'Nelly Nyawira Nkonge',
+            affiliation: 'National Genomics Infrastructure',
+            github: 'nkongenelly',
+            contribution: ['contributor'],
+        ],
+        [
+            name: 'Beatriz Vinhas',
+            affiliation: 'Clinical Genomics',
+            github: 'beatrizsavinhas',
+            contribution: ['contributor'],
+        ],
+        [
+            name: 'Júlia Mir Pedrol',
+            affiliation: 'Center For Genomics Regulation',
+            github: 'mirpedrol',
+            contribution: ['contributor'],
+        ],
+        [
+            name: 'Cristina Tuñí i Domínguez',
+            affiliation: 'Flowmics',
+            github: 'ctuni',
+            contribution: ['contributor'],
+        ],
+        [
+            name: 'Johannes Alneberg',
+            affiliation: 'National Genomics Infrastructure',
+            github: 'alneberg',
+            contribution: ['contributor'],
+        ],
+        [
+            name: 'Annick Renevey',
+            affiliation: 'Clinical Genomics',
+            github: 'rannick',
+            contribution: ['contributor'],
+        ],
+        [
+            name: 'Adam Talbot',
+            affiliation: 'Seqera',
+            github: 'adamrtalbot',
+            contribution: ['contributor'],
+        ],
+        [
+            name: 'Jonas Kjellin',
+            affiliation: 'National Genomics Infrastructure',
+            github: 'kjellinjonas',
+            contribution: ['contributor'],
+        ],
+        [
+            name: 'Tori Griffin',
+            affiliation: 'National Genomics Infrastructure',
+            github: 'torigiffin',
+            contribution: ['contributor'],
         ],
     ]
     homePage        = 'https://github.com/nf-core/seqinspector'
diff --git a/nf-test.config b/nf-test.config
index 71deaff9..ef5a466e 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -1,21 +1,21 @@
 config {
     // location for all nf-test tests
-    testsDir "."
+    testsDir = "."
 
     // nf-test directory including temporary files for each test
-    workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"
+    workDir = System.getenv("NFT_WORKDIR") ?: ".nf-test"
 
     // location of an optional nextflow.config file specific for executing tests
-    configFile "tests/nextflow.config"
+    configFile = "tests/nextflow.config"
 
     // ignore tests coming from the nf-core/modules repo
-    ignore 'modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*'
+    ignore = ['modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*']
 
     // run all test with defined profile(s) from the main nextflow.config
-    profile "test"
+    profile  ="test"
 
     // list of filenames or patterns that should be trigger a full test run
-    triggers 'nextflow.config', 'nf-test.config', 'conf/test.config', 'tests/nextflow.config', 'tests/.nftignore'
+    triggers = ['nextflow.config', 'nf-test.config', 'conf/test.config', 'tests/nextflow.config', 'tests/.nftignore']
 
     // load the necessary plugins
     plugins {
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 02d4357c..94830468 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,8 +22,8 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2025-11-24T14:37:12+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n<picture>\n  <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n  <source media=\"(prefers-color-scheme: light)\" srcset=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  <img alt=\"Fallback image description\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n</picture>\n\n<picture>\n  <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nfcore-seqinspector-logo-hex-dark.png\">\n  <source media=\"(prefers-color-scheme: light)\" srcset=\"docs/images/nfcore-seqinspector-logo-hex-light.png\">\n  <img alt=\"Fallback image description\" src=\"docs/images/nfcore-seqinspector-logo-hex-light.png\">\n</picture>\n\n**nf-core/seqinspector** is a bioinformatics pipeline that that processes raw sequence data (FASTQ) to provide comprehensive quality control. It can perform subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants. The pipeline generates detailed MultiQC reports with flexible output options, ranging from individual sample reports to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments. If provided, nf-core/seqinspector can also parse statistics from an Illumina run folder directory into the final MultiQC reports.\n\n<!-- TODO: add a search tool that accepts a tree for `Compatibility with Data`. -->\n\n| Tool Type           | Tool Name                                                                                                           | Tool Description                                                                              | Compatibility with Data | Dependencies                                                                                                              | Default tool |\n| ------------------- | ------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------- | ----------------------- | ------------------------------------------------------------------------------------------------------------------------- | ------------ |\n| `Subsampling`       | [`Seqtk`](https://github.com/lh3/seqtk)                                                                             | Global subsampling of reads. Only performs subsampling if `--sample_size` parameter is given. | [RNA, DNA, synthetic]   | [N/A]                                                                                                                     | no           |\n| `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2)                                                                   | Align reads to reference                                                                      | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `Indexing`          | [`SAMtools`](http://github.com/samtools)                                                                            | Index aligned BAM files, create FASTA index                                                   | [DNA]                   | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)                                              | Read QC                                                                                       | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)                                   | Basic contamination detection                                                                 | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`SeqFu Stats`](https://github.com/telatin/seqfu2)                                                                  | Sequence statistics                                                                           | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`Picard collect multiple metrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html)         | Collect multiple QC metrics                                                                   | [RNA, DNA]              | [Bwamem2, SAMtools, `--genome`]                                                                                           | yes          |\n| `QC`                | [`Picard_collecthsmetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard) | Collect alignment QC metrics of hybrid-selection data.                                        | [RNA, DNA]              | [Bwamem2, SAMtools, `--fasta`, `--run_picard_collecths_metrics`, `--bait_intervals`, `--target_intervals` (`--ref_dict`)] | no           |\n| `Reporting`         | [`MultiQC`](http://multiqc.info/)                                                                                   | Present QC for raw reads                                                                      | [RNA, DNA, synthetic]   | [N/A]                                                                                                                     | yes          |\n\n<picture>\n  <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/seqinspector_tubemap_V1.0_dark.png\">\n  <source media=\"(prefers-color-scheme: light)\" srcset=\"docs/images/seqinspector_tubemap_V1.0.png\">\n  <img alt=\"Fallback image description\" src=\"docs/images/seqinspector_tubemap_V1.0.png\">\n</picture>\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/) and [Clinical Genomics Stockholm](https://clinical.scilifelab.se/).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "datePublished": "2026-02-10T11:55:01+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that processes raw sequence data (FASTQ) to provide comprehensive quality control.\nIt can perform subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants.\nThe pipeline generates detailed MultiQC reports with flexible output options, ranging from individual sample reports to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments.\nIf provided, nf-core/seqinspector can also parse statistics from an Illumina run folder directory into the final MultiQC reports.\n\n<!-- TODO: add a search tool that accepts a tree for `Compatibility with Data`. -->\n\n| Tool Type           | Tool Name                                                                                                           | Tool Description                                                                              | Compatibility with Data | Dependencies                                                                                                              | Default tool |\n| ------------------- | ------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------- | ----------------------- | ------------------------------------------------------------------------------------------------------------------------- | ------------ |\n| `Subsampling`       | [`Seqtk`](https://github.com/lh3/seqtk)                                                                             | Global subsampling of reads. Only performs subsampling if `--sample_size` parameter is given. | [RNA, DNA, synthetic]   | [N/A]                                                                                                                     | no           |\n| `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2)                                                                   | Align reads to reference                                                                      | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `Indexing`          | [`SAMtools`](http://github.com/samtools)                                                                            | Index aligned BAM files, create FASTA index                                                   | [DNA]                   | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)                                              | Read QC                                                                                       | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)                                   | Basic contamination detection                                                                 | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`SeqFu Stats`](https://github.com/telatin/seqfu2)                                                                  | Sequence statistics                                                                           | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`Picard collect multiple metrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html)         | Collect multiple QC metrics                                                                   | [RNA, DNA]              | [Bwamem2, SAMtools, `--genome`]                                                                                           | yes          |\n| `QC`                | [`Picard_collecthsmetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard) | Collect alignment QC metrics of hybrid-selection data.                                        | [RNA, DNA]              | [Bwamem2, SAMtools, `--fasta`, `--run_picard_collecths_metrics`, `--bait_intervals`, `--target_intervals` (`--ref_dict`)] | no           |\n| `Reporting`         | [`MultiQC`](http://multiqc.info/)                                                                                   | Present QC for raw reads                                                                      | [RNA, DNA, synthetic]   | [N/A]                                                                                                                     | yes          |\n\n<picture>\n  <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/seqinspector_tubemap_V1.0_dark.png\">\n  <source media=\"(prefers-color-scheme: light)\" srcset=\"docs/images/seqinspector_tubemap_V1.0.png\">\n  <img alt=\"Fallback image description\" src=\"docs/images/seqinspector_tubemap_V1.0.png\">\n</picture>\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end with only `fastq_1`) or a pair of fastq files (paired end with `fastq_1` and `fastq_2`).\n`rundir` is the path to the runfolder.\n`tags` is a colon-separated list of tags that will be added to the MultiQC report for this `sample`.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by [@agrima2010](https://github.com/agrima2010), [@Aratz](https://github.com/Aratz), [@FranBonath](https://github.com/FranBonath), [@kedhammar](https://github.com/kedhammar), and [@MatthiasZepper](https://github.com/MatthiasZepper) from the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/) and [Clinical Genomics Stockholm](https://clinical.scilifelab.se/).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@adamrtalbot](https://github.com/adamrtalbot)\n- [@alneberg](https://github.com/alneberg)\n- [@beatrizsavinhas](https://github.com/beatrizsavinhas)\n- [@ctuni](https://github.com/ctuni)\n- [@edmundmiller](https://github.com/edmundmiller)\n- [@EliottBo](https://github.com/EliottBo)\n- [@KarNair](https://github.com/KarNair)\n- [@kjellinjonas](https://github.com/kjellinjonas)\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n- [@matrulda](https://github.com/matrulda)\n- [@maxulysse](https://github.com/maxulysse)\n- [@mirpedrol](https://github.com/mirpedrol)\n- [@nggvs](https://github.com/nggvs)\n- [@nkongenelly](https://github.com/nkongenelly)\n- [@Patricie34](https://github.com/Patricie34)\n- [@pontushojer](https://github.com/pontushojer)\n- [@ramprasadn](https://github.com/ramprasadn)\n- [@rannick](https://github.com/rannick)\n- [@torigiffin](https://github.com/torigiffin)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
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@@ -43,6 +43,9 @@
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@@ -99,7 +102,7 @@
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@@ -128,23 +131,23 @@
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-                    "@id": "https://orcid.org/0000-0003-2702-1103"
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-                    "@id": "https://orcid.org/0000-0003-1675-0677"
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-                    "@id": "https://orcid.org/0009-0004-5536-7210"
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             "dateCreated": "",
-            "dateModified": "2025-11-24T15:37:12Z",
+            "dateModified": "2026-02-10T12:55:01Z",
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             "keywords": [
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@@ -155,6 +158,23 @@
             "license": [
                 "MIT"
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+            "maintainer": [
+                {
+                    "@id": "#max.u.garcia@gmail.com"
+                },
+                {
+                    "@id": "https://orcid.org/0000-0003-1675-0677"
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+                    "@id": "https://orcid.org/0000-0003-2702-1103"
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@@ -185,11 +205,11 @@
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         {
-            "@id": "#5046cfd6-7adc-440b-8923-715e3d592be8",
+            "@id": "#4c91a6e5-517c-49a6-b553-2e7d9ffc1e5e",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/seqinspector",
             "resource": "repos/nf-core/seqinspector/actions/workflows/nf-test.yml",
@@ -240,6 +260,11 @@
             "@type": "Dataset",
             "description": "Modules used by the pipeline"
         },
+        {
+            "@id": "modules/local/",
+            "@type": "Dataset",
+            "description": "Pipeline-specific modules"
+        },
         {
             "@id": "modules/nf-core/",
             "@type": "Dataset",
@@ -326,24 +351,12 @@
             "name": "nf-core",
             "url": "https://nf-co.re/"
         },
-        {
-            "@id": "https://orcid.org/0000-0003-2702-1103",
-            "@type": "Person",
-            "email": "adrien.coulier@medsci.uu.se",
-            "name": "Adrien Coulier"
-        },
         {
             "@id": "#max.u.garcia@gmail.com",
             "@type": "Person",
             "email": "max.u.garcia@gmail.com",
             "name": "Maxime U Garcia"
         },
-        {
-            "@id": "#89784800+kedhammar@users.noreply.github.com",
-            "@type": "Person",
-            "email": "89784800+kedhammar@users.noreply.github.com",
-            "name": "Alfred Kedhammar"
-        },
         {
             "@id": "https://orcid.org/0000-0003-1675-0677",
             "@type": "Person",
@@ -355,6 +368,18 @@
             "@type": "Person",
             "email": "163723002+agrima2010@users.noreply.github.com",
             "name": "Agrima Bhatt"
+        },
+        {
+            "@id": "#89784800+kedhammar@users.noreply.github.com",
+            "@type": "Person",
+            "email": "89784800+kedhammar@users.noreply.github.com",
+            "name": "Alfred Kedhammar"
+        },
+        {
+            "@id": "https://orcid.org/0000-0003-2702-1103",
+            "@type": "Person",
+            "email": "adrien.coulier@medsci.uu.se",
+            "name": "Adrien Coulier"
         }
     ]
 }
\ No newline at end of file
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index 6f9cd5ed..37ec91ee 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -8,15 +8,15 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { UTILS_NFSCHEMA_PLUGIN     } from '../../nf-core/utils_nfschema_plugin'
-include { paramsSummaryMap          } from 'plugin/nf-schema'
-include { samplesheetToList         } from 'plugin/nf-schema'
-include { paramsHelp                } from 'plugin/nf-schema'
-include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
-include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
-include { imNotification            } from '../../nf-core/utils_nfcore_pipeline'
-include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
-include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
+include { UTILS_NFSCHEMA_PLUGIN   } from '../../nf-core/utils_nfschema_plugin'
+include { paramsSummaryMap        } from 'plugin/nf-schema'
+include { samplesheetToList       } from 'plugin/nf-schema'
+include { paramsHelp              } from 'plugin/nf-schema'
+include { completionEmail         } from '../../nf-core/utils_nfcore_pipeline'
+include { completionSummary       } from '../../nf-core/utils_nfcore_pipeline'
+include { imNotification          } from '../../nf-core/utils_nfcore_pipeline'
+include { UTILS_NFCORE_PIPELINE   } from '../../nf-core/utils_nfcore_pipeline'
+include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -25,17 +25,16 @@ include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipelin
 */
 
 workflow PIPELINE_INITIALISATION {
-
     take:
-    version           // boolean: Display version and exit
-    validate_params   // boolean: Boolean whether to validate parameters against the schema at runtime
-    monochrome_logs   // boolean: Do not use coloured log outputs
+    version // boolean: Display version and exit
+    validate_params // boolean: Boolean whether to validate parameters against the schema at runtime
+    _monochrome_logs // boolean: Do not use coloured log outputs
     nextflow_cli_args //   array: List of positional nextflow CLI args
-    outdir            //  string: The output directory where the results will be saved
-    input             //  string: Path to input samplesheet
-    help              // boolean: Display help message and exit
-    help_full         // boolean: Show the full help message
-    show_hidden       // boolean: Show hidden parameters in the help message
+    outdir //  string: The output directory where the results will be saved
+    input //  string: Path to input samplesheet
+    help // boolean: Display help message and exit
+    help_full // boolean: Show the full help message
+    show_hidden // boolean: Show hidden parameters in the help message
 
     main:
 
@@ -44,11 +43,11 @@ workflow PIPELINE_INITIALISATION {
     //
     // Print version and exit if required and dump pipeline parameters to JSON file
     //
-    UTILS_NEXTFLOW_PIPELINE (
+    UTILS_NEXTFLOW_PIPELINE(
         version,
         true,
         outdir,
-        workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1
+        workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1,
     )
 
     //
@@ -64,7 +63,7 @@ workflow PIPELINE_INITIALISATION {
 \033[0;35m  nf-core/seqinspector ${workflow.manifest.version}\033[0m
 -\033[2m----------------------------------------------------\033[0m-
 """
-    after_text = """${workflow.manifest.doi ? "\n* The pipeline\n" : ""}${workflow.manifest.doi.tokenize(",").collect { doi -> "    https://doi.org/${doi.trim().replace('https://doi.org/','')}"}.join("\n")}${workflow.manifest.doi ? "\n" : ""}
+    after_text = """${workflow.manifest.doi ? "\n* The pipeline\n" : ""}${workflow.manifest.doi.tokenize(",").collect { doi -> "    https://doi.org/${doi.trim().replace('https://doi.org/', '')}" }.join("\n")}${workflow.manifest.doi ? "\n" : ""}
 * The nf-core framework
     https://doi.org/10.1038/s41587-020-0439-x
 
@@ -73,7 +72,7 @@ workflow PIPELINE_INITIALISATION {
 """
     command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
 
-    UTILS_NFSCHEMA_PLUGIN (
+    UTILS_NFSCHEMA_PLUGIN(
         workflow,
         validate_params,
         null,
@@ -82,74 +81,69 @@ workflow PIPELINE_INITIALISATION {
         show_hidden,
         before_text,
         after_text,
-        command
+        command,
     )
 
     //
     // Check config provided to the pipeline
     //
-    UTILS_NFCORE_PIPELINE (
+    UTILS_NFCORE_PIPELINE(
         nextflow_cli_args
     )
 
     //
     // Custom validation for pipeline parameters
     //
-    validateInputParameters() // Runs additional validation that is not done by $projectDir/nextflow_schema.json
+    validateInputParameters()
+    // Runs additional validation that is not done by $projectDir/nextflow_schema.json
 
     //
-    // Create channel from input file provided through params.input
+    // Create channel from input file provided through params input
     //
-    nr_samples = Channel.fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
-        .toList().size()
+    nr_samples = channel.fromList(samplesheetToList(input, "${projectDir}/assets/schema_input.json"))
+        .toList()
+        .size()
 
-    channel
-        .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
+    channel.fromList(samplesheetToList(input, "${projectDir}/assets/schema_input.json"))
         .toList()
-        .flatMap { it.withIndex().collect {  entry, idx -> entry + "${idx+1}" } }
-        .map {
-            meta, fastq_1, fastq_2, idx ->
-                def tags = meta.tags ? meta.tags.tokenize(":") : []
-                def pad_positions = [nr_samples.length(), 2].max()
-                def zero_padded_idx = idx.padLeft(pad_positions, "0")
-                def updated_meta = meta + [ id:"${meta.sample}_${zero_padded_idx}", tags:tags ]
-                if (!fastq_2) {
-                    return [
-                        updated_meta.id,
-                        updated_meta + [ single_end:true ],
-                        [ fastq_1 ]
-                    ]
-                } else {
-                    return [
-                        updated_meta.id,
-                        updated_meta + [ single_end:false ],
-                        [ fastq_1, fastq_2 ]
-                    ]
-                }
+        .flatMap { item -> item.withIndex().collect { entry, idx -> entry + "${idx + 1}" } }
+        .map { meta, fastq_1, fastq_2, idx ->
+            def tags = meta.tags ? meta.tags.tokenize(":") : []
+            def pad_positions = [nr_samples.length(), 2].max()
+            def zero_padded_idx = idx.padLeft(pad_positions, "0")
+            def updated_meta = meta + [id: "${meta.sample}_${zero_padded_idx}", tags: tags]
+            if (!fastq_2) {
+                return [
+                    updated_meta.id,
+                    updated_meta + [single_end: true],
+                    [fastq_1],
+                ]
+            }
+            else {
+                return [
+                    updated_meta.id,
+                    updated_meta + [single_end: false],
+                    [fastq_1, fastq_2],
+                ]
+            }
         }
         .groupTuple()
-        .map {
-            validateInputSamplesheet(it) // Applies additional group validation checks that schema_input.json cannot do.
+        .map { meta ->
+            validateInputSamplesheet(meta)
         }
-        .transpose() // Replace the map below
-        // .map {
-        //     meta, fastqs ->
-        //         return [ meta, fastqs.flatten() ]
-        // }
+        .transpose()
         .set { ch_samplesheet }
 
     ch_samplesheet
-        .map {
-            meta, fastqs -> meta.tags
+        .map { meta, _fastqs ->
+            meta.tags
         }
         .flatten()
         .unique()
         .map { tag_name -> [tag_name.toLowerCase(), tag_name] }
         .groupTuple()
-        .map {
-            tag_lowercase, tags ->
-                assert tags.size() == 1 :
-                "Tag name collision: " + tags.join(", ")
+        .map { _tag_lowercase, tags ->
+            assert tags.size() == 1 : "Tag name collision: " + tags.join(", ")
         }
 
     emit:
@@ -164,15 +158,14 @@ workflow PIPELINE_INITIALISATION {
 */
 
 workflow PIPELINE_COMPLETION {
-
     take:
-    email           //  string: email address
-    email_on_fail   //  string: email address sent on pipeline failure
+    email //  string: email address
+    email_on_fail //  string: email address sent on pipeline failure
     plaintext_email // boolean: Send plain-text email instead of HTML
-    outdir          //    path: Path to output directory where results will be published
+    outdir //    path: Path to output directory where results will be published
     monochrome_logs // boolean: Disable ANSI colour codes in log output
-    hook_url        //  string: hook URL for notifications
-    multiqc_report  //  string: Path to MultiQC report
+    hook_url //  string: hook URL for notifications
+    multiqc_report //  string: Path to MultiQC report
 
     main:
     summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
@@ -201,7 +194,7 @@ workflow PIPELINE_COMPLETION {
     }
 
     workflow.onError {
-        log.error "Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting"
+        log.error("Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting")
     }
 }
 
@@ -214,8 +207,7 @@ workflow PIPELINE_COMPLETION {
 // Check and validate pipeline parameters
 //
 def validateInputParameters() {
-    // genomeExistsError()
-
+    genomeExistsError()
 }
 
 //
@@ -225,12 +217,12 @@ def validateInputSamplesheet(input) {
     def (metas, fastqs) = input[1..2]
 
     // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end
-    def endedness_ok = metas.collect{ meta -> meta.single_end }.unique().size == 1
+    def endedness_ok = metas.collect { meta -> meta.single_end }.unique().size == 1
     if (!endedness_ok) {
         error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}")
     }
 
-    return [ metas[0], fastqs ]
+    return [metas[0], fastqs]
 }
 
 //
@@ -238,11 +230,7 @@ def validateInputSamplesheet(input) {
 //
 def genomeExistsError() {
     if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
-        def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-            "  Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
-            "  Currently, the available genome keys are:\n" +
-            "  ${params.genomes.keySet().join(", ")}\n" +
-            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+        def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + "  Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + "  Currently, the available genome keys are:\n" + "  ${params.genomes.keySet().join(", ")}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
         error(error_string)
     }
 }
@@ -252,12 +240,16 @@ def genomeExistsError() {
 def toolCitationText() {
     def citation_text = [
         "Tools used in the workflow included:",
+        "Bowtie2 (Langmead et al. 2012)",
+        "BWAMEM2 (Vasimuddin et al. 2019)",
         "FastQC (Andrews 2010),",
-        "MultiQC (Ewels et al. 2016),",
         "FastQ Screen (Wingett & Andrews 2018)",
+        "MultiQC (Ewels et al. 2016),",
+        "Picard Tool (Broad Institute 2019),",
+        "SAMTOOLS (Danecek et al. 2021),",
         params.sample_size > 0 ? "Seqtk (Li 2021)," : "",
         "SeqFu (Telatin et al. 2021),",
-        "."
+        ".",
     ].join(' ').trim()
 
     return citation_text
@@ -265,11 +257,15 @@ def toolCitationText() {
 
 def toolBibliographyText() {
     def reference_text = [
+        "<li>Langmead S., & Salzberg SL. (2012). Fast gapped-read alignment with Bowtie 2.</li>",
+        "<li>Vasimuddin Md., Misra S., Li H, & Aluru S. (2019). Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems.</li>",
         "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.</li>",
+        "<li>Wingett SW., & Andrews S. FastQ Screen: A tool for multi-genome mapping and quality control. F1000Res. 2018 Aug 24 [revised 2018 Jan 1];7:1338. doi: 10.12688/f1000research.15931.2. eCollection</li>",
         "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics, 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>",
-        "<li>Wingett SW, Andrews S. FastQ Screen: A tool for multi-genome mapping and quality control. F1000Res. 2018 Aug 24 [revised 2018 Jan 1];7:1338. doi: 10.12688/f1000research.15931.2. eCollection</li>",
+        "<li>Broad Institute, (2019) Picard Tools, URL: https://broadinstitute.github.io/picard/.</li>",
+        "<li>Danecek P., Bonfield JK., Liddle J., & al. (2021). Twelve years of SAMtools and BCFtools.</li>",
         params.sample_size > 0 ? "<li>Li, H. SeqTk. Available online: https://github.com/lh3/seqtk (accessed on 6 May 2021)</li>" : "",
-        "<li>Telatin, A.; Fariselli, P.; Birolo, G. SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files. Bioengineering 2021, 8, 59. https://doi.org/10.3390/bioengineering8050059</li>"
+        "<li>Telatin, A.; Fariselli, P.; Birolo, G. SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files. Bioengineering 2021, 8, 59. https://doi.org/10.3390/bioengineering8050059</li>",
     ].join(' ').trim()
 
     return reference_text
@@ -292,7 +288,10 @@ def methodsDescriptionText(mqc_methods_yaml) {
             temp_doi_ref += "(doi: <a href=\'https://doi.org/${doi_ref.replace("https://doi.org/", "").replace(" ", "")}\'>${doi_ref.replace("https://doi.org/", "").replace(" ", "")}</a>), "
         }
         meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2)
-    } else meta["doi_text"] = ""
+    }
+    else {
+        meta["doi_text"] = ""
+    }
     meta["nodoi_text"] = meta.manifest_map.doi ? "" : "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
 
     // Tool references
@@ -301,7 +300,7 @@ def methodsDescriptionText(mqc_methods_yaml) {
 
     def methods_text = mqc_methods_yaml.text
 
-    def engine =  new groovy.text.SimpleTemplateEngine()
+    def engine = new groovy.text.SimpleTemplateEngine()
     def description_html = engine.createTemplate(methods_text).make(meta)
 
     return description_html.toString()
@@ -310,7 +309,7 @@ def methodsDescriptionText(mqc_methods_yaml) {
 //
 // Generate report index for MultiQC
 //
-def reportIndexMultiqc(tags, global=true) {
+def reportIndexMultiqc(tags, global = true) {
     def relative_path = global ? ".." : "../.."
 
     def a_attrs = "target=\"_blank\" class=\"list-group-item list-group-item-action\""
@@ -319,22 +318,21 @@ def reportIndexMultiqc(tags, global=true) {
     def index_section = "    <a href=\"${relative_path}/global_report/multiqc_report.html\" ${a_attrs}>Global report</a>\n"
 
     // Group report paths
-    tags
-        .each { tag ->
-            index_section += "    <a href=\"${relative_path}/group_reports/${tag}/multiqc_report.html\" ${a_attrs}>Group report: ${tag}</a>\n"
-        }
+    tags.each { tag ->
+        index_section += "    <a href=\"${relative_path}/group_reports/${tag}/multiqc_report.html\" ${a_attrs}>Group report: ${tag}</a>\n"
+    }
 
     def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-index'\n" as String
-    yaml_file_text     += "description: 'MultiQC reports collected from running the pipeline.'\n"
-    yaml_file_text     += "section_name: '${workflow.manifest.name} MultiQC Reports Index'\n"
-    yaml_file_text     += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
-    yaml_file_text     += "plot_type: 'html'\n"
-    yaml_file_text     += "data: |\n"
-    yaml_file_text     += "  <h4>Reports</h4>\n"
-    yaml_file_text     += "  <p>Select a report to view (open in a new tab):</p>\n"
-    yaml_file_text     += "  <div class=\"list-group\">\n"
-    yaml_file_text     += "${index_section}"
-    yaml_file_text     += "  </div>\n"
+    yaml_file_text += "description: 'MultiQC reports collected from running the pipeline.'\n"
+    yaml_file_text += "section_name: '${workflow.manifest.name} MultiQC Reports Index'\n"
+    yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
+    yaml_file_text += "plot_type: 'html'\n"
+    yaml_file_text += "data: |\n"
+    yaml_file_text += "  <h4>Reports</h4>\n"
+    yaml_file_text += "  <p>Select a report to view (open in a new tab):</p>\n"
+    yaml_file_text += "  <div class=\"list-group\">\n"
+    yaml_file_text += "${index_section}"
+    yaml_file_text += "  </div>\n"
 
     return yaml_file_text
 }
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test
deleted file mode 100644
index 68718e4f..00000000
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test
+++ /dev/null
@@ -1,54 +0,0 @@
-
-nextflow_function {
-
-    name "Test Functions"
-    script "subworkflows/nf-core/utils_nextflow_pipeline/main.nf"
-    config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config"
-    tag 'subworkflows'
-    tag 'utils_nextflow_pipeline'
-    tag 'subworkflows/utils_nextflow_pipeline'
-
-    test("Test Function getWorkflowVersion") {
-
-        function "getWorkflowVersion"
-
-        then {
-            assertAll(
-                { assert function.success },
-                { assert snapshot(function.result).match() }
-            )
-        }
-    }
-
-    test("Test Function dumpParametersToJSON") {
-
-        function "dumpParametersToJSON"
-
-        when {
-            function {
-                """
-                // define inputs of the function here. Example:
-                input[0] = "$outputDir"
-                """.stripIndent()
-            }
-        }
-
-        then {
-            assertAll(
-                { assert function.success }
-            )
-        }
-    }
-
-    test("Test Function checkCondaChannels") {
-
-        function "checkCondaChannels"
-
-        then {
-            assertAll(
-                { assert function.success },
-                { assert snapshot(function.result).match() }
-            )
-        }
-    }
-}
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap
deleted file mode 100644
index e3f0baf4..00000000
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap
+++ /dev/null
@@ -1,20 +0,0 @@
-{
-    "Test Function getWorkflowVersion": {
-        "content": [
-            "v9.9.9"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:02:05.308243"
-    },
-    "Test Function checkCondaChannels": {
-        "content": null,
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:02:12.425833"
-    }
-}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
deleted file mode 100644
index 02dbf094..00000000
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
+++ /dev/null
@@ -1,113 +0,0 @@
-nextflow_workflow {
-
-    name "Test Workflow UTILS_NEXTFLOW_PIPELINE"
-    script "../main.nf"
-    config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config"
-    workflow "UTILS_NEXTFLOW_PIPELINE"
-    tag 'subworkflows'
-    tag 'utils_nextflow_pipeline'
-    tag 'subworkflows/utils_nextflow_pipeline'
-
-    test("Should run no inputs") {
-
-        when {
-            workflow {
-                """
-                print_version        = false
-                dump_parameters      = false
-                outdir               = null
-                check_conda_channels = false
-
-                input[0] = print_version
-                input[1] = dump_parameters
-                input[2] = outdir
-                input[3] = check_conda_channels
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success }
-            )
-        }
-    }
-
-    test("Should print version") {
-
-        when {
-            workflow {
-                """
-                print_version        = true
-                dump_parameters      = false
-                outdir               = null
-                check_conda_channels = false
-
-                input[0] = print_version
-                input[1] = dump_parameters
-                input[2] = outdir
-                input[3] = check_conda_channels
-                """
-            }
-        }
-
-        then {
-            expect {
-                with(workflow) {
-                    assert success
-                    assert "nextflow_workflow v9.9.9" in stdout
-                }
-            }
-        }
-    }
-
-    test("Should dump params") {
-
-        when {
-            workflow {
-                """
-                print_version        = false
-                dump_parameters      = true
-                outdir               = 'results'
-                check_conda_channels = false
-
-                input[0] = false
-                input[1] = true
-                input[2] = outdir
-                input[3] = false
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success }
-            )
-        }
-    }
-
-    test("Should not create params JSON if no output directory") {
-
-        when {
-            workflow {
-                """
-                print_version        = false
-                dump_parameters      = true
-                outdir               = null
-                check_conda_channels = false
-
-                input[0] = false
-                input[1] = true
-                input[2] = outdir
-                input[3] = false
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success }
-            )
-        }
-    }
-}
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
deleted file mode 100644
index a09572e5..00000000
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-manifest {
-    name            = 'nextflow_workflow'
-    author          = """nf-core"""
-    homePage        = 'https://127.0.0.1'
-    description     = """Dummy pipeline"""
-    nextflowVersion = '!>=23.04.0'
-    version         = '9.9.9'
-    doi             = 'https://doi.org/10.5281/zenodo.5070524'
-}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
deleted file mode 100644
index f117040c..00000000
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
+++ /dev/null
@@ -1,126 +0,0 @@
-
-nextflow_function {
-
-    name "Test Functions"
-    script "../main.nf"
-    config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config"
-    tag "subworkflows"
-    tag "subworkflows_nfcore"
-    tag "utils_nfcore_pipeline"
-    tag "subworkflows/utils_nfcore_pipeline"
-
-    test("Test Function checkConfigProvided") {
-
-        function "checkConfigProvided"
-
-        then {
-            assertAll(
-                { assert function.success },
-                { assert snapshot(function.result).match() }
-            )
-        }
-    }
-
-    test("Test Function checkProfileProvided") {
-
-        function "checkProfileProvided"
-
-        when {
-            function {
-                """
-                input[0] = []
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert function.success },
-                { assert snapshot(function.result).match() }
-            )
-        }
-    }
-
-    test("Test Function without logColours") {
-
-        function "logColours"
-
-        when {
-            function {
-                """
-                input[0] = true
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert function.success },
-                { assert snapshot(function.result).match() }
-            )
-        }
-    }
-
-    test("Test Function with logColours") {
-        function "logColours"
-
-        when {
-            function {
-                """
-                input[0] = false
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert function.success },
-                { assert snapshot(function.result).match() }
-            )
-        }
-    }
-
-    test("Test Function getSingleReport with a single file") {
-        function "getSingleReport"
-
-        when {
-            function {
-                """
-                input[0] = file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true)
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert function.success },
-                { assert function.result.contains("test.tsv") }
-            )
-        }
-    }
-
-    test("Test Function getSingleReport with multiple files") {
-        function "getSingleReport"
-
-        when {
-            function {
-                """
-                input[0] = [
-                    file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true),
-                    file(params.modules_testdata_base_path + '/generic/tsv/network.tsv', checkIfExists: true),
-                    file(params.modules_testdata_base_path + '/generic/tsv/expression.tsv', checkIfExists: true)
-                ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert function.success },
-                { assert function.result.contains("test.tsv") },
-                { assert !function.result.contains("network.tsv") },
-                { assert !function.result.contains("expression.tsv") }
-            )
-        }
-    }
-}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
deleted file mode 100644
index 02c67014..00000000
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
+++ /dev/null
@@ -1,136 +0,0 @@
-{
-    "Test Function checkProfileProvided": {
-        "content": null,
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:03:03.360873"
-    },
-    "Test Function checkConfigProvided": {
-        "content": [
-            true
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:02:59.729647"
-    },
-    "Test Function without logColours": {
-        "content": [
-            {
-                "reset": "",
-                "bold": "",
-                "dim": "",
-                "underlined": "",
-                "blink": "",
-                "reverse": "",
-                "hidden": "",
-                "black": "",
-                "red": "",
-                "green": "",
-                "yellow": "",
-                "blue": "",
-                "purple": "",
-                "cyan": "",
-                "white": "",
-                "bblack": "",
-                "bred": "",
-                "bgreen": "",
-                "byellow": "",
-                "bblue": "",
-                "bpurple": "",
-                "bcyan": "",
-                "bwhite": "",
-                "ublack": "",
-                "ured": "",
-                "ugreen": "",
-                "uyellow": "",
-                "ublue": "",
-                "upurple": "",
-                "ucyan": "",
-                "uwhite": "",
-                "iblack": "",
-                "ired": "",
-                "igreen": "",
-                "iyellow": "",
-                "iblue": "",
-                "ipurple": "",
-                "icyan": "",
-                "iwhite": "",
-                "biblack": "",
-                "bired": "",
-                "bigreen": "",
-                "biyellow": "",
-                "biblue": "",
-                "bipurple": "",
-                "bicyan": "",
-                "biwhite": ""
-            }
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:03:17.969323"
-    },
-    "Test Function with logColours": {
-        "content": [
-            {
-                "reset": "\u001b[0m",
-                "bold": "\u001b[1m",
-                "dim": "\u001b[2m",
-                "underlined": "\u001b[4m",
-                "blink": "\u001b[5m",
-                "reverse": "\u001b[7m",
-                "hidden": "\u001b[8m",
-                "black": "\u001b[0;30m",
-                "red": "\u001b[0;31m",
-                "green": "\u001b[0;32m",
-                "yellow": "\u001b[0;33m",
-                "blue": "\u001b[0;34m",
-                "purple": "\u001b[0;35m",
-                "cyan": "\u001b[0;36m",
-                "white": "\u001b[0;37m",
-                "bblack": "\u001b[1;30m",
-                "bred": "\u001b[1;31m",
-                "bgreen": "\u001b[1;32m",
-                "byellow": "\u001b[1;33m",
-                "bblue": "\u001b[1;34m",
-                "bpurple": "\u001b[1;35m",
-                "bcyan": "\u001b[1;36m",
-                "bwhite": "\u001b[1;37m",
-                "ublack": "\u001b[4;30m",
-                "ured": "\u001b[4;31m",
-                "ugreen": "\u001b[4;32m",
-                "uyellow": "\u001b[4;33m",
-                "ublue": "\u001b[4;34m",
-                "upurple": "\u001b[4;35m",
-                "ucyan": "\u001b[4;36m",
-                "uwhite": "\u001b[4;37m",
-                "iblack": "\u001b[0;90m",
-                "ired": "\u001b[0;91m",
-                "igreen": "\u001b[0;92m",
-                "iyellow": "\u001b[0;93m",
-                "iblue": "\u001b[0;94m",
-                "ipurple": "\u001b[0;95m",
-                "icyan": "\u001b[0;96m",
-                "iwhite": "\u001b[0;97m",
-                "biblack": "\u001b[1;90m",
-                "bired": "\u001b[1;91m",
-                "bigreen": "\u001b[1;92m",
-                "biyellow": "\u001b[1;93m",
-                "biblue": "\u001b[1;94m",
-                "bipurple": "\u001b[1;95m",
-                "bicyan": "\u001b[1;96m",
-                "biwhite": "\u001b[1;97m"
-            }
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:03:21.714424"
-    }
-}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
deleted file mode 100644
index 8940d32d..00000000
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
+++ /dev/null
@@ -1,29 +0,0 @@
-nextflow_workflow {
-
-    name "Test Workflow UTILS_NFCORE_PIPELINE"
-    script "../main.nf"
-    config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config"
-    workflow "UTILS_NFCORE_PIPELINE"
-    tag "subworkflows"
-    tag "subworkflows_nfcore"
-    tag "utils_nfcore_pipeline"
-    tag "subworkflows/utils_nfcore_pipeline"
-
-    test("Should run without failures") {
-
-        when {
-            workflow {
-                """
-                input[0] = []
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(workflow.out).match() }
-            )
-        }
-    }
-}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap
deleted file mode 100644
index 859d1030..00000000
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap
+++ /dev/null
@@ -1,19 +0,0 @@
-{
-    "Should run without failures": {
-        "content": [
-            {
-                "0": [
-                    true
-                ],
-                "valid_config": [
-                    true
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:03:25.726491"
-    }
-}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
deleted file mode 100644
index d0a926bf..00000000
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-manifest {
-    name            = 'nextflow_workflow'
-    author          = """nf-core"""
-    homePage        = 'https://127.0.0.1'
-    description     = """Dummy pipeline"""
-    nextflowVersion  = '!>=23.04.0'
-    version         = '9.9.9'
-    doi             = 'https://doi.org/10.5281/zenodo.5070524'
-}
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
deleted file mode 100644
index c977917a..00000000
--- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
+++ /dev/null
@@ -1,173 +0,0 @@
-nextflow_workflow {
-
-    name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN"
-    script "../main.nf"
-    workflow "UTILS_NFSCHEMA_PLUGIN"
-
-    tag "subworkflows"
-    tag "subworkflows_nfcore"
-    tag "subworkflows/utils_nfschema_plugin"
-    tag "plugin/nf-schema"
-
-    config "./nextflow.config"
-
-    test("Should run nothing") {
-
-        when {
-
-            params {
-                test_data   = ''
-            }
-
-            workflow {
-                """
-                validate_params = false
-                input[0] = workflow
-                input[1] = validate_params
-                input[2] = ""
-                input[3] = false
-                input[4] = false
-                input[5] = false
-                input[6] = ""
-                input[7] = ""
-                input[8] = ""
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success }
-            )
-        }
-    }
-
-    test("Should validate params") {
-
-        when {
-
-            params {
-                test_data   = ''
-                outdir      = null
-            }
-
-            workflow {
-                """
-                validate_params = true
-                input[0] = workflow
-                input[1] = validate_params
-                input[2] = ""
-                input[3] = false
-                input[4] = false
-                input[5] = false
-                input[6] = ""
-                input[7] = ""
-                input[8] = ""
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.failed },
-                { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } }
-            )
-        }
-    }
-
-    test("Should run nothing - custom schema") {
-
-        when {
-
-            params {
-                test_data   = ''
-            }
-
-            workflow {
-                """
-                validate_params = false
-                input[0] = workflow
-                input[1] = validate_params
-                input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
-                input[3] = false
-                input[4] = false
-                input[5] = false
-                input[6] = ""
-                input[7] = ""
-                input[8] = ""
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success }
-            )
-        }
-    }
-
-    test("Should validate params - custom schema") {
-
-        when {
-
-            params {
-                test_data   = ''
-                outdir      = null
-            }
-
-            workflow {
-                """
-                validate_params = true
-                input[0] = workflow
-                input[1] = validate_params
-                input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
-                input[3] = false
-                input[4] = false
-                input[5] = false
-                input[6] = ""
-                input[7] = ""
-                input[8] = ""
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.failed },
-                { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } }
-            )
-        }
-    }
-
-    test("Should create a help message") {
-
-        when {
-
-            params {
-                test_data   = ''
-                outdir      = null
-            }
-
-            workflow {
-                """
-                validate_params = true
-                input[0] = workflow
-                input[1] = validate_params
-                input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
-                input[3] = true
-                input[4] = false
-                input[5] = false
-                input[6] = "Before"
-                input[7] = "After"
-                input[8] = "nextflow run test/test"
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success }
-            )
-        }
-    }
-}
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
deleted file mode 100644
index 8d8c7371..00000000
--- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
+++ /dev/null
@@ -1,8 +0,0 @@
-plugins {
-    id "nf-schema@2.5.1"
-}
-
-validation {
-    parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
-    monochromeLogs = true
-}
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
deleted file mode 100644
index 331e0d2f..00000000
--- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
+++ /dev/null
@@ -1,96 +0,0 @@
-{
-    "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
-    "title": ". pipeline parameters",
-    "description": "",
-    "type": "object",
-    "$defs": {
-        "input_output_options": {
-            "title": "Input/output options",
-            "type": "object",
-            "fa_icon": "fas fa-terminal",
-            "description": "Define where the pipeline should find input data and save output data.",
-            "required": ["outdir"],
-            "properties": {
-                "validate_params": {
-                    "type": "boolean",
-                    "description": "Validate parameters?",
-                    "default": true,
-                    "hidden": true
-                },
-                "outdir": {
-                    "type": "string",
-                    "format": "directory-path",
-                    "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
-                    "fa_icon": "fas fa-folder-open"
-                },
-                "test_data_base": {
-                    "type": "string",
-                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/modules",
-                    "description": "Base for test data directory",
-                    "hidden": true
-                },
-                "test_data": {
-                    "type": "string",
-                    "description": "Fake test data param",
-                    "hidden": true
-                }
-            }
-        },
-        "generic_options": {
-            "title": "Generic options",
-            "type": "object",
-            "fa_icon": "fas fa-file-import",
-            "description": "Less common options for the pipeline, typically set in a config file.",
-            "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
-            "properties": {
-                "help": {
-                    "type": "boolean",
-                    "description": "Display help text.",
-                    "fa_icon": "fas fa-question-circle",
-                    "hidden": true
-                },
-                "version": {
-                    "type": "boolean",
-                    "description": "Display version and exit.",
-                    "fa_icon": "fas fa-question-circle",
-                    "hidden": true
-                },
-                "logo": {
-                    "type": "boolean",
-                    "default": true,
-                    "description": "Display nf-core logo in console output.",
-                    "fa_icon": "fas fa-image",
-                    "hidden": true
-                },
-                "singularity_pull_docker_container": {
-                    "type": "boolean",
-                    "description": "Pull Singularity container from Docker?",
-                    "hidden": true
-                },
-                "publish_dir_mode": {
-                    "type": "string",
-                    "default": "copy",
-                    "description": "Method used to save pipeline results to output directory.",
-                    "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
-                    "fa_icon": "fas fa-copy",
-                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
-                    "hidden": true
-                },
-                "monochrome_logs": {
-                    "type": "boolean",
-                    "description": "Use monochrome_logs",
-                    "hidden": true
-                }
-            }
-        }
-    },
-    "allOf": [
-        {
-            "$ref": "#/$defs/input_output_options"
-        },
-        {
-            "$ref": "#/$defs/generic_options"
-        }
-    ]
-}

From 9df5cfcfb41ac3aa9ddedc16d4ef5129f0c9d524 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Wed, 11 Feb 2026 10:45:13 +0100
Subject: [PATCH 523/530] prepare release 1.0.0 (#169)

---
 .nf-core.yml                             |  2 +-
 CHANGELOG.md                             |  4 +-
 assets/multiqc_config.yml                |  6 +--
 main.nf                                  |  4 +-
 nextflow.config                          |  2 +-
 ro-crate-metadata.json                   | 48 ++++++++++++------------
 tests/MiSeq.nf.test                      |  6 +--
 tests/MiSeq.nf.test.snap                 | 34 ++++++++++-------
 tests/MiSeq_PairedEnd.nf.test            |  2 +-
 tests/MiSeq_PairedEnd.nf.test.snap       | 13 ++++---
 tests/NovaSeq6000.nf.test                |  4 +-
 tests/NovaSeq6000.nf.test.snap           | 28 ++++++++------
 tests/NovaSeq6000_subsample.nf.test      |  6 +--
 tests/NovaSeq6000_subsample.nf.test.snap | 39 +++++++++++--------
 tests/PromethION.nf.test                 |  2 +-
 tests/PromethION.nf.test.snap            | 10 ++---
 workflows/seqinspector.nf                | 11 +++---
 17 files changed, 123 insertions(+), 98 deletions(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index 6bfb94c6..3e335c69 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -21,4 +21,4 @@ template:
   name: seqinspector
   org: nf-core
   outdir: .
-  version: 1.0dev
+  version: 1.0.0
diff --git a/CHANGELOG.md b/CHANGELOG.md
index c3e85d71..ddf6ddff 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.0dev - [date]
+## [1.0.0](https://github.com/nf-core/seqinspector/releases/tag/1.0.0) - Inspector Gadget
 
 Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-co.re/) template.
 
@@ -52,6 +52,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#162](https://github.com/nf-core/seqinspector/pull/162) Fix bugs in qc_bam and prepare_genome subworkflows and add tests
 - [#163](https://github.com/nf-core/seqinspector/pull/163) Run fastqscreen with subsampled data if available
 - [#167](https://github.com/nf-core/seqinspector/pull/167) RunDirParser is now skipped if no Run Directory information is available
+- [#169](https://github.com/nf-core/seqinspector/pull/169) Rescue missing versions from PREPARE_GENOME subworkflow
 
 ### `Changed`
 
@@ -68,6 +69,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#158](https://github.com/nf-core/seqinspector/pull/158) Moved picard_collectmultiplemetrics to the subworkflow QC_BAM
 - [#164](https://github.com/nf-core/seqinspector/pull/164) Refactor local subworkflow and pipeline tests
 - [#168](https://github.com/nf-core/seqinspector/pull/168) Adhere to strict syntax
+- [#169](https://github.com/nf-core/seqinspector/pull/169) Prepare release 1.0.0
 
 ### `Dependencies`
 
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index dbd65efb..9f11f5fa 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,7 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/seqinspector/tree/dev" target="_blank">nf-core/seqinspector</a>
-  analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/seqinspector/dev/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/seqinspector/releases/tag/1.0.0" target="_blank">nf-core/seqinspector</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/seqinspector/1.0.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-seqinspector-index":
     order: -999
@@ -23,7 +21,7 @@ fn_clean_trim:
 # for SE: "SampleName_01" -> "SampleName #01"
 # for PE: "SampleName_01_1" -> "SampleName #01_1"
 #    and: "SampleName_01_2" -> "SampleName #01_2"
-sample_names_replace_regex: True
+sample_names_replace_regex: true
 sample_names_replace:
   "(.+)_(\\d{2,}|\\d{2,}_[12])$": "\\1 #\\2"
 
diff --git a/main.nf b/main.nf
index 3de00b77..f2b8507f 100644
--- a/main.nf
+++ b/main.nf
@@ -51,7 +51,7 @@ workflow NFCORE_SEQINSPECTOR {
         samplesheet,
         params.fasta,
         skip_tools,
-        params.bwamem2
+        params.bwamem2,
     )
 
     emit:
@@ -80,7 +80,7 @@ workflow {
         params.input,
         params.help,
         params.help_full,
-        params.show_hidden
+        params.show_hidden,
     )
 
     //
diff --git a/nextflow.config b/nextflow.config
index c4f142c9..3df58bb6 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -404,7 +404,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
     nextflowVersion = '!>=25.04.0'
-    version         = '1.0dev'
+    version         = '1.0.0'
     doi             = ''
 }
 
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 94830468..242fa244 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -21,8 +21,8 @@
         {
             "@id": "./",
             "@type": "Dataset",
-            "creativeWorkStatus": "InProgress",
-            "datePublished": "2026-02-10T11:55:01+00:00",
+            "creativeWorkStatus": "Stable",
+            "datePublished": "2026-02-10T15:24:32+00:00",
             "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that processes raw sequence data (FASTQ) to provide comprehensive quality control.\nIt can perform subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants.\nThe pipeline generates detailed MultiQC reports with flexible output options, ranging from individual sample reports to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments.\nIf provided, nf-core/seqinspector can also parse statistics from an Illumina run folder directory into the final MultiQC reports.\n\n<!-- TODO: add a search tool that accepts a tree for `Compatibility with Data`. -->\n\n| Tool Type           | Tool Name                                                                                                           | Tool Description                                                                              | Compatibility with Data | Dependencies                                                                                                              | Default tool |\n| ------------------- | ------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------- | ----------------------- | ------------------------------------------------------------------------------------------------------------------------- | ------------ |\n| `Subsampling`       | [`Seqtk`](https://github.com/lh3/seqtk)                                                                             | Global subsampling of reads. Only performs subsampling if `--sample_size` parameter is given. | [RNA, DNA, synthetic]   | [N/A]                                                                                                                     | no           |\n| `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2)                                                                   | Align reads to reference                                                                      | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `Indexing`          | [`SAMtools`](http://github.com/samtools)                                                                            | Index aligned BAM files, create FASTA index                                                   | [DNA]                   | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)                                              | Read QC                                                                                       | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)                                   | Basic contamination detection                                                                 | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`SeqFu Stats`](https://github.com/telatin/seqfu2)                                                                  | Sequence statistics                                                                           | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`Picard collect multiple metrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html)         | Collect multiple QC metrics                                                                   | [RNA, DNA]              | [Bwamem2, SAMtools, `--genome`]                                                                                           | yes          |\n| `QC`                | [`Picard_collecthsmetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard) | Collect alignment QC metrics of hybrid-selection data.                                        | [RNA, DNA]              | [Bwamem2, SAMtools, `--fasta`, `--run_picard_collecths_metrics`, `--bait_intervals`, `--target_intervals` (`--ref_dict`)] | no           |\n| `Reporting`         | [`MultiQC`](http://multiqc.info/)                                                                                   | Present QC for raw reads                                                                      | [RNA, DNA, synthetic]   | [N/A]                                                                                                                     | yes          |\n\n<picture>\n  <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/seqinspector_tubemap_V1.0_dark.png\">\n  <source media=\"(prefers-color-scheme: light)\" srcset=\"docs/images/seqinspector_tubemap_V1.0.png\">\n  <img alt=\"Fallback image description\" src=\"docs/images/seqinspector_tubemap_V1.0.png\">\n</picture>\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end with only `fastq_1`) or a pair of fastq files (paired end with `fastq_1` and `fastq_2`).\n`rundir` is the path to the runfolder.\n`tags` is a colon-separated list of tags that will be added to the MultiQC report for this `sample`.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by [@agrima2010](https://github.com/agrima2010), [@Aratz](https://github.com/Aratz), [@FranBonath](https://github.com/FranBonath), [@kedhammar](https://github.com/kedhammar), and [@MatthiasZepper](https://github.com/MatthiasZepper) from the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/) and [Clinical Genomics Stockholm](https://clinical.scilifelab.se/).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@adamrtalbot](https://github.com/adamrtalbot)\n- [@alneberg](https://github.com/alneberg)\n- [@beatrizsavinhas](https://github.com/beatrizsavinhas)\n- [@ctuni](https://github.com/ctuni)\n- [@edmundmiller](https://github.com/edmundmiller)\n- [@EliottBo](https://github.com/EliottBo)\n- [@KarNair](https://github.com/KarNair)\n- [@kjellinjonas](https://github.com/kjellinjonas)\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n- [@matrulda](https://github.com/matrulda)\n- [@maxulysse](https://github.com/maxulysse)\n- [@mirpedrol](https://github.com/mirpedrol)\n- [@nggvs](https://github.com/nggvs)\n- [@nkongenelly](https://github.com/nkongenelly)\n- [@Patricie34](https://github.com/Patricie34)\n- [@pontushojer](https://github.com/pontushojer)\n- [@ramprasadn](https://github.com/ramprasadn)\n- [@rannick](https://github.com/rannick)\n- [@torigiffin](https://github.com/torigiffin)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
@@ -102,7 +102,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#a88abaae-15ab-45e5-9040-debdc8473225"
+                    "@id": "#eb65e4a1-3330-4f79-98cb-e1b2a7f86b81"
                 }
             ],
             "name": "nf-core/seqinspector"
@@ -131,23 +131,23 @@
             ],
             "creator": [
                 {
-                    "@id": "#max.u.garcia@gmail.com"
+                    "@id": "https://orcid.org/0009-0004-5536-7210"
                 },
                 {
                     "@id": "https://orcid.org/0000-0003-1675-0677"
                 },
                 {
-                    "@id": "https://orcid.org/0009-0004-5536-7210"
+                    "@id": "https://orcid.org/0000-0003-2702-1103"
                 },
                 {
                     "@id": "#89784800+kedhammar@users.noreply.github.com"
                 },
                 {
-                    "@id": "https://orcid.org/0000-0003-2702-1103"
+                    "@id": "#max.u.garcia@gmail.com"
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2026-02-10T12:55:01Z",
+            "dateModified": "2026-02-10T16:24:32Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -160,19 +160,19 @@
             ],
             "maintainer": [
                 {
-                    "@id": "#max.u.garcia@gmail.com"
+                    "@id": "https://orcid.org/0009-0004-5536-7210"
                 },
                 {
                     "@id": "https://orcid.org/0000-0003-1675-0677"
                 },
                 {
-                    "@id": "https://orcid.org/0009-0004-5536-7210"
+                    "@id": "https://orcid.org/0000-0003-2702-1103"
                 },
                 {
                     "@id": "#89784800+kedhammar@users.noreply.github.com"
                 },
                 {
-                    "@id": "https://orcid.org/0000-0003-2702-1103"
+                    "@id": "#max.u.garcia@gmail.com"
                 }
             ],
             "name": [
@@ -186,10 +186,10 @@
             },
             "url": [
                 "https://github.com/nf-core/seqinspector",
-                "https://nf-co.re/seqinspector/dev/"
+                "https://nf-co.re/seqinspector/1.0.0/"
             ],
             "version": [
-                "1.0dev"
+                "1.0.0"
             ]
         },
         {
@@ -205,11 +205,11 @@
             "version": "!>=25.04.0"
         },
         {
-            "@id": "#a88abaae-15ab-45e5-9040-debdc8473225",
+            "@id": "#eb65e4a1-3330-4f79-98cb-e1b2a7f86b81",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#4c91a6e5-517c-49a6-b553-2e7d9ffc1e5e"
+                    "@id": "#58467589-6ef2-4f18-8ebc-b5ecd9967ecd"
                 }
             ],
             "mainEntity": {
@@ -218,7 +218,7 @@
             "name": "Test suite for nf-core/seqinspector"
         },
         {
-            "@id": "#4c91a6e5-517c-49a6-b553-2e7d9ffc1e5e",
+            "@id": "#58467589-6ef2-4f18-8ebc-b5ecd9967ecd",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/seqinspector",
             "resource": "repos/nf-core/seqinspector/actions/workflows/nf-test.yml",
@@ -352,10 +352,10 @@
             "url": "https://nf-co.re/"
         },
         {
-            "@id": "#max.u.garcia@gmail.com",
+            "@id": "https://orcid.org/0009-0004-5536-7210",
             "@type": "Person",
-            "email": "max.u.garcia@gmail.com",
-            "name": "Maxime U Garcia"
+            "email": "163723002+agrima2010@users.noreply.github.com",
+            "name": "Agrima Bhatt"
         },
         {
             "@id": "https://orcid.org/0000-0003-1675-0677",
@@ -364,10 +364,10 @@
             "name": "Mahesh Binzer-Panchal"
         },
         {
-            "@id": "https://orcid.org/0009-0004-5536-7210",
+            "@id": "https://orcid.org/0000-0003-2702-1103",
             "@type": "Person",
-            "email": "163723002+agrima2010@users.noreply.github.com",
-            "name": "Agrima Bhatt"
+            "email": "adrien.coulier@medsci.uu.se",
+            "name": "Adrien Coulier"
         },
         {
             "@id": "#89784800+kedhammar@users.noreply.github.com",
@@ -376,10 +376,10 @@
             "name": "Alfred Kedhammar"
         },
         {
-            "@id": "https://orcid.org/0000-0003-2702-1103",
+            "@id": "#max.u.garcia@gmail.com",
             "@type": "Person",
-            "email": "adrien.coulier@medsci.uu.se",
-            "name": "Adrien Coulier"
+            "email": "max.u.garcia@gmail.com",
+            "name": "Maxime U Garcia"
         }
     ]
 }
\ No newline at end of file
diff --git a/tests/MiSeq.nf.test b/tests/MiSeq.nf.test
index 8cd63574..dc822aa9 100644
--- a/tests/MiSeq.nf.test
+++ b/tests/MiSeq.nf.test
@@ -33,7 +33,7 @@ nextflow_pipeline {
             assertAll(
                 { assert snapshot(
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
+                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
                     // All stable path names, with a relative path
                     stable_name,
                     // All files with stable contents
@@ -72,7 +72,7 @@ nextflow_pipeline {
             assertAll(
                 { assert snapshot(
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
+                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
                     // All stable path names, with a relative path
                     stable_name,
                     // All files with stable contents
@@ -111,7 +111,7 @@ nextflow_pipeline {
             assertAll(
                 { assert snapshot(
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
+                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
                     // All stable path names, with a relative path
                     stable_name,
                     // All files with stable contents
diff --git a/tests/MiSeq.nf.test.snap b/tests/MiSeq.nf.test.snap
index d5df70ba..d6dac529 100644
--- a/tests/MiSeq.nf.test.snap
+++ b/tests/MiSeq.nf.test.snap
@@ -2,8 +2,8 @@
     "Miseq data test (skip all tools)": {
         "content": [
             {
-                "Workflow": {
-                    "nf-core/seqinspector": "v1.0dev"
+                "SAMTOOLS_FAIDX": {
+                    "samtools": "1.22.1"
                 }
             },
             [
@@ -33,13 +33,16 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2025-12-12T16:48:15.085074556"
+        "timestamp": "2026-02-10T17:15:27.612715634"
     },
     "MiSeq data test (single end reads)": {
         "content": [
             {
+                "BWAMEM2_INDEX": {
+                    "bwamem2": "2.2.1"
+                },
                 "BWAMEM2_MEM": {
                     "bwamem2": "2.2.1",
                     "samtools": "1.22.1"
@@ -53,14 +56,14 @@
                 "PICARD_COLLECTMULTIPLEMETRICS": {
                     "picard": "3.4.0"
                 },
+                "SAMTOOLS_FAIDX": {
+                    "samtools": "1.22.1"
+                },
                 "SAMTOOLS_INDEX": {
                     "samtools": "1.22.1"
                 },
                 "SEQFU_STATS": {
                     "seqfu": "1.22.3"
-                },
-                "Workflow": {
-                    "nf-core/seqinspector": "v1.0dev"
                 }
             },
             [
@@ -265,13 +268,16 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2025-12-12T16:45:20.420081882"
+        "timestamp": "2026-02-10T17:14:12.684188306"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
             {
+                "BWAMEM2_INDEX": {
+                    "bwamem2": "2.2.1"
+                },
                 "BWAMEM2_MEM": {
                     "bwamem2": "2.2.1",
                     "samtools": "1.22.1"
@@ -282,14 +288,14 @@
                 "PICARD_COLLECTMULTIPLEMETRICS": {
                     "picard": "3.4.0"
                 },
+                "SAMTOOLS_FAIDX": {
+                    "samtools": "1.22.1"
+                },
                 "SAMTOOLS_INDEX": {
                     "samtools": "1.22.1"
                 },
                 "SEQFU_STATS": {
                     "seqfu": "1.22.3"
-                },
-                "Workflow": {
-                    "nf-core/seqinspector": "v1.0dev"
                 }
             },
             [
@@ -439,8 +445,8 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2025-12-12T16:47:54.570558579"
+        "timestamp": "2026-02-10T17:14:58.212405529"
     }
 }
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.nf.test b/tests/MiSeq_PairedEnd.nf.test
index b77f5043..bb24f4db 100644
--- a/tests/MiSeq_PairedEnd.nf.test
+++ b/tests/MiSeq_PairedEnd.nf.test
@@ -33,7 +33,7 @@ nextflow_pipeline {
             assertAll(
                 { assert snapshot(
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
+                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
                     // All stable path names, with a relative path
                     stable_name,
                     // All files with stable contents
diff --git a/tests/MiSeq_PairedEnd.nf.test.snap b/tests/MiSeq_PairedEnd.nf.test.snap
index 346eaa7b..661eaec9 100644
--- a/tests/MiSeq_PairedEnd.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.nf.test.snap
@@ -2,6 +2,9 @@
     "MiSeq data test (paired end reads)": {
         "content": [
             {
+                "BWAMEM2_INDEX": {
+                    "bwamem2": "2.2.1"
+                },
                 "BWAMEM2_MEM": {
                     "bwamem2": "2.2.1",
                     "samtools": "1.22.1"
@@ -15,14 +18,14 @@
                 "PICARD_COLLECTMULTIPLEMETRICS": {
                     "picard": "3.4.0"
                 },
+                "SAMTOOLS_FAIDX": {
+                    "samtools": "1.22.1"
+                },
                 "SAMTOOLS_INDEX": {
                     "samtools": "1.22.1"
                 },
                 "SEQFU_STATS": {
                     "seqfu": "1.22.3"
-                },
-                "Workflow": {
-                    "nf-core/seqinspector": "v1.0dev"
                 }
             },
             [
@@ -418,8 +421,8 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2025-12-12T16:49:17.100345817"
+        "timestamp": "2026-02-10T17:16:28.42493386"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.nf.test b/tests/NovaSeq6000.nf.test
index df72a311..81641f40 100644
--- a/tests/NovaSeq6000.nf.test
+++ b/tests/NovaSeq6000.nf.test
@@ -32,7 +32,7 @@ nextflow_pipeline {
             assertAll(
                 { assert snapshot(
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
+                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
                     // All stable path names, with a relative path
                     stable_name,
                     // All files with stable contents
@@ -73,7 +73,7 @@ nextflow_pipeline {
             assertAll(
                 { assert snapshot(
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
+                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
                     // All stable path names, with a relative path
                     stable_name,
                     // All files with stable contents
diff --git a/tests/NovaSeq6000.nf.test.snap b/tests/NovaSeq6000.nf.test.snap
index 7ffaa3e9..d39d71a7 100644
--- a/tests/NovaSeq6000.nf.test.snap
+++ b/tests/NovaSeq6000.nf.test.snap
@@ -2,6 +2,9 @@
     "NovaSeq6000 data test": {
         "content": [
             {
+                "BWAMEM2_INDEX": {
+                    "bwamem2": "2.2.1"
+                },
                 "BWAMEM2_MEM": {
                     "bwamem2": "2.2.1",
                     "samtools": "1.22.1"
@@ -19,14 +22,14 @@
                     "PyYAML": "6.0.2",
                     "Python": "3.13.2"
                 },
+                "SAMTOOLS_FAIDX": {
+                    "samtools": "1.22.1"
+                },
                 "SAMTOOLS_INDEX": {
                     "samtools": "1.22.1"
                 },
                 "SEQFU_STATS": {
                     "seqfu": "1.22.3"
-                },
-                "Workflow": {
-                    "nf-core/seqinspector": "v1.0dev"
                 }
             },
             [
@@ -957,13 +960,16 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2025-12-12T16:50:45.065344275"
+        "timestamp": "2026-02-10T17:17:52.421091867"
     },
     "NovaSeq6000 data test - No rundirs": {
         "content": [
             {
+                "BWAMEM2_INDEX": {
+                    "bwamem2": "2.2.1"
+                },
                 "BWAMEM2_MEM": {
                     "bwamem2": "2.2.1",
                     "samtools": "1.22.1"
@@ -977,14 +983,14 @@
                 "PICARD_COLLECTMULTIPLEMETRICS": {
                     "picard": "3.4.0"
                 },
+                "SAMTOOLS_FAIDX": {
+                    "samtools": "1.22.1"
+                },
                 "SAMTOOLS_INDEX": {
                     "samtools": "1.22.1"
                 },
                 "SEQFU_STATS": {
                     "seqfu": "1.22.3"
-                },
-                "Workflow": {
-                    "nf-core/seqinspector": "v1.0dev"
                 }
             },
             [
@@ -1886,9 +1892,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.10.0"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2026-01-19T16:52:47.847449885"
+        "timestamp": "2026-02-10T17:18:55.46208782"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000_subsample.nf.test b/tests/NovaSeq6000_subsample.nf.test
index 14775ca5..d03cfbfe 100644
--- a/tests/NovaSeq6000_subsample.nf.test
+++ b/tests/NovaSeq6000_subsample.nf.test
@@ -31,7 +31,7 @@ nextflow_pipeline {
             assertAll(
                 { assert snapshot(
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
+                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
                     // All stable path names, with a relative path
                     stable_name,
                     // All files with stable contents
@@ -69,7 +69,7 @@ nextflow_pipeline {
             assertAll(
                 { assert snapshot(
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
+                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
                     // All stable path names, with a relative path
                     stable_name,
                     // All files with stable contents
@@ -106,7 +106,7 @@ nextflow_pipeline {
             assertAll(
                 { assert snapshot(
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
+                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
                     // All stable path names, with a relative path
                     stable_name,
                     // All files with stable contents
diff --git a/tests/NovaSeq6000_subsample.nf.test.snap b/tests/NovaSeq6000_subsample.nf.test.snap
index 98b4c72f..c80ed369 100644
--- a/tests/NovaSeq6000_subsample.nf.test.snap
+++ b/tests/NovaSeq6000_subsample.nf.test.snap
@@ -2,6 +2,9 @@
     "NovaSeq6000 data test sample size": {
         "content": [
             {
+                "BWAMEM2_INDEX": {
+                    "bwamem2": "2.2.1"
+                },
                 "BWAMEM2_MEM": {
                     "bwamem2": "2.2.1",
                     "samtools": "1.22.1"
@@ -19,6 +22,9 @@
                     "PyYAML": "6.0.2",
                     "Python": "3.13.2"
                 },
+                "SAMTOOLS_FAIDX": {
+                    "samtools": "1.22.1"
+                },
                 "SAMTOOLS_INDEX": {
                     "samtools": "1.22.1"
                 },
@@ -27,9 +33,6 @@
                 },
                 "SEQTK_SAMPLE": {
                     "seqtk": "1.4-r122"
-                },
-                "Workflow": {
-                    "nf-core/seqinspector": "v1.0dev"
                 }
             },
             [
@@ -971,13 +974,16 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2025-12-12T16:52:05.081506101"
+        "timestamp": "2026-02-10T17:20:02.068821333"
     },
     "NovaSeq6000 data test relative sample size": {
         "content": [
             {
+                "BWAMEM2_INDEX": {
+                    "bwamem2": "2.2.1"
+                },
                 "BWAMEM2_MEM": {
                     "bwamem2": "2.2.1",
                     "samtools": "1.22.1"
@@ -995,6 +1001,9 @@
                     "PyYAML": "6.0.2",
                     "Python": "3.13.2"
                 },
+                "SAMTOOLS_FAIDX": {
+                    "samtools": "1.22.1"
+                },
                 "SAMTOOLS_INDEX": {
                     "samtools": "1.22.1"
                 },
@@ -1003,9 +1012,6 @@
                 },
                 "SEQTK_SAMPLE": {
                     "seqtk": "1.4-r122"
-                },
-                "Workflow": {
-                    "nf-core/seqinspector": "v1.0dev"
                 }
             },
             [
@@ -1947,13 +1953,16 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2025-12-12T16:53:21.397671601"
+        "timestamp": "2026-02-10T17:21:13.638097598"
     },
     "NovaSeq6000 data test sample size exceeds available reads": {
         "content": [
             {
+                "BWAMEM2_INDEX": {
+                    "bwamem2": "2.2.1"
+                },
                 "BWAMEM2_MEM": {
                     "bwamem2": "2.2.1",
                     "samtools": "1.22.1"
@@ -1971,6 +1980,9 @@
                     "PyYAML": "6.0.2",
                     "Python": "3.13.2"
                 },
+                "SAMTOOLS_FAIDX": {
+                    "samtools": "1.22.1"
+                },
                 "SAMTOOLS_INDEX": {
                     "samtools": "1.22.1"
                 },
@@ -1979,9 +1991,6 @@
                 },
                 "SEQTK_SAMPLE": {
                     "seqtk": "1.4-r122"
-                },
-                "Workflow": {
-                    "nf-core/seqinspector": "v1.0dev"
                 }
             },
             [
@@ -2923,8 +2932,8 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2025-12-12T16:54:35.347526634"
+        "timestamp": "2026-02-10T17:22:24.323697018"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.nf.test b/tests/PromethION.nf.test
index 1af5ef06..32fbd529 100644
--- a/tests/PromethION.nf.test
+++ b/tests/PromethION.nf.test
@@ -34,7 +34,7 @@ nextflow_pipeline {
             assertAll(
                 { assert snapshot(
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
+                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
                     // All stable path names, with a relative path
                     stable_name,
                     // All files with stable contents
diff --git a/tests/PromethION.nf.test.snap b/tests/PromethION.nf.test.snap
index 0d421ffe..1de4b147 100644
--- a/tests/PromethION.nf.test.snap
+++ b/tests/PromethION.nf.test.snap
@@ -8,11 +8,11 @@
                 "FASTQSCREEN_FASTQSCREEN": {
                     "fastqscreen": "0.16.0"
                 },
+                "SAMTOOLS_FAIDX": {
+                    "samtools": "1.22.1"
+                },
                 "SEQFU_STATS": {
                     "seqfu": "1.22.3"
-                },
-                "Workflow": {
-                    "nf-core/seqinspector": "v1.0dev"
                 }
             },
             [
@@ -137,8 +137,8 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2025-12-12T16:55:17.977465362"
+        "timestamp": "2026-02-10T17:23:01.972294667"
     }
 }
\ No newline at end of file
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 40a65c4a..1e2c94b0 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -59,6 +59,8 @@ workflow SEQINSPECTOR {
         params.ref_dict,
     )
 
+    ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions)
+
     //
     // MODULE: Parse rundir info
     //
@@ -73,10 +75,9 @@ workflow SEQINSPECTOR {
             .set { ch_rundir_branched }
 
         // Log warnings for samples without rundir
-        ch_rundir_branched.without_rundir
-            .view { meta, reads ->
-                log.warn "Sample '${meta.id}' does not have a rundir specified"
-            }
+        ch_rundir_branched.without_rundir.view { meta, reads ->
+            log.warn("Sample '${meta.id}' does not have a rundir specified")
+        }
 
         // From samplesheet channel serving (sampleMetaObj, sampleReadsPath) tuples:
         // --> Create new rundir channel serving (rundirMetaObj, rundirPath) tuples
@@ -96,7 +97,7 @@ workflow SEQINSPECTOR {
                 [dir_meta, rundir]
             }
 
-        ch_rundir.ifEmpty { log.warn "No samples with rundir found, skipping RUNDIRPARSER" }
+        ch_rundir.ifEmpty { log.warn("No samples with rundir found, skipping RUNDIRPARSER") }
 
         RUNDIRPARSER(ch_rundir)
 

From 204b44dfb8f6619761316ac18bd25c60be1f88d3 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Wed, 11 Feb 2026 12:32:33 +0100
Subject: [PATCH 524/530] rescure size from the pipeline tests (#171)

---
 CHANGELOG.md                             |  1 +
 tests/MiSeq.nf.test                      |  3 +++
 tests/MiSeq.nf.test.snap                 | 15 +++++++++------
 tests/MiSeq_PairedEnd.nf.test            |  1 +
 tests/MiSeq_PairedEnd.nf.test.snap       |  5 +++--
 tests/NovaSeq6000.nf.test                |  2 ++
 tests/NovaSeq6000.nf.test.snap           | 10 ++++++----
 tests/NovaSeq6000_subsample.nf.test      |  3 +++
 tests/NovaSeq6000_subsample.nf.test.snap | 15 +++++++++------
 tests/PromethION.nf.test                 |  1 +
 tests/PromethION.nf.test.snap            |  5 +++--
 11 files changed, 41 insertions(+), 20 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ddf6ddff..d03126cf 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -53,6 +53,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#163](https://github.com/nf-core/seqinspector/pull/163) Run fastqscreen with subsampled data if available
 - [#167](https://github.com/nf-core/seqinspector/pull/167) RunDirParser is now skipped if no Run Directory information is available
 - [#169](https://github.com/nf-core/seqinspector/pull/169) Rescue missing versions from PREPARE_GENOME subworkflow
+- [#171](https://github.com/nf-core/seqinspector/pull/171) Rescue number of tasks in the pipeline level tests
 
 ### `Changed`
 
diff --git a/tests/MiSeq.nf.test b/tests/MiSeq.nf.test
index dc822aa9..6dbb1cc4 100644
--- a/tests/MiSeq.nf.test
+++ b/tests/MiSeq.nf.test
@@ -32,6 +32,7 @@ nextflow_pipeline {
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
                     // All stable path names, with a relative path
@@ -71,6 +72,7 @@ nextflow_pipeline {
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
                     // All stable path names, with a relative path
@@ -110,6 +112,7 @@ nextflow_pipeline {
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
                     // All stable path names, with a relative path
diff --git a/tests/MiSeq.nf.test.snap b/tests/MiSeq.nf.test.snap
index d6dac529..2e7d47be 100644
--- a/tests/MiSeq.nf.test.snap
+++ b/tests/MiSeq.nf.test.snap
@@ -1,6 +1,7 @@
 {
     "Miseq data test (skip all tools)": {
         "content": [
+            2,
             {
                 "SAMTOOLS_FAIDX": {
                     "samtools": "1.22.1"
@@ -33,12 +34,13 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-02-10T17:15:27.612715634"
+        "timestamp": "2026-02-11T11:04:44.656020406"
     },
     "MiSeq data test (single end reads)": {
         "content": [
+            9,
             {
                 "BWAMEM2_INDEX": {
                     "bwamem2": "2.2.1"
@@ -268,12 +270,13 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-02-10T17:14:12.684188306"
+        "timestamp": "2026-02-11T11:03:07.801122062"
     },
     "Miseq data test (skip fastqc)": {
         "content": [
+            8,
             {
                 "BWAMEM2_INDEX": {
                     "bwamem2": "2.2.1"
@@ -445,8 +448,8 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-02-10T17:14:58.212405529"
+        "timestamp": "2026-02-11T11:04:06.426745227"
     }
 }
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.nf.test b/tests/MiSeq_PairedEnd.nf.test
index bb24f4db..be862326 100644
--- a/tests/MiSeq_PairedEnd.nf.test
+++ b/tests/MiSeq_PairedEnd.nf.test
@@ -32,6 +32,7 @@ nextflow_pipeline {
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
                     // All stable path names, with a relative path
diff --git a/tests/MiSeq_PairedEnd.nf.test.snap b/tests/MiSeq_PairedEnd.nf.test.snap
index 661eaec9..db97a637 100644
--- a/tests/MiSeq_PairedEnd.nf.test.snap
+++ b/tests/MiSeq_PairedEnd.nf.test.snap
@@ -1,6 +1,7 @@
 {
     "MiSeq data test (paired end reads)": {
         "content": [
+            16,
             {
                 "BWAMEM2_INDEX": {
                     "bwamem2": "2.2.1"
@@ -421,8 +422,8 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-02-10T17:16:28.42493386"
+        "timestamp": "2026-02-11T11:06:18.529815388"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.nf.test b/tests/NovaSeq6000.nf.test
index 81641f40..3c207193 100644
--- a/tests/NovaSeq6000.nf.test
+++ b/tests/NovaSeq6000.nf.test
@@ -31,6 +31,7 @@ nextflow_pipeline {
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
                     // All stable path names, with a relative path
@@ -72,6 +73,7 @@ nextflow_pipeline {
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
                     // All stable path names, with a relative path
diff --git a/tests/NovaSeq6000.nf.test.snap b/tests/NovaSeq6000.nf.test.snap
index d39d71a7..980ab608 100644
--- a/tests/NovaSeq6000.nf.test.snap
+++ b/tests/NovaSeq6000.nf.test.snap
@@ -1,6 +1,7 @@
 {
     "NovaSeq6000 data test": {
         "content": [
+            38,
             {
                 "BWAMEM2_INDEX": {
                     "bwamem2": "2.2.1"
@@ -960,12 +961,13 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-02-10T17:17:52.421091867"
+        "timestamp": "2026-02-11T11:08:03.880392879"
     },
     "NovaSeq6000 data test - No rundirs": {
         "content": [
+            37,
             {
                 "BWAMEM2_INDEX": {
                     "bwamem2": "2.2.1"
@@ -1893,8 +1895,8 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-02-10T17:18:55.46208782"
+        "timestamp": "2026-02-11T11:09:20.902763656"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000_subsample.nf.test b/tests/NovaSeq6000_subsample.nf.test
index d03cfbfe..510500d2 100644
--- a/tests/NovaSeq6000_subsample.nf.test
+++ b/tests/NovaSeq6000_subsample.nf.test
@@ -30,6 +30,7 @@ nextflow_pipeline {
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
                     // All stable path names, with a relative path
@@ -68,6 +69,7 @@ nextflow_pipeline {
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
                     // All stable path names, with a relative path
@@ -105,6 +107,7 @@ nextflow_pipeline {
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
                     // All stable path names, with a relative path
diff --git a/tests/NovaSeq6000_subsample.nf.test.snap b/tests/NovaSeq6000_subsample.nf.test.snap
index c80ed369..2c4df709 100644
--- a/tests/NovaSeq6000_subsample.nf.test.snap
+++ b/tests/NovaSeq6000_subsample.nf.test.snap
@@ -1,6 +1,7 @@
 {
     "NovaSeq6000 data test sample size": {
         "content": [
+            43,
             {
                 "BWAMEM2_INDEX": {
                     "bwamem2": "2.2.1"
@@ -974,12 +975,13 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-02-10T17:20:02.068821333"
+        "timestamp": "2026-02-11T11:10:40.164111338"
     },
     "NovaSeq6000 data test relative sample size": {
         "content": [
+            43,
             {
                 "BWAMEM2_INDEX": {
                     "bwamem2": "2.2.1"
@@ -1953,12 +1955,13 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-02-10T17:21:13.638097598"
+        "timestamp": "2026-02-11T11:11:56.554513485"
     },
     "NovaSeq6000 data test sample size exceeds available reads": {
         "content": [
+            43,
             {
                 "BWAMEM2_INDEX": {
                     "bwamem2": "2.2.1"
@@ -2932,8 +2935,8 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-02-10T17:22:24.323697018"
+        "timestamp": "2026-02-11T11:13:08.854683994"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.nf.test b/tests/PromethION.nf.test
index 32fbd529..c2402d43 100644
--- a/tests/PromethION.nf.test
+++ b/tests/PromethION.nf.test
@@ -33,6 +33,7 @@ nextflow_pipeline {
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
                     // All stable path names, with a relative path
diff --git a/tests/PromethION.nf.test.snap b/tests/PromethION.nf.test.snap
index 1de4b147..71ce8690 100644
--- a/tests/PromethION.nf.test.snap
+++ b/tests/PromethION.nf.test.snap
@@ -1,6 +1,7 @@
 {
     "PromethION data test": {
         "content": [
+            5,
             {
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -137,8 +138,8 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-02-10T17:23:01.972294667"
+        "timestamp": "2026-02-11T11:13:50.566732998"
     }
 }
\ No newline at end of file

From 2a59538a55a061d61efe342be944939b78e7912a Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Wed, 11 Feb 2026 17:21:28 +0100
Subject: [PATCH 525/530] fix conda env for rundirparser (#172)

---
 CHANGELOG.md                               | 1 +
 modules/local/rundirparser/environment.yml | 4 +++-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d03126cf..b6015912 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -54,6 +54,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#167](https://github.com/nf-core/seqinspector/pull/167) RunDirParser is now skipped if no Run Directory information is available
 - [#169](https://github.com/nf-core/seqinspector/pull/169) Rescue missing versions from PREPARE_GENOME subworkflow
 - [#171](https://github.com/nf-core/seqinspector/pull/171) Rescue number of tasks in the pipeline level tests
+- [#172](https://github.com/nf-core/seqinspector/pull/172) More complete conda environment for rundir parser
 
 ### `Changed`
 
diff --git a/modules/local/rundirparser/environment.yml b/modules/local/rundirparser/environment.yml
index 046f88d8..82d343f1 100644
--- a/modules/local/rundirparser/environment.yml
+++ b/modules/local/rundirparser/environment.yml
@@ -2,6 +2,8 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - pip
+  - conda-forge::python=3.13.2
+  - pip=25.3
   - pip:
       - PyYAML==6.0.2
+      - xmltodict==1.0.2

From abe112d9befbb3514543443a0e874281476fd1db Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Mon, 16 Feb 2026 10:03:49 +0100
Subject: [PATCH 526/530] addess review comments (#173)

* addess review comments

* Update usage.md

* Apply suggestion from @maxulysse

* fix warning message about tag collision

* CHANGELOG

* Apply suggestion from @maxulysse

* update contributor
---
 CHANGELOG.md                                  |  2 +
 README.md                                     |  9 ++-
 docs/usage.md                                 | 39 ++++++++-----
 nextflow.config                               |  4 +-
 ro-crate-metadata.json                        | 58 +++++++++----------
 .../main.nf                                   |  4 +-
 6 files changed, 69 insertions(+), 47 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b6015912..f7c7ad46 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -55,6 +55,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#169](https://github.com/nf-core/seqinspector/pull/169) Rescue missing versions from PREPARE_GENOME subworkflow
 - [#171](https://github.com/nf-core/seqinspector/pull/171) Rescue number of tasks in the pipeline level tests
 - [#172](https://github.com/nf-core/seqinspector/pull/172) More complete conda environment for rundir parser
+- [#173](https://github.com/nf-core/seqinspector/pull/173) Fix warning message for tag name collision
 
 ### `Changed`
 
@@ -72,6 +73,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#164](https://github.com/nf-core/seqinspector/pull/164) Refactor local subworkflow and pipeline tests
 - [#168](https://github.com/nf-core/seqinspector/pull/168) Adhere to strict syntax
 - [#169](https://github.com/nf-core/seqinspector/pull/169) Prepare release 1.0.0
+- [#173](https://github.com/nf-core/seqinspector/pull/173) Improve documentation
 
 ### `Dependencies`
 
diff --git a/README.md b/README.md
index a249295e..7ea39662 100644
--- a/README.md
+++ b/README.md
@@ -26,6 +26,8 @@ It can perform subsampling, quality assessment, duplication level analysis, and
 The pipeline generates detailed MultiQC reports with flexible output options, ranging from individual sample reports to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments.
 If provided, nf-core/seqinspector can also parse statistics from an Illumina run folder directory into the final MultiQC reports.
 
+### Compatibility between tools and data type
+
 <!-- TODO: add a search tool that accepts a tree for `Compatibility with Data`. -->
 
 | Tool Type           | Tool Name                                                                                                           | Tool Description                                                                              | Compatibility with Data | Dependencies                                                                                                              | Default tool |
@@ -40,6 +42,8 @@ If provided, nf-core/seqinspector can also parse statistics from an Illumina run
 | `QC`                | [`Picard_collecthsmetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard) | Collect alignment QC metrics of hybrid-selection data.                                        | [RNA, DNA]              | [Bwamem2, SAMtools, `--fasta`, `--run_picard_collecths_metrics`, `--bait_intervals`, `--target_intervals` (`--ref_dict`)] | no           |
 | `Reporting`         | [`MultiQC`](http://multiqc.info/)                                                                                   | Present QC for raw reads                                                                      | [RNA, DNA, synthetic]   | [N/A]                                                                                                                     | yes          |
 
+### Workflow diagram
+
 <picture>
   <source media="(prefers-color-scheme: dark)" srcset="docs/images/seqinspector_tubemap_V1.0_dark.png">
   <source media="(prefers-color-scheme: light)" srcset="docs/images/seqinspector_tubemap_V1.0.png">
@@ -86,7 +90,9 @@ For more details about the output files and reports, please refer to the
 
 ## Credits
 
-nf-core/seqinspector was originally written by [@agrima2010](https://github.com/agrima2010), [@Aratz](https://github.com/Aratz), [@FranBonath](https://github.com/FranBonath), [@kedhammar](https://github.com/kedhammar), and [@MatthiasZepper](https://github.com/MatthiasZepper) from the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/) and [Clinical Genomics Stockholm](https://clinical.scilifelab.se/).
+nf-core/seqinspector was originally written by [@agrima2010](https://github.com/agrima2010), [@Aratz](https://github.com/Aratz), [@FranBonath](https://github.com/FranBonath), [@kedhammar](https://github.com/kedhammar), and [@MatthiasZepper](https://github.com/MatthiasZepper) from the Swedish [National Genomics Infrastructure](https://github.com/NationalGenomicsInfrastructure/) and [Clinical Genomics Stockholm](https://clinical.scilifelab.se/).
+
+Maintenance is now lead by Maxime U Garcia ([National Genomics Infrastructure](https://github.com/NationalGenomicsInfrastructure/))
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 
@@ -100,7 +106,6 @@ We thank the following people for their extensive assistance in the development
 - [@kjellinjonas](https://github.com/kjellinjonas)
 - [@mahesh-panchal](https://github.com/mahesh-panchal)
 - [@matrulda](https://github.com/matrulda)
-- [@maxulysse](https://github.com/maxulysse)
 - [@mirpedrol](https://github.com/mirpedrol)
 - [@nggvs](https://github.com/nggvs)
 - [@nkongenelly](https://github.com/nkongenelly)
diff --git a/docs/usage.md b/docs/usage.md
index e7ddeb0c..a58ba6af 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -6,13 +6,18 @@
 
 ### General points
 
-The nf-core/seqinspector pipeline is a general QC pipeline for sequencing data. The current version only supports data in fastq format.
-The pipeline is meant to include a large amount of possible QC tools to chose from, but not all of them may be relevant to your data. As such we highly recommend to familiarize yourself with the different QC tools available and to remove any QC tool you would like to exclude with the `--skip-tools` command line parameter. For repeated use we suggest to create a params file containing the `--skip-tools` parameters (for details see the "Running the pipeline" section).
-Be aware that some tools are skipped by default and will need to be included in the list of skipped tools when curating your own list. To identify defaults included or excluded please check out the overview table in the Introduction.
+The nf-core/seqinspector pipeline is a general QC pipeline for sequencing data.
+The current version only supports data in fastq format.
+The pipeline is meant to include a large amount of possible QC tools to chose from, but not all of them may be relevant to your data.
+As such we highly recommend to familiarize yourself with the different QC tools available and to remove any QC tool you would like to exclude with the `--skip-tools` command line parameter.
+For repeated use we suggest to create a params file containing the `--skip-tools` parameters (for details see the "Running the pipeline" section).
+Be aware that some tools are skipped by default and will need to be included in the list of skipped tools when curating your own list.
+To identify defaults included or excluded please check out [the overview compatibility between tools and data type table](../#compatibility-between-tools-and-data-type).
 
 ### What nf-core/seqinspector is not for
 
-The results of the nf-core/seqinspector pipeline are not meant to be used for any downstream analysis, but are exclusively for QC purposes. Even tools that may be used in other pipelines as a starting point for analysis are run in a QC perspective, most likely with a downsampled input.
+The results of the nf-core/seqinspector pipeline are not meant to be used for any downstream analysis, but are exclusively for QC purposes.
+Even tools that may be used in other pipelines as a starting point for analysis are run in a QC perspective, most likely with a downsampled input.
 
 ## Samplesheet input
 
@@ -26,7 +31,7 @@ You will need to create a samplesheet with information about the samples/fastq f
 
 The following simple run dir structure...
 
-```
+```bash
 run_dir
 ├── sample1_lane1_group1_r1.fq.gz
 ├── sample2_lane1_group1_r1.fq.gz
@@ -42,7 +47,6 @@ sample1 path/to/run_dir/sample1_lane1_group1_r1.fq.gz         path/to/run_dir pr
 sample2 path/to/run_dir/sample2_lane1_group1_r1.fq.gz         path/to/run_dir project1:group1
 sample3 path/to/run_dir/sample3_lane2_group2_r1.fq.gz         path/to/run_dir project1:group2
 sample4 path/to/run_dir/sample4_lane2_group3_r1.fq.gz         path/to/run_dir control
-
 ```
 
 | Column    | Description                                                                                                                                                                            |
@@ -100,17 +104,28 @@ genome: 'GRCh37'
 
 You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch).
 
-Optionally, the `sample_size` parameter allows you to subset a random number of reads to be analysed. Both absolute numbers (e.g 100) and relative numbers (e.g 0.25) can be specified.
+### Sample size selection
+
+Optionally, the `sample_size` parameter allows you to subset a random number of reads to be analysed.
+Both absolute numbers (e.g 100) and relative numbers (e.g 0.25) can be specified.
 
 ```bash
 nextflow run nf-core/seqinspector --input ./samplesheet.csv --outdir ./results --sample_size 1000000 -profile docker
 ```
 
+### Hybrid-selection QC metrics
+
+The pipeline supports hybrid-selection (HS) QC metrics collection .
+Use `--run_picard_collecthsmetrics true` to run the QC tool [picard CollectHSmetrics](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard).
+This tool is otherwise not run by default.
+
 ### Skipping tools
 
-Some tools might not be compatible with your data. In this case you can skip them by providing a comma-separated list of tools to be skipped with the `--skip_tools` parameter.
+Some tools might not be compatible with your data.
+In this case you can skip them by providing a comma-separated list of tools to be skipped with the `--skip_tools` parameter.
 
-In case you want to make this more permanent, it is recommended to specify this in a params file, or even in your own nextflow configuration file. The nextflow configuration file can also be use to customise tool arguments. See official [nexflow](https://www.nextflow.io/docs/latest/config.html) and [nf-core](https://nf-co.re/docs/usage/configuration#customising-tool-arguments) documentation for further details.
+The nextflow configuration file can also be use to customise tool arguments.
+See official [nexflow](https://www.nextflow.io/docs/latest/config.html) and [nf-core](https://nf-co.re/docs/usage/configuration#customising-tool-arguments) documentation for further details.
 
 ### Updating the pipeline
 
@@ -170,7 +185,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
 - `apptainer`
   - A generic configuration profile to be used with [Apptainer](https://apptainer.org/)
 - `wave`
-  - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later).
+  - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow `24.03.0-edge` or later).
 - `conda`
   - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer.
 
@@ -229,7 +244,3 @@ We recommend adding the following line to your environment to limit this (typica
 ```bash
 NXF_OPTS='-Xms1g -Xmx4g'
 ```
-
-## Hybrid-selection QC metrics
-
-The pipeline supports hybrid-selection (HS) QC metrics collection . Use `--run_picard_collecthsmetrics true` to run the QC tool [picard CollectHSmetrics](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard). This tool is otherwise not run by default.
diff --git a/nextflow.config b/nextflow.config
index 3df58bb6..4f3dd01a 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -256,6 +256,7 @@ manifest {
             affiliation: 'Pixelgen Technologies',
             github: 'Aratz',
             contribution: ['author'],
+            orcid: '0000-0003-2702-1103'
         ],
         [
             name: 'Alfred Kedhammar',
@@ -274,7 +275,7 @@ manifest {
             name: 'Maxime U Garcia',
             affiliation: 'National Genomics Infrastructure',
             github: 'maxulysse',
-            contribution: ['maintainer'],
+            contribution: ['contributor', 'maintainer'],
             orcid: '0000-0003-2827-9261',
         ],
         [
@@ -307,6 +308,7 @@ manifest {
             affiliation: 'National Bioinformatics Infrastructure Sweden',
             github: 'mahesh-panchal',
             contribution: ['contributor'],
+            orcid: '0000-0003-1675-0677'
         ],
         [
             name: 'Ramprasad Neethiraj',
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 242fa244..6c0c4e85 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,8 +22,8 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "Stable",
-            "datePublished": "2026-02-10T15:24:32+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that processes raw sequence data (FASTQ) to provide comprehensive quality control.\nIt can perform subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants.\nThe pipeline generates detailed MultiQC reports with flexible output options, ranging from individual sample reports to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments.\nIf provided, nf-core/seqinspector can also parse statistics from an Illumina run folder directory into the final MultiQC reports.\n\n<!-- TODO: add a search tool that accepts a tree for `Compatibility with Data`. -->\n\n| Tool Type           | Tool Name                                                                                                           | Tool Description                                                                              | Compatibility with Data | Dependencies                                                                                                              | Default tool |\n| ------------------- | ------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------- | ----------------------- | ------------------------------------------------------------------------------------------------------------------------- | ------------ |\n| `Subsampling`       | [`Seqtk`](https://github.com/lh3/seqtk)                                                                             | Global subsampling of reads. Only performs subsampling if `--sample_size` parameter is given. | [RNA, DNA, synthetic]   | [N/A]                                                                                                                     | no           |\n| `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2)                                                                   | Align reads to reference                                                                      | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `Indexing`          | [`SAMtools`](http://github.com/samtools)                                                                            | Index aligned BAM files, create FASTA index                                                   | [DNA]                   | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)                                              | Read QC                                                                                       | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)                                   | Basic contamination detection                                                                 | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`SeqFu Stats`](https://github.com/telatin/seqfu2)                                                                  | Sequence statistics                                                                           | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`Picard collect multiple metrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html)         | Collect multiple QC metrics                                                                   | [RNA, DNA]              | [Bwamem2, SAMtools, `--genome`]                                                                                           | yes          |\n| `QC`                | [`Picard_collecthsmetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard) | Collect alignment QC metrics of hybrid-selection data.                                        | [RNA, DNA]              | [Bwamem2, SAMtools, `--fasta`, `--run_picard_collecths_metrics`, `--bait_intervals`, `--target_intervals` (`--ref_dict`)] | no           |\n| `Reporting`         | [`MultiQC`](http://multiqc.info/)                                                                                   | Present QC for raw reads                                                                      | [RNA, DNA, synthetic]   | [N/A]                                                                                                                     | yes          |\n\n<picture>\n  <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/seqinspector_tubemap_V1.0_dark.png\">\n  <source media=\"(prefers-color-scheme: light)\" srcset=\"docs/images/seqinspector_tubemap_V1.0.png\">\n  <img alt=\"Fallback image description\" src=\"docs/images/seqinspector_tubemap_V1.0.png\">\n</picture>\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end with only `fastq_1`) or a pair of fastq files (paired end with `fastq_1` and `fastq_2`).\n`rundir` is the path to the runfolder.\n`tags` is a colon-separated list of tags that will be added to the MultiQC report for this `sample`.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by [@agrima2010](https://github.com/agrima2010), [@Aratz](https://github.com/Aratz), [@FranBonath](https://github.com/FranBonath), [@kedhammar](https://github.com/kedhammar), and [@MatthiasZepper](https://github.com/MatthiasZepper) from the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/) and [Clinical Genomics Stockholm](https://clinical.scilifelab.se/).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@adamrtalbot](https://github.com/adamrtalbot)\n- [@alneberg](https://github.com/alneberg)\n- [@beatrizsavinhas](https://github.com/beatrizsavinhas)\n- [@ctuni](https://github.com/ctuni)\n- [@edmundmiller](https://github.com/edmundmiller)\n- [@EliottBo](https://github.com/EliottBo)\n- [@KarNair](https://github.com/KarNair)\n- [@kjellinjonas](https://github.com/kjellinjonas)\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n- [@matrulda](https://github.com/matrulda)\n- [@maxulysse](https://github.com/maxulysse)\n- [@mirpedrol](https://github.com/mirpedrol)\n- [@nggvs](https://github.com/nggvs)\n- [@nkongenelly](https://github.com/nkongenelly)\n- [@Patricie34](https://github.com/Patricie34)\n- [@pontushojer](https://github.com/pontushojer)\n- [@ramprasadn](https://github.com/ramprasadn)\n- [@rannick](https://github.com/rannick)\n- [@torigiffin](https://github.com/torigiffin)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "datePublished": "2026-02-16T08:55:13+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that processes raw sequence data (FASTQ) to provide comprehensive quality control.\nIt can perform subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants.\nThe pipeline generates detailed MultiQC reports with flexible output options, ranging from individual sample reports to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments.\nIf provided, nf-core/seqinspector can also parse statistics from an Illumina run folder directory into the final MultiQC reports.\n\n### Compatibility between tools and data type\n\n<!-- TODO: add a search tool that accepts a tree for `Compatibility with Data`. -->\n\n| Tool Type           | Tool Name                                                                                                           | Tool Description                                                                              | Compatibility with Data | Dependencies                                                                                                              | Default tool |\n| ------------------- | ------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------- | ----------------------- | ------------------------------------------------------------------------------------------------------------------------- | ------------ |\n| `Subsampling`       | [`Seqtk`](https://github.com/lh3/seqtk)                                                                             | Global subsampling of reads. Only performs subsampling if `--sample_size` parameter is given. | [RNA, DNA, synthetic]   | [N/A]                                                                                                                     | no           |\n| `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2)                                                                   | Align reads to reference                                                                      | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `Indexing`          | [`SAMtools`](http://github.com/samtools)                                                                            | Index aligned BAM files, create FASTA index                                                   | [DNA]                   | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)                                              | Read QC                                                                                       | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)                                   | Basic contamination detection                                                                 | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`SeqFu Stats`](https://github.com/telatin/seqfu2)                                                                  | Sequence statistics                                                                           | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`Picard collect multiple metrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html)         | Collect multiple QC metrics                                                                   | [RNA, DNA]              | [Bwamem2, SAMtools, `--genome`]                                                                                           | yes          |\n| `QC`                | [`Picard_collecthsmetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard) | Collect alignment QC metrics of hybrid-selection data.                                        | [RNA, DNA]              | [Bwamem2, SAMtools, `--fasta`, `--run_picard_collecths_metrics`, `--bait_intervals`, `--target_intervals` (`--ref_dict`)] | no           |\n| `Reporting`         | [`MultiQC`](http://multiqc.info/)                                                                                   | Present QC for raw reads                                                                      | [RNA, DNA, synthetic]   | [N/A]                                                                                                                     | yes          |\n\n### Workflow diagram\n\n<picture>\n  <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/seqinspector_tubemap_V1.0_dark.png\">\n  <source media=\"(prefers-color-scheme: light)\" srcset=\"docs/images/seqinspector_tubemap_V1.0.png\">\n  <img alt=\"Fallback image description\" src=\"docs/images/seqinspector_tubemap_V1.0.png\">\n</picture>\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end with only `fastq_1`) or a pair of fastq files (paired end with `fastq_1` and `fastq_2`).\n`rundir` is the path to the runfolder.\n`tags` is a colon-separated list of tags that will be added to the MultiQC report for this `sample`.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by [@agrima2010](https://github.com/agrima2010), [@Aratz](https://github.com/Aratz), [@FranBonath](https://github.com/FranBonath), [@kedhammar](https://github.com/kedhammar), and [@MatthiasZepper](https://github.com/MatthiasZepper) from the Swedish [National Genomics Infrastructure](https://github.com/NationalGenomicsInfrastructure/) and [Clinical Genomics Stockholm](https://clinical.scilifelab.se/).\n\nMaintenance is now lead by Maxime U Garcia ([National Genomics Infrastructure](https://github.com/NationalGenomicsInfrastructure/))\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@adamrtalbot](https://github.com/adamrtalbot)\n- [@alneberg](https://github.com/alneberg)\n- [@beatrizsavinhas](https://github.com/beatrizsavinhas)\n- [@ctuni](https://github.com/ctuni)\n- [@edmundmiller](https://github.com/edmundmiller)\n- [@EliottBo](https://github.com/EliottBo)\n- [@KarNair](https://github.com/KarNair)\n- [@kjellinjonas](https://github.com/kjellinjonas)\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n- [@matrulda](https://github.com/matrulda)\n- [@mirpedrol](https://github.com/mirpedrol)\n- [@nggvs](https://github.com/nggvs)\n- [@nkongenelly](https://github.com/nkongenelly)\n- [@Patricie34](https://github.com/Patricie34)\n- [@pontushojer](https://github.com/pontushojer)\n- [@ramprasadn](https://github.com/ramprasadn)\n- [@rannick](https://github.com/rannick)\n- [@torigiffin](https://github.com/torigiffin)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
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@@ -102,7 +102,7 @@
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@@ -143,11 +140,14 @@
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-                    "@id": "#max.u.garcia@gmail.com"
+                    "@id": "https://orcid.org/0000-0003-1675-0677"
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-            "dateModified": "2026-02-10T16:24:32Z",
+            "dateModified": "2026-02-16T09:55:13Z",
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+                    "@id": "#max.u.garcia@gmail.com"
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@@ -172,7 +169,10 @@
                     "@id": "#89784800+kedhammar@users.noreply.github.com"
                 },
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-                    "@id": "#max.u.garcia@gmail.com"
+                    "@id": "https://orcid.org/0000-0003-1675-0677"
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@@ -205,11 +205,11 @@
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         {
-            "@id": "#eb65e4a1-3330-4f79-98cb-e1b2a7f86b81",
+            "@id": "#08014bc0-7c74-49f0-a201-fcc18504ce2b",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#58467589-6ef2-4f18-8ebc-b5ecd9967ecd"
+                    "@id": "#c3eeced1-9e95-4a6c-932f-c4ceae1158d2"
                 }
             ],
             "mainEntity": {
@@ -218,7 +218,7 @@
             "name": "Test suite for nf-core/seqinspector"
         },
         {
-            "@id": "#58467589-6ef2-4f18-8ebc-b5ecd9967ecd",
+            "@id": "#c3eeced1-9e95-4a6c-932f-c4ceae1158d2",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/seqinspector",
             "resource": "repos/nf-core/seqinspector/actions/workflows/nf-test.yml",
@@ -352,16 +352,10 @@
             "url": "https://nf-co.re/"
         },
         {
-            "@id": "https://orcid.org/0009-0004-5536-7210",
-            "@type": "Person",
-            "email": "163723002+agrima2010@users.noreply.github.com",
-            "name": "Agrima Bhatt"
-        },
-        {
-            "@id": "https://orcid.org/0000-0003-1675-0677",
+            "@id": "#max.u.garcia@gmail.com",
             "@type": "Person",
-            "email": "mahesh.binzer-panchal@nbis.se",
-            "name": "Mahesh Binzer-Panchal"
+            "email": "max.u.garcia@gmail.com",
+            "name": "Maxime U Garcia"
         },
         {
             "@id": "https://orcid.org/0000-0003-2702-1103",
@@ -376,10 +370,16 @@
             "name": "Alfred Kedhammar"
         },
         {
-            "@id": "#max.u.garcia@gmail.com",
+            "@id": "https://orcid.org/0000-0003-1675-0677",
             "@type": "Person",
-            "email": "max.u.garcia@gmail.com",
-            "name": "Maxime U Garcia"
+            "email": "mahesh.binzer-panchal@nbis.se",
+            "name": "Mahesh Binzer-Panchal"
+        },
+        {
+            "@id": "https://orcid.org/0009-0004-5536-7210",
+            "@type": "Person",
+            "email": "163723002+agrima2010@users.noreply.github.com",
+            "name": "Agrima Bhatt"
         }
     ]
 }
\ No newline at end of file
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index 37ec91ee..14748673 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -143,7 +143,9 @@ workflow PIPELINE_INITIALISATION {
         .map { tag_name -> [tag_name.toLowerCase(), tag_name] }
         .groupTuple()
         .map { _tag_lowercase, tags ->
-            assert tags.size() == 1 : "Tag name collision: " + tags.join(", ")
+            if (tags.size() == 1) {
+                log.warn("Tag name collision: " + tags)
+            }
         }
 
     emit:

From 25269d27127fa092086827ce25ff7871f93daa50 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Thu, 19 Feb 2026 11:01:47 +0100
Subject: [PATCH 527/530] Minor code polish (#174)

* code polish

* code polish

* Set NFT_WORKDIR dynamically

* simplify logic

* no params in workflows

* code polish

* code polish + view -> subscribe

* CHANGELOG
---
 .github/workflows/nf-test.yml                 |   11 +-
 CHANGELOG.md                                  |    6 +
 README.md                                     |    2 +-
 main.nf                                       |   51 +-
 modules.json                                  |    3 +-
 modules/local/rundirparser/main.nf            |    1 +
 .../fastqscreen-buildfromindex.diff           |   86 +
 .../fastqscreen/buildfromindex/main.nf        |   36 +-
 nextflow.config                               |    5 +-
 nf-test.config                                |    2 +-
 tests/MiSeq.nf.test                           |  159 +-
 tests/MiSeq.nf.test.snap                      |  455 ++-
 tests/MiSeq_PairedEnd.nf.test                 |   48 -
 tests/MiSeq_PairedEnd.nf.test.snap            |  429 ---
 tests/NovaSeq6000.nf.test                     |  120 +-
 tests/NovaSeq6000.nf.test.snap                | 3081 ++++++++++++++++-
 tests/NovaSeq6000_subsample.nf.test           |  123 -
 tests/NovaSeq6000_subsample.nf.test.snap      | 2942 ----------------
 tests/PromethION.nf.test                      |   58 +-
 tests/PromethION.nf.test.snap                 |    9 +-
 tests/lib/UTILS.groovy                        |  156 +
 workflows/seqinspector.nf                     |  199 +-
 22 files changed, 3983 insertions(+), 3999 deletions(-)
 create mode 100644 modules/nf-core/fastqscreen/buildfromindex/fastqscreen-buildfromindex.diff
 delete mode 100644 tests/MiSeq_PairedEnd.nf.test
 delete mode 100644 tests/MiSeq_PairedEnd.nf.test.snap
 delete mode 100644 tests/NovaSeq6000_subsample.nf.test
 delete mode 100644 tests/NovaSeq6000_subsample.nf.test.snap
 create mode 100644 tests/lib/UTILS.groovy

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index c98d76ec..a5e6e302 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -9,7 +9,7 @@ on:
       - "**/*.svg"
   release:
     types: [published]
-  workflow_dispatch:
+  workflow_dispatch: null
 
 # Cancel if a newer run is started
 concurrency:
@@ -19,7 +19,7 @@ concurrency:
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
   NFT_VER: "0.9.3"
-  NFT_WORKDIR: "~"
+  # NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
@@ -78,8 +78,8 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "25.04.0"
-          - "latest-everything"
+          - 25.10.4
+          - latest-everything
     env:
       NXF_ANSI_LOG: false
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
@@ -89,6 +89,9 @@ jobs:
         with:
           fetch-depth: 0
 
+      - name: Set NFT_WORKDIR dynamically
+        run: echo "NFT_WORKDIR=$HOME" >> $GITHUB_ENV
+
       - name: Run nf-test
         id: run_nf_test
         uses: ./.github/actions/nf-test
diff --git a/CHANGELOG.md b/CHANGELOG.md
index f7c7ad46..91065c5f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -38,6 +38,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#162](https://github.com/nf-core/seqinspector/pull/162) Add tests for prepare_genome subworkflow
 - [#168](https://github.com/nf-core/seqinspector/pull/168) Add contributors list
 - [#168](https://github.com/nf-core/seqinspector/pull/168) Add logo to the pipeline logo
+- [#174](https://github.com/nf-core/seqinspector/pull/174) Add nf-core-utils 0.4.0
 
 ### `Fixed`
 
@@ -56,6 +57,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#171](https://github.com/nf-core/seqinspector/pull/171) Rescue number of tasks in the pipeline level tests
 - [#172](https://github.com/nf-core/seqinspector/pull/172) More complete conda environment for rundir parser
 - [#173](https://github.com/nf-core/seqinspector/pull/173) Fix warning message for tag name collision
+- [#174](https://github.com/nf-core/seqinspector/pull/174) Fix null message when no rundir information is available
 
 ### `Changed`
 
@@ -74,9 +76,13 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#168](https://github.com/nf-core/seqinspector/pull/168) Adhere to strict syntax
 - [#169](https://github.com/nf-core/seqinspector/pull/169) Prepare release 1.0.0
 - [#173](https://github.com/nf-core/seqinspector/pull/173) Improve documentation
+- [#174](https://github.com/nf-core/seqinspector/pull/174) Refactor tests
+- [#174](https://github.com/nf-core/seqinspector/pull/174) More strict syntax
+- [#174](https://github.com/nf-core/seqinspector/pull/174) No params included in workflows
 
 ### `Dependencies`
 
 - [#116](https://github.com/nf-core/seqinspector/pull/116) Update MultiQC to 1.28
+- [#174](https://github.com/nf-core/seqinspector/pull/174) Update nf-schema to 2.6.1
 
 ### `Deprecated`
diff --git a/README.md b/README.md
index 7ea39662..6add6b59 100644
--- a/README.md
+++ b/README.md
@@ -10,7 +10,7 @@
 [![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
 [![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
diff --git a/main.nf b/main.nf
index f2b8507f..595494a2 100644
--- a/main.nf
+++ b/main.nf
@@ -10,22 +10,22 @@
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    GENOME PARAMETER VALUES
+    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-params.fasta = getGenomeAttribute('fasta')
-
+include { SEQINSPECTOR            } from './workflows/seqinspector'
+include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
+include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
+include { getGenomeAttribute      } from 'plugin/nf-core-utils'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
+    GENOME PARAMETER VALUES
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { SEQINSPECTOR            } from './workflows/seqinspector'
-include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
-include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
+params.fasta = getGenomeAttribute('fasta')
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -45,13 +45,22 @@ workflow NFCORE_SEQINSPECTOR {
     //
     // WORKFLOW: Run pipeline
     //
-    skip_tools = params.skip_tools ? params.skip_tools.split(',') : []
-
     SEQINSPECTOR(
         samplesheet,
-        params.fasta,
-        skip_tools,
+        params.bait_intervals,
         params.bwamem2,
+        params.fasta ? channel.fromPath(params.fasta, checkIfExists: true).map { file -> tuple([id: file.name], file) }.collect() : channel.value([[:], []]),
+        params.fastq_screen_references,
+        params.multiqc_config,
+        params.multiqc_logo,
+        params.multiqc_methods_description,
+        params.outdir,
+        params.ref_dict,
+        params.run_picard_collecthsmetrics,
+        params.sample_size,
+        params.skip_tools ? params.skip_tools.split(',') : ['no_skip_tools'],
+        params.sort_bam,
+        params.target_intervals,
     )
 
     emit:
@@ -66,7 +75,6 @@ workflow NFCORE_SEQINSPECTOR {
 
 workflow {
 
-
     //
     // SUBWORKFLOW: Run initialisation tasks
     //
@@ -102,22 +110,3 @@ workflow {
         NFCORE_SEQINSPECTOR.out.global_report,
     )
 }
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    FUNCTIONS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-//
-// Get attribute from genome config file e.g. fasta
-//
-
-def getGenomeAttribute(attribute) {
-    if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
-        if (params.genomes[params.genome].containsKey(attribute)) {
-            return params.genomes[params.genome][attribute]
-        }
-    }
-    return null
-}
diff --git a/modules.json b/modules.json
index 3476ca7d..e8a3d49f 100644
--- a/modules.json
+++ b/modules.json
@@ -29,7 +29,8 @@
                     "fastqscreen/buildfromindex": {
                         "branch": "master",
                         "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/fastqscreen/buildfromindex/fastqscreen-buildfromindex.diff"
                     },
                     "fastqscreen/fastqscreen": {
                         "branch": "master",
diff --git a/modules/local/rundirparser/main.nf b/modules/local/rundirparser/main.nf
index dd02b58c..3864b3ec 100644
--- a/modules/local/rundirparser/main.nf
+++ b/modules/local/rundirparser/main.nf
@@ -44,6 +44,7 @@ process RUNDIRPARSER {
     fi
 
     # TODO: check what kind of seq platfrom to decide which script to use
+    # or replace with a smarter solution, like the MultiQC_SAV plugin
     parse_illumina.py ${input_dir}
     """
 
diff --git a/modules/nf-core/fastqscreen/buildfromindex/fastqscreen-buildfromindex.diff b/modules/nf-core/fastqscreen/buildfromindex/fastqscreen-buildfromindex.diff
new file mode 100644
index 00000000..9333012d
--- /dev/null
+++ b/modules/nf-core/fastqscreen/buildfromindex/fastqscreen-buildfromindex.diff
@@ -0,0 +1,86 @@
+Changes in component 'nf-core/fastqscreen/buildfromindex'
+'modules/nf-core/fastqscreen/buildfromindex/meta.yml' is unchanged
+'modules/nf-core/fastqscreen/buildfromindex/environment.yml' is unchanged
+Changes in 'fastqscreen/buildfromindex/main.nf':
+--- modules/nf-core/fastqscreen/buildfromindex/main.nf
++++ modules/nf-core/fastqscreen/buildfromindex/main.nf
+@@ -2,39 +2,39 @@
+     label 'process_single'
+ 
+     conda "${moduleDir}/environment.yml"
+-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+-        'https://depot.galaxyproject.org/singularity/fastq-screen:0.15.3--pl5321hdfd78af_0':
+-        'biocontainers/fastq-screen:0.15.3--pl5321hdfd78af_0'}"
++    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
++        ? 'https://depot.galaxyproject.org/singularity/fastq-screen:0.15.3--pl5321hdfd78af_0'
++        : 'biocontainers/fastq-screen:0.15.3--pl5321hdfd78af_0'}"
+ 
+     input:
+-    val(genome_names)
+-    path(indexes), stageAs: "dir*"
++    val genome_names
++    path (indexes), stageAs: "dir*"
+ 
+     output:
+-    path("FastQ_Screen_Genomes"), emit: database
+-    path "versions.yml"         , emit: versions
++    path ("FastQ_Screen_Genomes"), emit: database
++    path "versions.yml", emit: versions
+ 
+     when:
+     task.ext.when == null || task.ext.when
+ 
+     script:
+     dir = "FastQ_Screen_Genomes"
+-    folder = indexes.collect { it.toString() }
++    folder = indexes.collect { index -> index.toString() }
+     database = [genome_names, folder].transpose()
+-    copy_indexes = folder.collect { "cp -r ${it} $dir/${it}"}.join(" && ")
++    copy_indexes = folder.collect { file -> "cp -r ${file} ${dir}/${file}" }.join(" && ")
+ 
+     // Folder name and index (within folder) name could be different - use bash to look for index name
+     config = database
+-        .collect { "########## ${it[0]} \nDATABASE ${it[0]} $dir/${it[1]}/${it[1] + '_to_be_replaced'}" }
++        .collect { file -> "########## ${file[0]} \nDATABASE ${file[0]} ${dir}/${file[1]}/${file[1] + '_to_be_replaced'}" }
+         .join("\n\n")
+         .replace("\n", "\\n")
+ 
+     """
+-    mkdir $dir
+-    $copy_indexes
++    mkdir ${dir}
++    ${copy_indexes}
+ 
+-    echo "$config" > fastq_screen.conf
+-    sed 's/\\\\n/\\n/g' fastq_screen.conf > $dir/fastq_screen.conf
++    echo "${config}" > fastq_screen.conf
++    sed 's/\\\\n/\\n/g' fastq_screen.conf > ${dir}/fastq_screen.conf
+     echo "Replace folder name real index name"
+ 
+     for f in ${folder.join(' ')}
+@@ -45,8 +45,8 @@
+         REPLACE_WITH=\$(basename \$REPLACE_WITH)
+         REPLACE_WITH=\${REPLACE_WITH%%.rev.1.bt2}
+ 
+-        sed "s/\$TO_REPLACE/\$REPLACE_WITH/g" $dir/fastq_screen.conf > new_conf.conf
+-        mv new_conf.conf $dir/fastq_screen.conf
++        sed "s/\$TO_REPLACE/\$REPLACE_WITH/g" ${dir}/fastq_screen.conf > new_conf.conf
++        mv new_conf.conf ${dir}/fastq_screen.conf
+     done
+ 
+     cat <<-END_VERSIONS > versions.yml
+@@ -58,8 +58,8 @@
+     stub:
+     dir = "FastQ_Screen_Genomes"
+     """
+-    mkdir $dir
+-    touch $dir/fastq_screen.conf
++    mkdir ${dir}
++    touch ${dir}/fastq_screen.conf
+ 
+     cat <<-END_VERSIONS > versions.yml
+     "${task.process}":
+
+'modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test' was removed
+'modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test.snap' was removed
+************************************************************
diff --git a/modules/nf-core/fastqscreen/buildfromindex/main.nf b/modules/nf-core/fastqscreen/buildfromindex/main.nf
index 33840120..6706111e 100644
--- a/modules/nf-core/fastqscreen/buildfromindex/main.nf
+++ b/modules/nf-core/fastqscreen/buildfromindex/main.nf
@@ -2,39 +2,39 @@ process FASTQSCREEN_BUILDFROMINDEX {
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/fastq-screen:0.15.3--pl5321hdfd78af_0':
-        'biocontainers/fastq-screen:0.15.3--pl5321hdfd78af_0'}"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/fastq-screen:0.15.3--pl5321hdfd78af_0'
+        : 'biocontainers/fastq-screen:0.15.3--pl5321hdfd78af_0'}"
 
     input:
-    val(genome_names)
-    path(indexes), stageAs: "dir*"
+    val genome_names
+    path (indexes), stageAs: "dir*"
 
     output:
-    path("FastQ_Screen_Genomes"), emit: database
-    path "versions.yml"         , emit: versions
+    path ("FastQ_Screen_Genomes"), emit: database
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     dir = "FastQ_Screen_Genomes"
-    folder = indexes.collect { it.toString() }
+    folder = indexes.collect { index -> index.toString() }
     database = [genome_names, folder].transpose()
-    copy_indexes = folder.collect { "cp -r ${it} $dir/${it}"}.join(" && ")
+    copy_indexes = folder.collect { file -> "cp -r ${file} ${dir}/${file}" }.join(" && ")
 
     // Folder name and index (within folder) name could be different - use bash to look for index name
     config = database
-        .collect { "########## ${it[0]} \nDATABASE ${it[0]} $dir/${it[1]}/${it[1] + '_to_be_replaced'}" }
+        .collect { file -> "########## ${file[0]} \nDATABASE ${file[0]} ${dir}/${file[1]}/${file[1] + '_to_be_replaced'}" }
         .join("\n\n")
         .replace("\n", "\\n")
 
     """
-    mkdir $dir
-    $copy_indexes
+    mkdir ${dir}
+    ${copy_indexes}
 
-    echo "$config" > fastq_screen.conf
-    sed 's/\\\\n/\\n/g' fastq_screen.conf > $dir/fastq_screen.conf
+    echo "${config}" > fastq_screen.conf
+    sed 's/\\\\n/\\n/g' fastq_screen.conf > ${dir}/fastq_screen.conf
     echo "Replace folder name real index name"
 
     for f in ${folder.join(' ')}
@@ -45,8 +45,8 @@ process FASTQSCREEN_BUILDFROMINDEX {
         REPLACE_WITH=\$(basename \$REPLACE_WITH)
         REPLACE_WITH=\${REPLACE_WITH%%.rev.1.bt2}
 
-        sed "s/\$TO_REPLACE/\$REPLACE_WITH/g" $dir/fastq_screen.conf > new_conf.conf
-        mv new_conf.conf $dir/fastq_screen.conf
+        sed "s/\$TO_REPLACE/\$REPLACE_WITH/g" ${dir}/fastq_screen.conf > new_conf.conf
+        mv new_conf.conf ${dir}/fastq_screen.conf
     done
 
     cat <<-END_VERSIONS > versions.yml
@@ -58,8 +58,8 @@ process FASTQSCREEN_BUILDFROMINDEX {
     stub:
     dir = "FastQ_Screen_Genomes"
     """
-    mkdir $dir
-    touch $dir/fastq_screen.conf
+    mkdir ${dir}
+    touch ${dir}/fastq_screen.conf
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/nextflow.config b/nextflow.config
index 4f3dd01a..40ca5ec9 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -405,14 +405,15 @@ manifest {
     description     = """Pipeline to QC your sequences"""
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
-    nextflowVersion = '!>=25.04.0'
+    nextflowVersion = '!>=25.10.4'
     version         = '1.0.0'
     doi             = ''
 }
 
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-core-utils@0.4.0' // nf-core-utils is a collection of utilities for Nextflow pipelines
+    id 'nf-schema@2.6.1'     // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 validation {
diff --git a/nf-test.config b/nf-test.config
index ef5a466e..6a25cc8c 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -20,6 +20,6 @@ config {
     // load the necessary plugins
     plugins {
         load "nft-bam@0.4.0"
-        load "nft-utils@0.0.8"
+        load "nft-utils@0.0.9"
     }
 }
diff --git a/tests/MiSeq.nf.test b/tests/MiSeq.nf.test
index 6dbb1cc4..0cf8aabe 100644
--- a/tests/MiSeq.nf.test
+++ b/tests/MiSeq.nf.test
@@ -1,128 +1,43 @@
+def pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
+
 nextflow_pipeline {
 
-    name "Test Workflow main.nf on MiSeq data with single end reads"
+    name "Test pipeline"
     script "../main.nf"
-    tag "seqinspector"
-    tag "PIPELINE"
-
-    test("MiSeq data test (single end reads)") {
-
-        when {
-            params {
-                pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
-                input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/MiSeq/samplesheet.csv'
-                outdir = "$outputDir"
-                skip_tools = "rundirparser"
-            }
-        }
-
-        then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(
-                params.outdir,
-                relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']
-            )
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(
-                params.outdir,
-                ignoreFile: 'tests/.nftignore'
-            )
-            // bam_files: All bam files
-            def bam_files  = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
-            assert workflow.success
-            assertAll(
-                { assert snapshot(
-                    workflow.trace.succeeded().size(),
-                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
-                    // All stable path names, with a relative path
-                    stable_name,
-                    // All files with stable contents
-                    stable_path,
-                    // All bam files
-                    bam_files.isEmpty() ? 'No BAM files' : bam_files.collect { file -> file.getName() + ":md5," +  bam(file.toString()).readsMD5 },
-                ).match() }
-            )
-        }
-    }
-
-    test("Miseq data test (skip fastqc)") {
-        when {
-            params {
-                pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
-                input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/MiSeq/samplesheet.csv'
-                outdir = "$outputDir"
-                skip_tools = "fastqc,rundirparser"
-            }
-        }
-
-        then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(
-                params.outdir,
-                relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']
-            )
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(
-                params.outdir,
-                ignoreFile: 'tests/.nftignore'
-            )
-            // bam_files: All bam files
-            def bam_files  = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
-            assert workflow.success
-            assertAll(
-                { assert snapshot(
-                    workflow.trace.succeeded().size(),
-                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
-                    // All stable path names, with a relative path
-                    stable_name,
-                    // All files with stable contents
-                    stable_path,
-                    // All bam files
-                    bam_files.isEmpty() ? 'No BAM files' : bam_files.collect { file -> file.getName() + ":md5," +  bam(file.toString()).readsMD5 },
-                ).match() }
-            )
-        }
-    }
-
-    test("Miseq data test (skip all tools)") {
-        when {
-            params {
-                pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
-                input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/MiSeq/samplesheet.csv'
-                outdir = "$outputDir"
-                skip_tools = "fastqc,fastqscreen,seqfu_stats,seqtk_sample,bwamem2_index,bwamem2_mem,rundirparser"
-            }
-        }
 
-        then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(
-                params.outdir,
-                relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']
-            )
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(
-                params.outdir,
-                ignoreFile: 'tests/.nftignore'
-            )
-            // bam_files: All bam files
-            def bam_files  = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
-            assert workflow.success
-            assertAll(
-                { assert snapshot(
-                    workflow.trace.succeeded().size(),
-                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
-                    // All stable path names, with a relative path
-                    stable_name,
-                    // All files with stable contents
-                    stable_path,
-                    // All bam files
-                    bam_files.isEmpty() ? 'No BAM files' : bam_files.collect { file -> file.getName() + ":md5," +  bam(file.toString()).readsMD5 },
-                ).match() }
-            )
-        }
+    def test_scenario = [
+        [
+            name: "MiSeq data test (single end reads)",
+            params: [
+                input: pipelines_testdata_base_path + 'seqinspector/testdata/MiSeq/samplesheet.csv',
+                skip_tools: 'rundirparser',
+            ]
+        ],
+        [
+            name: "Miseq data test (skip fastqc)",
+            params: [
+                input: pipelines_testdata_base_path + 'seqinspector/testdata/MiSeq/samplesheet.csv',
+                skip_tools: 'fastqc,rundirparser',
+            ]
+        ],
+        [
+            name: "Miseq data test (skip all tools)",
+            params: [
+                input: pipelines_testdata_base_path + 'seqinspector/testdata/MiSeq/samplesheet.csv',
+                skip_tools: 'fastqc,fastqscreen,seqfu_stats,seqtk_sample,bwamem2_index,bwamem2_mem,rundirparser',
+            ]
+        ],
+        [
+            name: "MiSeq data test (paired end reads)",
+            params: [
+                input: pipelines_testdata_base_path + 'seqinspector/testdata/Miseq_PairedEnd/samplesheet.csv',
+                skip_tools: 'rundirparser',
+            ]
+        ]
+    ]
+
+    // Generate tests for each scenario
+    test_scenario.each { scenario ->
+        test(scenario.name, UTILS.getTest(scenario))
     }
 }
diff --git a/tests/MiSeq.nf.test.snap b/tests/MiSeq.nf.test.snap
index 2e7d47be..617568de 100644
--- a/tests/MiSeq.nf.test.snap
+++ b/tests/MiSeq.nf.test.snap
@@ -30,13 +30,14 @@
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc"
             ],
-            "No BAM files"
+            "No BAM files",
+            "No warnings"
         ],
+        "timestamp": "2026-02-17T10:23:01.770390051",
         "meta": {
-            "nf-test": "0.9.3",
+            "nf-test": "0.9.4",
             "nextflow": "25.10.4"
-        },
-        "timestamp": "2026-02-11T11:04:44.656020406"
+        }
     },
     "MiSeq data test (single end reads)": {
         "content": [
@@ -266,13 +267,444 @@
             ],
             [
                 "SAMPLE_SINGLE_END_01.bam:md5,9acd4428f95f70c1393671680ab9270f"
+            ],
+            "No warnings"
+        ],
+        "timestamp": "2026-02-17T10:17:46.832632927",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
+    "MiSeq data test (paired end reads)": {
+        "content": [
+            16,
+            {
+                "BWAMEM2_INDEX": {
+                    "bwamem2": "2.2.1"
+                },
+                "BWAMEM2_MEM": {
+                    "bwamem2": "2.2.1",
+                    "samtools": "1.22.1"
+                },
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "FASTQSCREEN_FASTQSCREEN": {
+                    "fastqscreen": "0.16.0"
+                },
+                "PICARD_COLLECTMULTIPLEMETRICS": {
+                    "picard": "3.4.0"
+                },
+                "SAMTOOLS_FAIDX": {
+                    "samtools": "1.22.1"
+                },
+                "SAMTOOLS_INDEX": {
+                    "samtools": "1.22.1"
+                },
+                "SEQFU_STATS": {
+                    "seqfu": "1.22.3"
+                }
+            },
+            [
+                "bwamem2_index",
+                "bwamem2_index/bwamem2",
+                "bwamem2_index/bwamem2/genome.fa.0123",
+                "bwamem2_index/bwamem2/genome.fa.amb",
+                "bwamem2_index/bwamem2/genome.fa.ann",
+                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
+                "bwamem2_index/bwamem2/genome.fa.pac",
+                "bwamem2_mem",
+                "bwamem2_mem/SAMPLE_PAIRED_END_1_01.bam",
+                "bwamem2_mem/SAMPLE_PAIRED_END_1_01.bam.bai",
+                "bwamem2_mem/SAMPLE_PAIRED_END_2_02.bam",
+                "bwamem2_mem/SAMPLE_PAIRED_END_2_02.bam.bai",
+                "fastqc",
+                "fastqc/SAMPLE_PAIRED_END_1_01_1_fastqc.html",
+                "fastqc/SAMPLE_PAIRED_END_1_01_1_fastqc.zip",
+                "fastqc/SAMPLE_PAIRED_END_1_01_2_fastqc.html",
+                "fastqc/SAMPLE_PAIRED_END_1_01_2_fastqc.zip",
+                "fastqc/SAMPLE_PAIRED_END_2_02_1_fastqc.html",
+                "fastqc/SAMPLE_PAIRED_END_2_02_1_fastqc.zip",
+                "fastqc/SAMPLE_PAIRED_END_2_02_2_fastqc.html",
+                "fastqc/SAMPLE_PAIRED_END_2_02_2_fastqc.zip",
+                "fastqscreen",
+                "fastqscreen/SAMPLE_PAIRED_END_1_01_1_screen.html",
+                "fastqscreen/SAMPLE_PAIRED_END_1_01_1_screen.png",
+                "fastqscreen/SAMPLE_PAIRED_END_1_01_1_screen.txt",
+                "fastqscreen/SAMPLE_PAIRED_END_1_01_2_screen.html",
+                "fastqscreen/SAMPLE_PAIRED_END_1_01_2_screen.png",
+                "fastqscreen/SAMPLE_PAIRED_END_1_01_2_screen.txt",
+                "fastqscreen/SAMPLE_PAIRED_END_2_02_1_screen.html",
+                "fastqscreen/SAMPLE_PAIRED_END_2_02_1_screen.png",
+                "fastqscreen/SAMPLE_PAIRED_END_2_02_1_screen.txt",
+                "fastqscreen/SAMPLE_PAIRED_END_2_02_2_screen.html",
+                "fastqscreen/SAMPLE_PAIRED_END_2_02_2_screen.png",
+                "fastqscreen/SAMPLE_PAIRED_END_2_02_2_screen.txt",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/global_report/multiqc_data/fastqc_adapter_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/global_report/multiqc_data/llms-full.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc.parquet",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu_mqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_summary_Aligned_Bases.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_summary_Aligned_Reads.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
+                "multiqc/global_report/multiqc_plots",
+                "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu_mqc.pdf",
+                "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_adapter_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu_mqc.png",
+                "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu_mqc.svg",
+                "multiqc/global_report/multiqc_report.html",
+                "multiqc/group_reports",
+                "multiqc/group_reports/Bpacificus",
+                "multiqc/group_reports/Bpacificus/multiqc_data",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_adapter_content_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
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+                "SAMPLE_PAIRED_END_1_01_seqfu_mqc.txt:md5,0aca00c7f64454af520c7e08ec595d2b",
+                "SAMPLE_PAIRED_END_2_02_seqfu.tsv:md5,44a5cb826e001d58208a5855938fa82b",
+                "SAMPLE_PAIRED_END_2_02_seqfu_mqc.txt:md5,ac1740de9ef142c99c993fa9824ead63"
+            ],
+            [
+                "SAMPLE_PAIRED_END_1_01.bam:md5,ac811b20d56132f5e039b3e8fd217405",
+                "SAMPLE_PAIRED_END_2_02.bam:md5,57892fc4314e66e8e20de4f5d82f9b5d"
+            ],
+            [
+                "WARN: Tag name collision: [Bpacificus]"
             ]
         ],
+        "timestamp": "2026-02-17T10:18:50.450876782",
         "meta": {
-            "nf-test": "0.9.3",
+            "nf-test": "0.9.4",
             "nextflow": "25.10.4"
-        },
-        "timestamp": "2026-02-11T11:03:07.801122062"
+        }
     },
     "Miseq data test (skip fastqc)": {
         "content": [
@@ -444,12 +876,13 @@
             ],
             [
                 "SAMPLE_SINGLE_END_01.bam:md5,9acd4428f95f70c1393671680ab9270f"
-            ]
+            ],
+            "No warnings"
         ],
+        "timestamp": "2026-02-17T10:22:28.854774703",
         "meta": {
-            "nf-test": "0.9.3",
+            "nf-test": "0.9.4",
             "nextflow": "25.10.4"
-        },
-        "timestamp": "2026-02-11T11:04:06.426745227"
+        }
     }
 }
\ No newline at end of file
diff --git a/tests/MiSeq_PairedEnd.nf.test b/tests/MiSeq_PairedEnd.nf.test
deleted file mode 100644
index be862326..00000000
--- a/tests/MiSeq_PairedEnd.nf.test
+++ /dev/null
@@ -1,48 +0,0 @@
-nextflow_pipeline {
-
-    name "Test Workflow main.nf on MiSeq data with paired end reads"
-    script "../main.nf"
-    tag "seqinspector"
-    tag "PIPELINE"
-
-    test("MiSeq data test (paired end reads)") {
-
-        when {
-            params {
-                pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
-                outdir = "$outputDir"
-                skip_tools = "rundirparser"
-                input = params.pipelines_testdata_base_path + 'seqinspector/testdata/Miseq_PairedEnd/samplesheet.csv'
-            }
-        }
-
-        then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(
-                params.outdir,
-                relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']
-            )
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(
-                params.outdir,
-                ignoreFile: 'tests/.nftignore'
-            )
-            // bam_files: All bam files
-            def bam_files  = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
-            assert workflow.success
-            assertAll(
-                { assert snapshot(
-                    workflow.trace.succeeded().size(),
-                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
-                    // All stable path names, with a relative path
-                    stable_name,
-                    // All files with stable contents
-                    stable_path,
-                    // All bam files
-                    bam_files.isEmpty() ? 'No BAM files' : bam_files.collect { file -> file.getName() + ":md5," +  bam(file.toString()).readsMD5 },
-                ).match() }
-            )
-        }
-    }
-}
diff --git a/tests/MiSeq_PairedEnd.nf.test.snap b/tests/MiSeq_PairedEnd.nf.test.snap
deleted file mode 100644
index db97a637..00000000
--- a/tests/MiSeq_PairedEnd.nf.test.snap
+++ /dev/null
@@ -1,429 +0,0 @@
-{
-    "MiSeq data test (paired end reads)": {
-        "content": [
-            16,
-            {
-                "BWAMEM2_INDEX": {
-                    "bwamem2": "2.2.1"
-                },
-                "BWAMEM2_MEM": {
-                    "bwamem2": "2.2.1",
-                    "samtools": "1.22.1"
-                },
-                "FASTQC": {
-                    "fastqc": "0.12.1"
-                },
-                "FASTQSCREEN_FASTQSCREEN": {
-                    "fastqscreen": "0.16.0"
-                },
-                "PICARD_COLLECTMULTIPLEMETRICS": {
-                    "picard": "3.4.0"
-                },
-                "SAMTOOLS_FAIDX": {
-                    "samtools": "1.22.1"
-                },
-                "SAMTOOLS_INDEX": {
-                    "samtools": "1.22.1"
-                },
-                "SEQFU_STATS": {
-                    "seqfu": "1.22.3"
-                }
-            },
-            [
-                "bwamem2_index",
-                "bwamem2_index/bwamem2",
-                "bwamem2_index/bwamem2/genome.fa.0123",
-                "bwamem2_index/bwamem2/genome.fa.amb",
-                "bwamem2_index/bwamem2/genome.fa.ann",
-                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
-                "bwamem2_index/bwamem2/genome.fa.pac",
-                "bwamem2_mem",
-                "bwamem2_mem/SAMPLE_PAIRED_END_1_01.bam",
-                "bwamem2_mem/SAMPLE_PAIRED_END_1_01.bam.bai",
-                "bwamem2_mem/SAMPLE_PAIRED_END_2_02.bam",
-                "bwamem2_mem/SAMPLE_PAIRED_END_2_02.bam.bai",
-                "fastqc",
-                "fastqc/SAMPLE_PAIRED_END_1_01_1_fastqc.html",
-                "fastqc/SAMPLE_PAIRED_END_1_01_1_fastqc.zip",
-                "fastqc/SAMPLE_PAIRED_END_1_01_2_fastqc.html",
-                "fastqc/SAMPLE_PAIRED_END_1_01_2_fastqc.zip",
-                "fastqc/SAMPLE_PAIRED_END_2_02_1_fastqc.html",
-                "fastqc/SAMPLE_PAIRED_END_2_02_1_fastqc.zip",
-                "fastqc/SAMPLE_PAIRED_END_2_02_2_fastqc.html",
-                "fastqc/SAMPLE_PAIRED_END_2_02_2_fastqc.zip",
-                "fastqscreen",
-                "fastqscreen/SAMPLE_PAIRED_END_1_01_1_screen.html",
-                "fastqscreen/SAMPLE_PAIRED_END_1_01_1_screen.png",
-                "fastqscreen/SAMPLE_PAIRED_END_1_01_1_screen.txt",
-                "fastqscreen/SAMPLE_PAIRED_END_1_01_2_screen.html",
-                "fastqscreen/SAMPLE_PAIRED_END_1_01_2_screen.png",
-                "fastqscreen/SAMPLE_PAIRED_END_1_01_2_screen.txt",
-                "fastqscreen/SAMPLE_PAIRED_END_2_02_1_screen.html",
-                "fastqscreen/SAMPLE_PAIRED_END_2_02_1_screen.png",
-                "fastqscreen/SAMPLE_PAIRED_END_2_02_1_screen.txt",
-                "fastqscreen/SAMPLE_PAIRED_END_2_02_2_screen.html",
-                "fastqscreen/SAMPLE_PAIRED_END_2_02_2_screen.png",
-                "fastqscreen/SAMPLE_PAIRED_END_2_02_2_screen.txt",
-                "multiqc",
-                "multiqc/global_report",
-                "multiqc/global_report/multiqc_data",
-                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
-                "multiqc/global_report/multiqc_data/fastqc_adapter_content_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
-                "multiqc/global_report/multiqc_data/llms-full.txt",
-                "multiqc/global_report/multiqc_data/multiqc.log",
-                "multiqc/global_report/multiqc_data/multiqc.parquet",
-                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
-                "multiqc/global_report/multiqc_data/multiqc_data.json",
-                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
-                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
-                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
-                "multiqc/global_report/multiqc_data/multiqc_seqfu_mqc.txt",
-                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
-                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
-                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
-                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
-                "multiqc/global_report/multiqc_data/picard_alignment_summary_Aligned_Bases.txt",
-                "multiqc/global_report/multiqc_data/picard_alignment_summary_Aligned_Reads.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
-                "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt",
-                "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
-                "multiqc/global_report/multiqc_plots",
-                "multiqc/global_report/multiqc_plots/pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu_mqc.pdf",
-                "multiqc/global_report/multiqc_plots/png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_adapter_content_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-pct.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-pct.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
-                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
-                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu_mqc.png",
-                "multiqc/global_report/multiqc_plots/svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
-                "multiqc/global_report/multiqc_plots/svg/seqfu_mqc.svg",
-                "multiqc/global_report/multiqc_report.html",
-                "multiqc/group_reports",
-                "multiqc/group_reports/Bpacificus",
-                "multiqc/group_reports/Bpacificus/multiqc_data",
-                "multiqc/group_reports/Bpacificus/multiqc_data/fastq_screen_plot.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc-status-check-heatmap.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_adapter_content_plot.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_base_n_content_plot.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_sequence_counts_plot.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/llms-full.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc.log",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc.parquet",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_citations.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_data.json",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_fastq_screen.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_fastqc.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_baseContent.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_quality_by_cycle.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_quality_score_distribution.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_seqfu_mqc.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_software_versions.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_sources.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/picard_alignment_readlength_plot.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/picard_alignment_summary_Aligned_Bases.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/picard_alignment_summary_Aligned_Reads.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/picard_quality_by_cycle.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_data/picard_quality_score_distribution.txt",
-                "multiqc/group_reports/Bpacificus/multiqc_plots",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-cnt.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-pct.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-cnt.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-pct.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/seqfu_mqc.pdf",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_adapter_content_plot.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_readlength_plot.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-cnt.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-pct.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-cnt.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-pct.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_quality_by_cycle.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_quality_score_distribution.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/png/seqfu_mqc.png",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-cnt.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-pct.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-cnt.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-pct.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_quality_by_cycle.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_quality_score_distribution.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/seqfu_mqc.svg",
-                "multiqc/group_reports/Bpacificus/multiqc_report.html",
-                "picard_collectmultiplemetrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_01.CollectMultipleMetrics.alignment_summary_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_01.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_01.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_01.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_01.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_01.CollectMultipleMetrics.quality_distribution.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_01.CollectMultipleMetrics.quality_distribution_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_01.CollectMultipleMetrics.read_length_histogram.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_02.CollectMultipleMetrics.alignment_summary_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_02.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_02.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_02.CollectMultipleMetrics.quality_by_cycle.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_02.CollectMultipleMetrics.quality_by_cycle_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_02.CollectMultipleMetrics.quality_distribution.pdf",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_02.CollectMultipleMetrics.quality_distribution_metrics",
-                "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_02.CollectMultipleMetrics.read_length_histogram.pdf",
-                "pipeline_info",
-                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
-                "samtools_faidx",
-                "samtools_faidx/genome.fa.fai",
-                "samtools_faidx/genome.fa.sizes",
-                "seqfu_stats",
-                "seqfu_stats/SAMPLE_PAIRED_END_1_01_seqfu.tsv",
-                "seqfu_stats/SAMPLE_PAIRED_END_1_01_seqfu_mqc.txt",
-                "seqfu_stats/SAMPLE_PAIRED_END_2_02_seqfu.tsv",
-                "seqfu_stats/SAMPLE_PAIRED_END_2_02_seqfu_mqc.txt"
-            ],
-            [
-                "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
-                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
-                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
-                "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
-                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "SAMPLE_PAIRED_END_1_01_1_screen.png:md5,f52ddd0e65f23f68dd8d58d5453417db",
-                "SAMPLE_PAIRED_END_1_01_1_screen.txt:md5,921b08eeb461a2aa1bd42bba53900f70",
-                "SAMPLE_PAIRED_END_1_01_2_screen.png:md5,908f4fceea8aa546106efdaa7ca78f7d",
-                "SAMPLE_PAIRED_END_1_01_2_screen.txt:md5,e9ea5789e356f666de27ba658704e80d",
-                "SAMPLE_PAIRED_END_2_02_1_screen.png:md5,48d546767ed2a34a1eda59d97dd00c18",
-                "SAMPLE_PAIRED_END_2_02_1_screen.txt:md5,a5b047f495d01bf9dcb0ae516d3c7fc3",
-                "SAMPLE_PAIRED_END_2_02_2_screen.png:md5,e3684b17339d16e6fb64ace7593cc388",
-                "SAMPLE_PAIRED_END_2_02_2_screen.txt:md5,fc95e5058e764596d5da182cbc0614cf",
-                "fastq_screen_plot.txt:md5,24a7d3472f06fe6032bb7f12f5828b49",
-                "fastqc-status-check-heatmap.txt:md5,c1e87942bda9a4ccf519bf561ce18ed3",
-                "fastqc_adapter_content_plot.txt:md5,4b7007431bd26127365b0f25120d48f2",
-                "fastqc_per_base_n_content_plot.txt:md5,6bbf19be2aef3ef67dfe548bf9323011",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,2bd96b0c0413ee4871a53d41f067d809",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,1f56f6ca0f469bec9b25010c6f9cbfdd",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,64bc987cceac0396b8b650000493427e",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,4aa57cbe1f9da1facc1b588b4c166cec",
-                "fastqc_sequence_counts_plot.txt:md5,57f96ad90232887fec1480ef4071f8b6",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,62e93bfc80b0bf201a605802edbe0177",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,6f9cfa81bda7482142c640b9f0c82b90",
-                "multiqc_fastqc.txt:md5,85fe5c24576dc105adb8ca90ce6449b7",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,32c0a27891fabd36de3c7fa97d82c11f",
-                "multiqc_picard_baseContent.txt:md5,a2043541e3ce74b710ae2b69ef7bc593",
-                "multiqc_picard_quality_by_cycle.txt:md5,0eab2183e8852b165b09a9ea8a5f67c9",
-                "multiqc_picard_quality_score_distribution.txt:md5,33955f093524a0eff449e25226768d84",
-                "multiqc_seqfu_mqc.txt:md5,139354afd154804b4b77f997277f3ee9",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,0eab2183e8852b165b09a9ea8a5f67c9",
-                "picard_QualityScoreDistribution_histogram.txt:md5,33955f093524a0eff449e25226768d84",
-                "picard_alignment_readlength_plot.txt:md5,ed079bc433831b807d11b7b95b151b4e",
-                "picard_alignment_summary_Aligned_Bases.txt:md5,9f877e31c0f772644a91531717b8ce32",
-                "picard_alignment_summary_Aligned_Reads.txt:md5,3a1ff58d9f57eb88240116dea3e11a99",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,23b0d8572689f0eafb3adaa57814fdfd",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,c9a36624afb4251813e392ea7bc0d135",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,c68670e3254396cd3db5fc57064ab328",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,ae15c81a007c9316c7d1ccda8daace25",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,040f28a453cfca2155c65f1d8553ecfe",
-                "picard_quality_by_cycle.txt:md5,2497dd5ef1e5cedc1f88a9b67ef549d7",
-                "picard_quality_score_distribution.txt:md5,795138cccc8b97143f8bf0bf0adbd4b7",
-                "fastq_screen_plot.txt:md5,24a7d3472f06fe6032bb7f12f5828b49",
-                "fastqc-status-check-heatmap.txt:md5,c1e87942bda9a4ccf519bf561ce18ed3",
-                "fastqc_adapter_content_plot.txt:md5,4b7007431bd26127365b0f25120d48f2",
-                "fastqc_per_base_n_content_plot.txt:md5,6bbf19be2aef3ef67dfe548bf9323011",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,2bd96b0c0413ee4871a53d41f067d809",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,1f56f6ca0f469bec9b25010c6f9cbfdd",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,64bc987cceac0396b8b650000493427e",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,4aa57cbe1f9da1facc1b588b4c166cec",
-                "fastqc_sequence_counts_plot.txt:md5,57f96ad90232887fec1480ef4071f8b6",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,62e93bfc80b0bf201a605802edbe0177",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,6f9cfa81bda7482142c640b9f0c82b90",
-                "multiqc_fastqc.txt:md5,85fe5c24576dc105adb8ca90ce6449b7",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,32c0a27891fabd36de3c7fa97d82c11f",
-                "multiqc_picard_baseContent.txt:md5,a2043541e3ce74b710ae2b69ef7bc593",
-                "multiqc_picard_quality_by_cycle.txt:md5,0eab2183e8852b165b09a9ea8a5f67c9",
-                "multiqc_picard_quality_score_distribution.txt:md5,33955f093524a0eff449e25226768d84",
-                "multiqc_seqfu_mqc.txt:md5,139354afd154804b4b77f997277f3ee9",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,0eab2183e8852b165b09a9ea8a5f67c9",
-                "picard_QualityScoreDistribution_histogram.txt:md5,33955f093524a0eff449e25226768d84",
-                "picard_alignment_readlength_plot.txt:md5,ed079bc433831b807d11b7b95b151b4e",
-                "picard_alignment_summary_Aligned_Bases.txt:md5,9f877e31c0f772644a91531717b8ce32",
-                "picard_alignment_summary_Aligned_Reads.txt:md5,3a1ff58d9f57eb88240116dea3e11a99",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,23b0d8572689f0eafb3adaa57814fdfd",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,c9a36624afb4251813e392ea7bc0d135",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,c68670e3254396cd3db5fc57064ab328",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,ae15c81a007c9316c7d1ccda8daace25",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,040f28a453cfca2155c65f1d8553ecfe",
-                "picard_quality_by_cycle.txt:md5,2497dd5ef1e5cedc1f88a9b67ef549d7",
-                "picard_quality_score_distribution.txt:md5,795138cccc8b97143f8bf0bf0adbd4b7",
-                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
-                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
-                "SAMPLE_PAIRED_END_1_01_seqfu.tsv:md5,be29dfe848eab9a10ee0d46691223eae",
-                "SAMPLE_PAIRED_END_1_01_seqfu_mqc.txt:md5,0aca00c7f64454af520c7e08ec595d2b",
-                "SAMPLE_PAIRED_END_2_02_seqfu.tsv:md5,44a5cb826e001d58208a5855938fa82b",
-                "SAMPLE_PAIRED_END_2_02_seqfu_mqc.txt:md5,ac1740de9ef142c99c993fa9824ead63"
-            ],
-            [
-                "SAMPLE_PAIRED_END_1_01.bam:md5,ac811b20d56132f5e039b3e8fd217405",
-                "SAMPLE_PAIRED_END_2_02.bam:md5,57892fc4314e66e8e20de4f5d82f9b5d"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.4"
-        },
-        "timestamp": "2026-02-11T11:06:18.529815388"
-    }
-}
\ No newline at end of file
diff --git a/tests/NovaSeq6000.nf.test b/tests/NovaSeq6000.nf.test
index 3c207193..27a24359 100644
--- a/tests/NovaSeq6000.nf.test
+++ b/tests/NovaSeq6000.nf.test
@@ -1,89 +1,45 @@
+def pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
+def projectDir = new File('.').absolutePath
+
 nextflow_pipeline {
 
-    name "Test Workflow main.nf on NovaSeq6000 data"
+    name "Test pipeline"
     script "../main.nf"
-    tag "seqinspector"
-    tag "PIPELINE"
-
-    test("NovaSeq6000 data test") {
-
-        when {
-            params {
-                fastq_screen_references = "${projectDir}/assets/example_fastq_screen_references.csv"
-                genome = 'R64-1-1'
-                outdir = "$outputDir"
-            }
-        }
-
-        then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(
-                params.outdir,
-                relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']
-            )
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(
-                params.outdir,
-                ignoreFile: 'tests/.nftignore'
-            )
-            // bam_files: All bam files
-            def bam_files  = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
-            assert workflow.success
-            assertAll(
-                { assert snapshot(
-                    workflow.trace.succeeded().size(),
-                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
-                    // All stable path names, with a relative path
-                    stable_name,
-                    // All files with stable contents
-                    stable_path,
-                    // All bam files
-                    bam_files.isEmpty() ? 'No BAM files' : bam_files.collect { file -> file.getName() + ":md5," +  bam(file.toString()).readsMD5 },
-                ).match() }
-            )
-        }
-    }
-
-    test("NovaSeq6000 data test - No rundirs") {
 
-        when {
-            params {
-                fastq_screen_references = "${projectDir}/assets/example_fastq_screen_references.csv"
-                genome = 'R64-1-1'
-                outdir = "$outputDir"
-                pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
-                input = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet_no_rundirs.csv'
-            }
-        }
+    def test_scenario = [
+        [
+            name: "NovaSeq6000 data test",
+            params: [],
+            snapshot: 'stderr,stdout'
+        ],
+        [
+            name: "NovaSeq6000 data test sample size",
+            params: [
+                sample_size : 90
+            ]
+        ],
+        [
+            name: "NovaSeq6000 data test relative sample size",
+            params: [
+                sample_size : 0.9
+            ]
+        ],
+        [
+            name: "NovaSeq6000 data test sample size exceeds available reads",
+            params: [
+                sample_size : 120
+            ]
+        ],
+        [
+            name: "NovaSeq6000 data test - No rundirs",
+            params: [
+                input : pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet_no_rundirs.csv'
+            ]
+        ]
+    ]
 
-        then {
-           // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(
-                params.outdir,
-                relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']
-            )
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(
-                params.outdir,
-                ignoreFile: 'tests/.nftignore'
-            )
-            // bam_files: All bam files
-            def bam_files  = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
-            assert workflow.success
-            assertAll(
-                { assert snapshot(
-                    workflow.trace.succeeded().size(),
-                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
-                    // All stable path names, with a relative path
-                    stable_name,
-                    // All files with stable contents
-                    stable_path,
-                    // All bam files
-                    bam_files.isEmpty() ? 'No BAM files' : bam_files.collect { file -> file.getName() + ":md5," +  bam(file.toString()).readsMD5 },
-                ).match() }
-            )
-        }
+    // Generate tests for each scenario
+    test_scenario.each { scenario ->
+        test(scenario.name, UTILS.getTest(scenario))
     }
 }
diff --git a/tests/NovaSeq6000.nf.test.snap b/tests/NovaSeq6000.nf.test.snap
index 980ab608..695e66d5 100644
--- a/tests/NovaSeq6000.nf.test.snap
+++ b/tests/NovaSeq6000.nf.test.snap
@@ -957,17 +957,3011 @@
                 "SampleA_02.bam:md5,250d0031520e59ee59a7112ab1ea32e1",
                 "Undetermined_05.bam:md5,8fcc158f1e0736b366152d5e187644ca",
                 "sampletest_04.bam:md5,f80371e37421d97499b3bfd55221ed00"
+            ],
+            [
+                "N E X T F L O W  ~  version [VERSION]",
+                "Launching `[PATH]/tests/../main.nf` [RUN_NAME] DSL2 - revision: [REVISION]",
+                "------------------------------------------------------",
+                "                                        ,--./,-.",
+                "        ___     __   __   __   ___     /,-._.--~'",
+                "  |\\ | |__  __ /  ` /  \\ |__) |__         }  {",
+                "  | \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,",
+                "                                        `._,._,'",
+                "  nf-core/seqinspector [VERSION]",
+                "------------------------------------------------------",
+                "Input/output options",
+                "  input                     : https://raw.githubusercontent.com/nf-core/test-datasets/seqinspector/testdata/NovaSeq6000/samplesheet.csv",
+                "  outdir                    : [PATH]/tests/[NFT_HASH]/output",
+                "Reference genome options",
+                "  genome                    : R64-1-1",
+                "  fasta                     : s3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa",
+                "Institutional config options",
+                "  config_profile_name       : Test profile",
+                "  config_profile_description: Minimal test dataset to check pipeline function",
+                "Generic options",
+                "  trace_report_suffix       : [TIMESTAMP]",
+                "Core Nextflow options",
+                "  runName                   : [RUN_NAME]",
+                "  launchDir                 : [PATH]/tests/[NFT_HASH]",
+                "  workDir                   : [PATH]/tests/[NFT_HASH]/work",
+                "  projectDir                : [PATH]",
+                "  userName                  : [USER]",
+                "  profile                   : test,[CONTAINER]",
+                "  configFiles               : [PATH]/nextflow.config, [PATH]/nextflow.config, [PATH]/tests/nextflow.config",
+                "!! Only displaying parameters that differ from the pipeline defaults !!",
+                "------------------------------------------------------",
+                "* The nf-core framework",
+                "    https://doi.org/10.1038/s41587-020-0439-x",
+                "* Software dependencies",
+                "    https://github.com/nf-core/seqinspector/blob/master/CITATIONS.md",
+                "-[nf-core/seqinspector] Pipeline completed successfully-",
+                "WARN: Tag name collision: [group1]",
+                "WARN: Tag name collision: [group2]",
+                "WARN: Tag name collision: [lane1]",
+                "WARN: Tag name collision: [test]",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:BWAMEM2_MEM (Sample1_01)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:BWAMEM2_MEM (Sample23_03)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:BWAMEM2_MEM (SampleA_02)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:BWAMEM2_MEM (Undetermined_05)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:BWAMEM2_MEM (sampletest_04)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:FASTQC (Sample1_01)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:FASTQC (Sample23_03)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:FASTQC (SampleA_02)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:FASTQC (Undetermined_05)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:FASTQC (sampletest_04)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:FASTQSCREEN_FASTQSCREEN (Sample1_01)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:FASTQSCREEN_FASTQSCREEN (Sample23_03)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:FASTQSCREEN_FASTQSCREEN (SampleA_02)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:FASTQSCREEN_FASTQSCREEN (Undetermined_05)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:FASTQSCREEN_FASTQSCREEN (sampletest_04)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:MULTIQC_GLOBAL",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:MULTIQC_PER_TAG (1)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:MULTIQC_PER_TAG (2)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:MULTIQC_PER_TAG (3)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:MULTIQC_PER_TAG (4)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:PREPARE_GENOME:BWAMEM2_INDEX (genome.fa)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:PREPARE_GENOME:SAMTOOLS_FAIDX (genome.fa)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (Sample1_01)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (Sample23_03)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (SampleA_02)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (Undetermined_05)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (sampletest_04)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:RUNDIRPARSER (200624_A00834_0183_BHMTFYDRXX)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:SAMTOOLS_INDEX (Sample1_01)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:SAMTOOLS_INDEX (Sample23_03)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:SAMTOOLS_INDEX (SampleA_02)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:SAMTOOLS_INDEX (Undetermined_05)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:SAMTOOLS_INDEX (sampletest_04)",
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:SEQFU_STATS (seqfu)"
+            ]
+        ],
+        "timestamp": "2026-02-17T16:11:01.427075006",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
+    "NovaSeq6000 data test sample size": {
+        "content": [
+            43,
+            {
+                "BWAMEM2_INDEX": {
+                    "bwamem2": "2.2.1"
+                },
+                "BWAMEM2_MEM": {
+                    "bwamem2": "2.2.1",
+                    "samtools": "1.22.1"
+                },
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "FASTQSCREEN_FASTQSCREEN": {
+                    "fastqscreen": "0.16.0"
+                },
+                "PICARD_COLLECTMULTIPLEMETRICS": {
+                    "picard": "3.4.0"
+                },
+                "RUNDIRPARSER": {
+                    "PyYAML": "6.0.2",
+                    "Python": "3.13.2"
+                },
+                "SAMTOOLS_FAIDX": {
+                    "samtools": "1.22.1"
+                },
+                "SAMTOOLS_INDEX": {
+                    "samtools": "1.22.1"
+                },
+                "SEQFU_STATS": {
+                    "seqfu": "1.22.3"
+                },
+                "SEQTK_SAMPLE": {
+                    "seqtk": "1.4-r122"
+                }
+            },
+            [
+                "bwamem2_index",
+                "bwamem2_index/bwamem2",
+                "bwamem2_index/bwamem2/genome.fa.0123",
+                "bwamem2_index/bwamem2/genome.fa.amb",
+                "bwamem2_index/bwamem2/genome.fa.ann",
+                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
+                "bwamem2_index/bwamem2/genome.fa.pac",
+                "bwamem2_mem",
+                "bwamem2_mem/Sample1_01.bam",
+                "bwamem2_mem/Sample1_01.bam.bai",
+                "bwamem2_mem/Sample23_03.bam",
+                "bwamem2_mem/Sample23_03.bam.bai",
+                "bwamem2_mem/SampleA_02.bam",
+                "bwamem2_mem/SampleA_02.bam.bai",
+                "bwamem2_mem/Undetermined_05.bam",
+                "bwamem2_mem/Undetermined_05.bam.bai",
+                "bwamem2_mem/sampletest_04.bam",
+                "bwamem2_mem/sampletest_04.bam.bai",
+                "fastqc",
+                "fastqc/Sample1_01_fastqc.html",
+                "fastqc/Sample1_01_fastqc.zip",
+                "fastqc/Sample23_03_fastqc.html",
+                "fastqc/Sample23_03_fastqc.zip",
+                "fastqc/SampleA_02_fastqc.html",
+                "fastqc/SampleA_02_fastqc.zip",
+                "fastqc/Undetermined_05_fastqc.html",
+                "fastqc/Undetermined_05_fastqc.zip",
+                "fastqc/sampletest_04_fastqc.html",
+                "fastqc/sampletest_04_fastqc.zip",
+                "fastqscreen",
+                "fastqscreen/Sample1_01_screen.html",
+                "fastqscreen/Sample1_01_screen.png",
+                "fastqscreen/Sample1_01_screen.txt",
+                "fastqscreen/Sample23_03_screen.html",
+                "fastqscreen/Sample23_03_screen.png",
+                "fastqscreen/Sample23_03_screen.txt",
+                "fastqscreen/SampleA_02_screen.html",
+                "fastqscreen/SampleA_02_screen.png",
+                "fastqscreen/SampleA_02_screen.txt",
+                "fastqscreen/Undetermined_05_screen.html",
+                "fastqscreen/Undetermined_05_screen.png",
+                "fastqscreen/Undetermined_05_screen.txt",
+                "fastqscreen/sampletest_04_screen.html",
+                "fastqscreen/sampletest_04_screen.png",
+                "fastqscreen/sampletest_04_screen.txt",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/global_report/multiqc_data/llms-full.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc.parquet",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
+                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_mqc_seq_metadata.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
+                "multiqc/global_report/multiqc_data/multiqc_seqfu_mqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
+                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
+                "multiqc/global_report/multiqc_data/picard_alignment_summary.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
+                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt",
+                "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
+                "multiqc/global_report/multiqc_plots",
+                "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/mqc_seq_metadata.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/seqfu_mqc.pdf",
+                "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/mqc_seq_metadata.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
+                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
+                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
+                "multiqc/global_report/multiqc_plots/png/seqfu_mqc.png",
+                "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/mqc_seq_metadata.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
+                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
+                "multiqc/global_report/multiqc_plots/svg/seqfu_mqc.svg",
+                "multiqc/global_report/multiqc_report.html",
+                "multiqc/group_reports",
+                "multiqc/group_reports/group1",
+                "multiqc/group_reports/group1/multiqc_data",
+                "multiqc/group_reports/group1/multiqc_data/fastq_screen_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
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+                "picard_collectmultiplemetrics/Undetermined_05.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/Undetermined_05.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Undetermined_05.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Undetermined_05.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/Undetermined_05.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/Undetermined_05.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/Undetermined_05.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/Undetermined_05.CollectMultipleMetrics.read_length_histogram.pdf",
+                "picard_collectmultiplemetrics/sampletest_04.CollectMultipleMetrics.alignment_summary_metrics",
+                "picard_collectmultiplemetrics/sampletest_04.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "picard_collectmultiplemetrics/sampletest_04.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "picard_collectmultiplemetrics/sampletest_04.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "picard_collectmultiplemetrics/sampletest_04.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "picard_collectmultiplemetrics/sampletest_04.CollectMultipleMetrics.quality_distribution.pdf",
+                "picard_collectmultiplemetrics/sampletest_04.CollectMultipleMetrics.quality_distribution_metrics",
+                "picard_collectmultiplemetrics/sampletest_04.CollectMultipleMetrics.read_length_histogram.pdf",
+                "pipeline_info",
+                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "rundirparser",
+                "rundirparser/200624_A00834_0183_BHMTFYDRXX_illumina_mqc.yml",
+                "samtools_faidx",
+                "samtools_faidx/genome.fa.fai",
+                "samtools_faidx/genome.fa.sizes",
+                "seqfu_stats",
+                "seqfu_stats/Sample1_01_seqfu.tsv",
+                "seqfu_stats/Sample1_01_seqfu_mqc.txt",
+                "seqfu_stats/Sample23_03_seqfu.tsv",
+                "seqfu_stats/Sample23_03_seqfu_mqc.txt",
+                "seqfu_stats/SampleA_02_seqfu.tsv",
+                "seqfu_stats/SampleA_02_seqfu_mqc.txt",
+                "seqfu_stats/Undetermined_05_seqfu.tsv",
+                "seqfu_stats/Undetermined_05_seqfu_mqc.txt",
+                "seqfu_stats/sampletest_04_seqfu.tsv",
+                "seqfu_stats/sampletest_04_seqfu_mqc.txt",
+                "seqtk",
+                "seqtk/Sample1_01_Sample1_S1_L001_R1_001.fastq.gz",
+                "seqtk/Sample23_03_Sample23_S3_L001_R1_001.fastq.gz",
+                "seqtk/SampleA_02_SampleA_S2_L001_R1_001.fastq.gz",
+                "seqtk/Undetermined_05_Undetermined_S0_L001_R1_001.fastq.gz",
+                "seqtk/sampletest_04_sampletest_S4_L001_R1_001.fastq.gz"
+            ],
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+                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
+                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
+                "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
+                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
+                "Sample1_01_screen.png:md5,57b1664bc6c8e82cc0ce14802ad0dc0f",
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+                "Undetermined_05_screen.png:md5,12707698b2765c68566ccf5ac25479f5",
+                "Undetermined_05_screen.txt:md5,20926a4045b2ecf4bc76007047cc645a",
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+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,b78adce4744b3c5f9dd10caf5c3c16b3",
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+                "fastqc-status-check-heatmap.txt:md5,7a64380ec42aac56949a2d9a4176d4d9",
+                "fastqc_overrepresented_sequences_plot.txt:md5,c7908980f1dba22b45cf6de14a66a686",
+                "fastqc_per_base_n_content_plot.txt:md5,8aafe701b59b4e70ccec86748c7d6eb3",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,c2bbc52a285a46ab8c548bca3b721e13",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a422f61a00f0839ef0d630d2e4524589",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,0e5a0cd0b0f8e66b3617f1ac19822d77",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,cbaa7c7033c526483584376275a8b33e",
+                "fastqc_sequence_counts_plot.txt:md5,d8ab86dbfce0c740f4a66a080803a0b9",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,f86012b3074d697c9a2b3bd67a074288",
+                "fastqc_sequence_length_distribution_plot.txt:md5,9d4fd245e8e1d5baa473a8bdffcd3e38",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,62240561100f78af37e7e2438cb58f90",
+                "multiqc_fastqc.txt:md5,23b698f1e957a26f49a9ad9bbdece908",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,b113ea40790fa45fa739f224f2710556",
+                "multiqc_picard_baseContent.txt:md5,e06c0dea80cb5cef312436e005aa0095",
+                "multiqc_picard_quality_by_cycle.txt:md5,6e13ddbd97caa0eaa52c118966e5f9fa",
+                "multiqc_picard_quality_score_distribution.txt:md5,39d3430744e9139020d7af3eb15fc629",
+                "multiqc_seqfu_mqc.txt:md5,18dd2407d4a1791646785123028f69b5",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,6e13ddbd97caa0eaa52c118966e5f9fa",
+                "picard_QualityScoreDistribution_histogram.txt:md5,39d3430744e9139020d7af3eb15fc629",
+                "picard_alignment_readlength_plot.txt:md5,57ee2de637b69efc49290bb5d4b57905",
+                "picard_alignment_summary.txt:md5,3fee23a738a44ee84592cb1144b32775",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,dfb9e50700b61cdbc0344690db202559",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,5eec2a9bbb5db321c7cbbbee26d90357",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,5b100b42e93792fed754deb276645e61",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,d0317fe5ef2cf1b692526cb9a18aa50c",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,8aafe701b59b4e70ccec86748c7d6eb3",
+                "picard_quality_by_cycle.txt:md5,366ee22c93a11c1335f867020bb03da5",
+                "picard_quality_score_distribution.txt:md5,17d6f490cb59e16a7ed4b04ffaa1a100",
+                "fastq_screen_plot.txt:md5,db7c9231e756a6e5999399a7385e4687",
+                "fastqc-status-check-heatmap.txt:md5,fc37eaf184877ac80b92001a7bf2fa81",
+                "fastqc_overrepresented_sequences_plot.txt:md5,0693849fc324ddf580e2c5a4d910bb4f",
+                "fastqc_per_base_n_content_plot.txt:md5,0ed7f750b500e7c5387ea5309e1ef467",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,18016152915653e812818194a142e162",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,93f664e18c021aae79ad222fb4cfb393",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,ba96762be2aa842e1d2a606095ffcb7e",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,b9044bfe90fd5685137739f52a97ee2c",
+                "fastqc_sequence_counts_plot.txt:md5,42b26ad3758717659763c81852c4f197",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,818f13a5372bad79e54cd984758096c5",
+                "fastqc_sequence_length_distribution_plot.txt:md5,98316a2607a889ae1e7e79a4f64cc740",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,024e1e7f9db3b0906c7aa0904229e176",
+                "multiqc_fastqc.txt:md5,3407d8f06117a65efce4c70f19e91dd1",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,1debd96f9f64c60a8ec742411da51a28",
+                "multiqc_picard_baseContent.txt:md5,afb4046944e302b40faea2233bca535c",
+                "multiqc_picard_quality_by_cycle.txt:md5,6a7552b74dd22410c3cab2c750de792e",
+                "multiqc_picard_quality_score_distribution.txt:md5,d6343c5f39942bc3f10c194067e6e9bc",
+                "multiqc_seqfu_mqc.txt:md5,6cdb863a3686fbb772aae5a66925ff23",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,6a7552b74dd22410c3cab2c750de792e",
+                "picard_QualityScoreDistribution_histogram.txt:md5,d6343c5f39942bc3f10c194067e6e9bc",
+                "picard_alignment_readlength_plot.txt:md5,01140e65e813b4ae43aabe662ef2f49a",
+                "picard_alignment_summary.txt:md5,79312cf30761025cc6902811c4165290",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,3c3671ac2aa18d883691d59adbfe3b2b",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,6cc2ae1411899de5542321ff1592b192",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,326471bc846a9fb6b54ff38cbdfb8d90",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,3132dac406a9b9e1f18af658ab856a5c",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,0ed7f750b500e7c5387ea5309e1ef467",
+                "picard_quality_by_cycle.txt:md5,fe4e6ab1c849a4f833eae9a8554ea432",
+                "picard_quality_score_distribution.txt:md5,c0864f8a1269d8ffd7a51abb6bd3ca2e",
+                "fastq_screen_plot.txt:md5,4def6c6a888afe487ab6ebef3ba8a133",
+                "fastqc-status-check-heatmap.txt:md5,61857d2c45cf0c080348047aa34e7525",
+                "fastqc_overrepresented_sequences_plot.txt:md5,7949c64cc6cef77f29349a188fc09656",
+                "fastqc_per_base_n_content_plot.txt:md5,0f2fd628631d42ed5e6a1db22578daaa",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,0a8bfa32ab04eaaa509dec3c37acb2d2",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,8c85be0c70129ba739feceddd58f6c75",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,94b975906d8a07e1604e00d4004f7463",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,ec22c8e4836aa726680f0ca767c778a0",
+                "fastqc_sequence_counts_plot.txt:md5,f4341795bdeba588248a74a095a97f8d",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,8fc995cb2192a2926eee242681bc3af6",
+                "fastqc_sequence_length_distribution_plot.txt:md5,4513e22583677a4d6167b9094242eb0b",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,fd3074930c72b666f201ae71fa27744b",
+                "multiqc_fastqc.txt:md5,98111f17d1899cad6379e4e56ed11c53",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,3b1929de09267fc1c1a15804cb5bf536",
+                "multiqc_picard_baseContent.txt:md5,ff36be9e2642089aa711c637d3cdba29",
+                "multiqc_picard_quality_by_cycle.txt:md5,9521c83313eaf5f681ac9a75de83a4b7",
+                "multiqc_picard_quality_score_distribution.txt:md5,90b9e29f22fa16cf2b0c4d92caf2dbb0",
+                "multiqc_seqfu_mqc.txt:md5,f821357507fda2d4cfd9299f52fa7dc1",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,9521c83313eaf5f681ac9a75de83a4b7",
+                "picard_QualityScoreDistribution_histogram.txt:md5,90b9e29f22fa16cf2b0c4d92caf2dbb0",
+                "picard_alignment_readlength_plot.txt:md5,9c80659c5c9b2fe9926b789fb67ba6ac",
+                "picard_alignment_summary.txt:md5,27bbb1fcdeecd26641938e5622087c23",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,99c5e961a4d26754e68047c8eb983798",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,44981dd399013d8c06481958be338040",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,b6369a23d3926edb90ae9bfdc6d90526",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,b253d3fca7c07b6a6dfea91725c58102",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,0f2fd628631d42ed5e6a1db22578daaa",
+                "picard_quality_by_cycle.txt:md5,3c34ae2bd2442a816577b1a794add2d6",
+                "picard_quality_score_distribution.txt:md5,0d58c59eac2952e6f71cefc35d4c4477",
+                "fastq_screen_plot.txt:md5,5abb5b9ed2c976f0ad83216ca3186201",
+                "fastqc-status-check-heatmap.txt:md5,323d6082b73ddb6ee33385f5ea4301c1",
+                "fastqc_overrepresented_sequences_plot.txt:md5,4e71d8913d40eb06db0f18d74ce6898f",
+                "fastqc_per_base_n_content_plot.txt:md5,b317ce09cb7a2be2366b544ea9b20ce6",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,e6f44d08f4185f680d4748a3b37201e2",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a1dc8a968f32bcf8a9b4c5f43d299dfa",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,e41b6dc1344f1aee379993daff310187",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,76f792b939233b070562cc46617f6371",
+                "fastqc_sequence_counts_plot.txt:md5,36c68522023b8d536c9362403bf03c48",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,9ff0df466790d971b3c7ef838efc0f4f",
+                "fastqc_sequence_length_distribution_plot.txt:md5,9fda632b92e3453f11cd0226484fce8e",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,536c28d7fadc9a76944f93ac9d643272",
+                "multiqc_fastqc.txt:md5,396b4cc0466a6642ec8b954237c42263",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,153c6e6a407ec128b1a02798ca2f1115",
+                "multiqc_picard_baseContent.txt:md5,6349e514552a0b5a0530fa6f311878a5",
+                "multiqc_picard_quality_by_cycle.txt:md5,c0c8b4c0197428d4d50e2c532814e1e2",
+                "multiqc_picard_quality_score_distribution.txt:md5,40e0b6faa75e1b51af42407f7ededb0c",
+                "multiqc_seqfu_mqc.txt:md5,8cced36d66ca9d25d60c006e734aa7e9",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,c0c8b4c0197428d4d50e2c532814e1e2",
+                "picard_QualityScoreDistribution_histogram.txt:md5,40e0b6faa75e1b51af42407f7ededb0c",
+                "picard_alignment_readlength_plot.txt:md5,5a19b1f8e2ac49d97f36a7792429419c",
+                "picard_alignment_summary.txt:md5,f9f791b7c569cfae07aef70aa630d40e",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,0165f522c84da6b17a286d37dc30abec",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,6fa0d29d40fe7fa24c166b664b6d4f4b",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,bf2426e09ac1ca4773edfc284c220122",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,3cbace572471ccf6c58673181dd0c0ec",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,b317ce09cb7a2be2366b544ea9b20ce6",
+                "picard_quality_by_cycle.txt:md5,7cb705007bc97da8c0da7d93201e6975",
+                "picard_quality_score_distribution.txt:md5,47d684abae0a8f4f09df43e91d54fb9a",
+                "fastq_screen_plot.txt:md5,82ceb9f2109f865d6d1b943441c09550",
+                "fastqc-status-check-heatmap.txt:md5,56b426cd5c030288639533fce7c95ab1",
+                "fastqc_overrepresented_sequences_plot.txt:md5,8e83abdbe7362e64d63339ee31ab3361",
+                "fastqc_per_base_n_content_plot.txt:md5,33b70326d8f888ac5a3d99b85f365e43",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,40bc954cc0d58a3197fdf124a40f1ca4",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,e240e30996c81a34b5d1a6b5a98ae254",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,b44d3376d503af12857d494c58b514bb",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,66b5b6d44f398fc9429460c0b9ba3ea9",
+                "fastqc_sequence_counts_plot.txt:md5,6e5804f553f656cffb02f927015d1026",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,fbe41935ea2e2faf7104393b476e5ac5",
+                "fastqc_sequence_length_distribution_plot.txt:md5,e77dc4ab73252c2e09c7452c3b8e8ab3",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,4fc422d9cb06a1d0248cc578c1eebaa2",
+                "multiqc_fastqc.txt:md5,95c8ffb23baafec625aeb600047515ae",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,2d05e826f5152fd0143edf7270de1235",
+                "multiqc_picard_baseContent.txt:md5,f3f23899a30a96260d8b5b3020708703",
+                "multiqc_picard_quality_by_cycle.txt:md5,c7edfc271ab59ecedad0ab046afd3563",
+                "multiqc_picard_quality_score_distribution.txt:md5,7fa89b52b8bc96dd1074aa07cb5a5a54",
+                "multiqc_seqfu_mqc.txt:md5,ff4ce1c88f39ed24a88bae0a861f75c8",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,c7edfc271ab59ecedad0ab046afd3563",
+                "picard_QualityScoreDistribution_histogram.txt:md5,7fa89b52b8bc96dd1074aa07cb5a5a54",
+                "picard_alignment_readlength_plot.txt:md5,c1519319c4942162b05e6225fea10569",
+                "picard_alignment_summary.txt:md5,49f5c0d2cf21a13d5f363cb42cf3790e",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,466a14fc9c09f9f4de02a00e8763cd2a",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,d5854c22df4ac60b8c47c4002d975fe9",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,c27b5aa2b90397b1302b880dff3ec958",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,6f2a3e9d03f17a93c69476607a1a580d",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,33b70326d8f888ac5a3d99b85f365e43",
+                "picard_quality_by_cycle.txt:md5,0aa028d69d8bb02f0a2bcd0ed08f4235",
+                "picard_quality_score_distribution.txt:md5,a2882ff59902dc95830ed4bdb955561a",
+                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
+                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
+                "Sample1_01_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6",
+                "Sample1_01_seqfu_mqc.txt:md5,24d99524ccd0e6c6255a69d68a871c7a",
+                "Sample23_03_seqfu.tsv:md5,6fac5d3dbce3f3bee72341fe99a399dc",
+                "Sample23_03_seqfu_mqc.txt:md5,4d4f280911a08bb6b753142980178027",
+                "SampleA_02_seqfu.tsv:md5,aec811f267bb2a0ef066a7abb59d2775",
+                "SampleA_02_seqfu_mqc.txt:md5,a819409a5cb64e20c3e54ec5ada4aa27",
+                "Undetermined_05_seqfu.tsv:md5,3a42c5c66a0a118f1a6f6f6e560b0e7e",
+                "Undetermined_05_seqfu_mqc.txt:md5,bd8be908362c5cb08a72f8ae7ab41b0d",
+                "sampletest_04_seqfu.tsv:md5,a5bea0b9c6015dd1a201ffd433e9b377",
+                "sampletest_04_seqfu_mqc.txt:md5,2180961655bbc8a12f0152d6a4b803a2"
+            ],
+            [
+                "Sample1_01.bam:md5,d06ccfde49cc474faebcab2ebf71b324",
+                "Sample23_03.bam:md5,5ff9f554c6255fd07d3841c6616c5031",
+                "SampleA_02.bam:md5,250d0031520e59ee59a7112ab1ea32e1",
+                "Undetermined_05.bam:md5,8fcc158f1e0736b366152d5e187644ca",
+                "sampletest_04.bam:md5,f80371e37421d97499b3bfd55221ed00"
+            ],
+            [
+                "WARN: No samples with rundir found, skipping RUNDIRPARSER",
+                "WARN: Sample 'Sample1_01' does not have a rundir specified",
+                "WARN: Sample 'Sample23_03' does not have a rundir specified",
+                "WARN: Sample 'SampleA_02' does not have a rundir specified",
+                "WARN: Sample 'Undetermined_05' does not have a rundir specified",
+                "WARN: Sample 'sampletest_04' does not have a rundir specified",
+                "WARN: Tag name collision: [group1]",
+                "WARN: Tag name collision: [group2]",
+                "WARN: Tag name collision: [lane1]",
+                "WARN: Tag name collision: [test]"
             ]
         ],
+        "timestamp": "2026-02-17T10:46:58.253157108",
         "meta": {
-            "nf-test": "0.9.3",
+            "nf-test": "0.9.4",
             "nextflow": "25.10.4"
-        },
-        "timestamp": "2026-02-11T11:08:03.880392879"
+        }
     },
-    "NovaSeq6000 data test - No rundirs": {
+    "NovaSeq6000 data test sample size exceeds available reads": {
         "content": [
-            37,
+            43,
             {
                 "BWAMEM2_INDEX": {
                     "bwamem2": "2.2.1"
@@ -985,6 +3979,10 @@
                 "PICARD_COLLECTMULTIPLEMETRICS": {
                     "picard": "3.4.0"
                 },
+                "RUNDIRPARSER": {
+                    "PyYAML": "6.0.2",
+                    "Python": "3.13.2"
+                },
                 "SAMTOOLS_FAIDX": {
                     "samtools": "1.22.1"
                 },
@@ -993,6 +3991,9 @@
                 },
                 "SEQFU_STATS": {
                     "seqfu": "1.22.3"
+                },
+                "SEQTK_SAMPLE": {
+                    "seqtk": "1.4-r122"
                 }
             },
             [
@@ -1064,6 +4065,7 @@
                 "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/global_report/multiqc_data/multiqc_mqc_seq_metadata.txt",
                 "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
                 "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
                 "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
@@ -1099,6 +4101,7 @@
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/mqc_seq_metadata.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
@@ -1124,6 +4127,7 @@
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/global_report/multiqc_plots/png/mqc_seq_metadata.png",
                 "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
                 "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
@@ -1149,6 +4153,7 @@
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/global_report/multiqc_plots/svg/mqc_seq_metadata.svg",
                 "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
@@ -1184,6 +4189,7 @@
                 "multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_mqc_seq_metadata.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_picard_baseContent.txt",
                 "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
@@ -1219,6 +4225,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/mqc_seq_metadata.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
@@ -1244,6 +4251,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/mqc_seq_metadata.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_readlength_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-cnt.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-pct.png",
@@ -1269,6 +4277,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/mqc_seq_metadata.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-pct.svg",
@@ -1303,6 +4312,7 @@
                 "multiqc/group_reports/group2/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_mqc_seq_metadata.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_picard_baseContent.txt",
                 "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_by_cycle.txt",
@@ -1338,6 +4348,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/mqc_seq_metadata.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
@@ -1363,6 +4374,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/mqc_seq_metadata.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_readlength_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-cnt.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-pct.png",
@@ -1388,6 +4400,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/mqc_seq_metadata.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-pct.svg",
@@ -1422,6 +4435,7 @@
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_mqc_seq_metadata.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_baseContent.txt",
                 "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
@@ -1457,6 +4471,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/mqc_seq_metadata.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
@@ -1482,6 +4497,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/mqc_seq_metadata.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_readlength_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-cnt.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-pct.png",
@@ -1507,6 +4523,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/mqc_seq_metadata.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-pct.svg",
@@ -1541,6 +4558,7 @@
                 "multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_mqc_seq_metadata.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_picard_baseContent.txt",
                 "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_by_cycle.txt",
@@ -1576,6 +4594,7 @@
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/mqc_seq_metadata.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
@@ -1601,6 +4620,7 @@
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/group_reports/test/multiqc_plots/png/mqc_seq_metadata.png",
                 "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_readlength_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-cnt.png",
                 "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-pct.png",
@@ -1626,6 +4646,7 @@
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/mqc_seq_metadata.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-pct.svg",
@@ -1681,6 +4702,8 @@
                 "picard_collectmultiplemetrics/sampletest_04.CollectMultipleMetrics.read_length_histogram.pdf",
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
+                "rundirparser",
+                "rundirparser/200624_A00834_0183_BHMTFYDRXX_illumina_mqc.yml",
                 "samtools_faidx",
                 "samtools_faidx/genome.fa.fai",
                 "samtools_faidx/genome.fa.sizes",
@@ -1694,7 +4717,13 @@
                 "seqfu_stats/Undetermined_05_seqfu.tsv",
                 "seqfu_stats/Undetermined_05_seqfu_mqc.txt",
                 "seqfu_stats/sampletest_04_seqfu.tsv",
-                "seqfu_stats/sampletest_04_seqfu_mqc.txt"
+                "seqfu_stats/sampletest_04_seqfu_mqc.txt",
+                "seqtk",
+                "seqtk/Sample1_01_Sample1_S1_L001_R1_001.fastq.gz",
+                "seqtk/Sample23_03_Sample23_S3_L001_R1_001.fastq.gz",
+                "seqtk/SampleA_02_SampleA_S2_L001_R1_001.fastq.gz",
+                "seqtk/Undetermined_05_Undetermined_S0_L001_R1_001.fastq.gz",
+                "seqtk/sampletest_04_sampletest_S4_L001_R1_001.fastq.gz"
             ],
             [
                 "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
@@ -1702,15 +4731,15 @@
                 "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
                 "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
                 "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "Sample1_01_screen.png:md5,562256290643b51e4374c2225a15f463",
+                "Sample1_01_screen.png:md5,57b1664bc6c8e82cc0ce14802ad0dc0f",
                 "Sample1_01_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
-                "Sample23_03_screen.png:md5,6bb2caf67b9b2ed25d3d5f32c343e9ab",
+                "Sample23_03_screen.png:md5,41b4f556865a2f55a93f63e520812fad",
                 "Sample23_03_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
-                "SampleA_02_screen.png:md5,b2c3e95e034f5c038754bf108537de0e",
+                "SampleA_02_screen.png:md5,2f808877be53aa1433c1856bbf50feaf",
                 "SampleA_02_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
-                "Undetermined_05_screen.png:md5,fc5d53f8876dfae3d1a781fa512ea1db",
+                "Undetermined_05_screen.png:md5,12707698b2765c68566ccf5ac25479f5",
                 "Undetermined_05_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
-                "sampletest_04_screen.png:md5,1fb60070e8f4b70de0c1b3786b54f27e",
+                "sampletest_04_screen.png:md5,a88937eb54785ee921549d3c894df45d",
                 "sampletest_04_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28",
                 "fastq_screen_plot.txt:md5,990122d48fa4c1a170107a1ba034e4cf",
                 "fastqc-status-check-heatmap.txt:md5,7a64380ec42aac56949a2d9a4176d4d9",
@@ -1726,6 +4755,7 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,62240561100f78af37e7e2438cb58f90",
                 "multiqc_fastqc.txt:md5,23b698f1e957a26f49a9ad9bbdece908",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
                 "multiqc_picard_AlignmentSummaryMetrics.txt:md5,b113ea40790fa45fa739f224f2710556",
                 "multiqc_picard_baseContent.txt:md5,e06c0dea80cb5cef312436e005aa0095",
                 "multiqc_picard_quality_by_cycle.txt:md5,6e13ddbd97caa0eaa52c118966e5f9fa",
@@ -1758,6 +4788,7 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,024e1e7f9db3b0906c7aa0904229e176",
                 "multiqc_fastqc.txt:md5,3407d8f06117a65efce4c70f19e91dd1",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
                 "multiqc_picard_AlignmentSummaryMetrics.txt:md5,1debd96f9f64c60a8ec742411da51a28",
                 "multiqc_picard_baseContent.txt:md5,afb4046944e302b40faea2233bca535c",
                 "multiqc_picard_quality_by_cycle.txt:md5,6a7552b74dd22410c3cab2c750de792e",
@@ -1790,6 +4821,7 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,fd3074930c72b666f201ae71fa27744b",
                 "multiqc_fastqc.txt:md5,98111f17d1899cad6379e4e56ed11c53",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
                 "multiqc_picard_AlignmentSummaryMetrics.txt:md5,3b1929de09267fc1c1a15804cb5bf536",
                 "multiqc_picard_baseContent.txt:md5,ff36be9e2642089aa711c637d3cdba29",
                 "multiqc_picard_quality_by_cycle.txt:md5,9521c83313eaf5f681ac9a75de83a4b7",
@@ -1822,6 +4854,7 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,536c28d7fadc9a76944f93ac9d643272",
                 "multiqc_fastqc.txt:md5,396b4cc0466a6642ec8b954237c42263",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
                 "multiqc_picard_AlignmentSummaryMetrics.txt:md5,153c6e6a407ec128b1a02798ca2f1115",
                 "multiqc_picard_baseContent.txt:md5,6349e514552a0b5a0530fa6f311878a5",
                 "multiqc_picard_quality_by_cycle.txt:md5,c0c8b4c0197428d4d50e2c532814e1e2",
@@ -1854,6 +4887,7 @@
                 "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
                 "multiqc_fastq_screen.txt:md5,4fc422d9cb06a1d0248cc578c1eebaa2",
                 "multiqc_fastqc.txt:md5,95c8ffb23baafec625aeb600047515ae",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
                 "multiqc_picard_AlignmentSummaryMetrics.txt:md5,2d05e826f5152fd0143edf7270de1235",
                 "multiqc_picard_baseContent.txt:md5,f3f23899a30a96260d8b5b3020708703",
                 "multiqc_picard_quality_by_cycle.txt:md5,c7edfc271ab59ecedad0ab046afd3563",
@@ -1872,6 +4906,7 @@
                 "picard_base_distribution_by_cycle__Undetermined.txt:md5,33b70326d8f888ac5a3d99b85f365e43",
                 "picard_quality_by_cycle.txt:md5,0aa028d69d8bb02f0a2bcd0ed08f4235",
                 "picard_quality_score_distribution.txt:md5,a2882ff59902dc95830ed4bdb955561a",
+                "200624_A00834_0183_BHMTFYDRXX_illumina_mqc.yml:md5,29e05fed18bca0e9a857c992b6d59a40",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "Sample1_01_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6",
@@ -1883,7 +4918,12 @@
                 "Undetermined_05_seqfu.tsv:md5,3a42c5c66a0a118f1a6f6f6e560b0e7e",
                 "Undetermined_05_seqfu_mqc.txt:md5,bd8be908362c5cb08a72f8ae7ab41b0d",
                 "sampletest_04_seqfu.tsv:md5,a5bea0b9c6015dd1a201ffd433e9b377",
-                "sampletest_04_seqfu_mqc.txt:md5,2180961655bbc8a12f0152d6a4b803a2"
+                "sampletest_04_seqfu_mqc.txt:md5,2180961655bbc8a12f0152d6a4b803a2",
+                "Sample1_01_Sample1_S1_L001_R1_001.fastq.gz:md5,9f2f4855422bd18576efbc8af0368517",
+                "Sample23_03_Sample23_S3_L001_R1_001.fastq.gz:md5,036238392d51face00be9710c0c14523",
+                "SampleA_02_SampleA_S2_L001_R1_001.fastq.gz:md5,bcc1ed324745e894356ff3b66d023156",
+                "Undetermined_05_Undetermined_S0_L001_R1_001.fastq.gz:md5,2d64ba05e69ae081f95581cc8f0ffd36",
+                "sampletest_04_sampletest_S4_L001_R1_001.fastq.gz:md5,e81c2337941970a3bafa2c0adf8bebb1"
             ],
             [
                 "Sample1_01.bam:md5,d06ccfde49cc474faebcab2ebf71b324",
@@ -1891,12 +4931,23 @@
                 "SampleA_02.bam:md5,250d0031520e59ee59a7112ab1ea32e1",
                 "Undetermined_05.bam:md5,8fcc158f1e0736b366152d5e187644ca",
                 "sampletest_04.bam:md5,f80371e37421d97499b3bfd55221ed00"
+            ],
+            [
+                "WARN: Sample1_01: Requested sample_size (120) is larger than available reads (100). Pipeline will continue with 100 reads.",
+                "WARN: Sample23_03: Requested sample_size (120) is larger than available reads (100). Pipeline will continue with 100 reads.",
+                "WARN: SampleA_02: Requested sample_size (120) is larger than available reads (100). Pipeline will continue with 100 reads.",
+                "WARN: Tag name collision: [group1]",
+                "WARN: Tag name collision: [group2]",
+                "WARN: Tag name collision: [lane1]",
+                "WARN: Tag name collision: [test]",
+                "WARN: Undetermined_05: Requested sample_size (120) is larger than available reads (100). Pipeline will continue with 100 reads.",
+                "WARN: sampletest_04: Requested sample_size (120) is larger than available reads (100). Pipeline will continue with 100 reads."
             ]
         ],
+        "timestamp": "2026-02-17T15:53:46.460202138",
         "meta": {
-            "nf-test": "0.9.3",
+            "nf-test": "0.9.4",
             "nextflow": "25.10.4"
-        },
-        "timestamp": "2026-02-11T11:09:20.902763656"
+        }
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000_subsample.nf.test b/tests/NovaSeq6000_subsample.nf.test
deleted file mode 100644
index 510500d2..00000000
--- a/tests/NovaSeq6000_subsample.nf.test
+++ /dev/null
@@ -1,123 +0,0 @@
-nextflow_pipeline {
-
-    name "Test Workflow main.nf on NovaSeq6000 data with different sample sizes"
-    script "../main.nf"
-    tag "seqinspector"
-    tag "PIPELINE"
-
-    test("NovaSeq6000 data test sample size") {
-
-        when {
-            params {
-                sample_size = 90
-                outdir = "$outputDir"
-            }
-        }
-
-        then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(
-                params.outdir,
-                relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']
-            )
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(
-                params.outdir,
-                ignoreFile: 'tests/.nftignore'
-            )
-            // bam_files: All bam files
-            def bam_files  = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
-            assert workflow.success
-            assertAll(
-                { assert snapshot(
-                    workflow.trace.succeeded().size(),
-                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
-                    // All stable path names, with a relative path
-                    stable_name,
-                    // All files with stable contents
-                    stable_path,
-                    // All bam files
-                    bam_files.isEmpty() ? 'No BAM files' : bam_files.collect { file -> file.getName() + ":md5," +  bam(file.toString()).readsMD5 },
-                ).match() }
-            )
-        }
-    }
-
-    test("NovaSeq6000 data test relative sample size") {
-
-        when {
-            params {
-                outdir = "$outputDir"
-                sample_size = 0.9
-            }
-        }
-
-        then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(
-                params.outdir,
-                relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']
-            )
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(
-                params.outdir,
-                ignoreFile: 'tests/.nftignore'
-            )
-            // bam_files: All bam files
-            def bam_files  = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
-            assert workflow.success
-            assertAll(
-                { assert snapshot(
-                    workflow.trace.succeeded().size(),
-                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
-                    // All stable path names, with a relative path
-                    stable_name,
-                    // All files with stable contents
-                    stable_path,
-                    // All bam files
-                    bam_files.isEmpty() ? 'No BAM files' : bam_files.collect { file -> file.getName() + ":md5," +  bam(file.toString()).readsMD5 },
-                ).match() }
-            )
-        }
-    }
-
-    test("NovaSeq6000 data test sample size exceeds available reads") {
-        tag "warning"
-
-        when {
-            params {
-                outdir = "$outputDir"
-                sample_size = 120
-            }
-        }
-
-        then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(
-                params.outdir,
-                relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']
-            )
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(
-                params.outdir,
-                ignoreFile: 'tests/.nftignore'
-            )
-            assert workflow.success
-            assertAll(
-                { assert snapshot(
-                    workflow.trace.succeeded().size(),
-                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
-                    // All stable path names, with a relative path
-                    stable_name,
-                    // All files with stable contents
-                    stable_path,
-                    // get all messages containing Requested sample_size (120)
-                    filterNextflowOutput(workflow.stdout + workflow.stderr, ignore: ['Downloading plugin'], include:['Requested sample_size (120)'])
-                ).match() }
-            )
-        }
-    }
-}
diff --git a/tests/NovaSeq6000_subsample.nf.test.snap b/tests/NovaSeq6000_subsample.nf.test.snap
deleted file mode 100644
index 2c4df709..00000000
--- a/tests/NovaSeq6000_subsample.nf.test.snap
+++ /dev/null
@@ -1,2942 +0,0 @@
-{
-    "NovaSeq6000 data test sample size": {
-        "content": [
-            43,
-            {
-                "BWAMEM2_INDEX": {
-                    "bwamem2": "2.2.1"
-                },
-                "BWAMEM2_MEM": {
-                    "bwamem2": "2.2.1",
-                    "samtools": "1.22.1"
-                },
-                "FASTQC": {
-                    "fastqc": "0.12.1"
-                },
-                "FASTQSCREEN_FASTQSCREEN": {
-                    "fastqscreen": "0.16.0"
-                },
-                "PICARD_COLLECTMULTIPLEMETRICS": {
-                    "picard": "3.4.0"
-                },
-                "RUNDIRPARSER": {
-                    "PyYAML": "6.0.2",
-                    "Python": "3.13.2"
-                },
-                "SAMTOOLS_FAIDX": {
-                    "samtools": "1.22.1"
-                },
-                "SAMTOOLS_INDEX": {
-                    "samtools": "1.22.1"
-                },
-                "SEQFU_STATS": {
-                    "seqfu": "1.22.3"
-                },
-                "SEQTK_SAMPLE": {
-                    "seqtk": "1.4-r122"
-                }
-            },
-            [
-                "bwamem2_index",
-                "bwamem2_index/bwamem2",
-                "bwamem2_index/bwamem2/genome.fa.0123",
-                "bwamem2_index/bwamem2/genome.fa.amb",
-                "bwamem2_index/bwamem2/genome.fa.ann",
-                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
-                "bwamem2_index/bwamem2/genome.fa.pac",
-                "bwamem2_mem",
-                "bwamem2_mem/Sample1_01.bam",
-                "bwamem2_mem/Sample1_01.bam.bai",
-                "bwamem2_mem/Sample23_03.bam",
-                "bwamem2_mem/Sample23_03.bam.bai",
-                "bwamem2_mem/SampleA_02.bam",
-                "bwamem2_mem/SampleA_02.bam.bai",
-                "bwamem2_mem/Undetermined_05.bam",
-                "bwamem2_mem/Undetermined_05.bam.bai",
-                "bwamem2_mem/sampletest_04.bam",
-                "bwamem2_mem/sampletest_04.bam.bai",
-                "fastqc",
-                "fastqc/Sample1_01_fastqc.html",
-                "fastqc/Sample1_01_fastqc.zip",
-                "fastqc/Sample23_03_fastqc.html",
-                "fastqc/Sample23_03_fastqc.zip",
-                "fastqc/SampleA_02_fastqc.html",
-                "fastqc/SampleA_02_fastqc.zip",
-                "fastqc/Undetermined_05_fastqc.html",
-                "fastqc/Undetermined_05_fastqc.zip",
-                "fastqc/sampletest_04_fastqc.html",
-                "fastqc/sampletest_04_fastqc.zip",
-                "fastqscreen",
-                "fastqscreen/Sample1_01_screen.html",
-                "fastqscreen/Sample1_01_screen.png",
-                "fastqscreen/Sample1_01_screen.txt",
-                "fastqscreen/Sample23_03_screen.html",
-                "fastqscreen/Sample23_03_screen.png",
-                "fastqscreen/Sample23_03_screen.txt",
-                "fastqscreen/SampleA_02_screen.html",
-                "fastqscreen/SampleA_02_screen.png",
-                "fastqscreen/SampleA_02_screen.txt",
-                "fastqscreen/Undetermined_05_screen.html",
-                "fastqscreen/Undetermined_05_screen.png",
-                "fastqscreen/Undetermined_05_screen.txt",
-                "fastqscreen/sampletest_04_screen.html",
-                "fastqscreen/sampletest_04_screen.png",
-                "fastqscreen/sampletest_04_screen.txt",
-                "multiqc",
-                "multiqc/global_report",
-                "multiqc/global_report/multiqc_data",
-                "multiqc/global_report/multiqc_data/fastq_screen_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc-status-check-heatmap.txt",
-                "multiqc/global_report/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_base_n_content_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
-                "multiqc/global_report/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_counts_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
-                "multiqc/global_report/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
-                "multiqc/global_report/multiqc_data/llms-full.txt",
-                "multiqc/global_report/multiqc_data/multiqc.log",
-                "multiqc/global_report/multiqc_data/multiqc.parquet",
-                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
-                "multiqc/global_report/multiqc_data/multiqc_data.json",
-                "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt",
-                "multiqc/global_report/multiqc_data/multiqc_fastqc.txt",
-                "multiqc/global_report/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/global_report/multiqc_data/multiqc_mqc_seq_metadata.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt",
-                "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt",
-                "multiqc/global_report/multiqc_data/multiqc_seqfu_mqc.txt",
-                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
-                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
-                "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
-                "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt",
-                "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt",
-                "multiqc/global_report/multiqc_data/picard_alignment_summary.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt",
-                "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt",
-                "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt",
-                "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt",
-                "multiqc/global_report/multiqc_plots",
-                "multiqc/global_report/multiqc_plots/pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/mqc_seq_metadata.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf",
-                "multiqc/global_report/multiqc_plots/pdf/seqfu_mqc.pdf",
-                "multiqc/global_report/multiqc_plots/png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/global_report/multiqc_plots/png/mqc_seq_metadata.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png",
-                "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png",
-                "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png",
-                "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png",
-                "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png",
-                "multiqc/global_report/multiqc_plots/png/seqfu_mqc.png",
-                "multiqc/global_report/multiqc_plots/svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/global_report/multiqc_plots/svg/mqc_seq_metadata.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg",
-                "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg",
-                "multiqc/global_report/multiqc_plots/svg/seqfu_mqc.svg",
-                "multiqc/global_report/multiqc_report.html",
-                "multiqc/group_reports",
-                "multiqc/group_reports/group1",
-                "multiqc/group_reports/group1/multiqc_data",
-                "multiqc/group_reports/group1/multiqc_data/fastq_screen_plot.txt",
-                "multiqc/group_reports/group1/multiqc_data/fastqc-status-check-heatmap.txt",
-                "multiqc/group_reports/group1/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
-                "multiqc/group_reports/group1/multiqc_data/fastqc_per_base_n_content_plot.txt",
-                "multiqc/group_reports/group1/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
-                "multiqc/group_reports/group1/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
-                "multiqc/group_reports/group1/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
-                "multiqc/group_reports/group1/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
-                "multiqc/group_reports/group1/multiqc_data/fastqc_sequence_counts_plot.txt",
-                "multiqc/group_reports/group1/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
-                "multiqc/group_reports/group1/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
-                "multiqc/group_reports/group1/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
-                "multiqc/group_reports/group1/multiqc_data/llms-full.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc.log",
-                "multiqc/group_reports/group1/multiqc_data/multiqc.parquet",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_citations.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_data.json",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_mqc_seq_metadata.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_baseContent.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_by_cycle.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_score_distribution.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_seqfu_mqc.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt",
-                "multiqc/group_reports/group1/multiqc_data/multiqc_sources.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram.txt",
-                "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt",
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-                "multiqc_picard_baseContent.txt:md5,7ed6695c5554f6f1551f2567f308ea01",
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-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,d0d632d38536b19bc97f5ac62b444863",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,47304e11e4c0fd1c8c8042df11dca5db",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,0ff9eb3250403c1f9a9df4b6b82a22aa",
-                "fastqc_sequence_counts_plot.txt:md5,d5cfb1e359dba2b44d2b7fa472bc2fef",
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-                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,21a9dbbdd953f7ebb6c033ba306e1a01",
-                "multiqc_picard_baseContent.txt:md5,9b901100401ce73e796855de065df5af",
-                "multiqc_picard_quality_by_cycle.txt:md5,016dbbf3b0be86e17414a77c8e7c0381",
-                "multiqc_picard_quality_score_distribution.txt:md5,baf6e77f157dcc1996f3aa8db9da5b56",
-                "multiqc_seqfu_mqc.txt:md5,f821357507fda2d4cfd9299f52fa7dc1",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
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-                "picard_MeanQualityByCycle_histogram_1.txt:md5,016dbbf3b0be86e17414a77c8e7c0381",
-                "picard_QualityScoreDistribution_histogram.txt:md5,baf6e77f157dcc1996f3aa8db9da5b56",
-                "picard_alignment_readlength_plot.txt:md5,ee5232cd541865ddde9fc932d1130024",
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-                "picard_base_distribution_by_cycle__Adenine.txt:md5,9dc845e9ec5f5fb741910c264040cc20",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,2f0b3650a527e493d5453f2e553aa672",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,163cccc75b8cdd52a944ae6aeb310148",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,9e8533969c84fff8f21b0a59745b344d",
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-                "picard_quality_by_cycle.txt:md5,a91bd8ec5591b7691be3413de26a76f9",
-                "picard_quality_score_distribution.txt:md5,b3936076ba1dec38ebfed4b03683e25d",
-                "fastq_screen_plot.txt:md5,54da156526832b95f4ebcb8544a87f77",
-                "fastqc-status-check-heatmap.txt:md5,c762f9c764ff99a610ff1d20f2ed6ac9",
-                "fastqc_overrepresented_sequences_plot.txt:md5,c304e2ee82e3fd480a9261ac768f98b3",
-                "fastqc_per_base_n_content_plot.txt:md5,c91a58eb10a898afb7b46a7dd8e72e8e",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,3930d07c38244edfeaa3ef909e1d4ac6",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,939f27bfae0d13cbbc85ff87e1b3d0ac",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,0d2925e3cbbb6de2c7ec034c26f41066",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,4569ebf563c3fdb3b7bef648f72f3006",
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-                "fastqc_sequence_duplication_levels_plot.txt:md5,a25fb5ca8e2082719e7129975e7f8b10",
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-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
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-                "multiqc_fastqc.txt:md5,82b45154efad92fa6566283f39459d23",
-                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,16327d839dfc8bf38c43945fe6b6b1df",
-                "multiqc_picard_baseContent.txt:md5,41dee821ab6f6aee05ded4bf41accd56",
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-                "multiqc_picard_quality_score_distribution.txt:md5,2864d590f88cb98bd0c8446f1b023704",
-                "multiqc_seqfu_mqc.txt:md5,8cced36d66ca9d25d60c006e734aa7e9",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,0af7938734a17202d944927b64904da0",
-                "picard_QualityScoreDistribution_histogram.txt:md5,2864d590f88cb98bd0c8446f1b023704",
-                "picard_alignment_readlength_plot.txt:md5,d2a5ee7fc76fc836dd81f12954f01887",
-                "picard_alignment_summary.txt:md5,cd27671e33d03c39be8fdd1e2b4e0246",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,282d6515ae71162568393cb28407d690",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,8693a806def68f65092dfa13542ab364",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,05f621a1fbbf2164522bc7cbe8790120",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,bf1889ea4e03ad99640dc408dde567ac",
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-                "picard_quality_by_cycle.txt:md5,2ccee1b2cead246a4e784b15eac28361",
-                "picard_quality_score_distribution.txt:md5,9b79b5de2293427df2add8cffe505f06",
-                "fastq_screen_plot.txt:md5,70fc7c0be8d24dffcff69dd216345a07",
-                "fastqc-status-check-heatmap.txt:md5,56b426cd5c030288639533fce7c95ab1",
-                "fastqc_overrepresented_sequences_plot.txt:md5,04fc7769d72ff4af8bf5679944a4a875",
-                "fastqc_per_base_n_content_plot.txt:md5,e09d3616e0bb7a50f851736de22cdb85",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,2138b44091c3e1d237917e77b320e157",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,f44cfb45f4a6b980008e9c758ab0a5f4",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,c8b50edb245a50ab0f471d723ecd3f0e",
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-                "fastqc_sequence_counts_plot.txt:md5,0fac11b09160c9b8cd61721fafaab7a1",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,e2426a601d1706cd4e4ece85632d179a",
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-                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,edacee934f1117cde82eaf7c54558c6d",
-                "multiqc_picard_baseContent.txt:md5,1b238999a80cf0a2d3777bdf6874afcb",
-                "multiqc_picard_quality_by_cycle.txt:md5,ec4ad84c72e43ce0b4f700da56f6de8c",
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-                "multiqc_seqfu_mqc.txt:md5,ff4ce1c88f39ed24a88bae0a861f75c8",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,ec4ad84c72e43ce0b4f700da56f6de8c",
-                "picard_QualityScoreDistribution_histogram.txt:md5,c976a39d5e24cc258fea812e43d2c512",
-                "picard_alignment_readlength_plot.txt:md5,afcd9e8705eda64d2ea69af9be869329",
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-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,2f7d64788fb4f41a785893d7f296ca63",
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-                "200624_A00834_0183_BHMTFYDRXX_illumina_mqc.yml:md5,29e05fed18bca0e9a857c992b6d59a40",
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-                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
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-                "fastqc-status-check-heatmap.txt:md5,7a64380ec42aac56949a2d9a4176d4d9",
-                "fastqc_overrepresented_sequences_plot.txt:md5,c7908980f1dba22b45cf6de14a66a686",
-                "fastqc_per_base_n_content_plot.txt:md5,8aafe701b59b4e70ccec86748c7d6eb3",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,c2bbc52a285a46ab8c548bca3b721e13",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a422f61a00f0839ef0d630d2e4524589",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,0e5a0cd0b0f8e66b3617f1ac19822d77",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,cbaa7c7033c526483584376275a8b33e",
-                "fastqc_sequence_counts_plot.txt:md5,d8ab86dbfce0c740f4a66a080803a0b9",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,f86012b3074d697c9a2b3bd67a074288",
-                "fastqc_sequence_length_distribution_plot.txt:md5,9d4fd245e8e1d5baa473a8bdffcd3e38",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,62240561100f78af37e7e2438cb58f90",
-                "multiqc_fastqc.txt:md5,23b698f1e957a26f49a9ad9bbdece908",
-                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,b113ea40790fa45fa739f224f2710556",
-                "multiqc_picard_baseContent.txt:md5,e06c0dea80cb5cef312436e005aa0095",
-                "multiqc_picard_quality_by_cycle.txt:md5,6e13ddbd97caa0eaa52c118966e5f9fa",
-                "multiqc_picard_quality_score_distribution.txt:md5,39d3430744e9139020d7af3eb15fc629",
-                "multiqc_seqfu_mqc.txt:md5,18dd2407d4a1791646785123028f69b5",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,6e13ddbd97caa0eaa52c118966e5f9fa",
-                "picard_QualityScoreDistribution_histogram.txt:md5,39d3430744e9139020d7af3eb15fc629",
-                "picard_alignment_readlength_plot.txt:md5,57ee2de637b69efc49290bb5d4b57905",
-                "picard_alignment_summary.txt:md5,3fee23a738a44ee84592cb1144b32775",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,dfb9e50700b61cdbc0344690db202559",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,5eec2a9bbb5db321c7cbbbee26d90357",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,5b100b42e93792fed754deb276645e61",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,d0317fe5ef2cf1b692526cb9a18aa50c",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,8aafe701b59b4e70ccec86748c7d6eb3",
-                "picard_quality_by_cycle.txt:md5,366ee22c93a11c1335f867020bb03da5",
-                "picard_quality_score_distribution.txt:md5,17d6f490cb59e16a7ed4b04ffaa1a100",
-                "fastq_screen_plot.txt:md5,db7c9231e756a6e5999399a7385e4687",
-                "fastqc-status-check-heatmap.txt:md5,fc37eaf184877ac80b92001a7bf2fa81",
-                "fastqc_overrepresented_sequences_plot.txt:md5,0693849fc324ddf580e2c5a4d910bb4f",
-                "fastqc_per_base_n_content_plot.txt:md5,0ed7f750b500e7c5387ea5309e1ef467",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,18016152915653e812818194a142e162",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,93f664e18c021aae79ad222fb4cfb393",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,ba96762be2aa842e1d2a606095ffcb7e",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,b9044bfe90fd5685137739f52a97ee2c",
-                "fastqc_sequence_counts_plot.txt:md5,42b26ad3758717659763c81852c4f197",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,818f13a5372bad79e54cd984758096c5",
-                "fastqc_sequence_length_distribution_plot.txt:md5,98316a2607a889ae1e7e79a4f64cc740",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,024e1e7f9db3b0906c7aa0904229e176",
-                "multiqc_fastqc.txt:md5,3407d8f06117a65efce4c70f19e91dd1",
-                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,1debd96f9f64c60a8ec742411da51a28",
-                "multiqc_picard_baseContent.txt:md5,afb4046944e302b40faea2233bca535c",
-                "multiqc_picard_quality_by_cycle.txt:md5,6a7552b74dd22410c3cab2c750de792e",
-                "multiqc_picard_quality_score_distribution.txt:md5,d6343c5f39942bc3f10c194067e6e9bc",
-                "multiqc_seqfu_mqc.txt:md5,6cdb863a3686fbb772aae5a66925ff23",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,6a7552b74dd22410c3cab2c750de792e",
-                "picard_QualityScoreDistribution_histogram.txt:md5,d6343c5f39942bc3f10c194067e6e9bc",
-                "picard_alignment_readlength_plot.txt:md5,01140e65e813b4ae43aabe662ef2f49a",
-                "picard_alignment_summary.txt:md5,79312cf30761025cc6902811c4165290",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,3c3671ac2aa18d883691d59adbfe3b2b",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,6cc2ae1411899de5542321ff1592b192",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,326471bc846a9fb6b54ff38cbdfb8d90",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,3132dac406a9b9e1f18af658ab856a5c",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,0ed7f750b500e7c5387ea5309e1ef467",
-                "picard_quality_by_cycle.txt:md5,fe4e6ab1c849a4f833eae9a8554ea432",
-                "picard_quality_score_distribution.txt:md5,c0864f8a1269d8ffd7a51abb6bd3ca2e",
-                "fastq_screen_plot.txt:md5,4def6c6a888afe487ab6ebef3ba8a133",
-                "fastqc-status-check-heatmap.txt:md5,61857d2c45cf0c080348047aa34e7525",
-                "fastqc_overrepresented_sequences_plot.txt:md5,7949c64cc6cef77f29349a188fc09656",
-                "fastqc_per_base_n_content_plot.txt:md5,0f2fd628631d42ed5e6a1db22578daaa",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,0a8bfa32ab04eaaa509dec3c37acb2d2",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,8c85be0c70129ba739feceddd58f6c75",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,94b975906d8a07e1604e00d4004f7463",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,ec22c8e4836aa726680f0ca767c778a0",
-                "fastqc_sequence_counts_plot.txt:md5,f4341795bdeba588248a74a095a97f8d",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,8fc995cb2192a2926eee242681bc3af6",
-                "fastqc_sequence_length_distribution_plot.txt:md5,4513e22583677a4d6167b9094242eb0b",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,fd3074930c72b666f201ae71fa27744b",
-                "multiqc_fastqc.txt:md5,98111f17d1899cad6379e4e56ed11c53",
-                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,3b1929de09267fc1c1a15804cb5bf536",
-                "multiqc_picard_baseContent.txt:md5,ff36be9e2642089aa711c637d3cdba29",
-                "multiqc_picard_quality_by_cycle.txt:md5,9521c83313eaf5f681ac9a75de83a4b7",
-                "multiqc_picard_quality_score_distribution.txt:md5,90b9e29f22fa16cf2b0c4d92caf2dbb0",
-                "multiqc_seqfu_mqc.txt:md5,f821357507fda2d4cfd9299f52fa7dc1",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,9521c83313eaf5f681ac9a75de83a4b7",
-                "picard_QualityScoreDistribution_histogram.txt:md5,90b9e29f22fa16cf2b0c4d92caf2dbb0",
-                "picard_alignment_readlength_plot.txt:md5,9c80659c5c9b2fe9926b789fb67ba6ac",
-                "picard_alignment_summary.txt:md5,27bbb1fcdeecd26641938e5622087c23",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,99c5e961a4d26754e68047c8eb983798",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,44981dd399013d8c06481958be338040",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,b6369a23d3926edb90ae9bfdc6d90526",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,b253d3fca7c07b6a6dfea91725c58102",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,0f2fd628631d42ed5e6a1db22578daaa",
-                "picard_quality_by_cycle.txt:md5,3c34ae2bd2442a816577b1a794add2d6",
-                "picard_quality_score_distribution.txt:md5,0d58c59eac2952e6f71cefc35d4c4477",
-                "fastq_screen_plot.txt:md5,5abb5b9ed2c976f0ad83216ca3186201",
-                "fastqc-status-check-heatmap.txt:md5,323d6082b73ddb6ee33385f5ea4301c1",
-                "fastqc_overrepresented_sequences_plot.txt:md5,4e71d8913d40eb06db0f18d74ce6898f",
-                "fastqc_per_base_n_content_plot.txt:md5,b317ce09cb7a2be2366b544ea9b20ce6",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,e6f44d08f4185f680d4748a3b37201e2",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a1dc8a968f32bcf8a9b4c5f43d299dfa",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,e41b6dc1344f1aee379993daff310187",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,76f792b939233b070562cc46617f6371",
-                "fastqc_sequence_counts_plot.txt:md5,36c68522023b8d536c9362403bf03c48",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,9ff0df466790d971b3c7ef838efc0f4f",
-                "fastqc_sequence_length_distribution_plot.txt:md5,9fda632b92e3453f11cd0226484fce8e",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,536c28d7fadc9a76944f93ac9d643272",
-                "multiqc_fastqc.txt:md5,396b4cc0466a6642ec8b954237c42263",
-                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,153c6e6a407ec128b1a02798ca2f1115",
-                "multiqc_picard_baseContent.txt:md5,6349e514552a0b5a0530fa6f311878a5",
-                "multiqc_picard_quality_by_cycle.txt:md5,c0c8b4c0197428d4d50e2c532814e1e2",
-                "multiqc_picard_quality_score_distribution.txt:md5,40e0b6faa75e1b51af42407f7ededb0c",
-                "multiqc_seqfu_mqc.txt:md5,8cced36d66ca9d25d60c006e734aa7e9",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,c0c8b4c0197428d4d50e2c532814e1e2",
-                "picard_QualityScoreDistribution_histogram.txt:md5,40e0b6faa75e1b51af42407f7ededb0c",
-                "picard_alignment_readlength_plot.txt:md5,5a19b1f8e2ac49d97f36a7792429419c",
-                "picard_alignment_summary.txt:md5,f9f791b7c569cfae07aef70aa630d40e",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,0165f522c84da6b17a286d37dc30abec",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,6fa0d29d40fe7fa24c166b664b6d4f4b",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,bf2426e09ac1ca4773edfc284c220122",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,3cbace572471ccf6c58673181dd0c0ec",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,b317ce09cb7a2be2366b544ea9b20ce6",
-                "picard_quality_by_cycle.txt:md5,7cb705007bc97da8c0da7d93201e6975",
-                "picard_quality_score_distribution.txt:md5,47d684abae0a8f4f09df43e91d54fb9a",
-                "fastq_screen_plot.txt:md5,82ceb9f2109f865d6d1b943441c09550",
-                "fastqc-status-check-heatmap.txt:md5,56b426cd5c030288639533fce7c95ab1",
-                "fastqc_overrepresented_sequences_plot.txt:md5,8e83abdbe7362e64d63339ee31ab3361",
-                "fastqc_per_base_n_content_plot.txt:md5,33b70326d8f888ac5a3d99b85f365e43",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,40bc954cc0d58a3197fdf124a40f1ca4",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,e240e30996c81a34b5d1a6b5a98ae254",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,b44d3376d503af12857d494c58b514bb",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,66b5b6d44f398fc9429460c0b9ba3ea9",
-                "fastqc_sequence_counts_plot.txt:md5,6e5804f553f656cffb02f927015d1026",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,fbe41935ea2e2faf7104393b476e5ac5",
-                "fastqc_sequence_length_distribution_plot.txt:md5,e77dc4ab73252c2e09c7452c3b8e8ab3",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,4fc422d9cb06a1d0248cc578c1eebaa2",
-                "multiqc_fastqc.txt:md5,95c8ffb23baafec625aeb600047515ae",
-                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,2d05e826f5152fd0143edf7270de1235",
-                "multiqc_picard_baseContent.txt:md5,f3f23899a30a96260d8b5b3020708703",
-                "multiqc_picard_quality_by_cycle.txt:md5,c7edfc271ab59ecedad0ab046afd3563",
-                "multiqc_picard_quality_score_distribution.txt:md5,7fa89b52b8bc96dd1074aa07cb5a5a54",
-                "multiqc_seqfu_mqc.txt:md5,ff4ce1c88f39ed24a88bae0a861f75c8",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,c7edfc271ab59ecedad0ab046afd3563",
-                "picard_QualityScoreDistribution_histogram.txt:md5,7fa89b52b8bc96dd1074aa07cb5a5a54",
-                "picard_alignment_readlength_plot.txt:md5,c1519319c4942162b05e6225fea10569",
-                "picard_alignment_summary.txt:md5,49f5c0d2cf21a13d5f363cb42cf3790e",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,466a14fc9c09f9f4de02a00e8763cd2a",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,d5854c22df4ac60b8c47c4002d975fe9",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,c27b5aa2b90397b1302b880dff3ec958",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,6f2a3e9d03f17a93c69476607a1a580d",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,33b70326d8f888ac5a3d99b85f365e43",
-                "picard_quality_by_cycle.txt:md5,0aa028d69d8bb02f0a2bcd0ed08f4235",
-                "picard_quality_score_distribution.txt:md5,a2882ff59902dc95830ed4bdb955561a",
-                "200624_A00834_0183_BHMTFYDRXX_illumina_mqc.yml:md5,29e05fed18bca0e9a857c992b6d59a40",
-                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
-                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
-                "Sample1_01_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6",
-                "Sample1_01_seqfu_mqc.txt:md5,24d99524ccd0e6c6255a69d68a871c7a",
-                "Sample23_03_seqfu.tsv:md5,6fac5d3dbce3f3bee72341fe99a399dc",
-                "Sample23_03_seqfu_mqc.txt:md5,4d4f280911a08bb6b753142980178027",
-                "SampleA_02_seqfu.tsv:md5,aec811f267bb2a0ef066a7abb59d2775",
-                "SampleA_02_seqfu_mqc.txt:md5,a819409a5cb64e20c3e54ec5ada4aa27",
-                "Undetermined_05_seqfu.tsv:md5,3a42c5c66a0a118f1a6f6f6e560b0e7e",
-                "Undetermined_05_seqfu_mqc.txt:md5,bd8be908362c5cb08a72f8ae7ab41b0d",
-                "sampletest_04_seqfu.tsv:md5,a5bea0b9c6015dd1a201ffd433e9b377",
-                "sampletest_04_seqfu_mqc.txt:md5,2180961655bbc8a12f0152d6a4b803a2",
-                "Sample1_01_Sample1_S1_L001_R1_001.fastq.gz:md5,9f2f4855422bd18576efbc8af0368517",
-                "Sample23_03_Sample23_S3_L001_R1_001.fastq.gz:md5,036238392d51face00be9710c0c14523",
-                "SampleA_02_SampleA_S2_L001_R1_001.fastq.gz:md5,bcc1ed324745e894356ff3b66d023156",
-                "Undetermined_05_Undetermined_S0_L001_R1_001.fastq.gz:md5,2d64ba05e69ae081f95581cc8f0ffd36",
-                "sampletest_04_sampletest_S4_L001_R1_001.fastq.gz:md5,e81c2337941970a3bafa2c0adf8bebb1"
-            ],
-            [
-                "WARN: Sample1_01: Requested sample_size (120) is larger than available reads (100). Pipeline will continue with 100 reads.",
-                "WARN: Sample23_03: Requested sample_size (120) is larger than available reads (100). Pipeline will continue with 100 reads.",
-                "WARN: SampleA_02: Requested sample_size (120) is larger than available reads (100). Pipeline will continue with 100 reads.",
-                "WARN: Undetermined_05: Requested sample_size (120) is larger than available reads (100). Pipeline will continue with 100 reads.",
-                "WARN: sampletest_04: Requested sample_size (120) is larger than available reads (100). Pipeline will continue with 100 reads."
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.4"
-        },
-        "timestamp": "2026-02-11T11:13:08.854683994"
-    }
-}
\ No newline at end of file
diff --git a/tests/PromethION.nf.test b/tests/PromethION.nf.test
index c2402d43..c31f90e4 100644
--- a/tests/PromethION.nf.test
+++ b/tests/PromethION.nf.test
@@ -1,49 +1,23 @@
+def pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
+
 nextflow_pipeline {
 
-    name "Test Workflow main.nf on PromethION data"
+    name "Test pipeline"
     script "../main.nf"
-    tag "seqinspector"
-    tag "PIPELINE"
-
-    test("PromethION data test") {
 
-        when {
-            params {
-                pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
-                genome = 'EB1'
-                input  = params.pipelines_testdata_base_path + '/seqinspector/testdata/PromethION/samplesheet.csv'
-                outdir = "$outputDir"
-                skip_tools = "bwamem2_index,bwamem2_mem,rundirparser"
-            }
-        }
+    def test_scenario = [
+        [
+            name: "PromethION data test",
+            params: [
+                genome : 'EB1',
+                input: pipelines_testdata_base_path + 'seqinspector/testdata/PromethION/samplesheet.csv',
+                skip_tools: 'bwamem2_index,bwamem2_mem,rundirparser',
+            ]
+        ]
+    ]
 
-        then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(
-                params.outdir,
-                relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']
-            )
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(
-                params.outdir,
-                ignoreFile: 'tests/.nftignore'
-            )
-            // bam_files: All bam files
-            def bam_files  = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
-            assert workflow.success
-            assertAll(
-                { assert snapshot(
-                    workflow.trace.succeeded().size(),
-                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"),
-                    // All stable path names, with a relative path
-                    stable_name,
-                    // All files with stable contents
-                    stable_path,
-                    // All bam files
-                    bam_files.isEmpty() ? 'No BAM files' : bam_files.collect { file -> file.getName() + ":md5," +  bam(file.toString()).readsMD5 },
-                ).match() }
-            )
-        }
+    // Generate tests for each scenario
+    test_scenario.each { scenario ->
+        test(scenario.name, UTILS.getTest(scenario))
     }
 }
diff --git a/tests/PromethION.nf.test.snap b/tests/PromethION.nf.test.snap
index 71ce8690..1bbc1aa3 100644
--- a/tests/PromethION.nf.test.snap
+++ b/tests/PromethION.nf.test.snap
@@ -134,12 +134,13 @@
                 "hg001_01_seqfu.tsv:md5,b133752c897afbb4d8721b911fa117d4",
                 "hg001_01_seqfu_mqc.txt:md5,42e3506b02ceb72a6f05cb174505e722"
             ],
-            "No BAM files"
+            "No BAM files",
+            "No warnings"
         ],
+        "timestamp": "2026-02-17T10:30:18.833766777",
         "meta": {
-            "nf-test": "0.9.3",
+            "nf-test": "0.9.4",
             "nextflow": "25.10.4"
-        },
-        "timestamp": "2026-02-11T11:13:50.566732998"
+        }
     }
 }
\ No newline at end of file
diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy
new file mode 100644
index 00000000..e8549dad
--- /dev/null
+++ b/tests/lib/UTILS.groovy
@@ -0,0 +1,156 @@
+// Helper functions for pipeline tests
+
+class UTILS {
+
+    public static def getAssertions = { Map args ->
+        // Mandatory, as we always need an outdir
+        def outdir = args.outdir
+
+        // Get scenario and extract all properties dynamically
+        def scenario = args.scenario ?: [:]
+
+        // Pass down workflow for std capture
+        def workflow = args.workflow
+
+        // These strings are not stable and should be ignored
+        def snapshot_ignore_list = [
+            "Creating env using",
+            "Downloading plugin",
+            "Pulling Singularity image",
+            "Staging foreign file",
+            "unable to stage foreign file"
+        ]
+
+        // stable_name: All files + folders in ${outdir}/ with a stable name
+        def stable_name = getAllFilesFromDir(outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+        // stable_content: All files in ${outdir}/ with stable content
+        def stable_content = getAllFilesFromDir(outdir, ignoreFile: 'tests/.nftignore', ignore: [scenario.ignoreFiles ])
+        // bam_files: All bam files
+        def bam_files = getAllFilesFromDir(outdir, include: ['**/*.bam'], ignore: [scenario.ignoreFiles ])
+
+        def assertion = []
+
+        if (!scenario.failure) {
+            assertion.add(workflow.trace.succeeded().size())
+            assertion.add(removeFromYamlMap("${outdir}/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", "Workflow"))
+        }
+
+        // At least always pipeline_info/ is created and stable
+        assertion.add(stable_name)
+
+        if (!scenario.stub) {
+            assertion.add(stable_content.isEmpty() ? 'No stable content' : stable_content)
+            assertion.add(bam_files.isEmpty() ? 'No BAM files' : bam_files.collect { file -> file.getName() + ":md5," + bam(file.toString()).readsMD5 })
+        }
+
+        // If we have a snapshot options in scenario then we allow to capture either stderr, stdout or both
+        // With options to include specific stings
+        def workflow_std = []
+        // Otherwise, we always capture stdout and stderr for any WARN message
+        // Both have additional possibilities to ignore some strings
+        def filter_args = [ignore: snapshot_ignore_list + (scenario.snapshot_ignore ?: [])]
+
+        if (scenario.snapshot) {
+            workflow_std = scenario.snapshot.split(',')
+                .findAll { it in ['stderr', 'stdout'] }
+                .collect { workflow."$it" }
+                .flatten()
+
+            if (scenario.snapshot_include) { filter_args.include = [scenario.snapshot_include] }
+        } else {
+            workflow_std = workflow.stderr + workflow.stdout
+            filter_args.include = ["WARN"]
+        }
+
+        assertion.add(filterNextflowOutput(workflow_std, filter_args) ?: "No warnings")
+
+        return assertion
+    }
+
+    public static def getTest = { scenario ->
+        // This function returns a closure that will be used to run the test and the assertion
+        // It will create tags or options based on the scenario
+
+        return {
+            // If the test is for a gpu, we add the gpu tag
+            // Otherwise, we add the cpu tag
+            // If the tests has no conda incompatibilities
+            // then we append "_conda" to the cpu/gpu tag
+            // If the test is for a stub, we add options -stub
+            // And we append "_stub" to the cpu/gpu tag
+
+            // All options should be:
+            // gpu (this is the default for gpu)
+            // cpu (this is the default for tests without conda)
+            // gpu_conda (this should never happen)
+            // cpu_conda (this is the default for tests with conda compatibility)
+            // gpu_stub
+            // cpu_stub
+            // gpu_conda_stub (this should never happen)
+            // cpu_conda_stub
+
+            tag "pipeline"
+            tag "pipeline_seqinspector"
+
+            if (scenario.stub) {
+                options "-stub"
+            }
+
+            options "-output-dir $outputDir"
+
+            if (scenario.gpu) {
+                tag "gpu${!scenario.no_conda ? '_conda' : ''}${scenario.stub ? '_stub' : ''}"
+            }
+
+            if (!scenario.gpu) {
+                tag "cpu${!scenario.no_conda ? '_conda' : ''}${scenario.stub ? '_stub' : ''}"
+            }
+
+            // If a tag is provided, add it to the test
+            if (scenario.tag) {
+                tag scenario.tag
+            }
+
+            when {
+                params {
+                    // Mandatory, as we always need an outdir
+                    outdir = "${outputDir}"
+                    // Apply scenario-specific params
+                    scenario.params.each { key, value ->
+                        delegate."$key" = value
+                    }
+                }
+            }
+
+            then {
+                // Assert failure/success, and fails early so we don't pollute console with massive diffs
+                if (scenario.failure) {
+                    assert workflow.failed
+                } else {
+                    assert workflow.success
+                }
+                assertAll(
+                    { assert snapshot(
+                        // All assertions based on the scenario
+                        *UTILS.getAssertions(
+                            outdir: params.outdir,
+                            scenario: scenario,
+                            workflow: workflow
+                        )
+                    ).match() }
+                )
+            }
+            cleanup {
+                if (System.getenv('NFT_CLEANUP')) {
+                    println ""
+                    println "CLEANUP"
+                    println "Set NFT_CLEANUP to false to disable."
+                    println "The following folders will be deleted:"
+                    println "- ${workDir}"
+
+                    new File("${workDir}").deleteDir()
+                }
+            }
+        }
+    }
+}
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 1e2c94b0..3317f739 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -1,5 +1,3 @@
-include { samplesheetToList             } from 'plugin/nf-schema'
-
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS
@@ -28,7 +26,8 @@ include { methodsDescriptionText        } from '../subworkflows/local/utils_nfco
 include { paramsSummaryMap              } from 'plugin/nf-schema'
 include { paramsSummaryMultiqc          } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { reportIndexMultiqc            } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline'
-include { softwareVersionsToYAML        } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { samplesheetToList             } from 'plugin/nf-schema'
+include { softwareVersionsToYAML        } from 'plugin/nf-core-utils'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -39,9 +38,20 @@ include { softwareVersionsToYAML        } from '../subworkflows/nf-core/utils_nf
 workflow SEQINSPECTOR {
     take:
     ch_samplesheet // channel: samplesheet read in from --input
-    fasta_file
-    skip_tools
+    bait_intervals
     bwamem2
+    fasta_reference
+    fastq_screen_references
+    multiqc_config
+    multiqc_logo
+    multiqc_methods_description
+    outdir
+    ref_dict
+    run_picard_collecthsmetrics
+    sample_size
+    skip_tools
+    sort_bam
+    target_intervals
 
     main:
     ch_versions = channel.empty()
@@ -49,14 +59,13 @@ workflow SEQINSPECTOR {
     ch_multiqc_extra_files = channel.empty()
     ch_bwamem2_mem = channel.empty()
     ch_samtools_index = channel.empty()
-    ch_reference_fasta = fasta_file ? channel.fromPath(fasta_file, checkIfExists: true).map { file -> tuple([id: file.name], file) }.collect() : channel.value([[:], []])
 
     PREPARE_GENOME(
-        ch_reference_fasta,
+        fasta_reference,
         bwamem2,
         skip_tools,
-        params.run_picard_collecthsmetrics,
-        params.ref_dict,
+        run_picard_collecthsmetrics,
+        ref_dict,
     )
 
     ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions)
@@ -67,21 +76,19 @@ workflow SEQINSPECTOR {
     if (!("rundirparser" in skip_tools)) {
 
         // Branch the samplesheet channel based on rundir presence
-        ch_samplesheet
-            .branch { meta, reads ->
-                with_rundir: meta.rundir.size() > 0
-                without_rundir: true
-            }
-            .set { ch_rundir_branched }
+        ch_rundir_branch = ch_samplesheet.branch { meta, _reads ->
+            with_rundir: meta.rundir.size() > 0
+            without_rundir: true
+        }
 
         // Log warnings for samples without rundir
-        ch_rundir_branched.without_rundir.view { meta, reads ->
+        ch_rundir_branch.without_rundir.subscribe { meta, _reads ->
             log.warn("Sample '${meta.id}' does not have a rundir specified")
         }
 
         // From samplesheet channel serving (sampleMetaObj, sampleReadsPath) tuples:
         // --> Create new rundir channel serving (rundirMetaObj, rundirPath) tuples
-        ch_rundir = ch_rundir_branched.with_rundir
+        ch_rundir = ch_rundir_branch.with_rundir
             .map { meta, _reads -> [meta.rundir, meta] }
             .groupTuple()
             .map { rundir, metas ->
@@ -108,60 +115,45 @@ workflow SEQINSPECTOR {
     //
     // MODULE: Run Seqtk sample to perform subsampling
     //
-    if (!("seqtk_sample" in skip_tools) && params.sample_size > 0) {
-        ch_sample_sized = SEQTK_SAMPLE(
-            ch_samplesheet.map { meta, reads ->
-                [meta, reads, params.sample_size]
-            }
-        ).reads
+    if (!("seqtk_sample" in skip_tools) && sample_size > 0) {
+        SEQTK_SAMPLE(ch_samplesheet.map { meta, reads -> [meta, reads, sample_size] })
+
+        ch_sample = SEQTK_SAMPLE.out.reads
         ch_versions = ch_versions.mix(SEQTK_SAMPLE.out.versions)
     }
     else {
         // No subsampling
-        ch_sample_sized = ch_samplesheet
+        ch_sample = ch_samplesheet
     }
 
     //
     // MODULE: Run FastQC
     //
     if (!("fastqc" in skip_tools)) {
-        FASTQC(
-            ch_sample_sized.map { meta, subsampled ->
-                [meta, subsampled]
-            }
-        )
+        FASTQC(ch_sample)
+
         ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip)
         ch_versions = ch_versions.mix(FASTQC.out.versions)
     }
 
-
     //
     // Module: Run SeqFu stats
     //
     if (!("seqfu_stats" in skip_tools)) {
-        ch_seqfu_stats = SEQFU_STATS(
-            ch_samplesheet.map { meta, reads ->
-                [[id: "seqfu", sample_id: meta.id, tags: meta.tags], reads]
-            }
-        )
-        ch_seqfu_stats.stats
-            .map { meta, stats ->
-                {
-                    // Parse the stats TSV file
-                    [meta.sample_id, stats]
-                }
-            }
+        SEQFU_STATS(ch_samplesheet.map { meta, reads -> [[id: "seqfu", sample_id: meta.id, tags: meta.tags], reads] })
+
+        // Parse the stats TSV file
+        SEQFU_STATS.out.stats
+            .map { meta, stats -> [meta.sample_id, stats] }
             .splitCsv(header: true, sep: '\t')
             .map { sample_id, row ->
                 // Check if requested sample size exceeds available reads
                 def sample_reads = row['#Seq'].toInteger()
-                if (params.sample_size > sample_reads) {
-                    // prntln is used here instead of log.warn/log.info as nf-test captures stdout
-                    // from 'println' but buffers log messages making them unavailable for assertion
-                    // This message will appear in .nextflow.log file and temporarily on runtime stdout.
-                    log.warn("${sample_id}: Requested sample_size (${params.sample_size}) is larger than available reads (${sample_reads}). Pipeline will continue with ${sample_reads} reads.")
+                if (sample_size > sample_reads) {
+                    log.warn("${sample_id}: Requested sample_size (${sample_size}) is larger than available reads (${sample_reads}). Pipeline will continue with ${sample_reads} reads.")
                 }
             }
+
         ch_multiqc_files = ch_multiqc_files.mix(SEQFU_STATS.out.multiqc)
         ch_versions = ch_versions.mix(SEQFU_STATS.out.versions)
     }
@@ -176,7 +168,7 @@ workflow SEQINSPECTOR {
     if (!("fastqscreen" in skip_tools)) {
         ch_fastqscreen_refs = channel.fromList(
                 samplesheetToList(
-                    params.fastq_screen_references,
+                    fastq_screen_references,
                     "${projectDir}/assets/schema_fastq_screen_references.json",
                 )
             )
@@ -184,10 +176,8 @@ workflow SEQINSPECTOR {
             .transpose()
             .toList()
 
-        FASTQSCREEN_FASTQSCREEN(
-            ch_sample_sized,
-            ch_fastqscreen_refs,
-        )
+        FASTQSCREEN_FASTQSCREEN(ch_sample, ch_fastqscreen_refs)
+
         ch_multiqc_files = ch_multiqc_files.mix(FASTQSCREEN_FASTQSCREEN.out.txt)
         ch_versions = ch_versions.mix(FASTQSCREEN_FASTQSCREEN.out.versions)
     }
@@ -195,17 +185,16 @@ workflow SEQINSPECTOR {
     // MODULE: Align reads with BWA-MEM2
     if (!("bwamem2_mem" in skip_tools)) {
         BWAMEM2_MEM(
-            ch_sample_sized,
+            ch_sample,
             PREPARE_GENOME.out.bwamem2_index,
-            ch_reference_fasta,
-            params.sort_bam ?: true,
+            fasta_reference,
+            sort_bam ?: true,
         )
         ch_bwamem2_mem = BWAMEM2_MEM.out.bam
         ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions)
 
-        SAMTOOLS_INDEX(
-            ch_bwamem2_mem
-        )
+        SAMTOOLS_INDEX(ch_bwamem2_mem)
+
         ch_samtools_index = SAMTOOLS_INDEX.out.bai
         ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions)
     }
@@ -215,8 +204,8 @@ workflow SEQINSPECTOR {
 
         ch_reference_fai = PREPARE_GENOME.out.reference_fai
 
-        ch_bait_intervals = params.bait_intervals ? channel.fromPath(params.bait_intervals).collect() : channel.empty()
-        ch_target_intervals = params.target_intervals ? channel.fromPath(params.target_intervals).collect() : channel.empty()
+        ch_bait_intervals = bait_intervals ? channel.fromPath(bait_intervals).collect() : channel.empty()
+        ch_target_intervals = target_intervals ? channel.fromPath(target_intervals).collect() : channel.empty()
 
         ch_ref_dict = PREPARE_GENOME.out.ref_dict
 
@@ -224,9 +213,9 @@ workflow SEQINSPECTOR {
         QC_BAM(
             ch_bwamem2_mem,
             ch_samtools_index,
-            ch_reference_fasta,
+            fasta_reference,
             ch_reference_fai,
-            params.run_picard_collecthsmetrics,
+            run_picard_collecthsmetrics,
             ch_bait_intervals,
             ch_target_intervals,
             ch_ref_dict,
@@ -238,81 +227,46 @@ workflow SEQINSPECTOR {
 
     // Collate and save software versions
     //
-    def topic_versions = channel.topic("versions")
-        .distinct()
-        .branch { entry ->
-            versions_file: entry instanceof Path
-            versions_tuple: true
-        }
-
-    def topic_versions_string = topic_versions.versions_tuple
-        .map { process, tool, version ->
-            [process[process.lastIndexOf(':') + 1..-1], "  ${tool}: ${version}"]
-        }
-        .groupTuple(by: 0)
-        .map { process, tool_versions ->
-            tool_versions.unique().sort()
-            "${process}:\n${tool_versions.join('\n')}"
-        }
-
-    softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file))
-        .mix(topic_versions_string)
-        .collectFile(
-            storeDir: "${params.outdir}/pipeline_info",
-            name: 'nf_core_' + 'seqinspector_software_' + 'mqc_' + 'versions.yml',
-            sort: true,
-            newLine: true,
-        )
-        .set { ch_collated_versions }
-
+    def collated_versions = softwareVersionsToYAML(
+        softwareVersions: ch_versions.mix(channel.topic("versions")),
+        nextflowVersion: workflow.nextflow.version,
+    ).collectFile(
+        storeDir: "${outdir}/pipeline_info",
+        name: 'nf_core_' + 'seqinspector_software_' + 'mqc_' + 'versions.yml',
+        sort: true,
+        newLine: true,
+    )
 
     //
     // MODULE: MultiQC
     //
 
-    ch_tags = ch_multiqc_files
-        .map { meta, _sample -> meta.tags }
-        .flatten()
-        .unique()
+    ch_tags = ch_multiqc_files.map { meta, _sample -> meta.tags }.flatten().unique()
 
-    ch_multiqc_config = params.multiqc_config
-        ? channel.fromPath(params.multiqc_config, checkIfExists: true)
+    ch_multiqc_config = multiqc_config
+        ? channel.fromPath(multiqc_config, checkIfExists: true)
         : channel.fromPath("${projectDir}/assets/multiqc_config.yml", checkIfExists: true)
-    ch_multiqc_logo = params.multiqc_logo
-        ? channel.fromPath(params.multiqc_logo, checkIfExists: true)
+    ch_multiqc_logo = multiqc_logo
+        ? channel.fromPath(multiqc_logo, checkIfExists: true)
         : channel.empty()
 
-    summary_params = paramsSummaryMap(
-        workflow,
-        parameters_schema: "nextflow_schema.json"
-    )
-    ch_workflow_summary = channel.value(
-        paramsSummaryMultiqc(summary_params)
-    )
-    ch_multiqc_custom_methods_description = params.multiqc_methods_description
-        ? file(params.multiqc_methods_description, checkIfExists: true)
+    summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
+    ch_workflow_summary = channel.value(paramsSummaryMultiqc(summary_params))
+
+    ch_multiqc_custom_methods_description = multiqc_methods_description
+        ? file(multiqc_methods_description, checkIfExists: true)
         : file("${projectDir}/assets/methods_description_template.yml", checkIfExists: true)
-    ch_methods_description = channel.value(
-        methodsDescriptionText(ch_multiqc_custom_methods_description)
-    )
-    ch_multiqc_extra_files = ch_multiqc_extra_files.mix(
-        ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')
-    )
-    ch_multiqc_extra_files = ch_multiqc_extra_files.mix(ch_collated_versions)
+    ch_methods_description = channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
+
+    ch_multiqc_extra_files = ch_multiqc_extra_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+    ch_multiqc_extra_files = ch_multiqc_extra_files.mix(collated_versions)
     ch_multiqc_extra_files = ch_multiqc_extra_files.mix(
-        ch_methods_description.collectFile(
-            name: 'methods_description_mqc.yaml',
-            sort: true,
-        )
+        ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: true)
     )
     // Add index to other MultiQC reports
     //ch_multiqc_extra_files_global = channel.empty()
     ch_multiqc_extra_files_global = ch_multiqc_extra_files.mix(
-        ch_tags.toList().map { tag_list ->
-            reportIndexMultiqc(tag_list)
-        }.collectFile(
-            name: 'multiqc_index_mqc.yaml'
-        )
+        ch_tags.toList().map { tag_list -> reportIndexMultiqc(tag_list) }.collectFile(name: 'multiqc_index_mqc.yaml')
     )
 
     MULTIQC_GLOBAL(
@@ -343,7 +297,6 @@ workflow SEQINSPECTOR {
         .groupTuple()
         .tap { mqc_by_tag }
         .collectFile { sample_tag, _samples ->
-
             def prefix_tag = "[TAG:${sample_tag}]"
             [
                 "${prefix_tag}_multiqc_extra_config.yml",

From 57ce6cf766a69b47ccce9647e0fc31ab492df8ad Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 20 Feb 2026 13:11:29 +0100
Subject: [PATCH 528/530] Update all modules and subworkflows + migrate to
 topics versions (#175)

* update all modules and subworkflows

* snapshot for subworkflows

* fix conda setup

* update more modules

* no channel versions in qc_bam

* no channel versions in qc_bam

* update seqfu and picard
---
 .github/actions/nf-test/action.yml            |  2 +-
 CHANGELOG.md                                  |  2 +
 README.md                                     | 14 +++
 conf/modules.config                           | 31 +++---
 main.nf                                       |  1 -
 modules.json                                  | 35 ++++---
 modules/nf-core/bowtie2/build/main.nf         | 11 +--
 modules/nf-core/bowtie2/build/meta.yml        | 30 ++++--
 modules/nf-core/bwamem2/index/environment.yml |  6 +-
 modules/nf-core/bwamem2/index/main.nf         | 18 +---
 modules/nf-core/bwamem2/index/meta.yml        | 43 ++++++---
 modules/nf-core/bwamem2/mem/bwamem2-mem.diff  |  4 +-
 modules/nf-core/bwamem2/mem/main.nf           | 63 ++++++------
 modules/nf-core/bwamem2/mem/meta.yml          | 64 ++++++++++---
 modules/nf-core/fastqc/main.nf                | 18 +---
 modules/nf-core/fastqc/meta.yml               | 51 ++++++++--
 .../buildfromindex/environment.yml            |  3 +-
 .../fastqscreen-buildfromindex.diff           | 86 -----------------
 .../fastqscreen/buildfromindex/main.nf        | 20 +---
 .../fastqscreen/buildfromindex/meta.yml       | 32 +++++--
 .../fastqscreen/fastqscreen-fastqscreen.diff  | 87 +++--------------
 .../nf-core/fastqscreen/fastqscreen/main.nf   | 12 +--
 .../nf-core/fastqscreen/fastqscreen/meta.yml  | 26 +++--
 modules/nf-core/multiqc/environment.yml       |  2 +-
 modules/nf-core/multiqc/main.nf               | 43 ++++-----
 modules/nf-core/multiqc/meta.yml              | 45 +++++++--
 .../nf-core/picard/collecthsmetrics/main.nf   | 53 ++++-------
 .../nf-core/picard/collecthsmetrics/meta.yml  | 27 ++++--
 .../picard/collectmultiplemetrics/main.nf     | 37 +++-----
 .../picard/collectmultiplemetrics/meta.yml    | 28 ++++--
 .../picard/createsequencedictionary/main.nf   | 34 +++----
 .../picard/createsequencedictionary/meta.yml  | 26 +++--
 modules/nf-core/samtools/faidx/main.nf        | 16 +---
 modules/nf-core/samtools/faidx/meta.yml       | 38 +++++---
 modules/nf-core/samtools/index/main.nf        | 12 +--
 modules/nf-core/samtools/index/meta.yml       | 29 ++++--
 modules/nf-core/seqfu/stats/main.nf           | 28 ++----
 modules/nf-core/seqfu/stats/meta.yml          | 37 +++++---
 modules/nf-core/seqtk/sample/main.nf          | 12 +--
 modules/nf-core/seqtk/sample/meta.yml         | 30 ++++--
 ro-crate-metadata.json                        | 60 ++++++------
 subworkflows/local/prepare_genome/main.nf     | 10 +-
 .../local/prepare_genome/tests/main.nf.test   |  9 --
 .../prepare_genome/tests/main.nf.test.snap    | 65 +++----------
 subworkflows/local/qc_bam/main.nf             |  5 -
 subworkflows/local/qc_bam/tests/main.nf.test  |  6 --
 .../local/qc_bam/tests/main.nf.test.snap      | 35 ++-----
 .../nf-core/utils_nfschema_plugin/main.nf     |  3 +-
 tests/MiSeq.nf.test.snap                      | 29 +++---
 tests/NovaSeq6000.nf.test.snap                | 95 ++++++++++++++++---
 tests/PromethION.nf.test.snap                 |  7 +-
 workflows/seqinspector.nf                     | 13 +--
 52 files changed, 723 insertions(+), 770 deletions(-)
 delete mode 100644 modules/nf-core/fastqscreen/buildfromindex/fastqscreen-buildfromindex.diff

diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml
index 3b9724c7..356bc683 100644
--- a/.github/actions/nf-test/action.yml
+++ b/.github/actions/nf-test/action.yml
@@ -52,7 +52,7 @@ runs:
       with:
         auto-update-conda: true
         conda-solver: libmamba
-        channels: conda-forge
+        channels: conda-forge,bioconda
         channel-priority: strict
         conda-remove-defaults: true
 
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 91065c5f..b511d1ea 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -58,6 +58,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#172](https://github.com/nf-core/seqinspector/pull/172) More complete conda environment for rundir parser
 - [#173](https://github.com/nf-core/seqinspector/pull/173) Fix warning message for tag name collision
 - [#174](https://github.com/nf-core/seqinspector/pull/174) Fix null message when no rundir information is available
+- [#175](https://github.com/nf-core/seqinspector/pull/175) Fix conda setup in CI
 
 ### `Changed`
 
@@ -79,6 +80,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#174](https://github.com/nf-core/seqinspector/pull/174) Refactor tests
 - [#174](https://github.com/nf-core/seqinspector/pull/174) More strict syntax
 - [#174](https://github.com/nf-core/seqinspector/pull/174) No params included in workflows
+- [#175](https://github.com/nf-core/seqinspector/pull/175) Update all modules and migrate the whole pipeline to using topic versions
 
 ### `Dependencies`
 
diff --git a/README.md b/README.md
index 6add6b59..9c3da5b4 100644
--- a/README.md
+++ b/README.md
@@ -50,6 +50,20 @@ If provided, nf-core/seqinspector can also parse statistics from an Illumina run
   <img alt="Fallback image description" src="docs/images/seqinspector_tubemap_V1.0.png">
 </picture>
 
+### Summary of tools and version used in the pipeline
+
+| Tool        | Version |
+| ----------- | ------- |
+| bowtie2     | 2.5.4   |
+| bwamem2     | 2.3     |
+| fastqc      | 0.12.1  |
+| fastqscreen | 0.16.0  |
+| multiqc     | 1.33    |
+| picard      | 3.4.0   |
+| samtools    | 1.22.1  |
+| seqfu       | 1.22.3  |
+| seqtk       | 1.4     |
+
 ## Usage
 
 > [!NOTE]
diff --git a/conf/modules.config b/conf/modules.config
index a48d73ad..280b7b49 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -14,8 +14,7 @@ process {
 
     publishDir = [
         path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        mode: params.publish_dir_mode
     ]
 
     withName: 'SEQTK_SAMPLE' {
@@ -31,47 +30,42 @@ process {
         publishDir = [
             path: { "${params.outdir}/seqfu_stats" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.sample_id}_$filename" }
+            saveAs: { filename -> "${meta.sample_id}_${filename}" }
         ]
     }
 
     withName: 'BWAMEM2_INDEX' {
         publishDir = [
             path: { "${params.outdir}/bwamem2_index" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            mode: params.publish_dir_mode
         ]
     }
 
         withName: 'PICARD_CREATESEQUENCEDICTIONARY' {
         publishDir = [
             path: { "${params.outdir}/picard_createsequencedictionary" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            mode: params.publish_dir_mode
         ]
     }
 
     withName: 'BWAMEM2_MEM' {
         publishDir = [
             path: { "${params.outdir}/bwamem2_mem" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            mode: params.publish_dir_mode
         ]
     }
 
     withName: 'PICARD_COLLECTMULTIPLEMETRICS' {
         publishDir = [
             path: { "${params.outdir}/picard_collectmultiplemetrics" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            mode: params.publish_dir_mode
         ]
     }
 
     withName: 'PICARD_COLLECTHSMETRICS' {
         publishDir = [
             path: { "${params.outdir}/picard_collecthsmetrics" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            mode: params.publish_dir_mode
         ]
         ext.args = {"--TMP_DIR ."}
     }
@@ -79,16 +73,14 @@ process {
     withName: 'SAMTOOLS_FAIDX' {
         publishDir = [
             path: { "${params.outdir}/samtools_faidx" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            mode: params.publish_dir_mode
         ]
     }
 
     withName: 'SAMTOOLS_INDEX' {
         publishDir = [
             path: { "${params.outdir}/bwamem2_mem" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            mode: params.publish_dir_mode
         ]
     }
 
@@ -99,7 +91,7 @@ process {
             // The process _mqc.txt outputs should have identical names for the same sequencing platforms
             // in order to be grouped together in the MultiQC report, but here we need to enforce uniqueness
             // to avoid overwriting results in the publishDir.
-            saveAs: { filename -> "${meta.dirname}_$filename" }
+            saveAs: { filename -> "${meta.dirname}_${filename}" }
         ]
     }
 
@@ -107,8 +99,7 @@ process {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
             path: { "${params.outdir}/multiqc/global_report" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            mode: params.publish_dir_mode
         ]
     }
 
diff --git a/main.nf b/main.nf
index 595494a2..47460d4d 100644
--- a/main.nf
+++ b/main.nf
@@ -41,7 +41,6 @@ workflow NFCORE_SEQINSPECTOR {
     samplesheet // channel: samplesheet read in from --input
 
     main:
-
     //
     // WORKFLOW: Run pipeline
     //
diff --git a/modules.json b/modules.json
index e8a3d49f..b18b2a73 100644
--- a/modules.json
+++ b/modules.json
@@ -7,75 +7,74 @@
                 "nf-core": {
                     "bowtie2/build": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "447f7bc0fa41dfc2400c8cad4c0291880dc060cf",
                         "installed_by": ["modules"]
                     },
                     "bwamem2/index": {
                         "branch": "master",
-                        "git_sha": "b2902040b9cb9b7b32b62400f1c024a709bd4812",
+                        "git_sha": "5dd46a36fca68d6ad1a6b22ec47adc8c6863717d",
                         "installed_by": ["modules"]
                     },
                     "bwamem2/mem": {
                         "branch": "master",
-                        "git_sha": "d86336f3e7ae0d5f76c67b0859409769cfeb2af2",
+                        "git_sha": "8325a8155a77a336a613a504b8e4d6cea7a2344a",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/bwamem2/mem/bwamem2-mem.diff"
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "3009f27c4e4b6e99da4eeebe82799e13924a4a1f",
                         "installed_by": ["modules"]
                     },
                     "fastqscreen/buildfromindex": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/fastqscreen/buildfromindex/fastqscreen-buildfromindex.diff"
+                        "git_sha": "ab2e7b785ee4fa6d108472862edbf983cea7db49",
+                        "installed_by": ["modules"]
                     },
                     "fastqscreen/fastqscreen": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "ab2e7b785ee4fa6d108472862edbf983cea7db49",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff"
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "82a79183037a403ad1b6714e5dbcff25500efaf6",
+                        "git_sha": "575e1a4b51a9bad7a8cd1316a88fb85684ef7c7b",
                         "installed_by": ["modules"]
                     },
                     "picard/collecthsmetrics": {
                         "branch": "master",
-                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
+                        "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859",
                         "installed_by": ["modules"]
                     },
                     "picard/collectmultiplemetrics": {
                         "branch": "master",
-                        "git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255",
+                        "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859",
                         "installed_by": ["modules"]
                     },
                     "picard/createsequencedictionary": {
                         "branch": "master",
-                        "git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255",
+                        "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859",
                         "installed_by": ["modules"]
                     },
                     "samtools/faidx": {
                         "branch": "master",
-                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
+                        "git_sha": "b2e78932ef01165fd85829513eaca29eff8e640a",
                         "installed_by": ["modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
+                        "git_sha": "1d2fbdcbca677bbe8da0f9d0d2bb7c02f2cab1c9",
                         "installed_by": ["modules"]
                     },
                     "seqfu/stats": {
                         "branch": "master",
-                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
+                        "git_sha": "6b81c03dc4465ac9351b293dc6caada2a5e7556c",
                         "installed_by": ["modules"]
                     },
                     "seqtk/sample": {
                         "branch": "master",
-                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
+                        "git_sha": "a46713779030a5f508117080cbf4b693dd4c6e33",
                         "installed_by": ["modules"]
                     }
                 }
@@ -89,12 +88,12 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2",
+                        "git_sha": "65f5e638d901a51534c68fd5c1c19e8112fb4df1",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd",
+                        "git_sha": "fdc08b8b1ae74f56686ce21f7ea11ad11990ce57",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf
index fb7effec..1be06ac8 100644
--- a/modules/nf-core/bowtie2/build/main.nf
+++ b/modules/nf-core/bowtie2/build/main.nf
@@ -12,7 +12,7 @@ process BOWTIE2_BUILD {
 
     output:
     tuple val(meta), path('bowtie2')    , emit: index
-    path "versions.yml"                 , emit: versions
+    tuple val("${task.process}"), val('bowtie2'), eval('bowtie2 --version 2>&1 | head -1 | sed "s/^.*bowtie2-align-s version //; s/ .*//"'), emit: versions_bowtie2, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,10 +22,6 @@ process BOWTIE2_BUILD {
     """
     mkdir bowtie2
     bowtie2-build $args --threads $task.cpus $fasta bowtie2/${fasta.baseName}
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
-    END_VERSIONS
     """
 
     stub:
@@ -33,10 +29,5 @@ process BOWTIE2_BUILD {
     mkdir bowtie2
     touch bowtie2/${fasta.baseName}.{1..4}.bt2
     touch bowtie2/${fasta.baseName}.rev.{1,2}.bt2
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/bowtie2/build/meta.yml b/modules/nf-core/bowtie2/build/meta.yml
index 3e83ecb4..3a9d31cf 100644
--- a/modules/nf-core/bowtie2/build/meta.yml
+++ b/modules/nf-core/bowtie2/build/meta.yml
@@ -34,17 +34,33 @@ output:
             Groovy Map containing reference information
             e.g. [ id:'test', single_end:false ]
       - bowtie2:
-          type: file
+          type: directory
           description: Bowtie2 genome index files
           pattern: "*.bt2"
           ontologies: []
+  versions_bowtie2:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - bowtie2:
+          type: string
+          description: The name of the tool
+      - 'bowtie2 --version 2>&1 | head -1 | sed "s/^.*bowtie2-align-s version //; s/ .*//"':
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - bowtie2:
+          type: string
+          description: The name of the tool
+      - 'bowtie2 --version 2>&1 | head -1 | sed "s/^.*bowtie2-align-s version //; s/ .*//"':
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@joseespinosa"
   - "@drpatelh"
diff --git a/modules/nf-core/bwamem2/index/environment.yml b/modules/nf-core/bwamem2/index/environment.yml
index c069e281..f3637444 100644
--- a/modules/nf-core/bwamem2/index/environment.yml
+++ b/modules/nf-core/bwamem2/index/environment.yml
@@ -6,8 +6,8 @@ channels:
 
 dependencies:
   # renovate: datasource=conda depName=bioconda/bwa-mem2
-  - bwa-mem2=2.2.1
+  - bwa-mem2=2.3
   # renovate: datasource=conda depName=bioconda/htslib
-  - htslib=1.21
+  - htslib=1.22.1
   # renovate: datasource=conda depName=bioconda/samtools
-  - samtools=1.21
+  - samtools=1.22.1
diff --git a/modules/nf-core/bwamem2/index/main.nf b/modules/nf-core/bwamem2/index/main.nf
index 529c66e8..cb2c4bb2 100644
--- a/modules/nf-core/bwamem2/index/main.nf
+++ b/modules/nf-core/bwamem2/index/main.nf
@@ -2,19 +2,19 @@ process BWAMEM2_INDEX {
     tag "$fasta"
     // NOTE Requires 28N GB memory where N is the size of the reference sequence, floor of 280M
     // source: https://github.com/bwa-mem2/bwa-mem2/issues/9
-    memory { (280.MB * Math.ceil(fasta.size() / 10000000)) * task.attempt }
+    memory { 280.MB * Math.ceil(fasta.size() / 10000000) * task.attempt }
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9ac054213e67b3c9308e409b459080bbe438f8fd6c646c351bc42887f35a42e7/data' :
-        'community.wave.seqera.io/library/bwa-mem2_htslib_samtools:e1f420694f8e42bd' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e0/e05ce34b46ad42810eb29f74e4e304c0cb592b2ca15572929ed8bbaee58faf01/data' :
+        'community.wave.seqera.io/library/bwa-mem2_htslib_samtools:db98f81f55b64113' }"
 
     input:
     tuple val(meta), path(fasta)
 
     output:
     tuple val(meta), path("bwamem2"), emit: index
-    path "versions.yml"             , emit: versions
+    tuple val("${task.process}"), val('bwamem2'), eval('bwa-mem2 version | grep -o -E "[0-9]+(\\.[0-9]+)+"'), emit: versions_bwamem2, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -29,11 +29,6 @@ process BWAMEM2_INDEX {
         $args \\
         -p bwamem2/${prefix} \\
         $fasta
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
-    END_VERSIONS
     """
 
     stub:
@@ -46,10 +41,5 @@ process BWAMEM2_INDEX {
     touch bwamem2/${prefix}.pac
     touch bwamem2/${prefix}.amb
     touch bwamem2/${prefix}.bwt.2bit.64
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/bwamem2/index/meta.yml b/modules/nf-core/bwamem2/index/meta.yml
index b2aa45fb..12074860 100644
--- a/modules/nf-core/bwamem2/index/meta.yml
+++ b/modules/nf-core/bwamem2/index/meta.yml
@@ -12,7 +12,8 @@ tools:
         a large reference genome, such as the human genome.
       homepage: https://github.com/bwa-mem2/bwa-mem2
       documentation: https://github.com/bwa-mem2/bwa-mem2#usage
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: "biotools:bwa-mem2"
 input:
   - - meta:
@@ -24,8 +25,8 @@ input:
         type: file
         description: Input genome fasta file
         ontologies:
-          - edam: "http://edamontology.org/data_2044" # Sequence
-          - edam: "http://edamontology.org/format_1929" # FASTA
+          - edam: "http://edamontology.org/data_2044"
+          - edam: "http://edamontology.org/format_1929"
 output:
   index:
     - - meta:
@@ -34,18 +35,38 @@ output:
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
       - bwamem2:
-          type: file
+          type: string
           description: BWA genome index files
           pattern: "*.{0123,amb,ann,bwt.2bit.64,pac}"
           ontologies:
-            - edam: "http://edamontology.org/data_3210" # Genome index
+            - edam: "http://edamontology.org/data_3210"
+  versions_bwamem2:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - bwamem2:
+          type: string
+          description: BWA genome index files
+          pattern: "*.{0123,amb,ann,bwt.2bit.64,pac}"
+          ontologies:
+            - edam: "http://edamontology.org/data_3210"
+      - bwa-mem2 version | grep -o -E "[0-9]+(\.[0-9]+)+":
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - bwamem2:
+          type: string
+          description: BWA genome index files
+          pattern: "*.{0123,amb,ann,bwt.2bit.64,pac}"
+          ontologies:
+            - edam: "http://edamontology.org/data_3210"
+      - bwa-mem2 version | grep -o -E "[0-9]+(\.[0-9]+)+":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@maxulysse"
 maintainers:
diff --git a/modules/nf-core/bwamem2/mem/bwamem2-mem.diff b/modules/nf-core/bwamem2/mem/bwamem2-mem.diff
index be5074e8..c9127f46 100644
--- a/modules/nf-core/bwamem2/mem/bwamem2-mem.diff
+++ b/modules/nf-core/bwamem2/mem/bwamem2-mem.diff
@@ -6,12 +6,12 @@ Changes in 'bwamem2/mem/main.nf':
 +++ modules/nf-core/bwamem2/mem/main.nf
 @@ -1,6 +1,6 @@
  process BWAMEM2_MEM {
-     tag "$meta.id"
+     tag "${meta.id}"
 -    label 'process_high'
 +    label 'process_low'
  
      conda "${moduleDir}/environment.yml"
-     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+     container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
 
 'modules/nf-core/bwamem2/mem/tests/main.nf.test' is unchanged
 'modules/nf-core/bwamem2/mem/tests/main.nf.test.snap' is unchanged
diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf
index e12a68b0..92dfc72a 100644
--- a/modules/nf-core/bwamem2/mem/main.nf
+++ b/modules/nf-core/bwamem2/mem/main.nf
@@ -1,25 +1,26 @@
 process BWAMEM2_MEM {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e0/e05ce34b46ad42810eb29f74e4e304c0cb592b2ca15572929ed8bbaee58faf01/data' :
-        'community.wave.seqera.io/library/bwa-mem2_htslib_samtools:db98f81f55b64113' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e0/e05ce34b46ad42810eb29f74e4e304c0cb592b2ca15572929ed8bbaee58faf01/data'
+        : 'community.wave.seqera.io/library/bwa-mem2_htslib_samtools:db98f81f55b64113'}"
 
     input:
     tuple val(meta), path(reads)
     tuple val(meta2), path(index)
     tuple val(meta3), path(fasta)
-    val   sort_bam
+    val sort_bam
 
     output:
-    tuple val(meta), path("*.sam")  , emit: sam , optional:true
-    tuple val(meta), path("*.bam")  , emit: bam , optional:true
-    tuple val(meta), path("*.cram") , emit: cram, optional:true
-    tuple val(meta), path("*.crai") , emit: crai, optional:true
-    tuple val(meta), path("*.csi")  , emit: csi , optional:true
-    path  "versions.yml"            , emit: versions
+    tuple val(meta), path("*.sam"), emit: sam, optional: true
+    tuple val(meta), path("*.bam"), emit: bam, optional: true
+    tuple val(meta), path("*.cram"), emit: cram, optional: true
+    tuple val(meta), path("*.crai"), emit: crai, optional: true
+    tuple val(meta), path("*.csi"), emit: csi, optional: true
+    tuple val("${task.process}"), val('bwamem2'), eval('bwa-mem2 version | grep -o -E "[0-9]+(\\.[0-9]+)+"'), emit: versions_bwamem2, topic: versions
+    tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), emit: versions_samtools, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -31,53 +32,43 @@ process BWAMEM2_MEM {
     def samtools_command = sort_bam ? 'sort' : 'view'
 
     def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/
-    def extension_matcher =  (args2 =~ extension_pattern)
+    def extension_matcher = (args2 =~ extension_pattern)
     def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam"
-    def reference = fasta && extension=="cram"  ? "--reference ${fasta}" : ""
-    if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output"
-
+    def reference = fasta && extension == "cram" ? "--reference ${fasta}" : ""
+    if (!fasta && extension == "cram") {
+        error("Fasta reference is required for CRAM output")
+    }
     """
     INDEX=`find -L ./ -name "*.amb" | sed 's/\\.amb\$//'`
 
     bwa-mem2 \\
         mem \\
-        $args \\
-        -t $task.cpus \\
+        ${args} \\
+        -t ${task.cpus} \\
         \$INDEX \\
-        $reads \\
-        | samtools $samtools_command $args2 -@ $task.cpus ${reference} -o ${prefix}.${extension} -
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
+        ${reads} \\
+        | samtools ${samtools_command} ${args2} -@ ${task.cpus} ${reference} -o ${prefix}.${extension} -
     """
 
     stub:
-
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/
-    def extension_matcher =  (args2 =~ extension_pattern)
+    def extension_matcher = (args2 =~ extension_pattern)
     def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam"
-    if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output"
+    if (!fasta && extension == "cram") {
+        error("Fasta reference is required for CRAM output")
+    }
 
     def create_index = ""
     if (extension == "cram") {
         create_index = "touch ${prefix}.crai"
-    } else if (extension == "bam") {
+    }
+    else if (extension == "bam") {
         create_index = "touch ${prefix}.csi"
     }
-
     """
     touch ${prefix}.${extension}
     ${create_index}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/bwamem2/mem/meta.yml b/modules/nf-core/bwamem2/mem/meta.yml
index 6c7d1728..a60d6788 100644
--- a/modules/nf-core/bwamem2/mem/meta.yml
+++ b/modules/nf-core/bwamem2/mem/meta.yml
@@ -16,7 +16,8 @@ tools:
       homepage: https://github.com/bwa-mem2/bwa-mem2
       documentation: http://www.htslib.org/doc/samtools.html
       arxiv: arXiv:1303.3997
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: "biotools:bwa-mem2"
 input:
   - - meta:
@@ -30,8 +31,8 @@ input:
           List of input FastQ files of size 1 and 2 for single-end and paired-end data,
           respectively.
         ontologies:
-          - edam: "http://edamontology.org/data_2044" # Sequence
-          - edam: "http://edamontology.org/format_1930" # FASTQ
+          - edam: "http://edamontology.org/data_2044"
+          - edam: "http://edamontology.org/format_1930"
   - - meta2:
         type: map
         description: |
@@ -42,7 +43,7 @@ input:
         description: BWA genome index files
         pattern: "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}"
         ontologies:
-          - edam: "http://edamontology.org/data_3210" # Genome index
+          - edam: "http://edamontology.org/data_3210"
   - - meta3:
         type: map
         description: |
@@ -53,8 +54,8 @@ input:
         description: Reference genome in FASTA format
         pattern: "*.{fa,fasta,fna}"
         ontologies:
-          - edam: "http://edamontology.org/data_2044" # Sequence
-          - edam: "http://edamontology.org/format_1929" # FASTA
+          - edam: "http://edamontology.org/data_2044"
+          - edam: "http://edamontology.org/format_1929"
   - sort_bam:
       type: boolean
       description: use samtools sort (true) or samtools view (false)
@@ -71,7 +72,7 @@ output:
           description: Output SAM file containing read alignments
           pattern: "*.{sam}"
           ontologies:
-            - edam: "http://edamontology.org/format_2573" # SAM
+            - edam: "http://edamontology.org/format_2573"
   bam:
     - - meta:
           type: map
@@ -83,7 +84,7 @@ output:
           description: Output BAM file containing read alignments
           pattern: "*.{bam}"
           ontologies:
-            - edam: "http://edamontology.org/format_2572" # BAM
+            - edam: "http://edamontology.org/format_2572"
   cram:
     - - meta:
           type: map
@@ -95,7 +96,7 @@ output:
           description: Output CRAM file containing read alignments
           pattern: "*.{cram}"
           ontologies:
-            - edam: "http://edamontology.org/format_3462" # CRAM
+            - edam: "http://edamontology.org/format_3462"
   crai:
     - - meta:
           type: map
@@ -118,13 +119,46 @@ output:
           description: Index file for BAM file
           pattern: "*.{csi}"
           ontologies: []
+  versions_bwamem2:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - bwamem2:
+          type: string
+          description: The name of the tool
+      - bwa-mem2 version | grep -o -E "[0-9]+(\.[0-9]+)+":
+          type: eval
+          description: The expression to obtain the version of the tool
+  versions_samtools:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - samtools:
+          type: string
+          description: The name of the tool
+      - samtools version | sed '1!d;s/.* //':
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - bwamem2:
+          type: string
+          description: The name of the tool
+      - bwa-mem2 version | grep -o -E "[0-9]+(\.[0-9]+)+":
+          type: eval
+          description: The expression to obtain the version of the tool
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - samtools:
+          type: string
+          description: The name of the tool
+      - samtools version | sed '1!d;s/.* //':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@maxulysse"
   - "@matthdsm"
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 23e16634..f5629527 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -1,6 +1,6 @@
 process FASTQC {
     tag "${meta.id}"
-    label 'process_medium'
+    label 'process_low'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -11,9 +11,9 @@ process FASTQC {
     tuple val(meta), path(reads)
 
     output:
-    tuple val(meta), path("*.html"), emit: html
-    tuple val(meta), path("*.zip") , emit: zip
-    path  "versions.yml"           , emit: versions
+    tuple val(meta)             , path("*.html")                                                       , emit: html
+    tuple val(meta)             , path("*.zip")                                                        , emit: zip
+    tuple val("${task.process}"), val('fastqc'), eval('fastqc --version | sed "/FastQC v/!d; s/.*v//"'), emit: versions_fastqc, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -43,11 +43,6 @@ process FASTQC {
         --threads ${task.cpus} \\
         --memory ${fastqc_memory} \\
         ${renamed_files}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
-    END_VERSIONS
     """
 
     stub:
@@ -55,10 +50,5 @@ process FASTQC {
     """
     touch ${prefix}.html
     touch ${prefix}.zip
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
index c8d9d025..49164c88 100644
--- a/modules/nf-core/fastqc/meta.yml
+++ b/modules/nf-core/fastqc/meta.yml
@@ -53,13 +53,28 @@ output:
           description: FastQC report archive
           pattern: "*_{fastqc.zip}"
           ontologies: []
+  versions_fastqc:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - fastqc:
+          type: string
+          description: The tool name
+      - fastqc --version | sed "/FastQC v/!d; s/.*v//":
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - fastqc:
+          type: string
+          description: The tool name
+      - fastqc --version | sed "/FastQC v/!d; s/.*v//":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@drpatelh"
   - "@grst"
@@ -70,3 +85,27 @@ maintainers:
   - "@grst"
   - "@ewels"
   - "@FelixKrueger"
+containers:
+  conda:
+    linux_amd64:
+      lock_file: https://wave.seqera.io/v1alpha1/builds/bd-af7a5314d5015c29_1/condalock
+    linux_arm64:
+      lock_file: https://wave.seqera.io/v1alpha1/builds/bd-df99cb252670875a_2/condalock
+  docker:
+    linux_amd64:
+      build_id: bd-af7a5314d5015c29_1
+      name: community.wave.seqera.io/library/fastqc:0.12.1--af7a5314d5015c29
+      scanId: sc-a618548acbee5a8a_30
+    linux_arm64:
+      build_id: bd-df99cb252670875a_2
+      name: community.wave.seqera.io/library/fastqc:0.12.1--df99cb252670875a
+      scanId: sc-b5913ed5d42b22d2_18
+  singularity:
+    linux_amd64:
+      build_id: bd-104d26ddd9519960_1
+      name: oras://community.wave.seqera.io/library/fastqc:0.12.1--104d26ddd9519960
+      https: https://community.wave.seqera.io/v2/library/fastqc/blobs/sha256:e0c976cb2eca5fee72618a581537a4f8ea42fcae24c9b201e2e0f764fd28648a
+    linux_arm64:
+      build_id: bd-d56b505a93aef38a_1
+      name: oras://community.wave.seqera.io/library/fastqc:0.12.1--d56b505a93aef38a
+      https: https://community.wave.seqera.io/v2/library/fastqc/blobs/sha256:fd39534bf298698cbe3ee4d4a6f1e73330ec4bca44c38dd9a4d06cb5ea838017
diff --git a/modules/nf-core/fastqscreen/buildfromindex/environment.yml b/modules/nf-core/fastqscreen/buildfromindex/environment.yml
index 3b3ba521..9ff968c9 100644
--- a/modules/nf-core/fastqscreen/buildfromindex/environment.yml
+++ b/modules/nf-core/fastqscreen/buildfromindex/environment.yml
@@ -4,4 +4,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::fastq-screen=0.15.3
+  - bioconda::fastq-screen=0.16.0
+  - bioconda::perl-gdgraph=1.54
diff --git a/modules/nf-core/fastqscreen/buildfromindex/fastqscreen-buildfromindex.diff b/modules/nf-core/fastqscreen/buildfromindex/fastqscreen-buildfromindex.diff
deleted file mode 100644
index 9333012d..00000000
--- a/modules/nf-core/fastqscreen/buildfromindex/fastqscreen-buildfromindex.diff
+++ /dev/null
@@ -1,86 +0,0 @@
-Changes in component 'nf-core/fastqscreen/buildfromindex'
-'modules/nf-core/fastqscreen/buildfromindex/meta.yml' is unchanged
-'modules/nf-core/fastqscreen/buildfromindex/environment.yml' is unchanged
-Changes in 'fastqscreen/buildfromindex/main.nf':
---- modules/nf-core/fastqscreen/buildfromindex/main.nf
-+++ modules/nf-core/fastqscreen/buildfromindex/main.nf
-@@ -2,39 +2,39 @@
-     label 'process_single'
- 
-     conda "${moduleDir}/environment.yml"
--    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
--        'https://depot.galaxyproject.org/singularity/fastq-screen:0.15.3--pl5321hdfd78af_0':
--        'biocontainers/fastq-screen:0.15.3--pl5321hdfd78af_0'}"
-+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-+        ? 'https://depot.galaxyproject.org/singularity/fastq-screen:0.15.3--pl5321hdfd78af_0'
-+        : 'biocontainers/fastq-screen:0.15.3--pl5321hdfd78af_0'}"
- 
-     input:
--    val(genome_names)
--    path(indexes), stageAs: "dir*"
-+    val genome_names
-+    path (indexes), stageAs: "dir*"
- 
-     output:
--    path("FastQ_Screen_Genomes"), emit: database
--    path "versions.yml"         , emit: versions
-+    path ("FastQ_Screen_Genomes"), emit: database
-+    path "versions.yml", emit: versions
- 
-     when:
-     task.ext.when == null || task.ext.when
- 
-     script:
-     dir = "FastQ_Screen_Genomes"
--    folder = indexes.collect { it.toString() }
-+    folder = indexes.collect { index -> index.toString() }
-     database = [genome_names, folder].transpose()
--    copy_indexes = folder.collect { "cp -r ${it} $dir/${it}"}.join(" && ")
-+    copy_indexes = folder.collect { file -> "cp -r ${file} ${dir}/${file}" }.join(" && ")
- 
-     // Folder name and index (within folder) name could be different - use bash to look for index name
-     config = database
--        .collect { "########## ${it[0]} \nDATABASE ${it[0]} $dir/${it[1]}/${it[1] + '_to_be_replaced'}" }
-+        .collect { file -> "########## ${file[0]} \nDATABASE ${file[0]} ${dir}/${file[1]}/${file[1] + '_to_be_replaced'}" }
-         .join("\n\n")
-         .replace("\n", "\\n")
- 
-     """
--    mkdir $dir
--    $copy_indexes
-+    mkdir ${dir}
-+    ${copy_indexes}
- 
--    echo "$config" > fastq_screen.conf
--    sed 's/\\\\n/\\n/g' fastq_screen.conf > $dir/fastq_screen.conf
-+    echo "${config}" > fastq_screen.conf
-+    sed 's/\\\\n/\\n/g' fastq_screen.conf > ${dir}/fastq_screen.conf
-     echo "Replace folder name real index name"
- 
-     for f in ${folder.join(' ')}
-@@ -45,8 +45,8 @@
-         REPLACE_WITH=\$(basename \$REPLACE_WITH)
-         REPLACE_WITH=\${REPLACE_WITH%%.rev.1.bt2}
- 
--        sed "s/\$TO_REPLACE/\$REPLACE_WITH/g" $dir/fastq_screen.conf > new_conf.conf
--        mv new_conf.conf $dir/fastq_screen.conf
-+        sed "s/\$TO_REPLACE/\$REPLACE_WITH/g" ${dir}/fastq_screen.conf > new_conf.conf
-+        mv new_conf.conf ${dir}/fastq_screen.conf
-     done
- 
-     cat <<-END_VERSIONS > versions.yml
-@@ -58,8 +58,8 @@
-     stub:
-     dir = "FastQ_Screen_Genomes"
-     """
--    mkdir $dir
--    touch $dir/fastq_screen.conf
-+    mkdir ${dir}
-+    touch ${dir}/fastq_screen.conf
- 
-     cat <<-END_VERSIONS > versions.yml
-     "${task.process}":
-
-'modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test' was removed
-'modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test.snap' was removed
-************************************************************
diff --git a/modules/nf-core/fastqscreen/buildfromindex/main.nf b/modules/nf-core/fastqscreen/buildfromindex/main.nf
index 6706111e..c543e61b 100644
--- a/modules/nf-core/fastqscreen/buildfromindex/main.nf
+++ b/modules/nf-core/fastqscreen/buildfromindex/main.nf
@@ -3,8 +3,8 @@ process FASTQSCREEN_BUILDFROMINDEX {
 
     conda "${moduleDir}/environment.yml"
     container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'https://depot.galaxyproject.org/singularity/fastq-screen:0.15.3--pl5321hdfd78af_0'
-        : 'biocontainers/fastq-screen:0.15.3--pl5321hdfd78af_0'}"
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fc/fc53eee7ca23c32220a9662fbb63c67769756544b6d74a1ee85cf439ea79a7ee/data'
+        : 'community.wave.seqera.io/library/fastq-screen_perl-gdgraph:5c1786a5d5bc1309'}"
 
     input:
     val genome_names
@@ -12,7 +12,7 @@ process FASTQSCREEN_BUILDFROMINDEX {
 
     output:
     path ("FastQ_Screen_Genomes"), emit: database
-    path "versions.yml", emit: versions
+    tuple val("${task.process}"), val('fastqscreen'), eval('fastq_screen --version 2>&1 | sed "s/^.*FastQ Screen v//;"'), emit: versions_fastqscreen, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -21,11 +21,11 @@ process FASTQSCREEN_BUILDFROMINDEX {
     dir = "FastQ_Screen_Genomes"
     folder = indexes.collect { index -> index.toString() }
     database = [genome_names, folder].transpose()
-    copy_indexes = folder.collect { file -> "cp -r ${file} ${dir}/${file}" }.join(" && ")
+    copy_indexes = folder.collect { index -> "cp -r ${index} ${dir}/${index}" }.join(" && ")
 
     // Folder name and index (within folder) name could be different - use bash to look for index name
     config = database
-        .collect { file -> "########## ${file[0]} \nDATABASE ${file[0]} ${dir}/${file[1]}/${file[1] + '_to_be_replaced'}" }
+        .collect { index -> "########## ${index[0]} \nDATABASE ${index[0]} ${dir}/${index[1]}/${index[1] + '_to_be_replaced'}" }
         .join("\n\n")
         .replace("\n", "\\n")
 
@@ -48,11 +48,6 @@ process FASTQSCREEN_BUILDFROMINDEX {
         sed "s/\$TO_REPLACE/\$REPLACE_WITH/g" ${dir}/fastq_screen.conf > new_conf.conf
         mv new_conf.conf ${dir}/fastq_screen.conf
     done
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//')
-    END_VERSIONS
     """
 
     stub:
@@ -60,10 +55,5 @@ process FASTQSCREEN_BUILDFROMINDEX {
     """
     mkdir ${dir}
     touch ${dir}/fastq_screen.conf
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/fastqscreen/buildfromindex/meta.yml b/modules/nf-core/fastqscreen/buildfromindex/meta.yml
index 0291620b..62561b2e 100644
--- a/modules/nf-core/fastqscreen/buildfromindex/meta.yml
+++ b/modules/nf-core/fastqscreen/buildfromindex/meta.yml
@@ -14,7 +14,8 @@ tools:
       documentation: "https://stevenwingett.github.io/FastQ-Screen/"
       tool_dev_url: "https://github.com/StevenWingett/FastQ-Screen/archive/refs/tags/v0.15.3.zip"
       doi: "10.5281/zenodo.5838377"
-      licence: ["GPL-3.0-or-later"]
+      licence:
+        - "GPL-3.0-or-later"
       identifier: ""
 input:
   - genome_names:
@@ -27,15 +28,30 @@ output:
   database:
     - FastQ_Screen_Genomes:
         type: directory
-        description: fastq screen database folder containing config file and index folders
+        description: fastq screen database folder containing config file and index
+          folders
         pattern: "FastQ_Screen_Genomes"
+  versions_fastqscreen:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - fastqscreen:
+          type: string
+          description: The name of the tool
+      - fastq_screen --version 2>&1 | sed "s/^.*FastQ Screen v//;":
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - fastqscreen:
+          type: string
+          description: The name of the tool
+      - fastq_screen --version 2>&1 | sed "s/^.*FastQ Screen v//;":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@snesic"
   - "@JPejovicApis"
diff --git a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
index 9647dd39..f75616f0 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
+++ b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
@@ -1,55 +1,25 @@
 Changes in component 'nf-core/fastqscreen/fastqscreen'
 'modules/nf-core/fastqscreen/fastqscreen/meta.yml' is unchanged
-Changes in 'fastqscreen/fastqscreen/environment.yml':
---- modules/nf-core/fastqscreen/fastqscreen/environment.yml
-+++ modules/nf-core/fastqscreen/fastqscreen/environment.yml
-@@ -4,5 +4,5 @@
-   - conda-forge
-   - bioconda
- dependencies:
--  - bioconda::fastq-screen=0.15.3
-+  - bioconda::fastq-screen=0.16.0
-   - bioconda::perl-gdgraph=1.54
-
+'modules/nf-core/fastqscreen/fastqscreen/environment.yml' is unchanged
 Changes in 'fastqscreen/fastqscreen/main.nf':
 --- modules/nf-core/fastqscreen/fastqscreen/main.nf
 +++ modules/nf-core/fastqscreen/fastqscreen/main.nf
-@@ -1,22 +1,22 @@
- process FASTQSCREEN_FASTQSCREEN {
--    tag "$meta.id"
-+    tag "${meta.id}"
-     label 'process_medium'
- 
-     conda "${moduleDir}/environment.yml"
--    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
--        'https://depot.galaxyproject.org/singularity/fastq-screen:0.15.3--pl5321hdfd78af_0':
--        'biocontainers/fastq-screen:0.15.3--pl5321hdfd78af_0'}"
-+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fc/fc53eee7ca23c32220a9662fbb63c67769756544b6d74a1ee85cf439ea79a7ee/data'
-+        : 'community.wave.seqera.io/library/fastq-screen_perl-gdgraph:5c1786a5d5bc1309'}"
+@@ -8,8 +8,8 @@
+         : 'community.wave.seqera.io/library/fastq-screen_perl-gdgraph:5c1786a5d5bc1309'}"
  
      input:
--    tuple val(meta), path(reads)  // .fastq files
+-    tuple val(meta), path(reads)
 -    path database
 +    tuple val(meta), path(reads, arity: '1..2')
 +    tuple val(ref_names), path(ref_dirs, name: "ref*"), val(ref_basenames), val(ref_aligners)
  
      output:
--    tuple val(meta), path("*.txt")     , emit: txt
--    tuple val(meta), path("*.png")     , emit: png  , optional: true
--    tuple val(meta), path("*.html")    , emit: html
-+    tuple val(meta), path("*.txt"), emit: txt
-+    tuple val(meta), path("*.png"), emit: png, optional: true
-+    tuple val(meta), path("*.html"), emit: html
-     tuple val(meta), path("*.fastq.gz"), emit: fastq, optional: true
--    path "versions.yml"                , emit: versions
-+    path "versions.yml", emit: versions
- 
-     when:
+     tuple val(meta), path("*.txt"), emit: txt
+@@ -22,13 +22,33 @@
      task.ext.when == null || task.ext.when
-@@ -24,31 +24,46 @@
+ 
      script:
-     def prefix = task.ext.prefix ?: "${meta.id}"
++    def prefix = task.ext.prefix ?: "${meta.id}"
      def args = task.ext.args ?: ""
 +    def config_content = ref_names.withIndex().collect { name, i -> "DATABASE ${name} ./${ref_dirs[i]}/${ref_basenames[i]} ${ref_aligners[i]}" }.join('\n')
  
@@ -68,51 +38,22 @@ Changes in 'fastqscreen/fastqscreen/main.nf':
 +        .join(' && ')
      """
 -    fastq_screen --threads ${task.cpus} \\
--        --aligner bowtie2 \\
 -        --conf ${database}/fastq_screen.conf \\
--        $reads \\
--        $args \\
 +    echo '${config_content}' > fastq_screen.conf
- 
--    cat <<-END_VERSIONS > versions.yml
--    "${task.process}":
--        fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//')
--    END_VERSIONS
++
 +    fastq_screen \\
 +        --conf fastq_screen.conf \\
 +        --threads ${task.cpus} \\
-+        ${reads} \\
+         ${reads} \\
+-        ${args} \\
 +        ${args}
 +
 +    ${mv_cmd}
-+
-+    fastq_screen_version=\$(fastq_screen --version 2>&1 | sed 's/^.*FastQ Screen v//; s/ .*\$//')
-+    echo "\\\"${task.process}\\\":" > versions.yml
-+    echo "    fastqscreen: \$fastq_screen_version" >> versions.yml
      """
  
      stub:
-     def prefix = task.ext.prefix ?: "${meta.id}"
-     """
--    touch test_1_screen.html
--    touch test_1_screen.png
--    touch test_1_screen.txt
-+    touch ${prefix}_screen.html
-+    touch ${prefix}_screen.png
-+    touch ${prefix}_screen.txt
- 
--    cat <<-END_VERSIONS > versions.yml
--    "${task.process}":
--        fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//')
--    END_VERSIONS
-+    fastq_screen_version=\$(fastq_screen --version 2>&1 | sed 's/^.*FastQ Screen v//; s/ .*\$//')
-+    echo "\\\"${task.process}\\\":" > versions.yml
-+    echo "    fastqscreen: \$fastq_screen_version" >> versions.yml
-     """
--
- }
 
-'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test' was removed
-'modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config' was removed
-'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap' was removed
+'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap' is unchanged
 ************************************************************
diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index dc53ae21..cc5c0fa7 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -16,7 +16,7 @@ process FASTQSCREEN_FASTQSCREEN {
     tuple val(meta), path("*.png"), emit: png, optional: true
     tuple val(meta), path("*.html"), emit: html
     tuple val(meta), path("*.fastq.gz"), emit: fastq, optional: true
-    path "versions.yml", emit: versions
+    tuple val("${task.process}"), val('fastqscreen'), eval('fastq_screen --version 2>&1 | sed "s/^.*FastQ Screen v//;"'), emit: versions_fastqscreen, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -49,21 +49,13 @@ process FASTQSCREEN_FASTQSCREEN {
         ${args}
 
     ${mv_cmd}
-
-    fastq_screen_version=\$(fastq_screen --version 2>&1 | sed 's/^.*FastQ Screen v//; s/ .*\$//')
-    echo "\\\"${task.process}\\\":" > versions.yml
-    echo "    fastqscreen: \$fastq_screen_version" >> versions.yml
     """
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix = task.ext.prefix ?: meta.id
     """
     touch ${prefix}_screen.html
     touch ${prefix}_screen.png
     touch ${prefix}_screen.txt
-
-    fastq_screen_version=\$(fastq_screen --version 2>&1 | sed 's/^.*FastQ Screen v//; s/ .*\$//')
-    echo "\\\"${task.process}\\\":" > versions.yml
-    echo "    fastqscreen: \$fastq_screen_version" >> versions.yml
     """
 }
diff --git a/modules/nf-core/fastqscreen/fastqscreen/meta.yml b/modules/nf-core/fastqscreen/fastqscreen/meta.yml
index 81e15b02..f8d7e0ab 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/meta.yml
+++ b/modules/nf-core/fastqscreen/fastqscreen/meta.yml
@@ -74,13 +74,27 @@ output:
           pattern: "*.fastq.gz"
           ontologies:
             - edam: http://edamontology.org/format_3989 # GZIP format
+  versions_fastqscreen:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - fastqscreen:
+          type: string
+          description: The name of the tool
+      - fastq_screen --version 2>&1 | sed "s/^.*FastQ Screen v//;":
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - fastqscreen:
+          type: string
+          description: The name of the tool
+      - fastq_screen --version 2>&1 | sed "s/^.*FastQ Screen v//;":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@snesic"
   - "@JPejovicApis"
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index d02016a0..009874d4 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::multiqc=1.32
+  - bioconda::multiqc=1.33
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 5d0780af..3b0e975b 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,11 +3,11 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8c/8c6c120d559d7ee04c7442b61ad7cf5a9e8970be5feefb37d68eeaa60c1034eb/data' :
-        'community.wave.seqera.io/library/multiqc:1.32--d58f60e4deb769bf' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/34/34e733a9ae16a27e80fe00f863ea1479c96416017f24a907996126283e7ecd4d/data' :
+        'community.wave.seqera.io/library/multiqc:1.33--ee7739d47738383b' }"
 
     input:
-    path  multiqc_files, stageAs: "?/*"
+    path multiqc_files, stageAs: "?/*"
     path(multiqc_config)
     path(extra_multiqc_config)
     path(multiqc_logo)
@@ -15,10 +15,11 @@ process MULTIQC {
     path(sample_names)
 
     output:
-    path "*multiqc_report.html", emit: report
-    path "*_data"              , emit: data
-    path "*_plots"             , optional:true, emit: plots
-    path "versions.yml"        , emit: versions
+    path "*.html"      , emit: report
+    path "*_data"      , emit: data
+    path "*_plots"     , optional:true, emit: plots
+    tuple val("${task.process}"), val('multiqc'), eval('multiqc --version | sed "s/.* //g"'), emit: versions
+    // MultiQC should not push its versions to the `versions` topic. Its input depends on the versions topic to be resolved thus outputting to the topic will let the pipeline hang forever
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,27 +27,22 @@ process MULTIQC {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : ''
-    def config = multiqc_config ? "--config $multiqc_config" : ''
-    def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
+    def config = multiqc_config ? "--config ${multiqc_config}" : ''
+    def extra_config = extra_multiqc_config ? "--config ${extra_multiqc_config}" : ''
     def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : ''
     def replace = replace_names ? "--replace-names ${replace_names}" : ''
     def samples = sample_names ? "--sample-names ${sample_names}" : ''
     """
     multiqc \\
         --force \\
-        $args \\
-        $config \\
-        $prefix \\
-        $extra_config \\
-        $logo \\
-        $replace \\
-        $samples \\
+        ${args} \\
+        ${config} \\
+        ${prefix} \\
+        ${extra_config} \\
+        ${logo} \\
+        ${replace} \\
+        ${samples} \\
         .
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
-    END_VERSIONS
     """
 
     stub:
@@ -55,10 +51,5 @@ process MULTIQC {
     touch multiqc_data/.stub
     mkdir multiqc_plots
     touch multiqc_report.html
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index ce30eb73..9fd34f37 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -57,10 +57,10 @@ input:
         - edam: http://edamontology.org/format_3475 # TSV
 output:
   report:
-    - "*multiqc_report.html":
+    - "*.html":
         type: file
         description: MultiQC report file
-        pattern: "multiqc_report.html"
+        pattern: ".html"
         ontologies: []
   data:
     - "*_data":
@@ -71,15 +71,18 @@ output:
     - "*_plots":
         type: file
         description: Plots created by MultiQC
-        pattern: "*_data"
+        pattern: "*_plots"
         ontologies: []
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - multiqc:
+          type: string
+          description: The tool name
+      - multiqc --version | sed "s/.* //g":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@abhi18av"
   - "@bunop"
@@ -90,3 +93,27 @@ maintainers:
   - "@bunop"
   - "@drpatelh"
   - "@jfy133"
+containers:
+  conda:
+    linux/amd64:
+      lock_file: https://wave.seqera.io/v1alpha1/builds/bd-ee7739d47738383b_1/condalock
+    linux/arm64:
+      lock_file: https://wave.seqera.io/v1alpha1/builds/bd-58d7dee710ab3aa8_1/condalock
+  docker:
+    linux/amd64:
+      build_id: bd-ee7739d47738383b_1
+      name: community.wave.seqera.io/library/multiqc:1.33--ee7739d47738383b
+      scanId: sc-6ddec592dcadd583_4
+    linux/arm64:
+      build_id: bd-58d7dee710ab3aa8_1
+      name: community.wave.seqera.io/library/multiqc:1.33--58d7dee710ab3aa8
+      scanId: sc-a04c42273e34c55c_2
+  singularity:
+    linux/amd64:
+      build_id: bd-e3576ddf588fa00d_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/34/34e733a9ae16a27e80fe00f863ea1479c96416017f24a907996126283e7ecd4d/data
+      name: oras://community.wave.seqera.io/library/multiqc:1.33--e3576ddf588fa00d
+    linux/arm64:
+      build_id: bd-2537ca5f8445e3c2_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/78b89e91d89e9cc99ad5ade5be311f347838cb2acbfb4f13bc343b170be09ce4/data
+      name: oras://community.wave.seqera.io/library/multiqc:1.33--2537ca5f8445e3c2
diff --git a/modules/nf-core/picard/collecthsmetrics/main.nf b/modules/nf-core/picard/collecthsmetrics/main.nf
index b86053e5..96045b5d 100644
--- a/modules/nf-core/picard/collecthsmetrics/main.nf
+++ b/modules/nf-core/picard/collecthsmetrics/main.nf
@@ -1,22 +1,22 @@
 process PICARD_COLLECTHSMETRICS {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' :
-        'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data'
+        : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}"
 
     input:
     tuple val(meta), path(bam), path(bai), path(bait_intervals, stageAs: "baits/*"), path(target_intervals, stageAs: 'targets/*')
     tuple val(meta2), path(ref)
     tuple val(meta3), path(ref_fai)
     tuple val(meta4), path(ref_dict)
-    tuple val(meta5), path(ref_gzi) // ref_gzi only required if reference is gzipped
+    tuple val(meta5), path(ref_gzi)
 
     output:
-    tuple val(meta), path("*_metrics")  , emit: metrics
-    path "versions.yml"                 , emit: versions
+    tuple val(meta), path("*_metrics"), emit: metrics
+    tuple val("${task.process}"), val('picard'), eval("picard CollectHsMetrics --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard
 
     when:
     task.ext.when == null || task.ext.when
@@ -28,56 +28,43 @@ process PICARD_COLLECTHSMETRICS {
 
     def avail_mem = 3072
     if (!task.memory) {
-        log.info '[Picard CollectHsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
-    } else {
-        avail_mem = (task.memory.mega*0.8).intValue()
+        log.info('[Picard CollectHsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.')
+    }
+    else {
+        avail_mem = (task.memory.mega * 0.8).intValue()
     }
 
     def bait_interval_list = bait_intervals
     def bait_intervallist_cmd = ""
-    if (bait_intervals =~ /.(bed|bed.gz)$/){
+    if (bait_intervals =~ /.(bed|bed.gz)$/) {
         bait_interval_list = bait_intervals.toString().replaceAll(/.(bed|bed.gz)$/, ".interval_list")
         bait_intervallist_cmd = "picard -Xmx${avail_mem}M BedToIntervalList --INPUT ${bait_intervals} --OUTPUT ${bait_interval_list} --SEQUENCE_DICTIONARY ${ref_dict} --TMP_DIR ."
     }
 
     def target_interval_list = target_intervals
     def target_intervallist_cmd = ""
-    if (target_intervals =~ /.(bed|bed.gz)$/){
+    if (target_intervals =~ /.(bed|bed.gz)$/) {
         target_interval_list = target_intervals.toString().replaceAll(/.(bed|bed.gz)$/, ".interval_list")
         target_intervallist_cmd = "picard -Xmx${avail_mem}M BedToIntervalList --INPUT ${target_intervals} --OUTPUT ${target_interval_list} --SEQUENCE_DICTIONARY ${ref_dict} --TMP_DIR ."
     }
-
-
     """
-
-    $bait_intervallist_cmd
-    $target_intervallist_cmd
+    ${bait_intervallist_cmd}
+    ${target_intervallist_cmd}
 
     picard \\
         -Xmx${avail_mem}M \\
         CollectHsMetrics \\
-        $args \\
-        $reference \\
-        --BAIT_INTERVALS $bait_interval_list \\
-        --TARGET_INTERVALS $target_interval_list \\
-        --INPUT $bam \\
+        ${args} \\
+        ${reference} \\
+        --BAIT_INTERVALS ${bait_interval_list} \\
+        --TARGET_INTERVALS ${target_interval_list} \\
+        --INPUT ${bam} \\
         --OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics
-
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        picard: \$(echo \$(picard CollectHsMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.CollectHsMetrics.coverage_metrics
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        picard: \$(echo \$(picard CollectHsMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/picard/collecthsmetrics/meta.yml b/modules/nf-core/picard/collecthsmetrics/meta.yml
index 511ae959..89bc502c 100644
--- a/modules/nf-core/picard/collecthsmetrics/meta.yml
+++ b/modules/nf-core/picard/collecthsmetrics/meta.yml
@@ -99,13 +99,28 @@ output:
           description: Alignment metrics files generated by picard
           pattern: "*_{metrics}"
           ontologies: []
+  versions_picard:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - picard:
+          type: string
+          description: The tool name
+      - "picard CollectHsMetrics --version 2>&1 | sed -n 's/.*Version://p'":
+          type: string
+          description: The command used to generate the version of the tool
+
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - picard:
+          type: string
+          description: The tool name
+      - "picard CollectHsMetrics --version 2>&1 | sed -n 's/.*Version://p'":
+          type: string
+          description: The command used to generate the version of the tool
 authors:
   - "@projectoriented"
   - "@matthdsm"
diff --git a/modules/nf-core/picard/collectmultiplemetrics/main.nf b/modules/nf-core/picard/collectmultiplemetrics/main.nf
index eb4f6c60..9de927e6 100644
--- a/modules/nf-core/picard/collectmultiplemetrics/main.nf
+++ b/modules/nf-core/picard/collectmultiplemetrics/main.nf
@@ -1,21 +1,21 @@
 process PICARD_COLLECTMULTIPLEMETRICS {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' :
-        'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data'
+        : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}"
 
     input:
-    tuple val(meta) , path(bam), path(bai)
+    tuple val(meta), path(bam), path(bai)
     tuple val(meta2), path(fasta)
     tuple val(meta3), path(fai)
 
     output:
     tuple val(meta), path("*_metrics"), emit: metrics
-    tuple val(meta), path("*.pdf")    , emit: pdf, optional: true
-    path  "versions.yml"              , emit: versions
+    tuple val(meta), path("*.pdf"), emit: pdf, optional: true
+    tuple val("${task.process}"), val('picard'), eval("picard CollectMultipleMetrics --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,23 +26,19 @@ process PICARD_COLLECTMULTIPLEMETRICS {
     def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : ""
     def avail_mem = 3072
     if (!task.memory) {
-        log.info '[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
-    } else {
-        avail_mem = (task.memory.mega*0.8).intValue()
+        log.info('[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.')
+    }
+    else {
+        avail_mem = (task.memory.mega * 0.8).intValue()
     }
     """
     picard \\
         -Xmx${avail_mem}M \\
         CollectMultipleMetrics \\
-        $args \\
-        --INPUT $bam \\
+        ${args} \\
+        --INPUT ${bam} \\
         --OUTPUT ${prefix}.CollectMultipleMetrics \\
-        $reference
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        picard: \$(picard CollectMultipleMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:)
-    END_VERSIONS
+        ${reference}
     """
 
     stub:
@@ -58,10 +54,5 @@ process PICARD_COLLECTMULTIPLEMETRICS {
     touch ${prefix}.CollectMultipleMetrics.quality_by_cycle.pdf
     touch ${prefix}.CollectMultipleMetrics.insert_size_histogram.pdf
     touch ${prefix}.CollectMultipleMetrics.quality_distribution_metrics
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        picard: \$(echo \$(picard CollectMultipleMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/picard/collectmultiplemetrics/meta.yml b/modules/nf-core/picard/collectmultiplemetrics/meta.yml
index 3f0bf610..213d600b 100644
--- a/modules/nf-core/picard/collectmultiplemetrics/meta.yml
+++ b/modules/nf-core/picard/collectmultiplemetrics/meta.yml
@@ -74,13 +74,29 @@ output:
           description: PDF plots of metrics
           pattern: "*.{pdf}"
           ontologies: []
+  versions_picard:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - picard:
+          type: string
+          description: The tool name
+      - "picard CollectMultipleMetrics --version 2>&1 | sed -n 's/.*Version://p'":
+          type: string
+          description: The command used to generate the version of the tool
+
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - picard:
+          type: string
+          description: The tool name
+      - "picard CollectMultipleMetrics --version 2>&1 | sed -n 's/.*Version://p'":
+          type: string
+          description: The command used to generate the version of the tool
+
 authors:
   - "@drpatelh"
 maintainers:
diff --git a/modules/nf-core/picard/createsequencedictionary/main.nf b/modules/nf-core/picard/createsequencedictionary/main.nf
index 4e241979..c2aadd9f 100644
--- a/modules/nf-core/picard/createsequencedictionary/main.nf
+++ b/modules/nf-core/picard/createsequencedictionary/main.nf
@@ -1,18 +1,18 @@
 process PICARD_CREATESEQUENCEDICTIONARY {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' :
-        'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data'
+        : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}"
 
     input:
     tuple val(meta), path(fasta)
 
     output:
     tuple val(meta), path("*.dict"), emit: reference_dict
-    path "versions.yml"            , emit: versions
+    tuple val("${task.process}"), val('picard'), eval("picard CreateSequenceDictionary --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,33 +22,23 @@ process PICARD_CREATESEQUENCEDICTIONARY {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def avail_mem = 3072
     if (!task.memory) {
-        log.info '[Picard CreateSequenceDictionary] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
-    } else {
-        avail_mem = (task.memory.mega*0.8).intValue()
+        log.info('[Picard CreateSequenceDictionary] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.')
+    }
+    else {
+        avail_mem = (task.memory.mega * 0.8).intValue()
     }
     """
     picard \\
         -Xmx${avail_mem}M \\
-        CreateSequenceDictionary  \\
-        $args \\
-        --REFERENCE $fasta \\
+        CreateSequenceDictionary \\
+        ${args} \\
+        --REFERENCE ${fasta} \\
         --OUTPUT ${prefix}.dict
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        picard: \$(picard CreateSequenceDictionary --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.dict
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        picard: \$(echo \$(picard CreateSequenceDictionary --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
-    END_VERSIONS
     """
-
 }
diff --git a/modules/nf-core/picard/createsequencedictionary/meta.yml b/modules/nf-core/picard/createsequencedictionary/meta.yml
index 97e0ddea..02487d5f 100644
--- a/modules/nf-core/picard/createsequencedictionary/meta.yml
+++ b/modules/nf-core/picard/createsequencedictionary/meta.yml
@@ -36,13 +36,27 @@ output:
           description: picard dictionary file
           pattern: "*.{dict}"
           ontologies: []
+  versions_picard:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - picard:
+          type: string
+          description: The tool name
+      - "picard CreateSequenceDictionary --version 2>&1 | sed -n 's/.*Version://p'":
+          type: string
+          description: The command used to generate the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - picard:
+          type: string
+          description: The tool name
+      - "picard CreateSequenceDictionary --version 2>&1 | sed -n 's/.*Version://p'":
+          type: string
+          description: The command used to generate the version of the tool
 authors:
   - "@sateeshperi"
   - "@mjcipriano"
diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf
index ed2d70a6..97bfb578 100644
--- a/modules/nf-core/samtools/faidx/main.nf
+++ b/modules/nf-core/samtools/faidx/main.nf
@@ -8,8 +8,7 @@ process SAMTOOLS_FAIDX {
         'biocontainers/samtools:1.22.1--h96c455f_0' }"
 
     input:
-    tuple val(meta), path(fasta)
-    tuple val(meta2), path(fai)
+    tuple val(meta), path(fasta), path(fai)
     val get_sizes
 
     output:
@@ -17,7 +16,7 @@ process SAMTOOLS_FAIDX {
     tuple val(meta), path ("*.sizes")      , emit: sizes, optional: true
     tuple val(meta), path ("*.fai")        , emit: fai, optional: true
     tuple val(meta), path ("*.gzi")        , emit: gzi, optional: true
-    path "versions.yml"                    , emit: versions
+    tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), topic: versions, emit: versions_samtools
 
     when:
     task.ext.when == null || task.ext.when
@@ -32,11 +31,6 @@ process SAMTOOLS_FAIDX {
         $args
 
     ${get_sizes_command}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 
     stub:
@@ -51,11 +45,5 @@ process SAMTOOLS_FAIDX {
     fi
 
     ${get_sizes_command}
-
-    cat <<-END_VERSIONS > versions.yml
-
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml
index b7a2e0c1..80aae1da 100644
--- a/modules/nf-core/samtools/faidx/meta.yml
+++ b/modules/nf-core/samtools/faidx/meta.yml
@@ -1,5 +1,6 @@
 name: samtools_faidx
-description: Index FASTA file, and optionally generate a file of chromosome sizes
+description: Index FASTA file, and optionally generate a file of chromosome
+  sizes
 keywords:
   - index
   - fasta
@@ -14,7 +15,8 @@ tools:
       homepage: http://www.htslib.org/
       documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: biotools:samtools
 input:
   - - meta:
@@ -27,11 +29,6 @@ input:
         description: FASTA file
         pattern: "*.{fa,fasta}"
         ontologies: []
-  - - meta2:
-        type: map
-        description: |
-          Groovy Map containing reference information
-          e.g. [ id:'test' ]
     - fai:
         type: file
         description: FASTA index file
@@ -40,7 +37,6 @@ input:
   - get_sizes:
       type: boolean
       description: use cut to get the sizes of the index (true) or not (false)
-
 output:
   fa:
     - - meta:
@@ -86,13 +82,27 @@ output:
           description: Optional gzip index file for compressed inputs
           pattern: "*.gzi"
           ontologies: []
+  versions_samtools:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - samtools:
+          type: string
+          description: The tool name
+      - "samtools version | sed '1!d;s/.* //'":
+          type: eval
+          description: The command used to generate the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - samtools:
+          type: string
+          description: The tool name
+      - "samtools version | sed '1!d;s/.* //'":
+          type: eval
+          description: The command used to generate the version of the tool
 authors:
   - "@drpatelh"
   - "@ewels"
diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf
index a77ad821..e2a0e56d 100644
--- a/modules/nf-core/samtools/index/main.nf
+++ b/modules/nf-core/samtools/index/main.nf
@@ -14,7 +14,7 @@ process SAMTOOLS_INDEX {
     tuple val(meta), path("*.bai") , optional:true, emit: bai
     tuple val(meta), path("*.csi") , optional:true, emit: csi
     tuple val(meta), path("*.crai"), optional:true, emit: crai
-    path  "versions.yml"           , emit: versions
+    tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), emit: versions_samtools, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,11 +27,6 @@ process SAMTOOLS_INDEX {
         -@ ${task.cpus} \\
         $args \\
         $input
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 
     stub:
@@ -40,10 +35,5 @@ process SAMTOOLS_INDEX {
                     "crai" : args.contains("-c") ?  "csi" : "bai"
     """
     touch ${input}.${extension}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml
index 1bed6bca..c6d4ce25 100644
--- a/modules/nf-core/samtools/index/meta.yml
+++ b/modules/nf-core/samtools/index/meta.yml
@@ -14,7 +14,8 @@ tools:
       homepage: http://www.htslib.org/
       documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: biotools:samtools
 input:
   - - meta:
@@ -60,13 +61,27 @@ output:
           description: BAM/CRAM/SAM index file
           pattern: "*.{bai,crai,sai}"
           ontologies: []
+  versions_samtools:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - samtools:
+          type: string
+          description: The name of the tool
+      - samtools version | sed '1!d;s/.* //':
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - samtools:
+          type: string
+          description: The name of the tool
+      - samtools version | sed '1!d;s/.* //':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@drpatelh"
   - "@ewels"
diff --git a/modules/nf-core/seqfu/stats/main.nf b/modules/nf-core/seqfu/stats/main.nf
index ced2451c..2f98c852 100644
--- a/modules/nf-core/seqfu/stats/main.nf
+++ b/modules/nf-core/seqfu/stats/main.nf
@@ -1,20 +1,20 @@
 process SEQFU_STATS {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqfu:1.22.3--hfd12232_2':
-        'biocontainers/seqfu:1.22.3--hfd12232_2' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/seqfu:1.22.3--hfd12232_2'
+        : 'biocontainers/seqfu:1.22.3--hfd12232_2'}"
 
     input:
     // stats can get one or more fasta or fastq files
     tuple val(meta), path(files)
 
     output:
-    tuple val(meta), path("*.tsv")    , emit: stats
+    tuple val(meta), path("*.tsv"), emit: stats
     tuple val(meta), path("*_mqc.txt"), emit: multiqc
-    path "versions.yml"               , emit: versions
+    tuple val("${task.process}"), val('seqfu'), eval('seqfu version'), emit: versions_seqfu, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -25,28 +25,18 @@ process SEQFU_STATS {
     """
     seqfu \\
         stats \\
-        $args \\
+        ${args} \\
         --multiqc ${prefix}_mqc.txt \\
-        $files > ${prefix}.tsv
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        seqfu: \$(seqfu version)
-    END_VERSIONS
+        ${files} > ${prefix}.tsv
     """
 
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    echo $args
+    echo ${args}
 
     touch ${prefix}.tsv
     touch ${prefix}_mqc.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        seqfu: \$(seqfu version)
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/seqfu/stats/meta.yml b/modules/nf-core/seqfu/stats/meta.yml
index 573498c5..856e6f79 100644
--- a/modules/nf-core/seqfu/stats/meta.yml
+++ b/modules/nf-core/seqfu/stats/meta.yml
@@ -1,4 +1,3 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "seqfu_stats"
 description: Statistics for FASTA or FASTQ files
 keywords:
@@ -13,11 +12,10 @@ tools:
       documentation: "https://telatin.github.io/seqfu2/"
       tool_dev_url: "https://github.com/telatin/seqfu2"
       doi: "10.3390/bioengineering8050059"
-      licence: ["GPL v3"]
+      licence:
+        - "GPL v3"
       identifier: biotools:seqfu
-
 input:
-  # Only when we have meta
   - - meta:
         type: map
         description: |
@@ -28,9 +26,8 @@ input:
         description: One or more FASTA or FASTQ files
         pattern: "*.{fasta,fastq,fasta.gz,fastq.gz,fq,fq.gz}"
         ontologies:
-          - edam: http://edamontology.org/format_1930 # FASTQ
+          - edam: http://edamontology.org/format_1930
 output:
-  #Only when we have meta
   stats:
     - - meta:
           type: map
@@ -42,7 +39,7 @@ output:
           description: Tab-separated output file with basic sequence statistics.
           pattern: "*.{tsv}"
           ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+            - edam: http://edamontology.org/format_3475
   multiqc:
     - - meta:
           type: map
@@ -54,13 +51,27 @@ output:
           description: MultiQC ready table
           pattern: "*.{_mqc.txt}"
           ontologies: []
+  versions_seqfu:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - seqfu:
+          type: string
+          description: The name of the tool
+      - seqfu version:
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - seqfu:
+          type: string
+          description: The name of the tool
+      - seqfu version:
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@telatin"
 maintainers:
diff --git a/modules/nf-core/seqtk/sample/main.nf b/modules/nf-core/seqtk/sample/main.nf
index 0c2aaeda..1a5d8cd7 100644
--- a/modules/nf-core/seqtk/sample/main.nf
+++ b/modules/nf-core/seqtk/sample/main.nf
@@ -12,7 +12,7 @@ process SEQTK_SAMPLE {
 
     output:
     tuple val(meta), path("*.fastq.gz"), emit: reads
-    path "versions.yml"                , emit: versions
+    tuple val("${task.process}"), val('seqtk'), eval("seqtk 2>&1 | sed -n 's/^Version: //p'"), emit: versions_seqtk, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -36,11 +36,6 @@ process SEQTK_SAMPLE {
             $sample_size \\
             | gzip --no-name > ${prefix}_\$(basename \$f)
     done
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
-    END_VERSIONS
     """
 
     stub:
@@ -48,11 +43,6 @@ process SEQTK_SAMPLE {
 
     """
     echo "" | gzip > ${prefix}.fastq.gz
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
-    END_VERSIONS
     """
 
 }
diff --git a/modules/nf-core/seqtk/sample/meta.yml b/modules/nf-core/seqtk/sample/meta.yml
index ed1f3325..9574c705 100644
--- a/modules/nf-core/seqtk/sample/meta.yml
+++ b/modules/nf-core/seqtk/sample/meta.yml
@@ -6,8 +6,8 @@ keywords:
   - reads
 tools:
   - seqtk:
-      description: Seqtk is a fast and lightweight tool for processing sequences in
-        the FASTA or FASTQ format. Seqtk sample command subsamples sequences.
+      description: Seqtk is a fast and lightweight tool for processing sequences
+        in the FASTA or FASTQ format. Seqtk sample command subsamples sequences.
       homepage: https://github.com/lh3/seqtk
       documentation: https://docs.csc.fi/apps/seqtk/
       tool_dev_url: https://github.com/lh3/seqtk
@@ -39,13 +39,27 @@ output:
           description: Subsampled FastQ files
           pattern: "*.{fastq.gz}"
           ontologies: []
+  versions_seqtk:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - seqtk:
+          type: string
+          description: The name of the tool
+      - "seqtk 2>&1 | sed -n 's/^Version: //p'":
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - seqtk:
+          type: string
+          description: The name of the tool
+      - "seqtk 2>&1 | sed -n 's/^Version: //p'":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@kaurravneet4123"
   - "@sidorov-si"
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 6c0c4e85..32c34943 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,8 +22,8 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "Stable",
-            "datePublished": "2026-02-16T08:55:13+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that processes raw sequence data (FASTQ) to provide comprehensive quality control.\nIt can perform subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants.\nThe pipeline generates detailed MultiQC reports with flexible output options, ranging from individual sample reports to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments.\nIf provided, nf-core/seqinspector can also parse statistics from an Illumina run folder directory into the final MultiQC reports.\n\n### Compatibility between tools and data type\n\n<!-- TODO: add a search tool that accepts a tree for `Compatibility with Data`. -->\n\n| Tool Type           | Tool Name                                                                                                           | Tool Description                                                                              | Compatibility with Data | Dependencies                                                                                                              | Default tool |\n| ------------------- | ------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------- | ----------------------- | ------------------------------------------------------------------------------------------------------------------------- | ------------ |\n| `Subsampling`       | [`Seqtk`](https://github.com/lh3/seqtk)                                                                             | Global subsampling of reads. Only performs subsampling if `--sample_size` parameter is given. | [RNA, DNA, synthetic]   | [N/A]                                                                                                                     | no           |\n| `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2)                                                                   | Align reads to reference                                                                      | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `Indexing`          | [`SAMtools`](http://github.com/samtools)                                                                            | Index aligned BAM files, create FASTA index                                                   | [DNA]                   | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)                                              | Read QC                                                                                       | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)                                   | Basic contamination detection                                                                 | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`SeqFu Stats`](https://github.com/telatin/seqfu2)                                                                  | Sequence statistics                                                                           | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`Picard collect multiple metrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html)         | Collect multiple QC metrics                                                                   | [RNA, DNA]              | [Bwamem2, SAMtools, `--genome`]                                                                                           | yes          |\n| `QC`                | [`Picard_collecthsmetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard) | Collect alignment QC metrics of hybrid-selection data.                                        | [RNA, DNA]              | [Bwamem2, SAMtools, `--fasta`, `--run_picard_collecths_metrics`, `--bait_intervals`, `--target_intervals` (`--ref_dict`)] | no           |\n| `Reporting`         | [`MultiQC`](http://multiqc.info/)                                                                                   | Present QC for raw reads                                                                      | [RNA, DNA, synthetic]   | [N/A]                                                                                                                     | yes          |\n\n### Workflow diagram\n\n<picture>\n  <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/seqinspector_tubemap_V1.0_dark.png\">\n  <source media=\"(prefers-color-scheme: light)\" srcset=\"docs/images/seqinspector_tubemap_V1.0.png\">\n  <img alt=\"Fallback image description\" src=\"docs/images/seqinspector_tubemap_V1.0.png\">\n</picture>\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end with only `fastq_1`) or a pair of fastq files (paired end with `fastq_1` and `fastq_2`).\n`rundir` is the path to the runfolder.\n`tags` is a colon-separated list of tags that will be added to the MultiQC report for this `sample`.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by [@agrima2010](https://github.com/agrima2010), [@Aratz](https://github.com/Aratz), [@FranBonath](https://github.com/FranBonath), [@kedhammar](https://github.com/kedhammar), and [@MatthiasZepper](https://github.com/MatthiasZepper) from the Swedish [National Genomics Infrastructure](https://github.com/NationalGenomicsInfrastructure/) and [Clinical Genomics Stockholm](https://clinical.scilifelab.se/).\n\nMaintenance is now lead by Maxime U Garcia ([National Genomics Infrastructure](https://github.com/NationalGenomicsInfrastructure/))\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@adamrtalbot](https://github.com/adamrtalbot)\n- [@alneberg](https://github.com/alneberg)\n- [@beatrizsavinhas](https://github.com/beatrizsavinhas)\n- [@ctuni](https://github.com/ctuni)\n- [@edmundmiller](https://github.com/edmundmiller)\n- [@EliottBo](https://github.com/EliottBo)\n- [@KarNair](https://github.com/KarNair)\n- [@kjellinjonas](https://github.com/kjellinjonas)\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n- [@matrulda](https://github.com/matrulda)\n- [@mirpedrol](https://github.com/mirpedrol)\n- [@nggvs](https://github.com/nggvs)\n- [@nkongenelly](https://github.com/nkongenelly)\n- [@Patricie34](https://github.com/Patricie34)\n- [@pontushojer](https://github.com/pontushojer)\n- [@ramprasadn](https://github.com/ramprasadn)\n- [@rannick](https://github.com/rannick)\n- [@torigiffin](https://github.com/torigiffin)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "datePublished": "2026-02-19T15:27:56+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n    <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that processes raw sequence data (FASTQ) to provide comprehensive quality control.\nIt can perform subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants.\nThe pipeline generates detailed MultiQC reports with flexible output options, ranging from individual sample reports to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments.\nIf provided, nf-core/seqinspector can also parse statistics from an Illumina run folder directory into the final MultiQC reports.\n\n### Compatibility between tools and data type\n\n<!-- TODO: add a search tool that accepts a tree for `Compatibility with Data`. -->\n\n| Tool Type           | Tool Name                                                                                                           | Tool Description                                                                              | Compatibility with Data | Dependencies                                                                                                              | Default tool |\n| ------------------- | ------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------- | ----------------------- | ------------------------------------------------------------------------------------------------------------------------- | ------------ |\n| `Subsampling`       | [`Seqtk`](https://github.com/lh3/seqtk)                                                                             | Global subsampling of reads. Only performs subsampling if `--sample_size` parameter is given. | [RNA, DNA, synthetic]   | [N/A]                                                                                                                     | no           |\n| `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2)                                                                   | Align reads to reference                                                                      | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `Indexing`          | [`SAMtools`](http://github.com/samtools)                                                                            | Index aligned BAM files, create FASTA index                                                   | [DNA]                   | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)                                              | Read QC                                                                                       | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)                                   | Basic contamination detection                                                                 | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`SeqFu Stats`](https://github.com/telatin/seqfu2)                                                                  | Sequence statistics                                                                           | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |\n| `QC`                | [`Picard collect multiple metrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html)         | Collect multiple QC metrics                                                                   | [RNA, DNA]              | [Bwamem2, SAMtools, `--genome`]                                                                                           | yes          |\n| `QC`                | [`Picard_collecthsmetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard) | Collect alignment QC metrics of hybrid-selection data.                                        | [RNA, DNA]              | [Bwamem2, SAMtools, `--fasta`, `--run_picard_collecths_metrics`, `--bait_intervals`, `--target_intervals` (`--ref_dict`)] | no           |\n| `Reporting`         | [`MultiQC`](http://multiqc.info/)                                                                                   | Present QC for raw reads                                                                      | [RNA, DNA, synthetic]   | [N/A]                                                                                                                     | yes          |\n\n### Workflow diagram\n\n<picture>\n  <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/seqinspector_tubemap_V1.0_dark.png\">\n  <source media=\"(prefers-color-scheme: light)\" srcset=\"docs/images/seqinspector_tubemap_V1.0.png\">\n  <img alt=\"Fallback image description\" src=\"docs/images/seqinspector_tubemap_V1.0.png\">\n</picture>\n\n### Summary of tools and version used in the pipeline\n\n| Tool        | Version |\n| ----------- | ------- |\n| bowtie2     | 2.5.4   |\n| bwamem2     | 2.3     |\n| fastqc      | 0.12.1  |\n| fastqscreen | 0.16.0  |\n| multiqc     | 1.33    |\n| picard      | 3.4.0   |\n| samtools    | 1.22.1  |\n| seqfu       | 1.22.3  |\n| seqtk       | 1.4     |\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end with only `fastq_1`) or a pair of fastq files (paired end with `fastq_1` and `fastq_2`).\n`rundir` is the path to the runfolder.\n`tags` is a colon-separated list of tags that will be added to the MultiQC report for this `sample`.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by [@agrima2010](https://github.com/agrima2010), [@Aratz](https://github.com/Aratz), [@FranBonath](https://github.com/FranBonath), [@kedhammar](https://github.com/kedhammar), and [@MatthiasZepper](https://github.com/MatthiasZepper) from the Swedish [National Genomics Infrastructure](https://github.com/NationalGenomicsInfrastructure/) and [Clinical Genomics Stockholm](https://clinical.scilifelab.se/).\n\nMaintenance is now lead by Maxime U Garcia ([National Genomics Infrastructure](https://github.com/NationalGenomicsInfrastructure/))\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@adamrtalbot](https://github.com/adamrtalbot)\n- [@alneberg](https://github.com/alneberg)\n- [@beatrizsavinhas](https://github.com/beatrizsavinhas)\n- [@ctuni](https://github.com/ctuni)\n- [@edmundmiller](https://github.com/edmundmiller)\n- [@EliottBo](https://github.com/EliottBo)\n- [@KarNair](https://github.com/KarNair)\n- [@kjellinjonas](https://github.com/kjellinjonas)\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n- [@matrulda](https://github.com/matrulda)\n- [@mirpedrol](https://github.com/mirpedrol)\n- [@nggvs](https://github.com/nggvs)\n- [@nkongenelly](https://github.com/nkongenelly)\n- [@Patricie34](https://github.com/Patricie34)\n- [@pontushojer](https://github.com/pontushojer)\n- [@ramprasadn](https://github.com/ramprasadn)\n- [@rannick](https://github.com/rannick)\n- [@torigiffin](https://github.com/torigiffin)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
                     "@id": "main.nf"
@@ -102,7 +102,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#08014bc0-7c74-49f0-a201-fcc18504ce2b"
+                    "@id": "#4194f54b-797e-4fc8-8f8a-d74016164630"
                 }
             ],
             "name": "nf-core/seqinspector"
@@ -131,23 +131,23 @@
             ],
             "creator": [
                 {
-                    "@id": "#max.u.garcia@gmail.com"
+                    "@id": "https://orcid.org/0009-0004-5536-7210"
                 },
                 {
-                    "@id": "https://orcid.org/0000-0003-2702-1103"
+                    "@id": "#89784800+kedhammar@users.noreply.github.com"
                 },
                 {
-                    "@id": "#89784800+kedhammar@users.noreply.github.com"
+                    "@id": "#max.u.garcia@gmail.com"
                 },
                 {
-                    "@id": "https://orcid.org/0000-0003-1675-0677"
+                    "@id": "https://orcid.org/0000-0003-2702-1103"
                 },
                 {
-                    "@id": "https://orcid.org/0009-0004-5536-7210"
+                    "@id": "https://orcid.org/0000-0003-1675-0677"
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2026-02-16T09:55:13Z",
+            "dateModified": "2026-02-19T16:27:56Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -160,19 +160,19 @@
             ],
             "maintainer": [
                 {
-                    "@id": "#max.u.garcia@gmail.com"
+                    "@id": "https://orcid.org/0009-0004-5536-7210"
                 },
                 {
-                    "@id": "https://orcid.org/0000-0003-2702-1103"
+                    "@id": "#89784800+kedhammar@users.noreply.github.com"
                 },
                 {
-                    "@id": "#89784800+kedhammar@users.noreply.github.com"
+                    "@id": "#max.u.garcia@gmail.com"
                 },
                 {
-                    "@id": "https://orcid.org/0000-0003-1675-0677"
+                    "@id": "https://orcid.org/0000-0003-2702-1103"
                 },
                 {
-                    "@id": "https://orcid.org/0009-0004-5536-7210"
+                    "@id": "https://orcid.org/0000-0003-1675-0677"
                 }
             ],
             "name": [
@@ -202,14 +202,14 @@
             "url": {
                 "@id": "https://www.nextflow.io/"
             },
-            "version": "!>=25.04.0"
+            "version": "!>=25.10.4"
         },
         {
-            "@id": "#08014bc0-7c74-49f0-a201-fcc18504ce2b",
+            "@id": "#4194f54b-797e-4fc8-8f8a-d74016164630",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#c3eeced1-9e95-4a6c-932f-c4ceae1158d2"
+                    "@id": "#3c0042e5-6160-451c-8f37-2395b6ebc082"
                 }
             ],
             "mainEntity": {
@@ -218,7 +218,7 @@
             "name": "Test suite for nf-core/seqinspector"
         },
         {
-            "@id": "#c3eeced1-9e95-4a6c-932f-c4ceae1158d2",
+            "@id": "#3c0042e5-6160-451c-8f37-2395b6ebc082",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/seqinspector",
             "resource": "repos/nf-core/seqinspector/actions/workflows/nf-test.yml",
@@ -351,6 +351,18 @@
             "name": "nf-core",
             "url": "https://nf-co.re/"
         },
+        {
+            "@id": "https://orcid.org/0009-0004-5536-7210",
+            "@type": "Person",
+            "email": "163723002+agrima2010@users.noreply.github.com",
+            "name": "Agrima Bhatt"
+        },
+        {
+            "@id": "#89784800+kedhammar@users.noreply.github.com",
+            "@type": "Person",
+            "email": "89784800+kedhammar@users.noreply.github.com",
+            "name": "Alfred Kedhammar"
+        },
         {
             "@id": "#max.u.garcia@gmail.com",
             "@type": "Person",
@@ -363,23 +375,11 @@
             "email": "adrien.coulier@medsci.uu.se",
             "name": "Adrien Coulier"
         },
-        {
-            "@id": "#89784800+kedhammar@users.noreply.github.com",
-            "@type": "Person",
-            "email": "89784800+kedhammar@users.noreply.github.com",
-            "name": "Alfred Kedhammar"
-        },
         {
             "@id": "https://orcid.org/0000-0003-1675-0677",
             "@type": "Person",
             "email": "mahesh.binzer-panchal@nbis.se",
             "name": "Mahesh Binzer-Panchal"
-        },
-        {
-            "@id": "https://orcid.org/0009-0004-5536-7210",
-            "@type": "Person",
-            "email": "163723002+agrima2010@users.noreply.github.com",
-            "name": "Agrima Bhatt"
         }
     ]
 }
\ No newline at end of file
diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf
index 96811a78..3fe0bd39 100644
--- a/subworkflows/local/prepare_genome/main.nf
+++ b/subworkflows/local/prepare_genome/main.nf
@@ -18,7 +18,6 @@ workflow PREPARE_GENOME {
     ch_bwamem2_index = channel.empty()
     ch_reference_fai = channel.empty()
     ch_ref_dict = channel.empty()
-    ch_versions = channel.empty()
 
     if (!("bwamem2_index" in skip_tools)) {
         // Use pre-built index when --bwamem2 parameter is provided
@@ -31,18 +30,15 @@ workflow PREPARE_GENOME {
         else {
             BWAMEM2_INDEX(ch_reference_fasta)
             ch_bwamem2_index = BWAMEM2_INDEX.out.index
-            ch_versions = ch_versions.mix(BWAMEM2_INDEX.out.versions)
         }
     }
 
     if (!("samtools_faidx" in skip_tools)) {
         SAMTOOLS_FAIDX(
-            ch_reference_fasta,
-            [[:], []],
-            true,
+            ch_reference_fasta.map { meta, fasta -> [meta, fasta, []] },
+            false,
         )
         ch_reference_fai = SAMTOOLS_FAIDX.out.fai
-        ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions)
     }
 
     if (run_picard_collecthsmetrics) {
@@ -52,7 +48,6 @@ workflow PREPARE_GENOME {
         else {
             PICARD_CREATESEQUENCEDICTIONARY(ch_reference_fasta)
             ch_ref_dict = PICARD_CREATESEQUENCEDICTIONARY.out.reference_dict
-            ch_versions = ch_versions.mix(PICARD_CREATESEQUENCEDICTIONARY.out.versions)
         }
     }
 
@@ -60,5 +55,4 @@ workflow PREPARE_GENOME {
     bwamem2_index = ch_bwamem2_index
     reference_fai = ch_reference_fai
     ref_dict      = ch_ref_dict
-    versions      = ch_versions
 }
diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test b/subworkflows/local/prepare_genome/tests/main.nf.test
index b9199a6f..3ba2985c 100644
--- a/subworkflows/local/prepare_genome/tests/main.nf.test
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test
@@ -35,9 +35,6 @@ nextflow_workflow {
                 else if (key == "ref_dict") {
                     return [key, val.collect { file(it[1]).name }]
                 }
-                else if (key == "versions") {
-                    return [key, val.collect { path(it).yaml }]
-                }
                 return [key, val.collect { path(it[1]) }]
             }).match()
         }
@@ -72,9 +69,6 @@ nextflow_workflow {
                 else if (key == "ref_dict") {
                     return [key, val.collect { file(it[1]).name }]
                 }
-                else if (key == "versions") {
-                    return [key, val.collect { path(it).yaml }]
-                }
                 return [key, val.collect { path(it[1]) }]
             }).match()
         }
@@ -109,9 +103,6 @@ nextflow_workflow {
                 else if (key == "ref_dict") {
                     return [key, val.collect { file(it[1]).name }]
                 }
-                else if (key == "versions") {
-                    return [key, val.collect { path(it).yaml }]
-                }
                 return [key, val.collect { path(it[1]) }]
             }).match()
         }
diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test.snap b/subworkflows/local/prepare_genome/tests/main.nf.test.snap
index 6fbdc7e0..6b4bd3f0 100644
--- a/subworkflows/local/prepare_genome/tests/main.nf.test.snap
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test.snap
@@ -18,31 +18,14 @@
                 ],
                 "reference_fai": [
                     "reference.fasta.fai:md5,bf4047e05f95deb372eb8ffd601cbc29"
-                ],
-                "versions": [
-                    {
-                        "PREPARE_GENOME:SAMTOOLS_FAIDX": {
-                            "samtools": "1.22.1"
-                        }
-                    },
-                    {
-                        "PREPARE_GENOME:PICARD_CREATESEQUENCEDICTIONARY": {
-                            "picard": "3.4.0"
-                        }
-                    },
-                    {
-                        "PREPARE_GENOME:BWAMEM2_INDEX": {
-                            "bwamem2": "2.2.1"
-                        }
-                    }
                 ]
             }
         ],
+        "timestamp": "2026-02-20T11:14:59.592335797",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2025-12-15T11:57:16.786415613"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "Test without bwamem2 index file path, with run_picard_collecthsmetrics=true and with ref_dict": {
         "content": [
@@ -63,26 +46,14 @@
                 ],
                 "reference_fai": [
                     "reference.fasta.fai:md5,bf4047e05f95deb372eb8ffd601cbc29"
-                ],
-                "versions": [
-                    {
-                        "PREPARE_GENOME:SAMTOOLS_FAIDX": {
-                            "samtools": "1.22.1"
-                        }
-                    },
-                    {
-                        "PREPARE_GENOME:BWAMEM2_INDEX": {
-                            "bwamem2": "2.2.1"
-                        }
-                    }
                 ]
             }
         ],
+        "timestamp": "2026-02-19T12:12:39.549105919",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2025-12-15T11:56:46.871893037"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "Test without bwamem2 index file path and with run_picard_collecthsmetrics=false": {
         "content": [
@@ -100,25 +71,13 @@
                 ],
                 "reference_fai": [
                     "reference.fasta.fai:md5,bf4047e05f95deb372eb8ffd601cbc29"
-                ],
-                "versions": [
-                    {
-                        "PREPARE_GENOME:SAMTOOLS_FAIDX": {
-                            "samtools": "1.22.1"
-                        }
-                    },
-                    {
-                        "PREPARE_GENOME:BWAMEM2_INDEX": {
-                            "bwamem2": "2.2.1"
-                        }
-                    }
                 ]
             }
         ],
+        "timestamp": "2026-02-19T12:11:58.258098906",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2025-12-15T12:47:55.989932088"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }
\ No newline at end of file
diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf
index 75661ddd..68a4d9d9 100644
--- a/subworkflows/local/qc_bam/main.nf
+++ b/subworkflows/local/qc_bam/main.nf
@@ -17,10 +17,8 @@ workflow QC_BAM {
     ch_ref_dict // channel: [mandatory for picard_collecthsmetrics] [ val(meta), path(ref_dict) ]
 
     main:
-
     ch_multiple_metrics = channel.empty()
     ch_hs_metrics = channel.empty()
-    ch_versions = channel.empty()
 
     ch_bam_bai = ch_bam.join(ch_bai, failOnDuplicate: true, failOnMismatch: true)
 
@@ -31,7 +29,6 @@ workflow QC_BAM {
     )
 
     ch_multiple_metrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics
-    ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions)
 
     if (run_picard_collecthsmetrics) {
 
@@ -48,11 +45,9 @@ workflow QC_BAM {
         )
 
         ch_hs_metrics = PICARD_COLLECTHSMETRICS.out.metrics
-        ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions)
     }
 
     emit:
     multiple_metrics = ch_multiple_metrics
     hs_metrics       = ch_hs_metrics
-    versions         = ch_versions
 }
diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test
index 86605790..017dfa25 100644
--- a/subworkflows/local/qc_bam/tests/main.nf.test
+++ b/subworkflows/local/qc_bam/tests/main.nf.test
@@ -48,9 +48,6 @@ nextflow_workflow {
                     println val[0][1]
                     return [key, val.collect { it[1].collect{ file(it.toString()).name } } ]
                 }
-                else if (key == "versions") {
-                    return [key, val.collect { path(it).yaml }]
-                }
                 return [key, val]
             }).match()
         }
@@ -99,9 +96,6 @@ nextflow_workflow {
                     println val[0][1]
                     return [key, val.collect { it[1].collect{ file(it.toString()).name } } ]
                 }
-                else if (key == "versions") {
-                    return [key, val.collect { path(it).yaml }]
-                }
                 return [key, val]
             }).match()
         }
diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap
index 16fd63af..e8bf25f2 100644
--- a/subworkflows/local/qc_bam/tests/main.nf.test.snap
+++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap
@@ -10,21 +10,14 @@
                         "earlycasualcaiman.CollectMultipleMetrics.quality_by_cycle_metrics",
                         "earlycasualcaiman.CollectMultipleMetrics.quality_distribution_metrics"
                     ]
-                ],
-                "versions": [
-                    {
-                        "QC_BAM:PICARD_COLLECTMULTIPLEMETRICS": {
-                            "picard": "3.4.0"
-                        }
-                    }
                 ]
             }
         ],
+        "timestamp": "2026-02-19T12:13:55.371999049",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2025-12-15T13:01:33.166952245"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "Test with run_picard_collecthsmetrics=true": {
         "content": [
@@ -40,25 +33,13 @@
                         "earlycasualcaiman.CollectMultipleMetrics.quality_by_cycle_metrics",
                         "earlycasualcaiman.CollectMultipleMetrics.quality_distribution_metrics"
                     ]
-                ],
-                "versions": [
-                    {
-                        "QC_BAM:PICARD_COLLECTMULTIPLEMETRICS": {
-                            "picard": "3.4.0"
-                        }
-                    },
-                    {
-                        "QC_BAM:PICARD_COLLECTHSMETRICS": {
-                            "picard": "3.4.0"
-                        }
-                    }
                 ]
             }
         ],
+        "timestamp": "2026-02-19T12:15:28.332477673",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2025-12-15T13:02:46.733316125"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
index ee4738c8..1df8b76f 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf
+++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
@@ -38,7 +38,7 @@ workflow UTILS_NFSCHEMA_PLUGIN {
         }
         log.info paramsHelp(
             help_options,
-            params.help instanceof String ? params.help : "",
+            (params.help instanceof String && params.help != "true") ? params.help : "",
         )
         exit 0
     }
@@ -71,4 +71,3 @@ workflow UTILS_NFSCHEMA_PLUGIN {
     emit:
     dummy_emit = true
 }
-
diff --git a/tests/MiSeq.nf.test.snap b/tests/MiSeq.nf.test.snap
index 617568de..7339c9d5 100644
--- a/tests/MiSeq.nf.test.snap
+++ b/tests/MiSeq.nf.test.snap
@@ -22,18 +22,16 @@
                 "pipeline_info",
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "samtools_faidx",
-                "samtools_faidx/genome.fa.fai",
-                "samtools_faidx/genome.fa.sizes"
+                "samtools_faidx/genome.fa.fai"
             ],
             [
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
-                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc"
+                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b"
             ],
             "No BAM files",
             "No warnings"
         ],
-        "timestamp": "2026-02-17T10:23:01.770390051",
+        "timestamp": "2026-02-19T11:25:41.926154725",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -133,6 +131,7 @@
                 "multiqc/global_report/multiqc_plots/pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -157,6 +156,7 @@
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -181,6 +181,7 @@
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -216,7 +217,6 @@
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "samtools_faidx",
                 "samtools_faidx/genome.fa.fai",
-                "samtools_faidx/genome.fa.sizes",
                 "seqfu_stats",
                 "seqfu_stats/SAMPLE_SINGLE_END_01_seqfu.tsv",
                 "seqfu_stats/SAMPLE_SINGLE_END_01_seqfu_mqc.txt"
@@ -261,7 +261,6 @@
                 "picard_quality_by_cycle.txt:md5,d754b0c0d9aac602637d0c923dc88834",
                 "picard_quality_score_distribution.txt:md5,d86da8fb7d48098fd5ec4a8419a8bc9e",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
-                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "SAMPLE_SINGLE_END_01_seqfu.tsv:md5,33a9e44386f308d43881a58394b6b17c",
                 "SAMPLE_SINGLE_END_01_seqfu_mqc.txt:md5,e67e819605ab49182aacf1d676dc885d"
             ],
@@ -270,7 +269,7 @@
             ],
             "No warnings"
         ],
-        "timestamp": "2026-02-17T10:17:46.832632927",
+        "timestamp": "2026-02-19T16:04:51.402781572",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -387,6 +386,7 @@
                 "multiqc/global_report/multiqc_plots/pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -412,6 +412,7 @@
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_adapter_content_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -437,6 +438,7 @@
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -506,6 +508,7 @@
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -531,6 +534,7 @@
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_adapter_content_plot.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -556,6 +560,7 @@
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -600,7 +605,6 @@
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "samtools_faidx",
                 "samtools_faidx/genome.fa.fai",
-                "samtools_faidx/genome.fa.sizes",
                 "seqfu_stats",
                 "seqfu_stats/SAMPLE_PAIRED_END_1_01_seqfu.tsv",
                 "seqfu_stats/SAMPLE_PAIRED_END_1_01_seqfu_mqc.txt",
@@ -686,7 +690,6 @@
                 "picard_quality_by_cycle.txt:md5,2497dd5ef1e5cedc1f88a9b67ef549d7",
                 "picard_quality_score_distribution.txt:md5,795138cccc8b97143f8bf0bf0adbd4b7",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
-                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "SAMPLE_PAIRED_END_1_01_seqfu.tsv:md5,be29dfe848eab9a10ee0d46691223eae",
                 "SAMPLE_PAIRED_END_1_01_seqfu_mqc.txt:md5,0aca00c7f64454af520c7e08ec595d2b",
                 "SAMPLE_PAIRED_END_2_02_seqfu.tsv:md5,44a5cb826e001d58208a5855938fa82b",
@@ -700,7 +703,7 @@
                 "WARN: Tag name collision: [Bpacificus]"
             ]
         ],
-        "timestamp": "2026-02-17T10:18:50.450876782",
+        "timestamp": "2026-02-19T16:07:01.63849991",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -835,7 +838,6 @@
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "samtools_faidx",
                 "samtools_faidx/genome.fa.fai",
-                "samtools_faidx/genome.fa.sizes",
                 "seqfu_stats",
                 "seqfu_stats/SAMPLE_SINGLE_END_01_seqfu.tsv",
                 "seqfu_stats/SAMPLE_SINGLE_END_01_seqfu_mqc.txt"
@@ -870,7 +872,6 @@
                 "picard_quality_by_cycle.txt:md5,d754b0c0d9aac602637d0c923dc88834",
                 "picard_quality_score_distribution.txt:md5,d86da8fb7d48098fd5ec4a8419a8bc9e",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
-                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "SAMPLE_SINGLE_END_01_seqfu.tsv:md5,33a9e44386f308d43881a58394b6b17c",
                 "SAMPLE_SINGLE_END_01_seqfu_mqc.txt:md5,e67e819605ab49182aacf1d676dc885d"
             ],
@@ -879,7 +880,7 @@
             ],
             "No warnings"
         ],
-        "timestamp": "2026-02-17T10:22:28.854774703",
+        "timestamp": "2026-02-19T16:05:40.254319275",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
diff --git a/tests/NovaSeq6000.nf.test.snap b/tests/NovaSeq6000.nf.test.snap
index 695e66d5..7d90acba 100644
--- a/tests/NovaSeq6000.nf.test.snap
+++ b/tests/NovaSeq6000.nf.test.snap
@@ -127,6 +127,7 @@
                 "multiqc/global_report/multiqc_plots/pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -153,6 +154,7 @@
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -179,6 +181,7 @@
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -251,6 +254,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -277,6 +281,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -303,6 +308,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -374,6 +380,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -400,6 +407,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -426,6 +434,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -497,6 +506,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -523,6 +533,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -549,6 +560,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -620,6 +632,7 @@
                 "multiqc/group_reports/test/multiqc_plots/pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -646,6 +659,7 @@
                 "multiqc/group_reports/test/multiqc_plots/png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -672,6 +686,7 @@
                 "multiqc/group_reports/test/multiqc_plots/svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -743,7 +758,6 @@
                 "rundirparser/200624_A00834_0183_BHMTFYDRXX_illumina_mqc.yml",
                 "samtools_faidx",
                 "samtools_faidx/genome.fa.fai",
-                "samtools_faidx/genome.fa.sizes",
                 "seqfu_stats",
                 "seqfu_stats/Sample1_01_seqfu.tsv",
                 "seqfu_stats/Sample1_01_seqfu_mqc.txt",
@@ -939,7 +953,6 @@
                 "picard_quality_score_distribution.txt:md5,a2882ff59902dc95830ed4bdb955561a",
                 "200624_A00834_0183_BHMTFYDRXX_illumina_mqc.yml:md5,29e05fed18bca0e9a857c992b6d59a40",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
-                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "Sample1_01_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6",
                 "Sample1_01_seqfu_mqc.txt:md5,24d99524ccd0e6c6255a69d68a871c7a",
                 "Sample23_03_seqfu.tsv:md5,6fac5d3dbce3f3bee72341fe99a399dc",
@@ -1035,7 +1048,7 @@
                 "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:SEQFU_STATS (seqfu)"
             ]
         ],
-        "timestamp": "2026-02-17T16:11:01.427075006",
+        "timestamp": "2026-02-19T16:08:17.233872508",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -1172,6 +1185,7 @@
                 "multiqc/global_report/multiqc_plots/pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -1198,6 +1212,7 @@
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -1224,6 +1239,7 @@
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -1296,6 +1312,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -1322,6 +1339,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -1348,6 +1366,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -1419,6 +1438,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -1445,6 +1465,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -1471,6 +1492,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -1542,6 +1564,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -1568,6 +1591,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -1594,6 +1618,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -1665,6 +1690,7 @@
                 "multiqc/group_reports/test/multiqc_plots/pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -1691,6 +1717,7 @@
                 "multiqc/group_reports/test/multiqc_plots/png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -1717,6 +1744,7 @@
                 "multiqc/group_reports/test/multiqc_plots/svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -1788,7 +1816,6 @@
                 "rundirparser/200624_A00834_0183_BHMTFYDRXX_illumina_mqc.yml",
                 "samtools_faidx",
                 "samtools_faidx/genome.fa.fai",
-                "samtools_faidx/genome.fa.sizes",
                 "seqfu_stats",
                 "seqfu_stats/Sample1_01_seqfu.tsv",
                 "seqfu_stats/Sample1_01_seqfu_mqc.txt",
@@ -1990,7 +2017,6 @@
                 "picard_quality_score_distribution.txt:md5,0a04dad54cadfd660c935af9a0658e0c",
                 "200624_A00834_0183_BHMTFYDRXX_illumina_mqc.yml:md5,29e05fed18bca0e9a857c992b6d59a40",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
-                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "Sample1_01_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6",
                 "Sample1_01_seqfu_mqc.txt:md5,24d99524ccd0e6c6255a69d68a871c7a",
                 "Sample23_03_seqfu.tsv:md5,6fac5d3dbce3f3bee72341fe99a399dc",
@@ -2021,7 +2047,7 @@
                 "WARN: Tag name collision: [test]"
             ]
         ],
-        "timestamp": "2026-02-17T15:50:33.940454174",
+        "timestamp": "2026-02-19T16:09:22.487870402",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -2158,6 +2184,7 @@
                 "multiqc/global_report/multiqc_plots/pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -2184,6 +2211,7 @@
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -2210,6 +2238,7 @@
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -2282,6 +2311,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -2308,6 +2338,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -2334,6 +2365,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -2405,6 +2437,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -2431,6 +2464,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -2457,6 +2491,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -2528,6 +2563,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -2554,6 +2590,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -2580,6 +2617,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -2651,6 +2689,7 @@
                 "multiqc/group_reports/test/multiqc_plots/pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -2677,6 +2716,7 @@
                 "multiqc/group_reports/test/multiqc_plots/png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -2703,6 +2743,7 @@
                 "multiqc/group_reports/test/multiqc_plots/svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -2774,7 +2815,6 @@
                 "rundirparser/200624_A00834_0183_BHMTFYDRXX_illumina_mqc.yml",
                 "samtools_faidx",
                 "samtools_faidx/genome.fa.fai",
-                "samtools_faidx/genome.fa.sizes",
                 "seqfu_stats",
                 "seqfu_stats/Sample1_01_seqfu.tsv",
                 "seqfu_stats/Sample1_01_seqfu_mqc.txt",
@@ -2976,7 +3016,6 @@
                 "picard_quality_score_distribution.txt:md5,65f7be51589f047c63fe05151a8fbde4",
                 "200624_A00834_0183_BHMTFYDRXX_illumina_mqc.yml:md5,29e05fed18bca0e9a857c992b6d59a40",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
-                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "Sample1_01_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6",
                 "Sample1_01_seqfu_mqc.txt:md5,24d99524ccd0e6c6255a69d68a871c7a",
                 "Sample23_03_seqfu.tsv:md5,6fac5d3dbce3f3bee72341fe99a399dc",
@@ -3007,7 +3046,7 @@
                 "WARN: Tag name collision: [test]"
             ]
         ],
-        "timestamp": "2026-02-17T15:52:18.005537349",
+        "timestamp": "2026-02-19T16:10:37.885643273",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -3136,6 +3175,7 @@
                 "multiqc/global_report/multiqc_plots/pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -3161,6 +3201,7 @@
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -3186,6 +3227,7 @@
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -3256,6 +3298,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -3281,6 +3324,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -3306,6 +3350,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -3375,6 +3420,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -3400,6 +3446,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -3425,6 +3472,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -3494,6 +3542,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -3519,6 +3568,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -3544,6 +3594,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -3613,6 +3664,7 @@
                 "multiqc/group_reports/test/multiqc_plots/pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -3638,6 +3690,7 @@
                 "multiqc/group_reports/test/multiqc_plots/png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -3663,6 +3716,7 @@
                 "multiqc/group_reports/test/multiqc_plots/svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -3731,7 +3785,6 @@
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "samtools_faidx",
                 "samtools_faidx/genome.fa.fai",
-                "samtools_faidx/genome.fa.sizes",
                 "seqfu_stats",
                 "seqfu_stats/Sample1_01_seqfu.tsv",
                 "seqfu_stats/Sample1_01_seqfu_mqc.txt",
@@ -3921,7 +3974,6 @@
                 "picard_quality_by_cycle.txt:md5,0aa028d69d8bb02f0a2bcd0ed08f4235",
                 "picard_quality_score_distribution.txt:md5,a2882ff59902dc95830ed4bdb955561a",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
-                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "Sample1_01_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6",
                 "Sample1_01_seqfu_mqc.txt:md5,24d99524ccd0e6c6255a69d68a871c7a",
                 "Sample23_03_seqfu.tsv:md5,6fac5d3dbce3f3bee72341fe99a399dc",
@@ -3953,7 +4005,7 @@
                 "WARN: Tag name collision: [test]"
             ]
         ],
-        "timestamp": "2026-02-17T10:46:58.253157108",
+        "timestamp": "2026-02-19T16:13:03.499762737",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -4090,6 +4142,7 @@
                 "multiqc/global_report/multiqc_plots/pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -4116,6 +4169,7 @@
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -4142,6 +4196,7 @@
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -4214,6 +4269,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -4240,6 +4296,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/group_reports/group1/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -4266,6 +4323,7 @@
                 "multiqc/group_reports/group1/multiqc_plots/svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -4337,6 +4395,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -4363,6 +4422,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/group_reports/group2/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -4389,6 +4449,7 @@
                 "multiqc/group_reports/group2/multiqc_plots/svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -4460,6 +4521,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -4486,6 +4548,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -4512,6 +4575,7 @@
                 "multiqc/group_reports/lane1/multiqc_plots/svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -4583,6 +4647,7 @@
                 "multiqc/group_reports/test/multiqc_plots/pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -4609,6 +4674,7 @@
                 "multiqc/group_reports/test/multiqc_plots/png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/group_reports/test/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/group_reports/test/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -4635,6 +4701,7 @@
                 "multiqc/group_reports/test/multiqc_plots/svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/group_reports/test/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -4706,7 +4773,6 @@
                 "rundirparser/200624_A00834_0183_BHMTFYDRXX_illumina_mqc.yml",
                 "samtools_faidx",
                 "samtools_faidx/genome.fa.fai",
-                "samtools_faidx/genome.fa.sizes",
                 "seqfu_stats",
                 "seqfu_stats/Sample1_01_seqfu.tsv",
                 "seqfu_stats/Sample1_01_seqfu_mqc.txt",
@@ -4908,7 +4974,6 @@
                 "picard_quality_score_distribution.txt:md5,a2882ff59902dc95830ed4bdb955561a",
                 "200624_A00834_0183_BHMTFYDRXX_illumina_mqc.yml:md5,29e05fed18bca0e9a857c992b6d59a40",
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
-                "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "Sample1_01_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6",
                 "Sample1_01_seqfu_mqc.txt:md5,24d99524ccd0e6c6255a69d68a871c7a",
                 "Sample23_03_seqfu.tsv:md5,6fac5d3dbce3f3bee72341fe99a399dc",
@@ -4944,7 +5009,7 @@
                 "WARN: sampletest_04: Requested sample_size (120) is larger than available reads (100). Pipeline will continue with 100 reads."
             ]
         ],
-        "timestamp": "2026-02-17T15:53:46.460202138",
+        "timestamp": "2026-02-19T16:11:52.597356515",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
diff --git a/tests/PromethION.nf.test.snap b/tests/PromethION.nf.test.snap
index 1bbc1aa3..f9a0fdcc 100644
--- a/tests/PromethION.nf.test.snap
+++ b/tests/PromethION.nf.test.snap
@@ -55,6 +55,7 @@
                 "multiqc/global_report/multiqc_plots/pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/global_report/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
@@ -71,6 +72,7 @@
                 "multiqc/global_report/multiqc_plots/png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png",
                 "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png",
+                "multiqc/global_report/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_adapter_content_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/global_report/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
@@ -87,6 +89,7 @@
                 "multiqc/global_report/multiqc_plots/svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg",
+                "multiqc/global_report/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/global_report/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
@@ -105,7 +108,6 @@
                 "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
                 "samtools_faidx",
                 "samtools_faidx/genome.fa.fai",
-                "samtools_faidx/genome.fa.sizes",
                 "seqfu_stats",
                 "seqfu_stats/hg001_01_seqfu.tsv",
                 "seqfu_stats/hg001_01_seqfu_mqc.txt"
@@ -130,14 +132,13 @@
                 "multiqc_fastqc.txt:md5,b71aaffef9767dfe9d83fde0d31a3a1b",
                 "multiqc_seqfu_mqc.txt:md5,9595d608ff5709f2bdec8cb1016416c0",
                 "genome.fa.fai:md5,59557cd3a71ca5e0840285b6088ec1d6",
-                "genome.fa.sizes:md5,f154a58a25ba9c4d386003eaa1bb731b",
                 "hg001_01_seqfu.tsv:md5,b133752c897afbb4d8721b911fa117d4",
                 "hg001_01_seqfu_mqc.txt:md5,42e3506b02ceb72a6f05cb174505e722"
             ],
             "No BAM files",
             "No warnings"
         ],
-        "timestamp": "2026-02-17T10:30:18.833766777",
+        "timestamp": "2026-02-19T11:20:55.026861066",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 3317f739..635e1a0b 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -54,7 +54,6 @@ workflow SEQINSPECTOR {
     target_intervals
 
     main:
-    ch_versions = channel.empty()
     ch_multiqc_files = channel.empty()
     ch_multiqc_extra_files = channel.empty()
     ch_bwamem2_mem = channel.empty()
@@ -68,8 +67,6 @@ workflow SEQINSPECTOR {
         ref_dict,
     )
 
-    ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions)
-
     //
     // MODULE: Parse rundir info
     //
@@ -119,7 +116,6 @@ workflow SEQINSPECTOR {
         SEQTK_SAMPLE(ch_samplesheet.map { meta, reads -> [meta, reads, sample_size] })
 
         ch_sample = SEQTK_SAMPLE.out.reads
-        ch_versions = ch_versions.mix(SEQTK_SAMPLE.out.versions)
     }
     else {
         // No subsampling
@@ -133,7 +129,6 @@ workflow SEQINSPECTOR {
         FASTQC(ch_sample)
 
         ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip)
-        ch_versions = ch_versions.mix(FASTQC.out.versions)
     }
 
     //
@@ -155,7 +150,6 @@ workflow SEQINSPECTOR {
             }
 
         ch_multiqc_files = ch_multiqc_files.mix(SEQFU_STATS.out.multiqc)
-        ch_versions = ch_versions.mix(SEQFU_STATS.out.versions)
     }
 
     //
@@ -179,7 +173,6 @@ workflow SEQINSPECTOR {
         FASTQSCREEN_FASTQSCREEN(ch_sample, ch_fastqscreen_refs)
 
         ch_multiqc_files = ch_multiqc_files.mix(FASTQSCREEN_FASTQSCREEN.out.txt)
-        ch_versions = ch_versions.mix(FASTQSCREEN_FASTQSCREEN.out.versions)
     }
 
     // MODULE: Align reads with BWA-MEM2
@@ -191,12 +184,10 @@ workflow SEQINSPECTOR {
             sort_bam ?: true,
         )
         ch_bwamem2_mem = BWAMEM2_MEM.out.bam
-        ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions)
 
         SAMTOOLS_INDEX(ch_bwamem2_mem)
 
         ch_samtools_index = SAMTOOLS_INDEX.out.bai
-        ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions)
     }
 
 
@@ -222,13 +213,12 @@ workflow SEQINSPECTOR {
         )
 
         ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.multiple_metrics, QC_BAM.out.hs_metrics)
-        ch_versions = ch_versions.mix(QC_BAM.out.versions)
     }
 
     // Collate and save software versions
     //
     def collated_versions = softwareVersionsToYAML(
-        softwareVersions: ch_versions.mix(channel.topic("versions")),
+        softwareVersions: channel.topic("versions"),
         nextflowVersion: workflow.nextflow.version,
     ).collectFile(
         storeDir: "${outdir}/pipeline_info",
@@ -327,5 +317,4 @@ workflow SEQINSPECTOR {
     emit:
     global_report   = MULTIQC_GLOBAL.out.report.toList() // channel: [ /path/to/multiqc_report.html ]
     grouped_reports = MULTIQC_PER_TAG.out.report.toList() // channel: [ /path/to/multiqc_report.html ]
-    versions        = ch_versions // channel: [ path(versions.yml) ]
 }

From 1c4e615bad9fc46dc719ff1d3c33c654c4fc7ee2 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 20 Feb 2026 13:30:07 +0100
Subject: [PATCH 529/530] no modules binaries (#176)

---
 CHANGELOG.md                                              | 1 +
 .../resources/usr/bin => bin}/parse_illumina.py           | 0
 modules/local/rundirparser/tests/main.nf.test             | 1 -
 modules/local/rundirparser/tests/main.nf.test.snap        | 8 ++++----
 modules/local/rundirparser/tests/nextflow.config          | 1 -
 5 files changed, 5 insertions(+), 6 deletions(-)
 rename {modules/local/rundirparser/resources/usr/bin => bin}/parse_illumina.py (100%)
 delete mode 100644 modules/local/rundirparser/tests/nextflow.config

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b511d1ea..2ac691ec 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -81,6 +81,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#174](https://github.com/nf-core/seqinspector/pull/174) More strict syntax
 - [#174](https://github.com/nf-core/seqinspector/pull/174) No params included in workflows
 - [#175](https://github.com/nf-core/seqinspector/pull/175) Update all modules and migrate the whole pipeline to using topic versions
+- [#176](https://github.com/nf-core/seqinspector/pull/176) No modules binaries
 
 ### `Dependencies`
 
diff --git a/modules/local/rundirparser/resources/usr/bin/parse_illumina.py b/bin/parse_illumina.py
similarity index 100%
rename from modules/local/rundirparser/resources/usr/bin/parse_illumina.py
rename to bin/parse_illumina.py
diff --git a/modules/local/rundirparser/tests/main.nf.test b/modules/local/rundirparser/tests/main.nf.test
index 894ead33..9a0befcf 100644
--- a/modules/local/rundirparser/tests/main.nf.test
+++ b/modules/local/rundirparser/tests/main.nf.test
@@ -3,7 +3,6 @@ nextflow_process {
     name "Test Process RUNDIRPARSER"
     script "../main.nf"
     process "RUNDIRPARSER"
-    config "./nextflow.config"
 
     test("NovaSeq6000") {
 
diff --git a/modules/local/rundirparser/tests/main.nf.test.snap b/modules/local/rundirparser/tests/main.nf.test.snap
index 4031a773..59e9f50c 100644
--- a/modules/local/rundirparser/tests/main.nf.test.snap
+++ b/modules/local/rundirparser/tests/main.nf.test.snap
@@ -19,11 +19,11 @@
                 ]
             }
         ],
+        "timestamp": "2025-12-12T13:30:03.998435274",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
-        },
-        "timestamp": "2025-12-12T13:30:03.998435274"
+        }
     },
     "NovaSeq6000 - stub": {
         "content": [
@@ -45,10 +45,10 @@
                 ]
             }
         ],
+        "timestamp": "2025-12-12T13:30:11.388290534",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
-        },
-        "timestamp": "2025-12-12T13:30:11.388290534"
+        }
     }
 }
\ No newline at end of file
diff --git a/modules/local/rundirparser/tests/nextflow.config b/modules/local/rundirparser/tests/nextflow.config
deleted file mode 100644
index 651f0b86..00000000
--- a/modules/local/rundirparser/tests/nextflow.config
+++ /dev/null
@@ -1 +0,0 @@
-nextflow.enable.moduleBinaries = true

From 78ad48b6885d30b625607f2a9b9db6e4faa3ecff Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 20 Feb 2026 14:54:31 +0100
Subject: [PATCH 530/530] Remove unused modules (bowtie2/build,
 fastqscreen/buildfromindex) (#177)

* Remove unused modules + move PREPARE_GENOME to root main.nf

* Actually not using BOWTIE2

* CHANGELOG

* snapshot

* regenerate snapshot

* auto-format

* Apply suggestion from @maxulysse
---
 CHANGELOG.md                                  |   2 +
 CITATIONS.md                                  |   4 -
 README.md                                     |   1 -
 conf/base.config                              |  40 +-
 conf/igenomes.config                          | 816 +++++++++---------
 conf/modules.config                           |  68 +-
 conf/test.config                              |   7 +-
 conf/test_full.config                         |   4 +-
 main.nf                                       | 107 ++-
 modules.json                                  |  10 -
 modules/nf-core/bowtie2/build/environment.yml |  13 -
 modules/nf-core/bowtie2/build/main.nf         |  33 -
 modules/nf-core/bowtie2/build/meta.yml        |  69 --
 .../buildfromindex/environment.yml            |   8 -
 .../fastqscreen/buildfromindex/main.nf        |  59 --
 .../fastqscreen/buildfromindex/meta.yml       |  57 --
 nextflow.config                               | 215 +++--
 nextflow_schema.json                          |  19 +-
 nf-test.config                                |  10 +-
 subworkflows/local/prepare_genome/main.nf     |   6 +-
 .../local/prepare_genome/tests/main.nf.test   |   6 +-
 .../prepare_genome/tests/main.nf.test.snap    |   8 +-
 .../main.nf                                   |   2 -
 tests/NovaSeq6000.nf.test.snap                |   8 +-
 tests/nextflow.config                         |   3 +-
 workflows/seqinspector.nf                     |  57 +-
 26 files changed, 694 insertions(+), 938 deletions(-)
 delete mode 100644 modules/nf-core/bowtie2/build/environment.yml
 delete mode 100644 modules/nf-core/bowtie2/build/main.nf
 delete mode 100644 modules/nf-core/bowtie2/build/meta.yml
 delete mode 100644 modules/nf-core/fastqscreen/buildfromindex/environment.yml
 delete mode 100644 modules/nf-core/fastqscreen/buildfromindex/main.nf
 delete mode 100644 modules/nf-core/fastqscreen/buildfromindex/meta.yml

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2ac691ec..ea501326 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -82,6 +82,8 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#174](https://github.com/nf-core/seqinspector/pull/174) No params included in workflows
 - [#175](https://github.com/nf-core/seqinspector/pull/175) Update all modules and migrate the whole pipeline to using topic versions
 - [#176](https://github.com/nf-core/seqinspector/pull/176) No modules binaries
+- [#177](https://github.com/nf-core/seqinspector/pull/177) Remove non used modules
+- [#177](https://github.com/nf-core/seqinspector/pull/177) Move PREPARE_GENOME to the root main.nf script
 
 ### `Dependencies`
 
diff --git a/CITATIONS.md b/CITATIONS.md
index 6d46e83b..6b025bee 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -10,10 +10,6 @@
 
 ## Pipeline tools
 
-- [Bowtie2](https://www.nature.com/articles/nmeth.1923)
-
-  > Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012 Apr;9(4):357-9. doi: 10.1038/nmeth.1923. PubMed PMID: 22388286.
-
 - [BWAMEM2](https://ieeexplore.ieee.org/abstract/document/8820962)
 
   > Vasimuddin Md, Misra S, Li H, Aluru S. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. In: 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS). IEEE; 2019:314-324. doi:10.1109/IPDPS.2019.00041
diff --git a/README.md b/README.md
index 9c3da5b4..f48b9894 100644
--- a/README.md
+++ b/README.md
@@ -54,7 +54,6 @@ If provided, nf-core/seqinspector can also parse statistics from an Illumina run
 
 | Tool        | Version |
 | ----------- | ------- |
-| bowtie2     | 2.5.4   |
 | bwamem2     | 2.3     |
 | fastqc      | 0.12.1  |
 | fastqscreen | 0.16.0  |
diff --git a/conf/base.config b/conf/base.config
index 45099965..af915353 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -9,9 +9,9 @@
 */
 
 process {
-    cpus   = { 1      * task.attempt }
-    memory = { 6.GB   * task.attempt }
-    time   = { 4.h    * task.attempt }
+    cpus          = { 1 * task.attempt }
+    memory        = { 6.GB * task.attempt }
+    time          = { 4.h * task.attempt }
 
     errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' }
     maxRetries    = 1
@@ -23,36 +23,36 @@ process {
     //        If possible, it would be nice to keep the same label naming convention when
     //        adding in your local modules too.
     // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
-    withLabel:process_single {
-        cpus   = { 1                   }
+    withLabel: process_single {
+        cpus   = { 1 }
         memory = { 6.GB * task.attempt }
-        time   = { 4.h  * task.attempt }
+        time   = { 4.h * task.attempt }
     }
-    withLabel:process_low {
-        cpus   = { 2     * task.attempt }
+    withLabel: process_low {
+        cpus   = { 2 * task.attempt }
         memory = { 12.GB * task.attempt }
-        time   = { 4.h   * task.attempt }
+        time   = { 4.h * task.attempt }
     }
-    withLabel:process_medium {
-        cpus   = { 6     * task.attempt }
+    withLabel: process_medium {
+        cpus   = { 6 * task.attempt }
         memory = { 36.GB * task.attempt }
-        time   = { 8.h   * task.attempt }
+        time   = { 8.h * task.attempt }
     }
-    withLabel:process_high {
-        cpus   = { 12    * task.attempt }
+    withLabel: process_high {
+        cpus   = { 12 * task.attempt }
         memory = { 72.GB * task.attempt }
-        time   = { 16.h  * task.attempt }
+        time   = { 16.h * task.attempt }
     }
-    withLabel:process_long {
-        time   = { 20.h  * task.attempt }
+    withLabel: process_long {
+        time = { 20.h * task.attempt }
     }
-    withLabel:process_high_memory {
+    withLabel: process_high_memory {
         memory = { 200.GB * task.attempt }
     }
-    withLabel:error_ignore {
+    withLabel: error_ignore {
         errorStrategy = 'ignore'
     }
-    withLabel:error_retry {
+    withLabel: error_retry {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
diff --git a/conf/igenomes.config b/conf/igenomes.config
index 3f114377..9fb1acad 100644
--- a/conf/igenomes.config
+++ b/conf/igenomes.config
@@ -11,430 +11,430 @@
 params {
     // illumina iGenomes reference file paths
     genomes {
-        'GRCh37' {
-            fasta       = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt"
-            mito_name   = "MT"
-            macs_gsize  = "2.7e9"
-            blacklist   = "${projectDir}/assets/blacklists/GRCh37-blacklist.bed"
-        }
-        'GRCh38' {
-            fasta       = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-            macs_gsize  = "2.7e9"
-            blacklist   = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
-        }
-        'CHM13' {
-            fasta       = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/"
-            bwamem2     = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/"
-            gtf         = "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf"
-            gff         = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz"
-            mito_name   = "chrM"
-        }
-        'GRCm38' {
-            fasta       = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt"
-            mito_name   = "MT"
-            macs_gsize  = "1.87e9"
-            blacklist   = "${projectDir}/assets/blacklists/GRCm38-blacklist.bed"
-        }
-        'TAIR10' {
-            fasta       = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt"
-            mito_name   = "Mt"
-        }
-        'EB2' {
-            fasta       = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt"
+        GRCh37 {
+            fasta      = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa"
+            bwa        = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/"
+            bowtie2    = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/"
+            star       = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/"
+            bismark    = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/"
+            gtf        = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf"
+            bed12      = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed"
+            readme     = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt"
+            mito_name  = "MT"
+            macs_gsize = "2.7e9"
+            blacklist  = "${projectDir}/assets/blacklists/GRCh37-blacklist.bed"
+        }
+        GRCh38 {
+            fasta      = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
+            bwa        = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/"
+            bowtie2    = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/"
+            star       = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/"
+            bismark    = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/"
+            gtf        = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf"
+            bed12      = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed"
+            mito_name  = "chrM"
+            macs_gsize = "2.7e9"
+            blacklist  = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
+        }
+        CHM13 {
+            fasta     = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa"
+            bwa       = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/"
+            bwamem2   = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/"
+            gtf       = "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf"
+            gff       = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz"
+            mito_name = "chrM"
+        }
+        GRCm38 {
+            fasta      = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa"
+            bwa        = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/"
+            bowtie2    = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/"
+            star       = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/"
+            bismark    = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/"
+            gtf        = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf"
+            bed12      = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed"
+            readme     = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt"
+            mito_name  = "MT"
+            macs_gsize = "1.87e9"
+            blacklist  = "${projectDir}/assets/blacklists/GRCm38-blacklist.bed"
+        }
+        TAIR10 {
+            fasta     = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa"
+            bwa       = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/"
+            bowtie2   = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/"
+            star      = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/"
+            bismark   = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/"
+            gtf       = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf"
+            bed12     = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed"
+            readme    = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt"
+            mito_name = "Mt"
+        }
+        EB2 {
+            fasta   = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa"
+            bwa     = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/"
+            bowtie2 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/"
+            star    = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/"
+            bismark = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/"
+            gtf     = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf"
+            bed12   = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed"
+            readme  = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt"
         }
         'UMD3.1' {
-            fasta       = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt"
-            mito_name   = "MT"
-        }
-        'WBcel235' {
-            fasta       = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed"
-            mito_name   = "MtDNA"
-            macs_gsize  = "9e7"
+            fasta     = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
+            bwa       = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/"
+            bowtie2   = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/"
+            star      = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/"
+            bismark   = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/"
+            gtf       = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf"
+            bed12     = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed"
+            readme    = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt"
+            mito_name = "MT"
+        }
+        WBcel235 {
+            fasta      = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
+            bwa        = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/"
+            bowtie2    = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/"
+            star       = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/"
+            bismark    = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/"
+            gtf        = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf"
+            bed12      = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed"
+            mito_name  = "MtDNA"
+            macs_gsize = "9e7"
         }
         'CanFam3.1' {
-            fasta       = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt"
-            mito_name   = "MT"
-        }
-        'GRCz10' {
-            fasta       = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed"
-            mito_name   = "MT"
-        }
-        'BDGP6' {
-            fasta       = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed"
-            mito_name   = "M"
-            macs_gsize  = "1.2e8"
-        }
-        'EquCab2' {
-            fasta       = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt"
-            mito_name   = "MT"
-        }
-        'EB1' {
-            fasta       = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt"
-        }
-        'Galgal4' {
-            fasta       = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed"
-            mito_name   = "MT"
-        }
-        'Gm01' {
-            fasta       = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt"
-        }
-        'Mmul_1' {
-            fasta       = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt"
-            mito_name   = "MT"
+            fasta     = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa"
+            bwa       = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/"
+            bowtie2   = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/"
+            star      = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/"
+            bismark   = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/"
+            gtf       = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf"
+            bed12     = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed"
+            readme    = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt"
+            mito_name = "MT"
+        }
+        GRCz10 {
+            fasta     = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa"
+            bwa       = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/"
+            bowtie2   = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/"
+            star      = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/"
+            bismark   = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/"
+            gtf       = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf"
+            bed12     = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed"
+            mito_name = "MT"
+        }
+        BDGP6 {
+            fasta      = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa"
+            bwa        = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/"
+            bowtie2    = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/"
+            star       = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/"
+            bismark    = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/"
+            gtf        = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf"
+            bed12      = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed"
+            mito_name  = "M"
+            macs_gsize = "1.2e8"
+        }
+        EquCab2 {
+            fasta     = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa"
+            bwa       = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/"
+            bowtie2   = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/"
+            star      = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/"
+            bismark   = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/"
+            gtf       = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf"
+            bed12     = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed"
+            readme    = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt"
+            mito_name = "MT"
+        }
+        EB1 {
+            fasta   = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa"
+            bwa     = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/"
+            bowtie2 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/"
+            star    = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/"
+            bismark = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/"
+            gtf     = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf"
+            bed12   = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed"
+            readme  = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt"
+        }
+        Galgal4 {
+            fasta     = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa"
+            bwa       = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/"
+            bowtie2   = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/"
+            star      = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/"
+            bismark   = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/"
+            gtf       = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf"
+            bed12     = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed"
+            mito_name = "MT"
+        }
+        Gm01 {
+            fasta   = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa"
+            bwa     = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/"
+            bowtie2 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/"
+            star    = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/"
+            bismark = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/"
+            gtf     = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf"
+            bed12   = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed"
+            readme  = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt"
+        }
+        Mmul_1 {
+            fasta     = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa"
+            bwa       = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/"
+            bowtie2   = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/"
+            star      = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/"
+            bismark   = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/"
+            gtf       = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf"
+            bed12     = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed"
+            readme    = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt"
+            mito_name = "MT"
         }
         'IRGSP-1.0' {
-            fasta       = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed"
-            mito_name   = "Mt"
+            fasta     = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa"
+            bwa       = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/"
+            bowtie2   = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/"
+            star      = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/"
+            bismark   = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/"
+            gtf       = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf"
+            bed12     = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed"
+            mito_name = "Mt"
         }
         'CHIMP2.1.4' {
-            fasta       = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt"
-            mito_name   = "MT"
+            fasta     = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa"
+            bwa       = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/"
+            bowtie2   = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/"
+            star      = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/"
+            bismark   = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/"
+            gtf       = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf"
+            bed12     = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed"
+            readme    = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt"
+            mito_name = "MT"
         }
         'Rnor_5.0' {
-            fasta       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.bed"
-            mito_name   = "MT"
+            fasta     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa"
+            bwa       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/"
+            bowtie2   = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/"
+            star      = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/"
+            bismark   = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BismarkIndex/"
+            gtf       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.gtf"
+            bed12     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.bed"
+            mito_name = "MT"
         }
         'Rnor_6.0' {
-            fasta       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed"
-            mito_name   = "MT"
+            fasta     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa"
+            bwa       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/"
+            bowtie2   = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/"
+            star      = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/"
+            bismark   = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/"
+            gtf       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf"
+            bed12     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed"
+            mito_name = "MT"
         }
         'R64-1-1' {
-            fasta       = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed"
-            mito_name   = "MT"
-            macs_gsize  = "1.2e7"
-        }
-        'EF2' {
-            fasta       = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt"
-            mito_name   = "MT"
-            macs_gsize  = "1.21e7"
-        }
-        'Sbi1' {
-            fasta       = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt"
+            fasta      = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
+            bwa        = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/"
+            bowtie2    = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/"
+            star       = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/"
+            bismark    = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/"
+            gtf        = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf"
+            bed12      = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed"
+            mito_name  = "MT"
+            macs_gsize = "1.2e7"
+        }
+        EF2 {
+            fasta      = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa"
+            bwa        = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/"
+            bowtie2    = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/"
+            star       = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/"
+            bismark    = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/"
+            gtf        = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf"
+            bed12      = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed"
+            readme     = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt"
+            mito_name  = "MT"
+            macs_gsize = "1.21e7"
+        }
+        Sbi1 {
+            fasta   = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa"
+            bwa     = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/"
+            bowtie2 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/"
+            star    = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/"
+            bismark = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/"
+            gtf     = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf"
+            bed12   = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed"
+            readme  = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt"
         }
         'Sscrofa10.2' {
-            fasta       = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt"
-            mito_name   = "MT"
-        }
-        'AGPv3' {
-            fasta       = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed"
-            mito_name   = "Mt"
-        }
-        'hg38' {
-            fasta       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-            macs_gsize  = "2.7e9"
-            blacklist   = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
-        }
-        'hg19' {
-            fasta       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt"
-            mito_name   = "chrM"
-            macs_gsize  = "2.7e9"
-            blacklist   = "${projectDir}/assets/blacklists/hg19-blacklist.bed"
-        }
-        'mm10' {
-            fasta       = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt"
-            mito_name   = "chrM"
-            macs_gsize  = "1.87e9"
-            blacklist   = "${projectDir}/assets/blacklists/mm10-blacklist.bed"
-        }
-        'bosTau8' {
-            fasta       = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-        }
-        'ce10' {
-            fasta       = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt"
-            mito_name   = "chrM"
-            macs_gsize  = "9e7"
-        }
-        'canFam3' {
-            fasta       = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt"
-            mito_name   = "chrM"
-        }
-        'danRer10' {
-            fasta       = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-            macs_gsize  = "1.37e9"
-        }
-        'dm6' {
-            fasta       = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-            macs_gsize  = "1.2e8"
-        }
-        'equCab2' {
-            fasta       = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt"
-            mito_name   = "chrM"
-        }
-        'galGal4' {
-            fasta       = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt"
-            mito_name   = "chrM"
-        }
-        'panTro4' {
-            fasta       = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt"
-            mito_name   = "chrM"
-        }
-        'rn6' {
-            fasta       = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-        }
-        'sacCer3' {
-            fasta       = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/"
-            readme      = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt"
-            mito_name   = "chrM"
-            macs_gsize  = "1.2e7"
-        }
-        'susScr3' {
-            fasta       = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt"
-            mito_name   = "chrM"
+            fasta     = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa"
+            bwa       = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/"
+            bowtie2   = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/"
+            star      = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/"
+            bismark   = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/"
+            gtf       = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf"
+            bed12     = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed"
+            readme    = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt"
+            mito_name = "MT"
+        }
+        AGPv3 {
+            fasta     = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa"
+            bwa       = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/"
+            bowtie2   = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/"
+            star      = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/"
+            bismark   = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/"
+            gtf       = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf"
+            bed12     = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed"
+            mito_name = "Mt"
+        }
+        hg38 {
+            fasta      = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa"
+            bwa        = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/"
+            bowtie2    = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/"
+            star       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/"
+            bismark    = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/"
+            gtf        = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf"
+            bed12      = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed"
+            mito_name  = "chrM"
+            macs_gsize = "2.7e9"
+            blacklist  = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
+        }
+        hg19 {
+            fasta      = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa"
+            bwa        = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/"
+            bowtie2    = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/"
+            star       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/"
+            bismark    = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/"
+            gtf        = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf"
+            bed12      = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed"
+            readme     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt"
+            mito_name  = "chrM"
+            macs_gsize = "2.7e9"
+            blacklist  = "${projectDir}/assets/blacklists/hg19-blacklist.bed"
+        }
+        mm10 {
+            fasta      = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa"
+            bwa        = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/"
+            bowtie2    = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/"
+            star       = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/"
+            bismark    = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/"
+            gtf        = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf"
+            bed12      = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed"
+            readme     = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt"
+            mito_name  = "chrM"
+            macs_gsize = "1.87e9"
+            blacklist  = "${projectDir}/assets/blacklists/mm10-blacklist.bed"
+        }
+        bosTau8 {
+            fasta     = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa"
+            bwa       = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/"
+            bowtie2   = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/"
+            star      = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/"
+            bismark   = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/"
+            gtf       = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf"
+            bed12     = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed"
+            mito_name = "chrM"
+        }
+        ce10 {
+            fasta      = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa"
+            bwa        = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/"
+            bowtie2    = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/"
+            star       = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/"
+            bismark    = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/"
+            gtf        = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf"
+            bed12      = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed"
+            readme     = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt"
+            mito_name  = "chrM"
+            macs_gsize = "9e7"
+        }
+        canFam3 {
+            fasta     = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa"
+            bwa       = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/"
+            bowtie2   = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/"
+            star      = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/"
+            bismark   = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/"
+            gtf       = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf"
+            bed12     = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed"
+            readme    = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt"
+            mito_name = "chrM"
+        }
+        danRer10 {
+            fasta      = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa"
+            bwa        = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/"
+            bowtie2    = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/"
+            star       = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/"
+            bismark    = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/"
+            gtf        = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf"
+            bed12      = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed"
+            mito_name  = "chrM"
+            macs_gsize = "1.37e9"
+        }
+        dm6 {
+            fasta      = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa"
+            bwa        = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/"
+            bowtie2    = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/"
+            star       = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/"
+            bismark    = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/"
+            gtf        = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf"
+            bed12      = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed"
+            mito_name  = "chrM"
+            macs_gsize = "1.2e8"
+        }
+        equCab2 {
+            fasta     = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa"
+            bwa       = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/"
+            bowtie2   = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/"
+            star      = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/"
+            bismark   = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/"
+            gtf       = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf"
+            bed12     = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed"
+            readme    = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt"
+            mito_name = "chrM"
+        }
+        galGal4 {
+            fasta     = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa"
+            bwa       = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/"
+            bowtie2   = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/"
+            star      = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/"
+            bismark   = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/"
+            gtf       = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf"
+            bed12     = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed"
+            readme    = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt"
+            mito_name = "chrM"
+        }
+        panTro4 {
+            fasta     = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa"
+            bwa       = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/"
+            bowtie2   = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/"
+            star      = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/"
+            bismark   = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/"
+            gtf       = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf"
+            bed12     = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed"
+            readme    = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt"
+            mito_name = "chrM"
+        }
+        rn6 {
+            fasta     = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa"
+            bwa       = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/"
+            bowtie2   = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/"
+            star      = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/"
+            bismark   = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/"
+            gtf       = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf"
+            bed12     = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed"
+            mito_name = "chrM"
+        }
+        sacCer3 {
+            fasta      = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa"
+            bwa        = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/"
+            bowtie2    = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/"
+            star       = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/"
+            bismark    = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/"
+            readme     = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt"
+            mito_name  = "chrM"
+            macs_gsize = "1.2e7"
+        }
+        susScr3 {
+            fasta     = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa"
+            bwa       = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/"
+            bowtie2   = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/"
+            star      = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/"
+            bismark   = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/"
+            gtf       = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf"
+            bed12     = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed"
+            readme    = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt"
+            mito_name = "chrM"
         }
     }
 }
diff --git a/conf/modules.config b/conf/modules.config
index 280b7b49..f84f48ff 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -11,21 +11,20 @@
 */
 
 process {
-
     publishDir = [
         path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
         mode: params.publish_dir_mode
     ]
 
-    withName: 'SEQTK_SAMPLE' {
+    withName: SEQTK_SAMPLE {
         ext.args = '-s100'
     }
 
-    withName: 'FASTQC' {
+    withName: FASTQC {
         ext.args = '--quiet'
     }
 
-    withName: 'SEQFU_STATS' {
+    withName: SEQFU_STATS {
         ext.args   = ''
         publishDir = [
             path: { "${params.outdir}/seqfu_stats" },
@@ -34,93 +33,94 @@ process {
         ]
     }
 
-    withName: 'BWAMEM2_INDEX' {
+    withName: BWAMEM2_INDEX {
         publishDir = [
             path: { "${params.outdir}/bwamem2_index" },
             mode: params.publish_dir_mode
         ]
     }
 
-        withName: 'PICARD_CREATESEQUENCEDICTIONARY' {
+    withName: PICARD_CREATESEQUENCEDICTIONARY {
         publishDir = [
             path: { "${params.outdir}/picard_createsequencedictionary" },
             mode: params.publish_dir_mode
         ]
     }
 
-    withName: 'BWAMEM2_MEM' {
+    withName: BWAMEM2_MEM {
         publishDir = [
             path: { "${params.outdir}/bwamem2_mem" },
             mode: params.publish_dir_mode
         ]
     }
 
-    withName: 'PICARD_COLLECTMULTIPLEMETRICS' {
+    withName: PICARD_COLLECTMULTIPLEMETRICS {
         publishDir = [
             path: { "${params.outdir}/picard_collectmultiplemetrics" },
             mode: params.publish_dir_mode
         ]
     }
 
-    withName: 'PICARD_COLLECTHSMETRICS' {
+    withName: PICARD_COLLECTHSMETRICS {
+        ext.args   = { "--TMP_DIR ." }
         publishDir = [
             path: { "${params.outdir}/picard_collecthsmetrics" },
             mode: params.publish_dir_mode
         ]
-        ext.args = {"--TMP_DIR ."}
     }
 
-    withName: 'SAMTOOLS_FAIDX' {
+    withName: SAMTOOLS_FAIDX {
         publishDir = [
             path: { "${params.outdir}/samtools_faidx" },
             mode: params.publish_dir_mode
         ]
     }
 
-    withName: 'SAMTOOLS_INDEX' {
+    withName: SAMTOOLS_INDEX {
         publishDir = [
             path: { "${params.outdir}/bwamem2_mem" },
             mode: params.publish_dir_mode
         ]
     }
 
-    withName: 'RUNDIRPARSER' {
-        publishDir = [
-            path: { "${params.outdir}/rundirparser" },
-            mode: params.publish_dir_mode,
+    withName: RUNDIRPARSER {
             // The process _mqc.txt outputs should have identical names for the same sequencing platforms
             // in order to be grouped together in the MultiQC report, but here we need to enforce uniqueness
             // to avoid overwriting results in the publishDir.
-            saveAs: { filename -> "${meta.dirname}_${filename}" }
-        ]
+            publishDir = [
+            path: { "${params.outdir}/rundirparser" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> "${meta.dirname}_${filename}" }]
     }
 
-    withName: 'MULTIQC_GLOBAL' {
-        ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
+    withName: MULTIQC_GLOBAL {
+        ext.args   = { params.multiqc_title ? "--title \"${params.multiqc_title}\"" : '' }
         publishDir = [
             path: { "${params.outdir}/multiqc/global_report" },
             mode: params.publish_dir_mode
         ]
     }
 
-    withName: 'MULTIQC_PER_TAG' {
-        ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
+    withName: MULTIQC_PER_TAG {
+        ext.args   = { params.multiqc_title ? "--title \"${params.multiqc_title}\"" : '' }
         publishDir = [
             path: { "${params.outdir}/multiqc/group_reports" },
             mode: params.publish_dir_mode,
             saveAs: { filename ->
-                if (filename == 'versions.yml') {
-                    return null
-                } else if (filename  =~/\[TAG:.+\]_multiqc_(report\.html|plots|data)/) {
-                        def tag = (filename =~ /\[TAG:(.+)\]_multiqc_(report\.html|plots|data)/)[0][1]
-                        def new_filename = filename.replaceFirst(
-                            "(?<prefix>.*)\\[TAG:${tag}\\]_(?<suffix>multiqc_(report\\.html|plots|data).*)",
-                            '${prefix}${suffix}')
-                    return "${tag}/${new_filename}"
-                } else {
-                    return filename
-                }
+            if (filename == 'versions.yml') {
+                return null
             }
-        ]
+            else if (filename =~ /\[TAG:.+\]_multiqc_(report\.html|plots|data)/) {
+                def tag = (filename =~ /\[TAG:(.+)\]_multiqc_(report\.html|plots|data)/)[0][1]
+                def new_filename = filename.replaceFirst(
+                    "(?<prefix>.*)\\[TAG:${tag}\\]_(?<suffix>multiqc_(report\\.html|plots|data).*)",
+                    '${prefix}${suffix}',
+                )
+                return "${tag}/${new_filename}"
+            }
+            else {
+                return filename
+            }
+        }]
     }
 }
diff --git a/conf/test.config b/conf/test.config
index cb8f1ada..4ab15ba5 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -15,11 +15,11 @@ params {
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Input data
-    input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
-    fastq_screen_references = "${projectDir}/assets/example_fastq_screen_references.csv"
+    input                      = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
+    fastq_screen_references    = "${projectDir}/assets/example_fastq_screen_references.csv"
 
     // Genome references
-    genome = 'R64-1-1'
+    genome                     = 'R64-1-1'
 }
 
 process {
@@ -28,5 +28,4 @@ process {
         memory: '8.GB',
         time: '1.h'
     ]
-
 }
diff --git a/conf/test_full.config b/conf/test_full.config
index 65f0a532..d9ea691c 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -16,8 +16,8 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
-    input = params.pipelines_testdata_base_path + 'seqinspector/full_tests/SampleSheet.csv'
+    input                      = params.pipelines_testdata_base_path + 'seqinspector/full_tests/SampleSheet.csv'
 
     // Genome references
-    genome = 'R64-1-1'
+    genome                     = 'R64-1-1'
 }
diff --git a/main.nf b/main.nf
index 47460d4d..10bb5d94 100644
--- a/main.nf
+++ b/main.nf
@@ -17,6 +17,7 @@
 include { SEQINSPECTOR            } from './workflows/seqinspector'
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
+include { PREPARE_GENOME          } from './subworkflows/local/prepare_genome'
 include { getGenomeAttribute      } from 'plugin/nf-core-utils'
 
 /*
@@ -25,47 +26,10 @@ include { getGenomeAttribute      } from 'plugin/nf-core-utils'
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-params.fasta = getGenomeAttribute('fasta')
+params.fasta   = getGenomeAttribute('fasta')
+params.bwamem2 = getGenomeAttribute('bwamem2')
+params.dict    = getGenomeAttribute('dict')
 
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    NAMED WORKFLOWS FOR PIPELINE
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-//
-// WORKFLOW: Run main analysis pipeline depending on type of input
-//
-workflow NFCORE_SEQINSPECTOR {
-    take:
-    samplesheet // channel: samplesheet read in from --input
-
-    main:
-    //
-    // WORKFLOW: Run pipeline
-    //
-    SEQINSPECTOR(
-        samplesheet,
-        params.bait_intervals,
-        params.bwamem2,
-        params.fasta ? channel.fromPath(params.fasta, checkIfExists: true).map { file -> tuple([id: file.name], file) }.collect() : channel.value([[:], []]),
-        params.fastq_screen_references,
-        params.multiqc_config,
-        params.multiqc_logo,
-        params.multiqc_methods_description,
-        params.outdir,
-        params.ref_dict,
-        params.run_picard_collecthsmetrics,
-        params.sample_size,
-        params.skip_tools ? params.skip_tools.split(',') : ['no_skip_tools'],
-        params.sort_bam,
-        params.target_intervals,
-    )
-
-    emit:
-    global_report   = SEQINSPECTOR.out.global_report // channel: /path/to/multiqc_report.html
-    grouped_reports = SEQINSPECTOR.out.grouped_reports // channel: /path/to/multiqc_report.html
-}
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     RUN MAIN WORKFLOW
@@ -74,6 +38,10 @@ workflow NFCORE_SEQINSPECTOR {
 
 workflow {
 
+    def fasta = params.fasta
+        ? channel.fromPath(params.fasta, checkIfExists: true).map { file -> tuple([id: file.name], file) }.collect()
+        : channel.value([[:], []])
+
     //
     // SUBWORKFLOW: Run initialisation tasks
     //
@@ -90,11 +58,23 @@ workflow {
         params.show_hidden,
     )
 
+    PREPARE_GENOME(
+        fasta,
+        params.bwamem2,
+        params.skip_tools ? params.skip_tools.split(',') : ['no_skip_tools'],
+        params.run_picard_collecthsmetrics,
+        params.dict,
+    )
+
     //
     // WORKFLOW: Run main workflow
     //
     NFCORE_SEQINSPECTOR(
-        PIPELINE_INITIALISATION.out.samplesheet
+        PIPELINE_INITIALISATION.out.samplesheet,
+        fasta,
+        PREPARE_GENOME.out.bwamem2_index,
+        PREPARE_GENOME.out.reference_dict,
+        PREPARE_GENOME.out.reference_fai,
     )
     //
     // SUBWORKFLOW: Run completion tasks
@@ -109,3 +89,48 @@ workflow {
         NFCORE_SEQINSPECTOR.out.global_report,
     )
 }
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    NAMED WORKFLOWS FOR PIPELINE
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+//
+// WORKFLOW: Run main analysis pipeline depending on type of input
+//
+workflow NFCORE_SEQINSPECTOR {
+    take:
+    samplesheet // channel: samplesheet read in from --input
+    fasta
+    bwamem2_index
+    dict
+    fasta_fai
+
+    main:
+    //
+    // WORKFLOW: Run pipeline
+    //
+    SEQINSPECTOR(
+        samplesheet,
+        params.bait_intervals,
+        bwamem2_index,
+        fasta,
+        params.fastq_screen_references,
+        params.multiqc_config,
+        params.multiqc_logo,
+        params.multiqc_methods_description,
+        params.outdir,
+        dict,
+        fasta_fai,
+        params.run_picard_collecthsmetrics,
+        params.sample_size,
+        params.skip_tools ? params.skip_tools.split(',') : ['no_skip_tools'],
+        params.sort_bam,
+        params.target_intervals,
+    )
+
+    emit:
+    global_report   = SEQINSPECTOR.out.global_report // channel: /path/to/multiqc_report.html
+    grouped_reports = SEQINSPECTOR.out.grouped_reports // channel: /path/to/multiqc_report.html
+}
diff --git a/modules.json b/modules.json
index b18b2a73..e8f2421e 100644
--- a/modules.json
+++ b/modules.json
@@ -5,11 +5,6 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
-                    "bowtie2/build": {
-                        "branch": "master",
-                        "git_sha": "447f7bc0fa41dfc2400c8cad4c0291880dc060cf",
-                        "installed_by": ["modules"]
-                    },
                     "bwamem2/index": {
                         "branch": "master",
                         "git_sha": "5dd46a36fca68d6ad1a6b22ec47adc8c6863717d",
@@ -26,11 +21,6 @@
                         "git_sha": "3009f27c4e4b6e99da4eeebe82799e13924a4a1f",
                         "installed_by": ["modules"]
                     },
-                    "fastqscreen/buildfromindex": {
-                        "branch": "master",
-                        "git_sha": "ab2e7b785ee4fa6d108472862edbf983cea7db49",
-                        "installed_by": ["modules"]
-                    },
                     "fastqscreen/fastqscreen": {
                         "branch": "master",
                         "git_sha": "ab2e7b785ee4fa6d108472862edbf983cea7db49",
diff --git a/modules/nf-core/bowtie2/build/environment.yml b/modules/nf-core/bowtie2/build/environment.yml
deleted file mode 100644
index 066ff52e..00000000
--- a/modules/nf-core/bowtie2/build/environment.yml
+++ /dev/null
@@ -1,13 +0,0 @@
----
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-channels:
-  - conda-forge
-  - bioconda
-dependencies:
-  # renovate: datasource=conda depName=bioconda/bowtie2
-  - bioconda::bowtie2=2.5.4
-  # renovate: datasource=conda depName=bioconda/htslib
-  - bioconda::htslib=1.21
-  # renovate: datasource=conda depName=bioconda/samtools
-  - bioconda::samtools=1.21
-  - conda-forge::pigz=2.8
diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf
deleted file mode 100644
index 1be06ac8..00000000
--- a/modules/nf-core/bowtie2/build/main.nf
+++ /dev/null
@@ -1,33 +0,0 @@
-process BOWTIE2_BUILD {
-    tag "$fasta"
-    label 'process_high'
-
-    conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b41b403e81883126c3227fc45840015538e8e2212f13abc9ae84e4b98891d51c/data' :
-        'community.wave.seqera.io/library/bowtie2_htslib_samtools_pigz:edeb13799090a2a6' }"
-
-    input:
-    tuple val(meta), path(fasta)
-
-    output:
-    tuple val(meta), path('bowtie2')    , emit: index
-    tuple val("${task.process}"), val('bowtie2'), eval('bowtie2 --version 2>&1 | head -1 | sed "s/^.*bowtie2-align-s version //; s/ .*//"'), emit: versions_bowtie2, topic: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    """
-    mkdir bowtie2
-    bowtie2-build $args --threads $task.cpus $fasta bowtie2/${fasta.baseName}
-    """
-
-    stub:
-    """
-    mkdir bowtie2
-    touch bowtie2/${fasta.baseName}.{1..4}.bt2
-    touch bowtie2/${fasta.baseName}.rev.{1,2}.bt2
-    """
-}
diff --git a/modules/nf-core/bowtie2/build/meta.yml b/modules/nf-core/bowtie2/build/meta.yml
deleted file mode 100644
index 3a9d31cf..00000000
--- a/modules/nf-core/bowtie2/build/meta.yml
+++ /dev/null
@@ -1,69 +0,0 @@
-name: bowtie2_build
-description: Builds bowtie index for reference genome
-keywords:
-  - build
-  - index
-  - fasta
-  - genome
-  - reference
-tools:
-  - bowtie2:
-      description: |
-        Bowtie 2 is an ultrafast and memory-efficient tool for aligning
-        sequencing reads to long reference sequences.
-      homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
-      documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
-      doi: 10.1038/nmeth.1923
-      licence: ["GPL-3.0-or-later"]
-      identifier: ""
-input:
-  - - meta:
-        type: map
-        description: |
-          Groovy Map containing reference information
-          e.g. [ id:'test', single_end:false ]
-    - fasta:
-        type: file
-        description: Input genome fasta file
-        ontologies: []
-output:
-  index:
-    - - meta:
-          type: map
-          description: |
-            Groovy Map containing reference information
-            e.g. [ id:'test', single_end:false ]
-      - bowtie2:
-          type: directory
-          description: Bowtie2 genome index files
-          pattern: "*.bt2"
-          ontologies: []
-  versions_bowtie2:
-    - - ${task.process}:
-          type: string
-          description: The name of the process
-      - bowtie2:
-          type: string
-          description: The name of the tool
-      - 'bowtie2 --version 2>&1 | head -1 | sed "s/^.*bowtie2-align-s version //; s/ .*//"':
-          type: eval
-          description: The expression to obtain the version of the tool
-
-topics:
-  versions:
-    - - ${task.process}:
-          type: string
-          description: The name of the process
-      - bowtie2:
-          type: string
-          description: The name of the tool
-      - 'bowtie2 --version 2>&1 | head -1 | sed "s/^.*bowtie2-align-s version //; s/ .*//"':
-          type: eval
-          description: The expression to obtain the version of the tool
-
-authors:
-  - "@joseespinosa"
-  - "@drpatelh"
-maintainers:
-  - "@joseespinosa"
-  - "@drpatelh"
diff --git a/modules/nf-core/fastqscreen/buildfromindex/environment.yml b/modules/nf-core/fastqscreen/buildfromindex/environment.yml
deleted file mode 100644
index 9ff968c9..00000000
--- a/modules/nf-core/fastqscreen/buildfromindex/environment.yml
+++ /dev/null
@@ -1,8 +0,0 @@
----
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-channels:
-  - conda-forge
-  - bioconda
-dependencies:
-  - bioconda::fastq-screen=0.16.0
-  - bioconda::perl-gdgraph=1.54
diff --git a/modules/nf-core/fastqscreen/buildfromindex/main.nf b/modules/nf-core/fastqscreen/buildfromindex/main.nf
deleted file mode 100644
index c543e61b..00000000
--- a/modules/nf-core/fastqscreen/buildfromindex/main.nf
+++ /dev/null
@@ -1,59 +0,0 @@
-process FASTQSCREEN_BUILDFROMINDEX {
-    label 'process_single'
-
-    conda "${moduleDir}/environment.yml"
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fc/fc53eee7ca23c32220a9662fbb63c67769756544b6d74a1ee85cf439ea79a7ee/data'
-        : 'community.wave.seqera.io/library/fastq-screen_perl-gdgraph:5c1786a5d5bc1309'}"
-
-    input:
-    val genome_names
-    path (indexes), stageAs: "dir*"
-
-    output:
-    path ("FastQ_Screen_Genomes"), emit: database
-    tuple val("${task.process}"), val('fastqscreen'), eval('fastq_screen --version 2>&1 | sed "s/^.*FastQ Screen v//;"'), emit: versions_fastqscreen, topic: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    dir = "FastQ_Screen_Genomes"
-    folder = indexes.collect { index -> index.toString() }
-    database = [genome_names, folder].transpose()
-    copy_indexes = folder.collect { index -> "cp -r ${index} ${dir}/${index}" }.join(" && ")
-
-    // Folder name and index (within folder) name could be different - use bash to look for index name
-    config = database
-        .collect { index -> "########## ${index[0]} \nDATABASE ${index[0]} ${dir}/${index[1]}/${index[1] + '_to_be_replaced'}" }
-        .join("\n\n")
-        .replace("\n", "\\n")
-
-    """
-    mkdir ${dir}
-    ${copy_indexes}
-
-    echo "${config}" > fastq_screen.conf
-    sed 's/\\\\n/\\n/g' fastq_screen.conf > ${dir}/fastq_screen.conf
-    echo "Replace folder name real index name"
-
-    for f in ${folder.join(' ')}
-    do
-        TO_REPLACE=\${f}_to_be_replaced
-
-        REPLACE_WITH=(\$f"/*.rev.1.bt2")
-        REPLACE_WITH=\$(basename \$REPLACE_WITH)
-        REPLACE_WITH=\${REPLACE_WITH%%.rev.1.bt2}
-
-        sed "s/\$TO_REPLACE/\$REPLACE_WITH/g" ${dir}/fastq_screen.conf > new_conf.conf
-        mv new_conf.conf ${dir}/fastq_screen.conf
-    done
-    """
-
-    stub:
-    dir = "FastQ_Screen_Genomes"
-    """
-    mkdir ${dir}
-    touch ${dir}/fastq_screen.conf
-    """
-}
diff --git a/modules/nf-core/fastqscreen/buildfromindex/meta.yml b/modules/nf-core/fastqscreen/buildfromindex/meta.yml
deleted file mode 100644
index 62561b2e..00000000
--- a/modules/nf-core/fastqscreen/buildfromindex/meta.yml
+++ /dev/null
@@ -1,57 +0,0 @@
-name: "fastqscreen_buildfromindex"
-description: Build fastq screen config file from bowtie index files
-keywords:
-  - build
-  - index
-  - genome
-  - reference
-tools:
-  - "fastqscreen":
-      description: "FastQ Screen allows you to screen a library of sequences in FastQ
-        format against a set of sequence databases so you can see if the composition
-        of the library matches with what you expect."
-      homepage: "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/"
-      documentation: "https://stevenwingett.github.io/FastQ-Screen/"
-      tool_dev_url: "https://github.com/StevenWingett/FastQ-Screen/archive/refs/tags/v0.15.3.zip"
-      doi: "10.5281/zenodo.5838377"
-      licence:
-        - "GPL-3.0-or-later"
-      identifier: ""
-input:
-  - genome_names:
-      type: string
-      description: List of names for each index
-  - indexes:
-      type: directory
-      description: Bowtie2 genome directories containing index files
-output:
-  database:
-    - FastQ_Screen_Genomes:
-        type: directory
-        description: fastq screen database folder containing config file and index
-          folders
-        pattern: "FastQ_Screen_Genomes"
-  versions_fastqscreen:
-    - - ${task.process}:
-          type: string
-          description: The name of the process
-      - fastqscreen:
-          type: string
-          description: The name of the tool
-      - fastq_screen --version 2>&1 | sed "s/^.*FastQ Screen v//;":
-          type: eval
-          description: The expression to obtain the version of the tool
-topics:
-  versions:
-    - - ${task.process}:
-          type: string
-          description: The name of the process
-      - fastqscreen:
-          type: string
-          description: The name of the tool
-      - fastq_screen --version 2>&1 | sed "s/^.*FastQ Screen v//;":
-          type: eval
-          description: The expression to obtain the version of the tool
-authors:
-  - "@snesic"
-  - "@JPejovicApis"
diff --git a/nextflow.config b/nextflow.config
index 40ca5ec9..6f51793f 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -6,31 +6,28 @@
 ----------------------------------------------------------------------------------------
 */
 
-// Enable use of module binaries for e.g. module specific Python scripts
-nextflow.enable.moduleBinaries = true
-
 // Global default params, used in configs
 params {
-
     // Input options
-    input                      = null
-    sample_size                = 0
-    skip_tools                 = ''
+    input                        = null
+    sample_size                  = 0
+    skip_tools                   = ''
+
     // References
-    genome                     = null
-    igenomes_base              = 's3://ngi-igenomes/igenomes/'
-    igenomes_ignore            = false
-    sort_bam                   = true
-    bwamem2                    = null
+    genome                       = null
+    igenomes_base                = 's3://ngi-igenomes/igenomes/'
+    igenomes_ignore              = false
+    sort_bam                     = true
+
     // Fastqscreen options
-    fastq_screen_references    = "${projectDir}/assets/example_fastq_screen_references.csv"
+    fastq_screen_references      = "${projectDir}/assets/example_fastq_screen_references.csv"
 
     // MultiQC options
-    multiqc_config             = null
-    multiqc_title              = null
-    multiqc_logo               = null
-    max_multiqc_email_size     = '25.MB'
-    multiqc_methods_description = null
+    multiqc_config               = null
+    multiqc_title                = null
+    multiqc_logo                 = null
+    max_multiqc_email_size       = '25.MB'
+    multiqc_methods_description  = null
 
     // Boilerplate options
     outdir                       = null
@@ -46,26 +43,24 @@ params {
     version                      = false
     modules_testdata_base_path   = 's3://ngi-igenomes/testdata/nf-core/modules/'
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
-    trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
+    trace_report_suffix          = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')
 
     // picard_collecthsmetrics options
-    run_picard_collecthsmetrics = false
-    bait_intervals              = null
-    target_intervals            = null
-    ref_dict                    = null
+    run_picard_collecthsmetrics  = false
+    bait_intervals               = null
+    target_intervals             = null
 
     // Config options
-    config_profile_name        = null
-    config_profile_description = null
-
-    custom_config_version      = 'master'
-    custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
-    config_profile_contact     = null
-    config_profile_url         = null
+    config_profile_name          = null
+    config_profile_description   = null
 
+    custom_config_version        = 'master'
+    custom_config_base           = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
+    config_profile_contact       = null
+    config_profile_url           = null
 
     // Schema validation default options
-    validate_params            = true
+    validate_params              = true
 }
 
 // Load base.config by default for all pipelines
@@ -73,40 +68,40 @@ includeConfig 'conf/base.config'
 
 profiles {
     debug {
-        dumpHashes              = true
-        process.beforeScript    = 'echo $HOSTNAME'
-        cleanup                 = false
+        dumpHashes                                   = true
+        process.beforeScript                         = 'echo $HOSTNAME'
+        cleanup                                      = false
         nextflow.enable.configProcessNamesValidation = true
     }
     conda {
-        conda.enabled           = true
-        docker.enabled          = false
-        singularity.enabled     = false
-        podman.enabled          = false
-        shifter.enabled         = false
-        charliecloud.enabled    = false
-        conda.channels          = ['conda-forge', 'bioconda']
-        apptainer.enabled       = false
+        conda.enabled        = true
+        docker.enabled       = false
+        singularity.enabled  = false
+        podman.enabled       = false
+        shifter.enabled      = false
+        charliecloud.enabled = false
+        conda.channels       = ['conda-forge', 'bioconda']
+        apptainer.enabled    = false
     }
     mamba {
-        conda.enabled           = true
-        conda.useMamba          = true
-        docker.enabled          = false
-        singularity.enabled     = false
-        podman.enabled          = false
-        shifter.enabled         = false
-        charliecloud.enabled    = false
-        apptainer.enabled       = false
+        conda.enabled        = true
+        conda.useMamba       = true
+        docker.enabled       = false
+        singularity.enabled  = false
+        podman.enabled       = false
+        shifter.enabled      = false
+        charliecloud.enabled = false
+        apptainer.enabled    = false
     }
     docker {
-        docker.enabled          = true
-        conda.enabled           = false
-        singularity.enabled     = false
-        podman.enabled          = false
-        shifter.enabled         = false
-        charliecloud.enabled    = false
-        apptainer.enabled       = false
-        docker.runOptions       = '-u $(id -u):$(id -g)'
+        docker.enabled       = true
+        conda.enabled        = false
+        singularity.enabled  = false
+        podman.enabled       = false
+        shifter.enabled      = false
+        charliecloud.enabled = false
+        apptainer.enabled    = false
+        docker.runOptions    = '-u $(id -u):$(id -g)'
     }
     arm64 {
         process.arch            = 'arm64'
@@ -120,54 +115,54 @@ profiles {
         wave.strategy           = 'conda,container'
     }
     emulate_amd64 {
-        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
+        docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
     }
     singularity {
-        singularity.enabled     = true
-        singularity.autoMounts  = true
-        conda.enabled           = false
-        docker.enabled          = false
-        podman.enabled          = false
-        shifter.enabled         = false
-        charliecloud.enabled    = false
-        apptainer.enabled       = false
+        singularity.enabled    = true
+        singularity.autoMounts = true
+        conda.enabled          = false
+        docker.enabled         = false
+        podman.enabled         = false
+        shifter.enabled        = false
+        charliecloud.enabled   = false
+        apptainer.enabled      = false
     }
     podman {
-        podman.enabled          = true
-        conda.enabled           = false
-        docker.enabled          = false
-        singularity.enabled     = false
-        shifter.enabled         = false
-        charliecloud.enabled    = false
-        apptainer.enabled       = false
+        podman.enabled       = true
+        conda.enabled        = false
+        docker.enabled       = false
+        singularity.enabled  = false
+        shifter.enabled      = false
+        charliecloud.enabled = false
+        apptainer.enabled    = false
     }
     shifter {
-        shifter.enabled         = true
-        conda.enabled           = false
-        docker.enabled          = false
-        singularity.enabled     = false
-        podman.enabled          = false
-        charliecloud.enabled    = false
-        apptainer.enabled       = false
+        shifter.enabled      = true
+        conda.enabled        = false
+        docker.enabled       = false
+        singularity.enabled  = false
+        podman.enabled       = false
+        charliecloud.enabled = false
+        apptainer.enabled    = false
     }
     charliecloud {
-        charliecloud.enabled    = true
-        conda.enabled           = false
-        docker.enabled          = false
-        singularity.enabled     = false
-        podman.enabled          = false
-        shifter.enabled         = false
-        apptainer.enabled       = false
+        charliecloud.enabled = true
+        conda.enabled        = false
+        docker.enabled       = false
+        singularity.enabled  = false
+        podman.enabled       = false
+        shifter.enabled      = false
+        apptainer.enabled    = false
     }
     apptainer {
-        apptainer.enabled       = true
-        apptainer.autoMounts    = true
-        conda.enabled           = false
-        docker.enabled          = false
-        singularity.enabled     = false
-        podman.enabled          = false
-        shifter.enabled         = false
-        charliecloud.enabled    = false
+        apptainer.enabled    = true
+        apptainer.autoMounts = true
+        conda.enabled        = false
+        docker.enabled       = false
+        singularity.enabled  = false
+        podman.enabled       = false
+        shifter.enabled      = false
+        charliecloud.enabled = false
     }
     wave {
         apptainer.ociAutoPull   = true
@@ -177,12 +172,16 @@ profiles {
         wave.strategy           = 'conda,container'
     }
     gpu {
-        docker.runOptions       = '-u $(id -u):$(id -g) --gpus all'
-        apptainer.runOptions    = '--nv'
-        singularity.runOptions  = '--nv'
+        docker.runOptions      = '-u $(id -u):$(id -g) --gpus all'
+        apptainer.runOptions   = '--nv'
+        singularity.runOptions = '--nv'
+    }
+    test {
+        includeConfig 'conf/test.config'
+    }
+    test_full {
+        includeConfig 'conf/test_full.config'
     }
-    test      { includeConfig 'conf/test.config'      }
-    test_full { includeConfig 'conf/test_full.config' }
 }
 
 // Load nf-core custom profiles from different institutions
@@ -198,10 +197,10 @@ includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !pa
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
 // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
 // Set to your registry if you have a mirror of containers
-apptainer.registry    = 'quay.io'
-docker.registry       = 'quay.io'
-podman.registry       = 'quay.io'
-singularity.registry  = 'quay.io'
+apptainer.registry = 'quay.io'
+docker.registry = 'quay.io'
+podman.registry = 'quay.io'
+singularity.registry = 'quay.io'
 charliecloud.registry = 'quay.io'
 
 // Load igenomes.config if required
@@ -256,7 +255,7 @@ manifest {
             affiliation: 'Pixelgen Technologies',
             github: 'Aratz',
             contribution: ['author'],
-            orcid: '0000-0003-2702-1103'
+            orcid: '0000-0003-2702-1103',
         ],
         [
             name: 'Alfred Kedhammar',
@@ -308,7 +307,7 @@ manifest {
             affiliation: 'National Bioinformatics Infrastructure Sweden',
             github: 'mahesh-panchal',
             contribution: ['contributor'],
-            orcid: '0000-0003-1675-0677'
+            orcid: '0000-0003-1675-0677',
         ],
         [
             name: 'Ramprasad Neethiraj',
@@ -418,7 +417,7 @@ plugins {
 
 validation {
     defaultIgnoreParams = ["genomes"]
-    monochromeLogs = params.monochrome_logs
+    monochromeLogs      = params.monochrome_logs
 }
 
 // Load modules.config for DSL2 module specific options
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 404846c5..0332ca15 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -103,7 +103,16 @@
                     "exists": true,
                     "fa_icon": "fas fa-copy",
                     "description": "Path to BWA mem indices.",
-                    "help_text": "If you wish to recompute indices available on igenomes, set `--bwa false`.\n\n> **NB** If none provided, will be generated automatically from the FASTA reference. Combine with `--save_reference` to save for future runs.\n\nIf you use AWS iGenomes, this has already been set for you appropriately."
+                    "help_text": "If you wish to recompute indices available on igenomes, set `--bwamem2 false`.\n\n> **NB** If none provided, will be generated automatically from the FASTA reference.\n\nIf you use AWS iGenomes, this has already been set for you appropriately."
+                },
+                "dict": {
+                    "type": "string",
+                    "hidden": true,
+                    "description": "Sequence dictionary for the reference fasta file provided.",
+                    "help_text": "If you wish to recompute indices available on igenomes, set `--ic false`.\n\n> **NB** If none provided, will be generated automatically from the FASTA reference.\n\nIf you use AWS iGenomes, this has already been set for you appropriately.",
+                    "pattern": "^\\S+.dict$",
+                    "format": "file-path",
+                    "exists": true
                 }
             }
         },
@@ -302,14 +311,6 @@
                     "pattern": "^\\S+.(bed|bed.gz|interval_list)$",
                     "format": "file-path",
                     "exists": true
-                },
-                "ref_dict": {
-                    "type": "string",
-                    "hidden": true,
-                    "description": "Sequence dictionary for the reference fasta file provided.",
-                    "pattern": "^\\S+.dict$",
-                    "format": "file-path",
-                    "exists": true
                 }
             }
         }
diff --git a/nf-test.config b/nf-test.config
index 6a25cc8c..3b7f95dc 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -1,21 +1,21 @@
 config {
     // location for all nf-test tests
-    testsDir = "."
+    testsDir   = "."
 
     // nf-test directory including temporary files for each test
-    workDir = System.getenv("NFT_WORKDIR") ?: ".nf-test"
+    workDir    = System.getenv("NFT_WORKDIR") ?: ".nf-test"
 
     // location of an optional nextflow.config file specific for executing tests
     configFile = "tests/nextflow.config"
 
     // ignore tests coming from the nf-core/modules repo
-    ignore = ['modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*']
+    ignore     = ['modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*']
 
     // run all test with defined profile(s) from the main nextflow.config
-    profile  ="test"
+    profile    = "test"
 
     // list of filenames or patterns that should be trigger a full test run
-    triggers = ['nextflow.config', 'nf-test.config', 'conf/test.config', 'tests/nextflow.config', 'tests/.nftignore']
+    triggers   = ['nextflow.config', 'nf-test.config', 'conf/test.config', 'tests/nextflow.config', 'tests/.nftignore']
 
     // load the necessary plugins
     plugins {
diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf
index 3fe0bd39..176036b1 100644
--- a/subworkflows/local/prepare_genome/main.nf
+++ b/subworkflows/local/prepare_genome/main.nf
@@ -52,7 +52,7 @@ workflow PREPARE_GENOME {
     }
 
     emit:
-    bwamem2_index = ch_bwamem2_index
-    reference_fai = ch_reference_fai
-    ref_dict      = ch_ref_dict
+    bwamem2_index  = ch_bwamem2_index
+    reference_fai  = ch_reference_fai
+    reference_dict = ch_ref_dict
 }
diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test b/subworkflows/local/prepare_genome/tests/main.nf.test
index 3ba2985c..21fd5f50 100644
--- a/subworkflows/local/prepare_genome/tests/main.nf.test
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test
@@ -32,7 +32,7 @@ nextflow_workflow {
                 else if (key == "bwamem2_index") {
                     return [key, val.collect { [path(it[1]).list().collect { it }] }]
                 }
-                else if (key == "ref_dict") {
+                else if (key == "reference_dict") {
                     return [key, val.collect { file(it[1]).name }]
                 }
                 return [key, val.collect { path(it[1]) }]
@@ -66,7 +66,7 @@ nextflow_workflow {
                 else if (key == "bwamem2_index") {
                     return [key, val.collect { [path(it[1]).list().collect { it }] }]
                 }
-                else if (key == "ref_dict") {
+                else if (key == "reference_dict") {
                     return [key, val.collect { file(it[1]).name }]
                 }
                 return [key, val.collect { path(it[1]) }]
@@ -100,7 +100,7 @@ nextflow_workflow {
                 else if (key == "bwamem2_index") {
                     return [key, val.collect { [path(it[1]).list().collect { it }] }]
                 }
-                else if (key == "ref_dict") {
+                else if (key == "reference_dict") {
                     return [key, val.collect { file(it[1]).name }]
                 }
                 return [key, val.collect { path(it[1]) }]
diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test.snap b/subworkflows/local/prepare_genome/tests/main.nf.test.snap
index 6b4bd3f0..4bb1683e 100644
--- a/subworkflows/local/prepare_genome/tests/main.nf.test.snap
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test.snap
@@ -13,7 +13,7 @@
                         ]
                     ]
                 ],
-                "ref_dict": [
+                "reference_dict": [
                     "genome.dict"
                 ],
                 "reference_fai": [
@@ -21,7 +21,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-02-20T11:14:59.592335797",
+        "timestamp": "2026-02-20T14:08:10.135732184",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -41,7 +41,7 @@
                         ]
                     ]
                 ],
-                "ref_dict": [
+                "reference_dict": [
                     "reference.dict"
                 ],
                 "reference_fai": [
@@ -49,7 +49,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-02-19T12:12:39.549105919",
+        "timestamp": "2026-02-20T14:07:30.247480534",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index 14748673..148a3959 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -242,7 +242,6 @@ def genomeExistsError() {
 def toolCitationText() {
     def citation_text = [
         "Tools used in the workflow included:",
-        "Bowtie2 (Langmead et al. 2012)",
         "BWAMEM2 (Vasimuddin et al. 2019)",
         "FastQC (Andrews 2010),",
         "FastQ Screen (Wingett & Andrews 2018)",
@@ -259,7 +258,6 @@ def toolCitationText() {
 
 def toolBibliographyText() {
     def reference_text = [
-        "<li>Langmead S., & Salzberg SL. (2012). Fast gapped-read alignment with Bowtie 2.</li>",
         "<li>Vasimuddin Md., Misra S., Li H, & Aluru S. (2019). Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems.</li>",
         "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.</li>",
         "<li>Wingett SW., & Andrews S. FastQ Screen: A tool for multi-genome mapping and quality control. F1000Res. 2018 Aug 24 [revised 2018 Jan 1];7:1338. doi: 10.12688/f1000research.15931.2. eCollection</li>",
diff --git a/tests/NovaSeq6000.nf.test.snap b/tests/NovaSeq6000.nf.test.snap
index 7d90acba..713edfa5 100644
--- a/tests/NovaSeq6000.nf.test.snap
+++ b/tests/NovaSeq6000.nf.test.snap
@@ -1032,8 +1032,6 @@
                 "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:MULTIQC_PER_TAG (2)",
                 "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:MULTIQC_PER_TAG (3)",
                 "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:MULTIQC_PER_TAG (4)",
-                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:PREPARE_GENOME:BWAMEM2_INDEX (genome.fa)",
-                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:PREPARE_GENOME:SAMTOOLS_FAIDX (genome.fa)",
                 "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (Sample1_01)",
                 "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (Sample23_03)",
                 "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (SampleA_02)",
@@ -1045,10 +1043,12 @@
                 "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:SAMTOOLS_INDEX (SampleA_02)",
                 "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:SAMTOOLS_INDEX (Undetermined_05)",
                 "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:SAMTOOLS_INDEX (sampletest_04)",
-                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:SEQFU_STATS (seqfu)"
+                "[NXF_HASH] Submitted process > NFCORE_SEQINSPECTOR:SEQINSPECTOR:SEQFU_STATS (seqfu)",
+                "[NXF_HASH] Submitted process > PREPARE_GENOME:BWAMEM2_INDEX (genome.fa)",
+                "[NXF_HASH] Submitted process > PREPARE_GENOME:SAMTOOLS_FAIDX (genome.fa)"
             ]
         ],
-        "timestamp": "2026-02-19T16:08:17.233872508",
+        "timestamp": "2026-02-20T14:19:24.909594023",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
diff --git a/tests/nextflow.config b/tests/nextflow.config
index 5d979d45..8d6d7704 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -4,4 +4,5 @@
 ========================================================================================
 */
 
-aws.client.anonymous = true // fixes S3 access issues on self-hosted runners
+// fixes S3 access issues on self-hosted runners
+aws.client.anonymous = true
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 635e1a0b..79d7f536 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -5,29 +5,26 @@
 */
 
 // modules
-include { BWAMEM2_MEM                   } from '../modules/nf-core/bwamem2/mem'
-include { FASTQC                        } from '../modules/nf-core/fastqc'
-include { FASTQSCREEN_FASTQSCREEN       } from '../modules/nf-core/fastqscreen/fastqscreen'
-include { MULTIQC as MULTIQC_GLOBAL     } from '../modules/nf-core/multiqc'
-include { MULTIQC as MULTIQC_PER_TAG    } from '../modules/nf-core/multiqc'
-include { PICARD_COLLECTMULTIPLEMETRICS } from '../modules/nf-core/picard/collectmultiplemetrics'
-include { RUNDIRPARSER                  } from '../modules/local/rundirparser'
-include { SAMTOOLS_FAIDX                } from '../modules/nf-core/samtools/faidx'
-include { SAMTOOLS_INDEX                } from '../modules/nf-core/samtools/index'
-include { SEQFU_STATS                   } from '../modules/nf-core/seqfu/stats'
-include { SEQTK_SAMPLE                  } from '../modules/nf-core/seqtk/sample'
+include { BWAMEM2_MEM                } from '../modules/nf-core/bwamem2/mem'
+include { FASTQC                     } from '../modules/nf-core/fastqc'
+include { FASTQSCREEN_FASTQSCREEN    } from '../modules/nf-core/fastqscreen/fastqscreen'
+include { MULTIQC as MULTIQC_GLOBAL  } from '../modules/nf-core/multiqc'
+include { MULTIQC as MULTIQC_PER_TAG } from '../modules/nf-core/multiqc'
+include { RUNDIRPARSER               } from '../modules/local/rundirparser'
+include { SAMTOOLS_INDEX             } from '../modules/nf-core/samtools/index'
+include { SEQFU_STATS                } from '../modules/nf-core/seqfu/stats'
+include { SEQTK_SAMPLE               } from '../modules/nf-core/seqtk/sample'
 
 // subworkflow
-include { PREPARE_GENOME                } from '../subworkflows/local/prepare_genome'
-include { QC_BAM                        } from '../subworkflows/local/qc_bam'
+include { QC_BAM                     } from '../subworkflows/local/qc_bam'
 
 // functions
-include { methodsDescriptionText        } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline'
-include { paramsSummaryMap              } from 'plugin/nf-schema'
-include { paramsSummaryMultiqc          } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-include { reportIndexMultiqc            } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline'
-include { samplesheetToList             } from 'plugin/nf-schema'
-include { softwareVersionsToYAML        } from 'plugin/nf-core-utils'
+include { methodsDescriptionText     } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline'
+include { paramsSummaryMap           } from 'plugin/nf-schema'
+include { paramsSummaryMultiqc       } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { reportIndexMultiqc         } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline'
+include { samplesheetToList          } from 'plugin/nf-schema'
+include { softwareVersionsToYAML     } from 'plugin/nf-core-utils'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -39,7 +36,7 @@ workflow SEQINSPECTOR {
     take:
     ch_samplesheet // channel: samplesheet read in from --input
     bait_intervals
-    bwamem2
+    bwamem2_index
     fasta_reference
     fastq_screen_references
     multiqc_config
@@ -47,6 +44,7 @@ workflow SEQINSPECTOR {
     multiqc_methods_description
     outdir
     ref_dict
+    ref_fai
     run_picard_collecthsmetrics
     sample_size
     skip_tools
@@ -59,14 +57,6 @@ workflow SEQINSPECTOR {
     ch_bwamem2_mem = channel.empty()
     ch_samtools_index = channel.empty()
 
-    PREPARE_GENOME(
-        fasta_reference,
-        bwamem2,
-        skip_tools,
-        run_picard_collecthsmetrics,
-        ref_dict,
-    )
-
     //
     // MODULE: Parse rundir info
     //
@@ -179,7 +169,7 @@ workflow SEQINSPECTOR {
     if (!("bwamem2_mem" in skip_tools)) {
         BWAMEM2_MEM(
             ch_sample,
-            PREPARE_GENOME.out.bwamem2_index,
+            bwamem2_index,
             fasta_reference,
             sort_bam ?: true,
         )
@@ -193,23 +183,18 @@ workflow SEQINSPECTOR {
 
     if (!("picard_collectmultiplemetrics" in skip_tools)) {
 
-        ch_reference_fai = PREPARE_GENOME.out.reference_fai
-
         ch_bait_intervals = bait_intervals ? channel.fromPath(bait_intervals).collect() : channel.empty()
         ch_target_intervals = target_intervals ? channel.fromPath(target_intervals).collect() : channel.empty()
 
-        ch_ref_dict = PREPARE_GENOME.out.ref_dict
-
-
         QC_BAM(
             ch_bwamem2_mem,
             ch_samtools_index,
             fasta_reference,
-            ch_reference_fai,
+            ref_fai,
             run_picard_collecthsmetrics,
             ch_bait_intervals,
             ch_target_intervals,
-            ch_ref_dict,
+            ref_dict,
         )
 
         ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.multiple_metrics, QC_BAM.out.hs_metrics)