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",
+                "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"
+            ],
+            [
+                "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",
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-                "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",
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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",
+                "Sample1_01_screen.txt:md5,14d10b0c3b63e18f223a0dc589abee36",
+                "Sample23_03_screen.png:md5,41b4f556865a2f55a93f63e520812fad",
+                "Sample23_03_screen.txt:md5,14d10b0c3b63e18f223a0dc589abee36",
+                "SampleA_02_screen.png:md5,2f808877be53aa1433c1856bbf50feaf",
+                "SampleA_02_screen.txt:md5,14d10b0c3b63e18f223a0dc589abee36",
+                "Undetermined_05_screen.png:md5,12707698b2765c68566ccf5ac25479f5",
+                "Undetermined_05_screen.txt:md5,14d10b0c3b63e18f223a0dc589abee36",
+                "sampletest_04_screen.png:md5,a88937eb54785ee921549d3c894df45d",
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+                "fastq_screen_plot.txt:md5,a9fac509f9eb26a068afbad8268544f3",
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+                "fastqc_per_base_n_content_plot.txt:md5,69d2d50e3947cac30beaef2b5f418631",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,a2812a2ba7918fedbecca506fbbeb0ff",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,040e1375843c2eeabd2818d605192a98",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,73f8b87eeed241bd7b96d98990f6972d",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,f74c1fcdb82a26f0c8592b9dc4016b98",
+                "fastqc_sequence_counts_plot.txt:md5,ba8082207f7c927301754a997b4e220f",
+                "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:md5,5af2d6080364385c05d50f9ffa7996e6",
+                "multiqc_fastqc.txt:md5,a9a9fc06badaade2d09486d2adaac1ce",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
+                "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",
+                "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:md5,14d33a39b52346515edfd7e8542e5c7b",
+                "multiqc_fastqc.txt:md5,e87c99cac0c4956521d9c660183722bb",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
+                "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",
+                "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:md5,179b14566daf82ccd294f54443cf9b5e",
+                "multiqc_fastqc.txt:md5,8b808265a3cfe52846f7d6a0c9624beb",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
+                "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",
+                "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,a84c2882a4ab93afd9599c7aebf3e897",
+                "multiqc_fastqc.txt:md5,b8f6f4ed32e60ff57c64bb0ba029adba",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
+                "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",
+                "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,db504d3eec12c5431e2b66d4880beb66",
+                "multiqc_fastqc.txt:md5,284597d876abc5a1242d8efb2d69f0d5",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
+                "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:md5,28ba1f3017af64453cd191cf6f895e17",
+                "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",
+                "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",
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+                "fastqc_overrepresented_sequences_plot.txt:md5,58f05a5aec002a72d7f6828378b78a9c",
+                "fastqc_per_base_n_content_plot.txt:md5,87299c06b90293903f4030c4e47a653d",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,c11ceffc34f32026754ad9ec14897246",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,b8a157fce78777d3787bc4023bc95ad5",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,b78adce4744b3c5f9dd10caf5c3c16b3",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,d339ebd1df4fef62cf01c18ccfadc8d4",
+                "fastqc_sequence_counts_plot.txt:md5,f92c2f7d8a08af4534273a473f909629",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,e605b0869e968ab483324c3e72dcc210",
+                "fastqc_sequence_length_distribution_plot.txt:md5,024386d10341fd18eb4e8bd55337777a",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,06da849fd9e7941fec86bb1a4068a020",
+                "multiqc_fastqc.txt:md5,64a5bf2de1edd567eacf4ad490bdbb20",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,963af5ca1c83a87e9eb8396c60ca0185",
+                "multiqc_picard_baseContent.txt:md5,7ed6695c5554f6f1551f2567f308ea01",
+                "multiqc_picard_quality_by_cycle.txt:md5,8299530bdcc6341bf87d8b3a344f1b35",
+                "multiqc_picard_quality_score_distribution.txt:md5,c7978efc924f1de12dd3c3a8a5182cac",
+                "multiqc_seqfu_mqc.txt:md5,18dd2407d4a1791646785123028f69b5",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram_1.txt:md5,8299530bdcc6341bf87d8b3a344f1b35",
+                "picard_QualityScoreDistribution_histogram.txt:md5,c7978efc924f1de12dd3c3a8a5182cac",
+                "picard_alignment_readlength_plot.txt:md5,9e70861ee11a1842de2d19adc2965c6e",
+                "picard_alignment_summary.txt:md5,46803cf45344b63078de59b4ad617005",
+                "picard_base_distribution_by_cycle__Adenine.txt:md5,da954ca1a4904484c5561b5559780670",
+                "picard_base_distribution_by_cycle__Cytosine.txt:md5,ff364d12f449a7fc7ec6e4f747376235",
+                "picard_base_distribution_by_cycle__Guanine.txt:md5,074489f5906aef06a5067abc3fb75776",
+                "picard_base_distribution_by_cycle__Thymine.txt:md5,e64e5c05cc4488dc316502b8ecd34c05",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,6b667bfe051130fe8fa3f92cab174b64",
+                "picard_quality_by_cycle.txt:md5,22a848260595b3c2eb8aaea9a5b7de16",
+                "picard_quality_score_distribution.txt:md5,a5704f2105a9aa9c719035bf1711307a",
+                "fastq_screen_plot.txt:md5,e2b256c1041a352c0d24186af7d04a02",
+                "fastqc-status-check-heatmap.txt:md5,6ecc7673865cff5b867a6e07f922aab6",
+                "fastqc_overrepresented_sequences_plot.txt:md5,b8049dce93ce38332c50f0b5e10804f3",
+                "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",
+                "fastqc_sequence_counts_plot.txt:md5,43444c6e5ee34c92b0e7cb4d903a07f0",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,818f13a5372bad79e54cd984758096c5",
+                "fastqc_sequence_length_distribution_plot.txt:md5,9c4f3aeac31f2ccca52468fb20cb794e",
+                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
+                "multiqc_fastq_screen.txt:md5,438e559fc0ce65fc5db989a50a769d6c",
+                "multiqc_fastqc.txt:md5,85b56748619f3553daecdd9f9acc7b10",
+                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
+                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,a8164399dfbc104ec98f0590d506f557",
+                "multiqc_picard_baseContent.txt:md5,2f35f7d55e96e55a97bab9a9509072f8",
+                "multiqc_picard_quality_by_cycle.txt:md5,41de636e329213c91de9811bcfacd1e1",
+                "multiqc_picard_quality_score_distribution.txt:md5,502b9469dea25bc742ae2016c2f62417",
+                "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",
+                "picard_alignment_summary.txt:md5,e576a6a6bf7bbe9ff1e86f5198bf6751",
+                "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",
+                "picard_base_distribution_by_cycle__Undetermined.txt:md5,19e2ac5ff90d4544555cf5361841513e",
+                "picard_quality_by_cycle.txt:md5,07609521a4b40b9b9aa5fbc911713545",
+                "picard_quality_score_distribution.txt:md5,b811a5ed7a63dba9b9514a27c8ac1ee1",
+                "fastq_screen_plot.txt:md5,4767010b30457fc1f2fb78d7ca727bee",
+                "fastqc-status-check-heatmap.txt:md5,61857d2c45cf0c080348047aa34e7525",
+                "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",
+                "fastqc_sequence_counts_plot.txt:md5,3b8b8a75232eccb934025ec75a590c6f",
+                "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"
+            ],
+            [
+                "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"
+            ],
+            [
+                "WARN: Tag name collision: [group1]",
+                "WARN: Tag name collision: [group2]",
+                "WARN: Tag name collision: [lane1]",
+                "WARN: Tag name collision: [test]"
+            ]
+        ],
+        "timestamp": "2026-02-17T15:52:18.005537349",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
+    "NovaSeq6000 data test - No rundirs": {
+        "content": [
+            37,
+            {
+                "BWAMEM2_INDEX": {
+                    "bwamem2": "2.2.1"
+                },
+                "BWAMEM2_MEM": {
+                    "bwamem2": "2.2.1",
+                    "samtools": "1.22.1"
+                },
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "FASTQSCREEN_FASTQSCREEN": {
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+                "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",
-                "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/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",
-                "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_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",
-                "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",
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-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,27ac8815e031784c1928f8ff7d2e8687",
-                "multiqc_picard_baseContent.txt:md5,b8f3650cf18daa57ae2b67c5b89f5b8b",
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-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,4caf3948c2fd99d795c1f6791221a02d",
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-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,097425295aec6d2235b3ce2efdeadc2f",
-                "multiqc_picard_baseContent.txt:md5,e866142c080aadf520f3533344b078f7",
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-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,ae01bdfe32a1adbde8bc90b5cfad3745",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,f7980b8f02897f644b07d15554d83998",
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-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,b9175f19bb7881a189d0f061089ee090",
-                "multiqc_picard_baseContent.txt:md5,fdfa6dc50f83f3966bc33caf796dddda",
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-                "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",