diff --git a/CHANGELOG.md b/CHANGELOG.md
index b28bb77d2..a235dd00f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -23,7 +23,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #1054](https://github.com/nf-core/rnaseq/pull/1054) - Template update to nf-core/tools v2.9
 - [PR #1058](https://github.com/nf-core/rnaseq/pull/1058) - Use `nf-validation` plugin for parameter and samplesheet validation
 - [PR #1068](https://github.com/nf-core/rnaseq/pull/1068) - Update `grep` version for `untar` module
-- [PR #1073](https://github.com/nf-core/rnaseq/pull/1073) - Update documentation to discourage --genome
+- [PR #1073](https://github.com/nf-core/rnaseq/pull/1073) - Update documentation to discourage use of `--genome`
 - [PR #1078](https://github.com/nf-core/rnaseq/pull/1078) - Updated pipeline template to [nf-core/tools 2.10](https://github.com/nf-core/tools/releases/tag/2.10)
 - [PR #1083](https://github.com/nf-core/rnaseq/pull/1083) - Move local modules and subworkflows to subfolders
 - [PR #1088](https://github.com/nf-core/rnaseq/pull/1088) - Updates contributing and code of conduct documents with nf-core template 2.10
@@ -31,9 +31,11 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 
 ### Software dependencies
 
-| Dependency | Old version | New version |
-| ---------- | ----------- | ----------- |
-| `fastqc`   | 0.11.9      | 0.12.1      |
+| Dependency              | Old version | New version |
+| ----------------------- | ----------- | ----------- |
+| `fastqc`                | 0.11.9      | 0.12.1      |
+| `multiqc`               | 1.14        | 1.15        |
+| `ucsc-bedgraphtobigwig` | 377         | 445         |
 
 > **NB:** Dependency has been **updated** if both old and new version information is present.
 >
diff --git a/docs/usage.md b/docs/usage.md
index 9f50fa4c1..9748aa5de 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -150,6 +150,7 @@ These files can then be specified to the workflow with the `--fasta` and `--gtf`
 Notes:
 
 - Compressed reference files are supported by the pipeline i.e. standard files with the `.gz` extension and indices folders with the `tar.gz` extension.
+
 - If `--gff` is provided as input then this will be converted to a GTF file, or the latter will be used if both are provided.
 - If `--gene_bed` is not provided then it will be generated from the GTF file.
 - If `--additional_fasta` is provided then the features in this file (e.g. ERCC spike-ins) will be automatically concatenated onto both the reference FASTA file as well as the GTF annotation before building the appropriate indices.
diff --git a/modules.json b/modules.json
index bbe00aa0c..3ae59acc3 100644
--- a/modules.json
+++ b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "bbmap/bbsplit": {
                         "branch": "master",
-                        "git_sha": "e228790f2957152ad2534e39abd7b3878963e89d",
+                        "git_sha": "de3e6fc949dcffb8d3508c015f435ace5773ff08",
                         "installed_by": ["modules"]
                     },
                     "cat/fastq": {
@@ -17,7 +17,7 @@
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "1b372269755a5c4a13c23bc130ebada8cb9d4cd0",
                         "installed_by": ["modules"]
                     },
                     "custom/getchromsizes": {
@@ -47,17 +47,17 @@
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
+                        "git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57",
                         "installed_by": ["modules"]
                     },
                     "hisat2/align": {
                         "branch": "master",
-                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
+                        "git_sha": "a1881f6374506f9e031b7af814768cdb44a6a7d3",
                         "installed_by": ["fastq_align_hisat2"]
                     },
                     "hisat2/build": {
                         "branch": "master",
-                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
+                        "git_sha": "f2f48836bf5c59434966a6c3b2211b29363f31ab",
                         "installed_by": ["modules"]
                     },
                     "hisat2/extractsplicesites": {
@@ -67,7 +67,7 @@
                     },
                     "picard/markduplicates": {
                         "branch": "master",
-                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
+                        "git_sha": "2ee934606f1fdf7fc1cb05d6e8abc13bec8ab448",
                         "installed_by": ["bam_markduplicates_picard"]
                     },
                     "preseq/lcextrap": {
@@ -77,7 +77,7 @@
                     },
                     "qualimap/rnaseq": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "4657d98bc9f565e067c4d924126ce107056f5e2f",
                         "installed_by": ["modules"]
                     },
                     "rsem/calculateexpression": {
@@ -137,17 +137,17 @@
                     },
                     "salmon/quant": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "c5b528d0a51c31621b485ab3bcc008f483619ea6",
                         "installed_by": ["modules", "fastq_subsample_fq_salmon"]
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "570ec5bcfe19c49e16c9ca35a7a116563af6cc1c",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "e662ab16e0c11f1e62983e21de9871f59371a639",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/index": {
@@ -176,12 +176,12 @@
                     },
                     "star/align": {
                         "branch": "master",
-                        "git_sha": "57d75dbac06812c59798a48585032f6e50bb1914",
+                        "git_sha": "cc08a888069f67cab8120259bddab8032d4c0fe3",
                         "installed_by": ["modules"]
                     },
                     "star/genomegenerate": {
                         "branch": "master",
-                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
+                        "git_sha": "cc08a888069f67cab8120259bddab8032d4c0fe3",
                         "installed_by": ["modules"]
                     },
                     "stringtie/stringtie": {
@@ -201,17 +201,17 @@
                     },
                     "ucsc/bedclip": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "240937a2a9c30298110753292be041188891f2cb",
                         "installed_by": ["bedgraph_bedclip_bedgraphtobigwig"]
                     },
                     "ucsc/bedgraphtobigwig": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "66290981ab6038ea86177ade40b9449bc790b0ce",
                         "installed_by": ["bedgraph_bedclip_bedgraphtobigwig"]
                     },
                     "umitools/dedup": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "7297204bf49273300a3dbfa4b7a4027c8683f1bd",
                         "installed_by": ["bam_dedup_stats_samtools_umitools"]
                     },
                     "umitools/extract": {
@@ -230,12 +230,12 @@
                 "nf-core": {
                     "bam_dedup_stats_samtools_umitools": {
                         "branch": "master",
-                        "git_sha": "e228790f2957152ad2534e39abd7b3878963e89d",
+                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_markduplicates_picard": {
                         "branch": "master",
-                        "git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
+                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_rseqc": {
@@ -245,26 +245,26 @@
                     },
                     "bam_sort_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
+                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
                         "installed_by": ["fastq_align_hisat2"]
                     },
                     "bam_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
+                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
                         "installed_by": [
-                            "bam_markduplicates_picard",
                             "bam_sort_stats_samtools",
+                            "bam_markduplicates_picard",
                             "bam_dedup_stats_samtools_umitools"
                         ]
                     },
                     "bedgraph_bedclip_bedgraphtobigwig": {
                         "branch": "master",
-                        "git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
+                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_align_hisat2": {
                         "branch": "master",
-                        "git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
+                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_fastqc_umitools_fastp": {
@@ -279,7 +279,7 @@
                     },
                     "fastq_subsample_fq_salmon": {
                         "branch": "master",
-                        "git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
+                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/local/multiqc/main.nf b/modules/local/multiqc/main.nf
index 6beb43310..44565a9f7 100644
--- a/modules/local/multiqc/main.nf
+++ b/modules/local/multiqc/main.nf
@@ -1,10 +1,10 @@
 process MULTIQC {
     label 'process_medium'
 
-    conda "bioconda::multiqc=1.14"
+    conda "bioconda::multiqc=1.15"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.14--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.15--pyhdfd78af_0' }"
 
     input:
     path multiqc_config
diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf
index 67190ff1d..f82bb9e47 100644
--- a/modules/nf-core/bbmap/bbsplit/main.nf
+++ b/modules/nf-core/bbmap/bbsplit/main.nf
@@ -1,4 +1,5 @@
 process BBMAP_BBSPLIT {
+    tag "$meta.id"
     label 'process_high'
     label 'error_retry'
 
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
index ebc872733..c9d014b11 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/main.nf
+++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf
@@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     label 'process_single'
 
     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
-    conda "bioconda::multiqc=1.14"
+    conda "bioconda::multiqc=1.15"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.14--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.15--pyhdfd78af_0' }"
 
     input:
     path versions
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
new file mode 100644
index 000000000..d528d3cb8
--- /dev/null
+++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
@@ -0,0 +1,37 @@
+nextflow_process {
+
+    name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS"
+    script "modules/nf-core/custom/dumpsoftwareversions/main.nf"
+    process "CUSTOM_DUMPSOFTWAREVERSIONS"
+    tag "custom"
+    tag "dumpsoftwareversions"
+    tag "custom/dumpsoftwareversions"
+    tag "modules_nfcore"
+
+    test("Should run without failures") {
+        when {
+            process {
+                """
+                def tool1_version = '''
+                TOOL1:
+                    tool1: 0.11.9
+                '''.stripIndent()
+
+                def tool2_version = '''
+                TOOL2:
+                    tool2: 1.9
+                '''.stripIndent()
+
+                input[0] = Channel.of(tool1_version, tool2_version).collectFile()
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
new file mode 100644
index 000000000..8713b9216
--- /dev/null
+++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
@@ -0,0 +1,27 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    "software_versions.yml:md5,a027f820f30b8191a20ca16465daaf37"
+                ],
+                "1": [
+                    "software_versions_mqc.yml:md5,ee4a1d028ad29987f9ac511f4668f17c"
+                ],
+                "2": [
+                    "versions.yml:md5,f47ebd22aba1dd987b7e5d5247b766c3"
+                ],
+                "mqc_yml": [
+                    "software_versions_mqc.yml:md5,ee4a1d028ad29987f9ac511f4668f17c"
+                ],
+                "versions": [
+                    "versions.yml:md5,f47ebd22aba1dd987b7e5d5247b766c3"
+                ],
+                "yml": [
+                    "software_versions.yml:md5,a027f820f30b8191a20ca16465daaf37"
+                ]
+            }
+        ],
+        "timestamp": "2023-10-11T17:10:02.930699"
+    }
+}
diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf
index e7189d2fb..73bf08cde 100644
--- a/modules/nf-core/gunzip/main.nf
+++ b/modules/nf-core/gunzip/main.nf
@@ -21,10 +21,14 @@ process GUNZIP {
     def args = task.ext.args ?: ''
     gunzip = archive.toString() - '.gz'
     """
-    gunzip \\
-        -f \\
+    # Not calling gunzip itself because it creates files
+    # with the original group ownership rather than the
+    # default one for that user / the work directory
+    gzip \\
+        -cd \\
         $args \\
-        $archive
+        $archive \\
+        > $gunzip
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/hisat2/align/main.nf b/modules/nf-core/hisat2/align/main.nf
index e69204692..db8e8bb6d 100644
--- a/modules/nf-core/hisat2/align/main.nf
+++ b/modules/nf-core/hisat2/align/main.nf
@@ -33,6 +33,7 @@ process HISAT2_ALIGN {
     } else if (meta.strandedness == 'reverse') {
         strandedness = meta.single_end ? '--rna-strandness R' : '--rna-strandness RF'
     }
+    ss = "$splicesites" ? "--known-splicesite-infile $splicesites" : ''
     def seq_center = params.seq_center ? "--rg-id ${prefix} --rg SM:$prefix --rg CN:${params.seq_center.replaceAll('\\s','_')}" : "--rg-id ${prefix} --rg SM:$prefix"
     if (meta.single_end) {
         def unaligned = params.save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
@@ -42,7 +43,7 @@ process HISAT2_ALIGN {
             -x \$INDEX \\
             -U $reads \\
             $strandedness \\
-            --known-splicesite-infile $splicesites \\
+            $ss \\
             --summary-file ${prefix}.hisat2.summary.log \\
             --threads $task.cpus \\
             $seq_center \\
@@ -65,7 +66,7 @@ process HISAT2_ALIGN {
             -1 ${reads[0]} \\
             -2 ${reads[1]} \\
             $strandedness \\
-            --known-splicesite-infile $splicesites \\
+            $ss \\
             --summary-file ${prefix}.hisat2.summary.log \\
             --threads $task.cpus \\
             $seq_center \\
diff --git a/modules/nf-core/hisat2/build/main.nf b/modules/nf-core/hisat2/build/main.nf
index 5ad36a548..90f8efcc6 100644
--- a/modules/nf-core/hisat2/build/main.nf
+++ b/modules/nf-core/hisat2/build/main.nf
@@ -37,9 +37,9 @@ process HISAT2_BUILD {
     def hisat2_build_memory = params.hisat2_build_memory ? (params.hisat2_build_memory as nextflow.util.MemoryUnit).toGiga() : 0
     if (avail_mem >= hisat2_build_memory) {
         log.info "[HISAT2 index build] At least ${hisat2_build_memory} GB available, so using splice sites and exons to build HISAT2 index"
-        extract_exons = "hisat2_extract_exons.py $gtf > ${gtf.baseName}.exons.txt"
-        ss = "--ss $splicesites"
-        exon = "--exon ${gtf.baseName}.exons.txt"
+        extract_exons = gtf ? "hisat2_extract_exons.py $gtf > ${gtf.baseName}.exons.txt" : ""
+        ss = splicesites ? "--ss $splicesites" : ""
+        exon = gtf ? "--exon ${gtf.baseName}.exons.txt" : ""
     } else {
         log.info "[HISAT2 index build] Less than ${hisat2_build_memory} GB available, so NOT using splice sites and exons to build HISAT2 index."
         log.info "[HISAT2 index build] Use --hisat2_build_memory [small number] to skip this check."
diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf
index facd7efb9..ebfa0864d 100644
--- a/modules/nf-core/picard/markduplicates/main.nf
+++ b/modules/nf-core/picard/markduplicates/main.nf
@@ -30,6 +30,9 @@ process PICARD_MARKDUPLICATES {
     } else {
         avail_mem = (task.memory.mega*0.8).intValue()
     }
+
+    if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+
     """
     picard \\
         -Xmx${avail_mem}M \\
@@ -48,6 +51,7 @@ process PICARD_MARKDUPLICATES {
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
+    if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     touch ${prefix}.bam
     touch ${prefix}.bam.bai
diff --git a/modules/nf-core/qualimap/rnaseq/main.nf b/modules/nf-core/qualimap/rnaseq/main.nf
index 2c0e4105f..044c983fc 100644
--- a/modules/nf-core/qualimap/rnaseq/main.nf
+++ b/modules/nf-core/qualimap/rnaseq/main.nf
@@ -9,7 +9,7 @@ process QUALIMAP_RNASEQ {
 
     input:
     tuple val(meta), path(bam)
-    path  gtf
+    tuple val(meta2), path(gtf)
 
     output:
     tuple val(meta), path("${prefix}"), emit: results
diff --git a/modules/nf-core/qualimap/rnaseq/meta.yml b/modules/nf-core/qualimap/rnaseq/meta.yml
new file mode 100644
index 000000000..7738f08d8
--- /dev/null
+++ b/modules/nf-core/qualimap/rnaseq/meta.yml
@@ -0,0 +1,52 @@
+name: qualimap_rnaseq
+description: Evaluate alignment data
+keywords:
+  - quality control
+  - qc
+  - rnaseq
+tools:
+  - qualimap:
+      description: |
+        Qualimap 2 is a platform-independent application written in
+        Java and R that provides both a Graphical User Interface and
+        a command-line interface to facilitate the quality control of
+        alignment sequencing data and its derivatives like feature counts.
+      homepage: http://qualimap.bioinfo.cipf.es/
+      documentation: http://qualimap.conesalab.org/doc_html/index.html
+      doi: 10.1093/bioinformatics/bts503
+      licence: ["GPL-2.0-only"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM file
+      pattern: "*.{bam}"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'test' ]
+  - gtf:
+      type: file
+      description: GTF file of the reference genome
+      pattern: "*.{gtf}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - results:
+      type: directory
+      description: Qualimap results dir
+      pattern: "*/*"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@FriederikeHanssen"
diff --git a/modules/nf-core/salmon/quant/main.nf b/modules/nf-core/salmon/quant/main.nf
index e356af26d..f11b6c2e2 100644
--- a/modules/nf-core/salmon/quant/main.nf
+++ b/modules/nf-core/salmon/quant/main.nf
@@ -28,7 +28,9 @@ process SALMON_QUANT {
     prefix   = task.ext.prefix ?: "${meta.id}"
 
     def reference   = "--index $index"
-    def input_reads = meta.single_end ? "-r $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
+    def reads1 = [], reads2 = []
+    meta.single_end ? [reads].flatten().each{reads1 << it} : reads.eachWithIndex{ v, ix -> ( ix & 1 ? reads2 : reads1) << v }
+    def input_reads = meta.single_end ? "-r ${reads1.join(" ")}" : "-1 ${reads1.join(" ")} -2 ${reads2.join(" ")}"
     if (alignment_mode) {
         reference   = "-t $transcript_fasta"
         input_reads = "-a $reads"
diff --git a/modules/nf-core/salmon/quant/meta.yml b/modules/nf-core/salmon/quant/meta.yml
index ea01e0df8..e809ade2b 100644
--- a/modules/nf-core/salmon/quant/meta.yml
+++ b/modules/nf-core/salmon/quant/meta.yml
@@ -22,8 +22,9 @@ input:
   - reads:
       type: file
       description: |
-        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-        respectively.
+        List of input FastQ files for single-end or paired-end data.
+        Multiple single-end fastqs or pairs of paired-end fastqs are
+        handled.
   - index:
       type: directory
       description: Folder containing the star index files
diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf
index eb7e72fc6..b75707eca 100644
--- a/modules/nf-core/samtools/flagstat/main.nf
+++ b/modules/nf-core/samtools/flagstat/main.nf
@@ -32,4 +32,15 @@ process SAMTOOLS_FLAGSTAT {
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.flagstat
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf
index a257d7002..83c7c34b9 100644
--- a/modules/nf-core/samtools/idxstats/main.nf
+++ b/modules/nf-core/samtools/idxstats/main.nf
@@ -33,4 +33,16 @@ process SAMTOOLS_IDXSTATS {
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch ${prefix}.idxstats
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf
index 8cb8e9a4d..d0e203848 100644
--- a/modules/nf-core/star/align/main.nf
+++ b/modules/nf-core/star/align/main.nf
@@ -9,8 +9,8 @@ process STAR_ALIGN {
 
     input:
     tuple val(meta), path(reads, stageAs: "input*/*")
-    path index
-    path gtf
+    tuple val(meta2), path(index)
+    tuple val(meta3), path(gtf)
     val star_ignore_sjdbgtf
     val seq_platform
     val seq_center
diff --git a/modules/nf-core/star/align/meta.yml b/modules/nf-core/star/align/meta.yml
index bce16d360..3d8fed0cc 100644
--- a/modules/nf-core/star/align/meta.yml
+++ b/modules/nf-core/star/align/meta.yml
@@ -25,10 +25,34 @@ input:
       description: |
         List of input FastQ files of size 1 and 2 for single-end and paired-end data,
         respectively.
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'test' ]
   - index:
       type: directory
       description: STAR genome index
       pattern: "star"
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'test' ]
+  - gtf:
+      type: file
+      description: Annotation GTF file
+      pattern: "*.{gtf}"
+  - star_ignore_sjdbgtf:
+      type: boolean
+      description: Ignore annotation GTF file
+  - seq_platform:
+      type: string
+      description: Sequencing platform
+  - seq_center:
+      type: string
+      description: Sequencing center
+
 output:
   - bam:
       type: file
diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf
index 2407d0066..434240427 100644
--- a/modules/nf-core/star/genomegenerate/main.nf
+++ b/modules/nf-core/star/genomegenerate/main.nf
@@ -8,12 +8,12 @@ process STAR_GENOMEGENERATE {
         'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }"
 
     input:
-    path fasta
-    path gtf
+    tuple val(meta), path(fasta)
+    tuple val(meta2), path(gtf)
 
     output:
-    path "star"        , emit: index
-    path "versions.yml", emit: versions
+    tuple val(meta), path("star")  , emit: index
+    path "versions.yml"            , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/star/genomegenerate/meta.yml b/modules/nf-core/star/genomegenerate/meta.yml
index 8181157a1..eba2d9cf1 100644
--- a/modules/nf-core/star/genomegenerate/meta.yml
+++ b/modules/nf-core/star/genomegenerate/meta.yml
@@ -15,14 +15,29 @@ tools:
       doi: 10.1093/bioinformatics/bts635
       licence: ["MIT"]
 input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - fasta:
       type: file
       description: Fasta file of the reference genome
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'test' ]
   - gtf:
       type: file
       description: GTF file of the reference genome
 
 output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - index:
       type: directory
       description: Folder containing the star index files
diff --git a/modules/nf-core/ucsc/bedclip/meta.yml b/modules/nf-core/ucsc/bedclip/meta.yml
index ca278552a..cc5d9d715 100755
--- a/modules/nf-core/ucsc/bedclip/meta.yml
+++ b/modules/nf-core/ucsc/bedclip/meta.yml
@@ -1,7 +1,9 @@
 name: ucsc_bedclip
-description: See http://hgdownload.cse.ucsc.edu/admin/exe/
+description: Remove lines from bed file that refer to off-chromosome locations.
 keywords:
-  - sort
+  - bed
+  - genomics
+  - ucsc
 tools:
   - ucsc:
       description: Remove lines from bed file that refer to off-chromosome locations.
diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf
index 054924e7e..06bb47099 100644
--- a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf
+++ b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf
@@ -3,10 +3,10 @@ process UCSC_BEDGRAPHTOBIGWIG {
     label 'process_single'
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
-    conda "bioconda::ucsc-bedgraphtobigwig=377"
+    conda "bioconda::ucsc-bedgraphtobigwig=445"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:377--h446ed27_1' :
-        'biocontainers/ucsc-bedgraphtobigwig:377--h446ed27_1' }"
+        'https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:445--h954228d_0' :
+        'biocontainers/ucsc-bedgraphtobigwig:445--h954228d_0' }"
 
     input:
     tuple val(meta), path(bedgraph)
@@ -22,7 +22,7 @@ process UCSC_BEDGRAPHTOBIGWIG {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '377' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = '445' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     bedGraphToBigWig \\
         $bedgraph \\
@@ -34,4 +34,16 @@ process UCSC_BEDGRAPHTOBIGWIG {
         ucsc: $VERSION
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '445' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    """
+    touch ${prefix}.bigWig
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ucsc: $VERSION
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/meta.yml b/modules/nf-core/ucsc/bedgraphtobigwig/meta.yml
index ba8915bed..416c91e07 100755
--- a/modules/nf-core/ucsc/bedgraphtobigwig/meta.yml
+++ b/modules/nf-core/ucsc/bedgraphtobigwig/meta.yml
@@ -3,6 +3,9 @@ description: Convert a bedGraph file to bigWig format.
 keywords:
   - bedgraph
   - bigwig
+  - ucsc
+  - bedgraphtobigwig
+  - converter
 tools:
   - ucsc:
       description: Convert a bedGraph file to bigWig format.
diff --git a/modules/nf-core/umitools/dedup/main.nf b/modules/nf-core/umitools/dedup/main.nf
index 2bd95da7c..56ea04691 100644
--- a/modules/nf-core/umitools/dedup/main.nf
+++ b/modules/nf-core/umitools/dedup/main.nf
@@ -12,7 +12,8 @@ process UMITOOLS_DEDUP {
     val get_output_stats
 
     output:
-    tuple val(meta), path("*.bam")             , emit: bam
+    tuple val(meta), path("${prefix}.bam")     , emit: bam
+    tuple val(meta), path("*.log")             , emit: log
     tuple val(meta), path("*edit_distance.tsv"), optional:true, emit: tsv_edit_distance
     tuple val(meta), path("*per_umi.tsv")      , optional:true, emit: tsv_per_umi
     tuple val(meta), path("*per_position.tsv") , optional:true, emit: tsv_umi_per_position
@@ -23,9 +24,10 @@ process UMITOOLS_DEDUP {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     def paired = meta.single_end ? "" : "--paired"
-    def stats = get_output_stats ? "--output-stats $prefix" : ""
+    stats = get_output_stats ? "--output-stats ${prefix}" : ""
+    if ("$bam" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
 
     if (!(args ==~ /.*--random-seed.*/)) {args += " --random-seed=100"}
     """
@@ -33,6 +35,7 @@ process UMITOOLS_DEDUP {
         dedup \\
         -I $bam \\
         -S ${prefix}.bam \\
+        -L ${prefix}.log \\
         $stats \\
         $paired \\
         $args
@@ -42,4 +45,18 @@ process UMITOOLS_DEDUP {
         umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//')
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch ${prefix}.bam
+    touch ${prefix}.log
+    touch ${prefix}_edit_distance.tsv
+    touch ${prefix}_per_umi.tsv
+    touch ${prefix}_per_position.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/umitools/dedup/meta.yml b/modules/nf-core/umitools/dedup/meta.yml
index 0719a9552..534d4c6b0 100644
--- a/modules/nf-core/umitools/dedup/meta.yml
+++ b/modules/nf-core/umitools/dedup/meta.yml
@@ -3,6 +3,7 @@ description: Deduplicate reads based on the mapping co-ordinate and the UMI atta
 keywords:
   - umitools
   - deduplication
+  - dedup
 tools:
   - umi_tools:
       description: >
@@ -40,6 +41,10 @@ output:
       type: file
       description: BAM file with deduplicated UMIs.
       pattern: "*.{bam}"
+  - log:
+      type: file
+      description: File with logging information
+      pattern: "*.{log}"
   - tsv_edit_distance:
       type: file
       description: Reports the (binned) average edit distance between the UMIs at each position.
diff --git a/subworkflows/local/align_star/main.nf b/subworkflows/local/align_star/main.nf
index 479ed2379..1dba0c085 100644
--- a/subworkflows/local/align_star/main.nf
+++ b/subworkflows/local/align_star/main.nf
@@ -9,8 +9,8 @@ include { BAM_SORT_STATS_SAMTOOLS } from '../../nf-core/bam_sort_stats_samtools'
 workflow ALIGN_STAR {
     take:
     reads               // channel: [ val(meta), [ reads ] ]
-    index               // channel: /path/to/star/index/
-    gtf                 // channel: /path/to/genome.gtf
+    index               // channel: [ val(meta), [ index ] ]
+    gtf                 // channel: [ val(meta), [ gtf ] ]
     star_ignore_sjdbgtf // boolean: when using pre-built STAR indices do not re-extract and use splice junctions from the GTF file 
     seq_platform        // string : sequencing platform
     seq_center          // string : sequencing center
diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf
index 200957cda..eceb2c1ce 100644
--- a/subworkflows/local/prepare_genome/main.nf
+++ b/subworkflows/local/prepare_genome/main.nf
@@ -191,7 +191,7 @@ workflow PREPARE_GENOME {
                 ch_star_index = STAR_GENOMEGENERATE_IGENOMES ( ch_fasta, ch_gtf ).index
                 ch_versions   = ch_versions.mix(STAR_GENOMEGENERATE_IGENOMES.out.versions)
             } else {
-                ch_star_index = STAR_GENOMEGENERATE ( ch_fasta, ch_gtf ).index
+                ch_star_index = STAR_GENOMEGENERATE ( ch_fasta.map { [ [:], it ] }, ch_gtf.map { [ [:], it ] } ).index.map { it[1] }
                 ch_versions   = ch_versions.mix(STAR_GENOMEGENERATE.out.versions)
             }
         }
diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/meta.yml b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/meta.yml
index 3af412fab..f11e7ab6f 100644
--- a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/meta.yml
+++ b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/meta.yml
@@ -8,12 +8,13 @@ keywords:
   - bam
   - sam
   - cram
-modules:
+components:
   - umitools/dedup
   - samtools/index
   - samtools/stats
   - samtools/idxstats
   - samtools/flagstat
+  - bam_stats_samtools
 input:
   - ch_bam_bai:
       description: |
diff --git a/subworkflows/nf-core/bam_markduplicates_picard/meta.yml b/subworkflows/nf-core/bam_markduplicates_picard/meta.yml
index d5e716092..b924596d8 100644
--- a/subworkflows/nf-core/bam_markduplicates_picard/meta.yml
+++ b/subworkflows/nf-core/bam_markduplicates_picard/meta.yml
@@ -7,12 +7,13 @@ keywords:
   - sam
   - cram
 
-modules:
+components:
   - picard/markduplicates
   - samtools/index
   - samtools/stats
   - samtools/idxstats
   - samtools/flagstat
+  - bam_stats_samtools
 
 input:
   - ch_bam:
diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml b/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml
index 8dfbd58df..69c16be41 100644
--- a/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml
+++ b/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml
@@ -6,12 +6,13 @@ keywords:
   - bam
   - sam
   - cram
-modules:
+components:
   - samtools/sort
   - samtools/index
   - samtools/stats
   - samtools/idxstats
   - samtools/flagstat
+  - bam_stats_samtools
 input:
   - meta:
       type: map
diff --git a/subworkflows/nf-core/bam_stats_samtools/meta.yml b/subworkflows/nf-core/bam_stats_samtools/meta.yml
index b05086bc2..87863b11b 100644
--- a/subworkflows/nf-core/bam_stats_samtools/meta.yml
+++ b/subworkflows/nf-core/bam_stats_samtools/meta.yml
@@ -7,7 +7,7 @@ keywords:
   - bam
   - sam
   - cram
-modules:
+components:
   - samtools/stats
   - samtools/idxstats
   - samtools/flagstat
diff --git a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/meta.yml b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/meta.yml
index 8d3257773..5ad4db7db 100644
--- a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/meta.yml
+++ b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/meta.yml
@@ -6,7 +6,7 @@ keywords:
   - bigwig
   - clip
   - conversion
-modules:
+components:
   - ucsc/bedclip
   - ucsc/bedgraphtobigwig
 input:
diff --git a/subworkflows/nf-core/fastq_align_hisat2/meta.yml b/subworkflows/nf-core/fastq_align_hisat2/meta.yml
index 36c7c78ec..2b05beb68 100644
--- a/subworkflows/nf-core/fastq_align_hisat2/meta.yml
+++ b/subworkflows/nf-core/fastq_align_hisat2/meta.yml
@@ -10,11 +10,12 @@ keywords:
   - bam
   - sam
   - cram
-modules:
+components:
   - hisat2/align
   - samtools/stats
   - samtools/idxstats
   - samtools/flagstat
+  - bam_sort_stats_samtools
 input:
   - meta:
       type: map
diff --git a/subworkflows/nf-core/fastq_subsample_fq_salmon/meta.yml b/subworkflows/nf-core/fastq_subsample_fq_salmon/meta.yml
index db96312aa..d144269ba 100644
--- a/subworkflows/nf-core/fastq_subsample_fq_salmon/meta.yml
+++ b/subworkflows/nf-core/fastq_subsample_fq_salmon/meta.yml
@@ -5,9 +5,10 @@ keywords:
   - fastq
   - subsample
   - strandedness
-modules:
+components:
   - fq/subsample
   - salmon/quant
+  - salmon/index
 input:
   - meta:
       type: map
diff --git a/workflows/rnaseq.nf b/workflows/rnaseq.nf
index f2dd49a0b..955a727c3 100755
--- a/workflows/rnaseq.nf
+++ b/workflows/rnaseq.nf
@@ -382,8 +382,8 @@ workflow RNASEQ {
     if (!params.skip_alignment && params.aligner == 'star_salmon') {
         ALIGN_STAR (
             ch_filtered_reads,
-            PREPARE_GENOME.out.star_index,
-            PREPARE_GENOME.out.gtf,
+            PREPARE_GENOME.out.star_index.map { [ [:], it ] },
+            PREPARE_GENOME.out.gtf.map { [ [:], it ] },
             params.star_ignore_sjdbgtf,
             '',
             params.seq_center ?: '',
@@ -729,7 +729,7 @@ workflow RNASEQ {
         if (!params.skip_qualimap) {
             QUALIMAP_RNASEQ (
                 ch_genome_bam,
-                PREPARE_GENOME.out.gtf
+                PREPARE_GENOME.out.gtf.map { [ [:], it ] }
             )
             ch_qualimap_multiqc = QUALIMAP_RNASEQ.out.results
             ch_versions = ch_versions.mix(QUALIMAP_RNASEQ.out.versions.first())