From d7d2d3f58d478cd77f4b2956273f570cdc067c15 Mon Sep 17 00:00:00 2001
From: Kevin-Brockers <kevin.brockers@yahoo.de>
Date: Fri, 20 Mar 2026 19:34:10 +0100
Subject: [PATCH 01/20] Updated python, added topic channel and enviroment.yml

---
 CHANGELOG.md                                    |  5 +++--
 modules/local/samplesheet_check/environment.yml |  7 +++++++
 modules/local/samplesheet_check/main.nf         | 13 ++++---------
 3 files changed, 14 insertions(+), 11 deletions(-)
 create mode 100644 modules/local/samplesheet_check/environment.yml

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 17c7b08d5..b2dfd43c0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -64,13 +64,14 @@ the last release have been listed below for reference.
 | r-tidyverse                 | 1.3.0       | 2.0.0       |
 | bioconductor-complexheatmap | 2.6.2       | 2.26.1      |
 | star                        | 2.6.1d      | 2.7.11b     |
+| python                      | 3.8.3       | 3.12.12     |
 |                             |             |             |
 
 ### Local modules refactoring and topic channels update
 
 | Module                              | Updated to wave containers | Topic channel added | refactoring (adding .yml files) |
 | ----------------------------------- | -------------------------- | ------------------- | ------------------------------- |
-| annotate_boolean_peaks              |                            |                     |                                 |
+| annotate_boolean_peaks              |                            | x                   | x                               |
 | bam_remove_orphans                  | x                          | x                   | x                               |
 | bamtools_filter                     | x                          | x                   | x                               |
 | deseq2_qc                           |                            |                     |                                 |
@@ -84,7 +85,7 @@ the last release have been listed below for reference.
 | multiqc_custom_phantompeakqualtools |                            |                     |                                 |
 | plot_homer_annotatepeaks            | x                          | x                   | x                               |
 | plot_macs3_qc                       | x                          | x                   | x                               |
-| samplesheet_check                   |                            |                     |                                 |
+| samplesheet_check                   | x                          | x                   | x                               |
 | star_align                          | x                          | x                   | x                               |
 | star_genomegenerate                 | x                          | x                   | x                               |
 |                                     |                            |                     |                                 |
diff --git a/modules/local/samplesheet_check/environment.yml b/modules/local/samplesheet_check/environment.yml
new file mode 100644
index 000000000..d34414278
--- /dev/null
+++ b/modules/local/samplesheet_check/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::python=3.12.3
\ No newline at end of file
diff --git a/modules/local/samplesheet_check/main.nf b/modules/local/samplesheet_check/main.nf
index 216e9fb78..2cce1a1db 100644
--- a/modules/local/samplesheet_check/main.nf
+++ b/modules/local/samplesheet_check/main.nf
@@ -2,17 +2,17 @@ process SAMPLESHEET_CHECK {
     tag "$samplesheet"
     label 'process_single'
 
-    conda "conda-forge::python=3.8.3"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/python:3.8.3' :
-        'biocontainers/python:3.8.3' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/62/622d8944750bc95bb56b4c3ed5c2b827e677c14073d48a5231e0f2bec0718add/data' :
+        'community.wave.seqera.io/library/python:3.12.12--74abbf3898230efd' }"
 
     input:
     path samplesheet
 
     output:
     path '*.csv'       , emit: csv
-    path "versions.yml", emit: versions
+    tuple val("${task.process}"), val('python'), eval("python --version | sed 's/Python //'"), topic: versions, emit: versions_python
 
     when:
     task.ext.when == null || task.ext.when
@@ -23,10 +23,5 @@ process SAMPLESHEET_CHECK {
     check_samplesheet.py \\
         $samplesheet \\
         $args
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        python: \$(python --version | sed 's/Python //g')
-    END_VERSIONS
     """
 }

From 1c2dc34e3636c4059681532bc48f07a126d7ba2c Mon Sep 17 00:00:00 2001
From: Kevin-Brockers <kevin.brockers@yahoo.de>
Date: Fri, 20 Mar 2026 19:37:24 +0100
Subject: [PATCH 02/20] added topic channels and enviroment.yml

---
 modules/local/annotate_boolean_peaks/environment.yml | 7 +++++++
 modules/local/annotate_boolean_peaks/main.nf         | 9 ++-------
 2 files changed, 9 insertions(+), 7 deletions(-)
 create mode 100644 modules/local/annotate_boolean_peaks/environment.yml

diff --git a/modules/local/annotate_boolean_peaks/environment.yml b/modules/local/annotate_boolean_peaks/environment.yml
new file mode 100644
index 000000000..ccfc67291
--- /dev/null
+++ b/modules/local/annotate_boolean_peaks/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::sed=4.7
\ No newline at end of file
diff --git a/modules/local/annotate_boolean_peaks/main.nf b/modules/local/annotate_boolean_peaks/main.nf
index 77baf5c40..463cb86af 100644
--- a/modules/local/annotate_boolean_peaks/main.nf
+++ b/modules/local/annotate_boolean_peaks/main.nf
@@ -2,7 +2,7 @@ process ANNOTATE_BOOLEAN_PEAKS {
     tag "$meta.id"
     label 'process_low'
 
-    conda "conda-forge::sed=4.7"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
         'docker.io/library/ubuntu:20.04' }"
@@ -12,17 +12,12 @@ process ANNOTATE_BOOLEAN_PEAKS {
 
     output:
     path '*.boolean.annotatePeaks.txt', emit: annotate_peaks_txt
-    path "versions.yml"               , emit: versions
+    tuple val("${task.process}"), val('sed'), eval("sed --version 2>&1 | sed '1!d;s/^.*) //'"), topic: versions, emit: versions_sed
 
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     cut -f2- ${homer_peaks} | awk 'NR==1; NR > 1 {print \$0 | "sort -T '.' -k1,1 -k2,2n"}' | cut -f6- > tmp.txt
     paste $boolean_txt tmp.txt > ${prefix}.boolean.annotatePeaks.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
-    END_VERSIONS
     """
 }

From 02be6884a08397340e8abe0877d6c77f8c2a27ff Mon Sep 17 00:00:00 2001
From: Kevin-Brockers <kevin.brockers@yahoo.de>
Date: Fri, 20 Mar 2026 19:55:37 +0100
Subject: [PATCH 03/20] added topic channels and environment.yml, did not
 update containers, see comment in main.mf

---
 modules/local/deseq2_qc/environment.yml | 15 +++++++++++++++
 modules/local/deseq2_qc/main.nf         | 11 +++--------
 2 files changed, 18 insertions(+), 8 deletions(-)
 create mode 100644 modules/local/deseq2_qc/environment.yml

diff --git a/modules/local/deseq2_qc/environment.yml b/modules/local/deseq2_qc/environment.yml
new file mode 100644
index 000000000..e0baa7b65
--- /dev/null
+++ b/modules/local/deseq2_qc/environment.yml
@@ -0,0 +1,15 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::r-base
+  - bioconda::bioconductor-deseq2
+  - bioconda::bioconductor-biocparallel
+  - bioconda::bioconductor-tximport
+  - bioconda::bioconductor-complexheatmap
+  - conda-forge::r-optparse
+  - conda-forge::r-ggplot2
+  - conda-forge::r-rcolorbrewer
+  - conda-forge::r-pheatmap
diff --git a/modules/local/deseq2_qc/main.nf b/modules/local/deseq2_qc/main.nf
index 4b5cae510..c201b1946 100644
--- a/modules/local/deseq2_qc/main.nf
+++ b/modules/local/deseq2_qc/main.nf
@@ -4,7 +4,7 @@ process DESEQ2_QC {
 
     // (Bio)conda packages have intentionally not been pinned to a specific version
     // This was to avoid the pipeline failing due to package conflicts whilst creating the environment when using -profile conda
-    conda "conda-forge::r-base bioconda::bioconductor-deseq2 bioconda::bioconductor-biocparallel bioconda::bioconductor-tximport bioconda::bioconductor-complexheatmap conda-forge::r-optparse conda-forge::r-ggplot2 conda-forge::r-rcolorbrewer conda-forge::r-pheatmap"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0' :
         'biocontainers/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0' }"
@@ -24,7 +24,8 @@ process DESEQ2_QC {
     path "*sample.dists_mqc.tsv", optional:true, emit: dists_multiqc
     path "*.log"                , optional:true, emit: log
     path "size_factors"         , optional:true, emit: size_factors
-    path "versions.yml"         , emit: versions
+    tuple val("${task.process}"), val('R'), eval('R --version | sed "1!d; s/.*version //; s/ .*//"'), topic: versions, emit: versions_r
+    tuple val("${task.process}"), val('DESeq2'), eval('Rscript -e "library(DESeq2); cat(as.character(packageVersion(\'DESeq2\')))"'), topic: versions, emit: versions_deseq2
 
     when:
     task.ext.when == null || task.ext.when
@@ -49,11 +50,5 @@ process DESEQ2_QC {
     sed 's/deseq2_clustering/deseq2_clustering_${task.index}/g' <$deseq2_clustering_header >tmp.txt
     sed -i -e 's/DESeq2 /${meta.id} DESeq2 /g' tmp.txt
     cat tmp.txt ${prefix}.sample.dists.txt > ${prefix}.sample.dists_mqc.tsv
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
-        bioconductor-deseq2: \$(Rscript -e "library(DESeq2); cat(as.character(packageVersion('DESeq2')))")
-    END_VERSIONS
     """
 }

From e5fcd86a673077093b3ed2b1fe5ec399f4a6fce6 Mon Sep 17 00:00:00 2001
From: Kevin-Brockers <kevin.brockers@yahoo.de>
Date: Fri, 20 Mar 2026 20:08:29 +0100
Subject: [PATCH 04/20] Topic channels - suggestion: see #494

---
 modules/local/gtf2bed/environment.yml |  7 +++++++
 modules/local/gtf2bed/main.nf         | 10 +++-------
 2 files changed, 10 insertions(+), 7 deletions(-)
 create mode 100644 modules/local/gtf2bed/environment.yml

diff --git a/modules/local/gtf2bed/environment.yml b/modules/local/gtf2bed/environment.yml
new file mode 100644
index 000000000..dc0f53163
--- /dev/null
+++ b/modules/local/gtf2bed/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::perl=5.26.2
\ No newline at end of file
diff --git a/modules/local/gtf2bed/main.nf b/modules/local/gtf2bed/main.nf
index bc0eef549..180ba7bf8 100644
--- a/modules/local/gtf2bed/main.nf
+++ b/modules/local/gtf2bed/main.nf
@@ -2,7 +2,7 @@ process GTF2BED {
     tag "$gtf"
     label 'process_low'
 
-    conda "conda-forge::perl=5.26.2"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/perl:5.26.2':
         'biocontainers/perl:5.26.2' }"
@@ -12,7 +12,8 @@ process GTF2BED {
 
     output:
     path '*.bed'       , emit: bed
-    path "versions.yml", emit: versions
+    tuple val({"${task.process}"}), val('perl'), eval("perl --version 2>&1 | sed 's/.*v\\(.*\\)) built.*/\\1/'"), topic:versions, emit: versions_perl
+
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,10 +23,5 @@ process GTF2BED {
     gtf2bed \\
         $gtf \\
         > ${gtf.baseName}.bed
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        perl: \$(echo \$(perl --version 2>&1) | sed 's/.*v\\(.*\\)) built.*/\\1/')
-    END_VERSIONS
     """
 }

From 55c1488fbc393011e2240ab362215bc681168927 Mon Sep 17 00:00:00 2001
From: Kevin-Brockers <kevin.brockers@yahoo.de>
Date: Fri, 20 Mar 2026 20:13:10 +0100
Subject: [PATCH 05/20] added topic channels, environment.yml and updated
 python

---
 modules/local/igv/environment.yml |  7 +++++++
 modules/local/igv/main.nf         | 13 ++++---------
 2 files changed, 11 insertions(+), 9 deletions(-)
 create mode 100644 modules/local/igv/environment.yml

diff --git a/modules/local/igv/environment.yml b/modules/local/igv/environment.yml
new file mode 100644
index 000000000..d34414278
--- /dev/null
+++ b/modules/local/igv/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::python=3.12.3
\ No newline at end of file
diff --git a/modules/local/igv/main.nf b/modules/local/igv/main.nf
index 7d9afe1c8..2b0a6c87f 100644
--- a/modules/local/igv/main.nf
+++ b/modules/local/igv/main.nf
@@ -3,10 +3,10 @@
  */
 process IGV {
 
-    conda "conda-forge::python=3.8.3"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/python:3.8.3':
-        'biocontainers/python:3.8.3' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/62/622d8944750bc95bb56b4c3ed5c2b827e677c14073d48a5231e0f2bec0718add/data' :
+        'community.wave.seqera.io/library/python:3.12.12--74abbf3898230efd' }"
 
     input:
     val aligner_dir
@@ -21,7 +21,7 @@ process IGV {
     path "*files.txt"  , emit: txt
     path "*.xml"       , emit: xml
     path fasta         , emit: fasta
-    path "versions.yml", emit: versions
+    tuple val("${task.process}"), val('python'), eval("python --version | sed 's/Python //'"), topic: versions, emit: versions_python
 
     when:
     task.ext.when == null || task.ext.when
@@ -42,10 +42,5 @@ process IGV {
 
     cat *.igv.txt > igv_files_orig.txt
     igv_files_to_session.py igv_session.xml igv_files_orig.txt replace_paths.txt ../../genome/${fasta.getName()} --path_prefix '../../'
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        python: \$(python --version | sed 's/Python //g')
-    END_VERSIONS
     """
 }

From 6d80159072311550ec941216e45e3cba810d3b6a Mon Sep 17 00:00:00 2001
From: Kevin-Brockers <kevin.brockers@yahoo.de>
Date: Fri, 20 Mar 2026 20:21:00 +0100
Subject: [PATCH 06/20] Updated multiqc version, added env, removed versions
 yml, see comment in main.nf not emitting to topic

---
 modules/local/multiqc/environment.yml |  7 +++++++
 modules/local/multiqc/main.nf         | 19 ++++++-------------
 2 files changed, 13 insertions(+), 13 deletions(-)
 create mode 100644 modules/local/multiqc/environment.yml

diff --git a/modules/local/multiqc/environment.yml b/modules/local/multiqc/environment.yml
new file mode 100644
index 000000000..7c525f913
--- /dev/null
+++ b/modules/local/multiqc/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::multiqc=1.33
\ No newline at end of file
diff --git a/modules/local/multiqc/main.nf b/modules/local/multiqc/main.nf
index 620529ce0..ae55b8687 100644
--- a/modules/local/multiqc/main.nf
+++ b/modules/local/multiqc/main.nf
@@ -1,9 +1,10 @@
 process MULTIQC {
     label 'process_medium'
-    conda "bioconda::multiqc=1.25.1"
+
+    conda "${moduleDir}/environment.yml"
     container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0'
-        : 'biocontainers/multiqc:1.25.1--pyhdfd78af_0'}"
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/34/34e733a9ae16a27e80fe00f863ea1479c96416017f24a907996126283e7ecd4d/data'
+        : 'community.wave.seqera.io/library/multiqc:1.33--ee7739d47738383b'}"
 
     input:
     path workflow_summary
@@ -52,6 +53,8 @@ process MULTIQC {
     path "*_data"              , emit: data
     path "*_plots"             , optional: true, emit: plots
     path "versions.yml"        , emit: versions
+    // From the nf-core/moduel: MultiQC should not push its versions to the `versions` topic. Its input depends on the versions topic to be resolved thus outputting to the topic will let the pipeline hang forever
+    tuple val("${task.process}"), val('multiqc'), eval('multiqc --version | sed "s/.* //g"'), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -65,11 +68,6 @@ process MULTIQC {
         ${args} \\
         ${custom_config} \\
         .
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
-    END_VERSIONS
     """
 
     stub:
@@ -77,10 +75,5 @@ process MULTIQC {
     mkdir -p multiqc_data
     touch multiqc_report.html
     touch multiqc_data/multiqc.log
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
-    END_VERSIONS
     """
 }

From 13466ff45c8506b2e8f40d1b117e2f47091b6238 Mon Sep 17 00:00:00 2001
From: Kevin-Brockers <kevin.brockers@yahoo.de>
Date: Fri, 20 Mar 2026 20:30:36 +0100
Subject: [PATCH 07/20] Added topic channels, environment.yml

---
 modules/local/multiqc_custom_peaks/environment.yml | 7 +++++++
 modules/local/multiqc_custom_peaks/main.nf         | 9 ++-------
 2 files changed, 9 insertions(+), 7 deletions(-)
 create mode 100644 modules/local/multiqc_custom_peaks/environment.yml

diff --git a/modules/local/multiqc_custom_peaks/environment.yml b/modules/local/multiqc_custom_peaks/environment.yml
new file mode 100644
index 000000000..ccfc67291
--- /dev/null
+++ b/modules/local/multiqc_custom_peaks/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::sed=4.7
\ No newline at end of file
diff --git a/modules/local/multiqc_custom_peaks/main.nf b/modules/local/multiqc_custom_peaks/main.nf
index eb3e5cbbc..69a7118ef 100644
--- a/modules/local/multiqc_custom_peaks/main.nf
+++ b/modules/local/multiqc_custom_peaks/main.nf
@@ -1,7 +1,7 @@
 process MULTIQC_CUSTOM_PEAKS {
     tag "$meta.id"
 
-    conda "conda-forge::sed=4.7"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
         'nf-core/ubuntu:20.04' }"
@@ -14,7 +14,7 @@ process MULTIQC_CUSTOM_PEAKS {
     output:
     tuple val(meta), path("*.peak_count_mqc.tsv"), emit: count
     tuple val(meta), path("*.FRiP_mqc.tsv")      , emit: frip
-    path "versions.yml"                          , emit: versions
+    tuple val("${task.process}"), val('sed'), eval("sed --version 2>&1 | sed '1!d;s/^.*) //'"), topic: versions, emit: versions_sed
 
     when:
     task.ext.when == null || task.ext.when
@@ -24,10 +24,5 @@ process MULTIQC_CUSTOM_PEAKS {
     """
     cat $peak | wc -l | awk -v OFS='\t' '{ print "${prefix}", \$1 }' | cat $peak_count_header - > ${prefix}.peak_count_mqc.tsv
     cat $frip_score_header $frip > ${prefix}.FRiP_mqc.tsv
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
-    END_VERSIONS
     """
 }

From 6155f0ec5472445e0915d7a71981a348149006bd Mon Sep 17 00:00:00 2001
From: Kevin-Brockers <kevin.brockers@yahoo.de>
Date: Fri, 20 Mar 2026 20:38:48 +0100
Subject: [PATCH 08/20] added topic channel and environment.yml

---
 .../environment.yml                               |  7 +++++++
 .../multiqc_custom_phantompeakqualtools/main.nf   | 15 +++------------
 2 files changed, 10 insertions(+), 12 deletions(-)
 create mode 100644 modules/local/multiqc_custom_phantompeakqualtools/environment.yml

diff --git a/modules/local/multiqc_custom_phantompeakqualtools/environment.yml b/modules/local/multiqc_custom_phantompeakqualtools/environment.yml
new file mode 100644
index 000000000..a3e06170f
--- /dev/null
+++ b/modules/local/multiqc_custom_phantompeakqualtools/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::r-base=4.5.3
\ No newline at end of file
diff --git a/modules/local/multiqc_custom_phantompeakqualtools/main.nf b/modules/local/multiqc_custom_phantompeakqualtools/main.nf
index 57341b532..368281e72 100644
--- a/modules/local/multiqc_custom_phantompeakqualtools/main.nf
+++ b/modules/local/multiqc_custom_phantompeakqualtools/main.nf
@@ -2,8 +2,8 @@ process MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS {
     tag "$meta.id"
     conda "conda-forge::r-base=4.3.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/45/4569ff9993578b8402d00230ab9dd75ce6e63529731eb24f21579845e6bd5cdb/data':
-        'community.wave.seqera.io/library/r-base:4.3.3--14bb33ac537aea22' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c7/c73daa0b0040137fbea15fc8ee54c9bf4e0a9c5e9412cc7c13f7b38cc9c8bbd9/data':
+        'community.wave.seqera.io/library/r-base:4.5.3--6814a4ccafc04d08' }"
 
     input:
     tuple val(meta), path(spp), path(rdata)
@@ -15,6 +15,7 @@ process MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS {
     tuple val(meta), path("*.spp_nsc_mqc.tsv")        , emit: nsc
     tuple val(meta), path("*.spp_rsc_mqc.tsv")        , emit: rsc
     tuple val(meta), path("*.spp_correlation_mqc.tsv"), emit: correlation
+    tuple val("${task.process}"), val('R'), eval('R --version | sed "1!d; s/.*version //; s/ .*//"'), topic: versions, emit: versions_r
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,11 +28,6 @@ process MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS {
 
     awk -v OFS='\t' '{print "${meta.id}", \$9}'  $spp | cat $nsc_header - > ${prefix}.spp_nsc_mqc.tsv
     awk -v OFS='\t' '{print "${meta.id}", \$10}' $spp | cat $rsc_header - > ${prefix}.spp_rsc_mqc.tsv
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
-    END_VERSIONS
     """
 
     stub:
@@ -40,10 +36,5 @@ process MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS {
     touch ${prefix}.spp_nsc_mqc.tsv
     touch ${prefix}.spp_rsc_mqc.tsv
     touch ${prefix}.spp_correlation_mqc.tsv
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
-    END_VERSIONS
     """
 }

From ba78068d99cc55b13700533ea5e3badd290ea96e Mon Sep 17 00:00:00 2001
From: Kevin-Brockers <kevin.brockers@yahoo.de>
Date: Fri, 20 Mar 2026 20:39:11 +0100
Subject: [PATCH 09/20] Updated progress

---
 CHANGELOG.md | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b2dfd43c0..831828bba 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -65,6 +65,7 @@ the last release have been listed below for reference.
 | bioconductor-complexheatmap | 2.6.2       | 2.26.1      |
 | star                        | 2.6.1d      | 2.7.11b     |
 | python                      | 3.8.3       | 3.12.12     |
+| multiqc                     | 1.25.1      | 1.33        |
 |                             |             |             |
 
 ### Local modules refactoring and topic channels update
@@ -74,15 +75,15 @@ the last release have been listed below for reference.
 | annotate_boolean_peaks              |                            | x                   | x                               |
 | bam_remove_orphans                  | x                          | x                   | x                               |
 | bamtools_filter                     | x                          | x                   | x                               |
-| deseq2_qc                           |                            |                     |                                 |
+| deseq2_qc                           |                            | x                   | x                               |
 | frip_score                          | x                          | x                   | x                               |
 | genome_blacklist_regions            | x                          | x                   | x                               |
-| gtf2bed                             |                            |                     |                                 |
-| igv                                 |                            |                     |                                 |
+| gtf2bed                             |                            | x                   | x                               |
+| igv                                 | x                          | x                   | x                               |
 | macs3_consensus                     | x                          | x                   | x                               |
-| multiqc                             |                            |                     |                                 |
-| multiqc_custom_peaks                |                            |                     |                                 |
-| multiqc_custom_phantompeakqualtools |                            |                     |                                 |
+| multiqc                             | x                          | x                   | x                               |
+| multiqc_custom_peaks                |                            | x                   | x                               |
+| multiqc_custom_phantompeakqualtools | x                          | x                   | x                               |
 | plot_homer_annotatepeaks            | x                          | x                   | x                               |
 | plot_macs3_qc                       | x                          | x                   | x                               |
 | samplesheet_check                   | x                          | x                   | x                               |

From 2159fa4fad8543c2e4ca7b81bdb1eba07fcebc8b Mon Sep 17 00:00:00 2001
From: Kevin-Brockers <kevin.brockers@yahoo.de>
Date: Wed, 25 Mar 2026 21:07:21 +0100
Subject: [PATCH 10/20] Removed progress for local module refactoring

---
 CHANGELOG.md | 23 -----------------------
 1 file changed, 23 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 37cb85b80..e9641d847 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -59,29 +59,6 @@ the last release have been listed below for reference.
 | multiqc                     | 1.25.1      | 1.33        |
 |                             |             |             |
 
-### Local modules refactoring and topic channels update
-
-| Module                              | Updated to wave containers | Topic channel added | refactoring (adding .yml files) |
-| ----------------------------------- | -------------------------- | ------------------- | ------------------------------- |
-| annotate_boolean_peaks              |                            | x                   | x                               |
-| bam_remove_orphans                  | x                          | x                   | x                               |
-| bamtools_filter                     | x                          | x                   | x                               |
-| deseq2_qc                           |                            | x                   | x                               |
-| frip_score                          | x                          | x                   | x                               |
-| genome_blacklist_regions            | x                          | x                   | x                               |
-| gtf2bed                             |                            | x                   | x                               |
-| igv                                 | x                          | x                   | x                               |
-| macs3_consensus                     | x                          | x                   | x                               |
-| multiqc                             | x                          | x                   | x                               |
-| multiqc_custom_peaks                |                            | x                   | x                               |
-| multiqc_custom_phantompeakqualtools | x                          | x                   | x                               |
-| plot_homer_annotatepeaks            | x                          | x                   | x                               |
-| plot_macs3_qc                       | x                          | x                   | x                               |
-| samplesheet_check                   | x                          | x                   | x                               |
-| star_align                          | x                          | x                   | x                               |
-| star_genomegenerate                 | x                          | x                   | x                               |
-|                                     |                            |                     |                                 |
-
 ## [[2.1.0](https://github.com/nf-core/chipseq/releases/tag/2.1.0)] - 2024-10-07
 
 ### Credits

From 4cc18cee51d8b59b67cf0ca316601468391c8473 Mon Sep 17 00:00:00 2001
From: Kevin-Brockers <kevin.brockers@yahoo.de>
Date: Wed, 25 Mar 2026 21:08:31 +0100
Subject: [PATCH 11/20] fixed formating issues

---
 modules/local/annotate_boolean_peaks/environment.yml            | 2 +-
 modules/local/gtf2bed/environment.yml                           | 2 +-
 modules/local/igv/environment.yml                               | 2 +-
 modules/local/multiqc/environment.yml                           | 2 +-
 modules/local/multiqc_custom_peaks/environment.yml              | 2 +-
 .../local/multiqc_custom_phantompeakqualtools/environment.yml   | 2 +-
 modules/local/samplesheet_check/environment.yml                 | 2 +-
 7 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/modules/local/annotate_boolean_peaks/environment.yml b/modules/local/annotate_boolean_peaks/environment.yml
index ccfc67291..4ea414c04 100644
--- a/modules/local/annotate_boolean_peaks/environment.yml
+++ b/modules/local/annotate_boolean_peaks/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::sed=4.7
\ No newline at end of file
+  - conda-forge::sed=4.7
diff --git a/modules/local/gtf2bed/environment.yml b/modules/local/gtf2bed/environment.yml
index dc0f53163..b827837b7 100644
--- a/modules/local/gtf2bed/environment.yml
+++ b/modules/local/gtf2bed/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::perl=5.26.2
\ No newline at end of file
+  - conda-forge::perl=5.26.2
diff --git a/modules/local/igv/environment.yml b/modules/local/igv/environment.yml
index d34414278..3ac6303f3 100644
--- a/modules/local/igv/environment.yml
+++ b/modules/local/igv/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::python=3.12.3
\ No newline at end of file
+  - conda-forge::python=3.12.3
diff --git a/modules/local/multiqc/environment.yml b/modules/local/multiqc/environment.yml
index 7c525f913..009874d4c 100644
--- a/modules/local/multiqc/environment.yml
+++ b/modules/local/multiqc/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::multiqc=1.33
\ No newline at end of file
+  - bioconda::multiqc=1.33
diff --git a/modules/local/multiqc_custom_peaks/environment.yml b/modules/local/multiqc_custom_peaks/environment.yml
index ccfc67291..4ea414c04 100644
--- a/modules/local/multiqc_custom_peaks/environment.yml
+++ b/modules/local/multiqc_custom_peaks/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::sed=4.7
\ No newline at end of file
+  - conda-forge::sed=4.7
diff --git a/modules/local/multiqc_custom_phantompeakqualtools/environment.yml b/modules/local/multiqc_custom_phantompeakqualtools/environment.yml
index a3e06170f..11bc999f2 100644
--- a/modules/local/multiqc_custom_phantompeakqualtools/environment.yml
+++ b/modules/local/multiqc_custom_phantompeakqualtools/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::r-base=4.5.3
\ No newline at end of file
+  - conda-forge::r-base=4.5.3
diff --git a/modules/local/samplesheet_check/environment.yml b/modules/local/samplesheet_check/environment.yml
index d34414278..3ac6303f3 100644
--- a/modules/local/samplesheet_check/environment.yml
+++ b/modules/local/samplesheet_check/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::python=3.12.3
\ No newline at end of file
+  - conda-forge::python=3.12.3

From aa56bb9da23eb8992b00eccf7b9eb2cd97648e59 Mon Sep 17 00:00:00 2001
From: Kevin-Brockers <kevin.brockers@yahoo.de>
Date: Wed, 25 Mar 2026 23:07:20 +0100
Subject: [PATCH 12/20] removed versions.yml

---
 modules/local/multiqc/main.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/local/multiqc/main.nf b/modules/local/multiqc/main.nf
index ae55b8687..78c85fb54 100644
--- a/modules/local/multiqc/main.nf
+++ b/modules/local/multiqc/main.nf
@@ -52,7 +52,6 @@ process MULTIQC {
     path "*multiqc_report.html", emit: report
     path "*_data"              , emit: data
     path "*_plots"             , optional: true, emit: plots
-    path "versions.yml"        , emit: versions
     // From the nf-core/moduel: MultiQC should not push its versions to the `versions` topic. Its input depends on the versions topic to be resolved thus outputting to the topic will let the pipeline hang forever
     tuple val("${task.process}"), val('multiqc'), eval('multiqc --version | sed "s/.* //g"'), emit: versions
 

From 7c4edfe892d45860456173f3fc2d8357da9d01ce Mon Sep 17 00:00:00 2001
From: Kevin-Brockers <kevin.brockers@yahoo.de>
Date: Thu, 26 Mar 2026 09:12:58 +0100
Subject: [PATCH 13/20] Fixed topic emission

---
 modules/local/gtf2bed/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/local/gtf2bed/main.nf b/modules/local/gtf2bed/main.nf
index 180ba7bf8..1248e978b 100644
--- a/modules/local/gtf2bed/main.nf
+++ b/modules/local/gtf2bed/main.nf
@@ -12,8 +12,8 @@ process GTF2BED {
 
     output:
     path '*.bed'       , emit: bed
-    tuple val({"${task.process}"}), val('perl'), eval("perl --version 2>&1 | sed 's/.*v\\(.*\\)) built.*/\\1/'"), topic:versions, emit: versions_perl
-
+    tuple val({"${task.process}"}), val('perl'), eval("perl -V:version | sed \"s/version='//; s/';//\""), topic:versions, emit: versions_perl
+                                                      
 
     when:
     task.ext.when == null || task.ext.when

From 5eef9a60dda2ac6b9818660af38243ddcab8b47a Mon Sep 17 00:00:00 2001
From: Kevin-Brockers <kevin.brockers@yahoo.de>
Date: Thu, 26 Mar 2026 09:13:59 +0100
Subject: [PATCH 14/20] Removed version channel

---
 main.nf                                                      | 1 -
 .../local/bam_peaks_call_qc_annotate_macs3_homer/main.nf     | 4 ----
 .../main.nf                                                  | 5 -----
 subworkflows/local/input_check/main.nf                       | 1 -
 subworkflows/local/prepare_genome/main.nf                    | 2 --
 workflows/chipseq.nf                                         | 5 -----
 6 files changed, 18 deletions(-)

diff --git a/main.nf b/main.nf
index 64450355f..ad8cd3ffe 100755
--- a/main.nf
+++ b/main.nf
@@ -66,7 +66,6 @@ workflow NFCORE_CHIPSEQ {
         params.chromap_index,
         params.star_index,
     )
-    ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions)
 
     //
     // WORKFLOW: Run nf-core/chipseq workflow
diff --git a/subworkflows/local/bam_peaks_call_qc_annotate_macs3_homer/main.nf b/subworkflows/local/bam_peaks_call_qc_annotate_macs3_homer/main.nf
index ce85b867d..e1d2fa85f 100644
--- a/subworkflows/local/bam_peaks_call_qc_annotate_macs3_homer/main.nf
+++ b/subworkflows/local/bam_peaks_call_qc_annotate_macs3_homer/main.nf
@@ -81,7 +81,6 @@ workflow BAM_PEAKS_CALL_QC_ANNOTATE_MACS3_HOMER {
         ch_peak_count_header_multiqc,
         ch_frip_score_multiqc
     )
-    ch_versions = ch_versions.mix(MULTIQC_CUSTOM_PEAKS.out.versions.first())
 
     ch_homer_annotatepeaks          = channel.empty()
     ch_plot_macs3_qc_txt            = channel.empty()
@@ -99,7 +98,6 @@ workflow BAM_PEAKS_CALL_QC_ANNOTATE_MACS3_HOMER {
             ch_gtf
         )
         ch_homer_annotatepeaks = HOMER_ANNOTATEPEAKS.out.txt
-        ch_versions = ch_versions.mix(HOMER_ANNOTATEPEAKS.out.versions.first())
 
         if (!skip_peak_qc) {
             //
@@ -146,6 +144,4 @@ workflow BAM_PEAKS_CALL_QC_ANNOTATE_MACS3_HOMER {
     plot_homer_annotatepeaks_txt = ch_plot_homer_annotatepeaks_txt  // channel: [ txt ]
     plot_homer_annotatepeaks_pdf = ch_plot_homer_annotatepeaks_pdf  // channel: [ pdf ]
     plot_homer_annotatepeaks_tsv = ch_plot_homer_annotatepeaks_tsv  // channel: [ tsv ]
-
-    versions                     = ch_versions                      // channel: [ versions.yml ]
 }
diff --git a/subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2/main.nf b/subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2/main.nf
index f91b5ae81..e07ceb3be 100644
--- a/subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2/main.nf
+++ b/subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2/main.nf
@@ -68,7 +68,6 @@ workflow BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2 {
             ch_fasta,
             ch_gtf
         )
-        ch_versions = ch_versions.mix(HOMER_ANNOTATEPEAKS.out.versions)
 
         //
         // MODULE: Add boolean fields to annotated consensus peaks to aid filtering
@@ -76,7 +75,6 @@ workflow BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2 {
         ANNOTATE_BOOLEAN_PEAKS (
             MACS3_CONSENSUS.out.boolean_txt.join(HOMER_ANNOTATEPEAKS.out.txt, by: [0]),
         )
-        ch_versions = ch_versions.mix(ANNOTATE_BOOLEAN_PEAKS.out.versions)
     }
 
     // Create channels: [ meta, [ ip_bams ], saf ]
@@ -128,7 +126,6 @@ workflow BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2 {
         ch_deseq2_qc_dists_multiqc = DESEQ2_QC.out.dists_multiqc
         ch_deseq2_qc_log           = DESEQ2_QC.out.log
         ch_deseq2_qc_size_factors  = DESEQ2_QC.out.size_factors
-        ch_versions = ch_versions.mix(DESEQ2_QC.out.versions)
     }
 
     emit:
@@ -151,6 +148,4 @@ workflow BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2 {
     deseq2_qc_dists_multiqc = ch_deseq2_qc_dists_multiqc        // channel: [ txt ]
     deseq2_qc_log           = ch_deseq2_qc_log                  // channel: [ txt ]
     deseq2_qc_size_factors  = ch_deseq2_qc_size_factors         // channel: [ txt ]
-
-    versions                = ch_versions                       // channel: [ versions.yml ]
 }
diff --git a/subworkflows/local/input_check/main.nf b/subworkflows/local/input_check/main.nf
index e5ee66055..7c5b25d58 100644
--- a/subworkflows/local/input_check/main.nf
+++ b/subworkflows/local/input_check/main.nf
@@ -18,7 +18,6 @@ workflow INPUT_CHECK {
 
     emit:
     reads                                     // channel: [ val(meta), [ reads ] ]
-    versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ]
 }
 
 // Function to get list of [ meta, [ fastq_1, fastq_2 ] ]
diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf
index 727769ac3..36bb7e609 100644
--- a/subworkflows/local/prepare_genome/main.nf
+++ b/subworkflows/local/prepare_genome/main.nf
@@ -102,7 +102,6 @@ workflow PREPARE_GENOME {
 
     if (make_bed) {
         ch_gene_bed = GTF2BED(ch_gtf).bed
-        ch_versions = ch_versions.mix(GTF2BED.out.versions)
     } else {
         if (gene_bed.endsWith('.gz')) {
             ch_gene_bed = GUNZIP_GENE_BED([[:], gene_bed]).gunzip.map { it[1] }
@@ -207,5 +206,4 @@ workflow PREPARE_GENOME {
     bowtie2_index = ch_bowtie2_index          //    path: bowtie2/index/
     chromap_index = ch_chromap_index          //    path: genome.index
     star_index    = ch_star_index             //    path: star/index/
-    versions      = ch_versions       //    path: versions.yml
 }
diff --git a/workflows/chipseq.nf b/workflows/chipseq.nf
index d805ad2c9..9d61bdf92 100644
--- a/workflows/chipseq.nf
+++ b/workflows/chipseq.nf
@@ -462,7 +462,6 @@ workflow CHIPSEQ {
         params.skip_peak_annotation,
         params.skip_peak_qc
     )
-    ch_versions = ch_versions.mix(BAM_PEAKS_CALL_QC_ANNOTATE_MACS3_HOMER.out.versions)
 
     //
     //  Consensus peaks analysis
@@ -502,7 +501,6 @@ workflow CHIPSEQ {
         ch_subreadfeaturecounts_multiqc  = BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2.out.featurecounts_summary
         ch_deseq2_pca_multiqc            = BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2.out.deseq2_qc_pca_multiqc
         ch_deseq2_clustering_multiqc     = BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2.out.deseq2_qc_dists_multiqc
-        ch_versions = ch_versions.mix(BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2.out.versions)
     }
 
     //
@@ -518,14 +516,11 @@ workflow CHIPSEQ {
             ch_macs3_consensus_bed_lib.collect{it[1]}.ifEmpty([]),
             ch_macs3_consensus_txt_lib.collect{it[1]}.ifEmpty([])
         )
-        ch_versions = ch_versions.mix(IGV.out.versions)
     }
 
     //
     // Collate and save software versions
     //
-    ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
-    ch_versions = ch_versions.mix(BAM_PEAKS_CALL_QC_ANNOTATE_MACS3_HOMER.out.versions)
 
     ch_collated_versions = softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file))
         .mix(topic_versions_string)

From 0925f309f45f3256d2035cdb9da4a5049f37e866 Mon Sep 17 00:00:00 2001
From: Kevin-Brockers <kevin.brockers@yahoo.de>
Date: Thu, 26 Mar 2026 10:41:32 +0100
Subject: [PATCH 15/20] Updated snapshots

---
 tests/bowtie2.nf.test.snap              | 222 +++++++++++-------------
 tests/chromap.nf.test.snap              | 222 +++++++++++-------------
 tests/default.nf.test.snap              | 218 +++++++++++------------
 tests/skip_consensus_peaks.nf.test.snap | 218 +++++++++++------------
 tests/skip_trimming.nf.test.snap        | 198 ++++++++++-----------
 tests/star.nf.test.snap                 | 222 +++++++++++-------------
 6 files changed, 614 insertions(+), 686 deletions(-)

diff --git a/tests/bowtie2.nf.test.snap b/tests/bowtie2.nf.test.snap
index 051fb49bb..fb78b3a3d 100644
--- a/tests/bowtie2.nf.test.snap
+++ b/tests/bowtie2.nf.test.snap
@@ -37,8 +37,8 @@
                     "deeptools": "3.5.6"
                 },
                 "DESEQ2_QC": {
-                    "bioconductor-deseq2": "1.28.0",
-                    "r-base": "4.0.3"
+                    "DESeq2": "1.28.0",
+                    "R": "4.0.3"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -53,11 +53,8 @@
                 "GTF2BED": {
                     "perl": "5.26.2"
                 },
-                "HOMER_ANNOTATEPEAKS": {
-                    "homer": 4.11
-                },
                 "IGV": {
-                    "python": "3.8.3"
+                    "python": "3.12.12"
                 },
                 "MACS3_CALLPEAK": {
                     "macs3": "3.0.4"
@@ -69,6 +66,9 @@
                 "MULTIQC_CUSTOM_PEAKS": {
                     "sed": 4.7
                 },
+                "MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS": {
+                    "R": "4.5.3"
+                },
                 "PICARD_COLLECTMULTIPLEMETRICS": {
                     "picard": "3.4.0"
                 },
@@ -85,7 +85,7 @@
                     "R": "4.5.3"
                 },
                 "SAMPLESHEET_CHECK": {
-                    "python": "3.8.3"
+                    "python": "3.12.12"
                 },
                 "SAMTOOLS_FAIDX": {
                     "samtools": "1.22.1"
@@ -439,65 +439,65 @@
                 "multiqc/broad_peak/multiqc_data/fastqc_sequence_length_distribution_plot.yaml",
                 "multiqc/broad_peak/multiqc_data/fastqc_top_overrepresented_sequences_table.yaml",
                 "multiqc/broad_peak/multiqc_data/featureCounts_assignment_plot.yaml",
+                "multiqc/broad_peak/multiqc_data/llms-full.txt",
                 "multiqc/broad_peak/multiqc_data/multiqc.log",
+                "multiqc/broad_peak/multiqc_data/multiqc.parquet",
                 "multiqc/broad_peak/multiqc_data/multiqc_citations.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_cutadapt.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_data.json",
                 "multiqc/broad_peak/multiqc_data/multiqc_deseq2_clustering_1.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_deseq2_pca_1.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_fastqc.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_fastqc_1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_fastqc_fastqc-1.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_featurecounts.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_frip_score.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_nsc_coefficient.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_peak_annotation.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_peak_count.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_phantompeakqualtools.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_AlignmentSummaryMetrics.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_insertSize.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_quality_by_cycle.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_quality_score_distribution.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard_baseContent.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_AlignmentSummaryMetrics_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_insertSize_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_quality_by_cycle_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_quality_score_distribution_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard_baseContent_picard-1.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_picard_dups.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_rsc_coefficient.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat_1.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat_2.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat_samtools-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat_samtools-2.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats_1.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats_2.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats_samtools-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats_samtools-2.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats_1.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats_2.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats_samtools-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats_samtools-2.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_software_versions.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_sources.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_strand_shift_correlation.yaml",
+                "multiqc/broad_peak/multiqc_data/picard-1_MarkIlluminaAdapters_histogram_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/picard-1_MeanQualityByCycle_histogram_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/picard-1_MeanQualityByCycle_histogram_picard-1_1.yaml",
+                "multiqc/broad_peak/multiqc_data/picard-1_QualityScoreDistribution_histogram_picard-1.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_alignment_readlength_plot.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_alignment_summary_Aligned_Bases.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_alignment_summary_Aligned_Reads.yaml",
-                "multiqc/broad_peak/multiqc_data/picard-1_histogram.yaml",
-                "multiqc/broad_peak/multiqc_data/picard-1_histogram_1.yaml",
-                "multiqc/broad_peak/multiqc_data/picard-1_histogram_2.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_insert_size_Counts.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_insert_size_Percentages.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_quality_by_cycle.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_quality_score_distribution.yaml",
+                "multiqc/broad_peak/multiqc_data/picard_MarkIlluminaAdapters_histogram.yaml",
+                "multiqc/broad_peak/multiqc_data/picard_MeanQualityByCycle_histogram.yaml",
+                "multiqc/broad_peak/multiqc_data/picard_MeanQualityByCycle_histogram_1.yaml",
+                "multiqc/broad_peak/multiqc_data/picard_QualityScoreDistribution_histogram.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Adenine.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Cytosine.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Guanine.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Thymine.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Undetermined.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_deduplication.yaml",
-                "multiqc/broad_peak/multiqc_data/picard_histogram.yaml",
-                "multiqc/broad_peak/multiqc_data/picard_histogram_1.yaml",
-                "multiqc/broad_peak/multiqc_data/picard_histogram_2.yaml",
                 "multiqc/broad_peak/multiqc_data/read_distribution_profile.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Percentage_of_total-1.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Percentage_of_total-2.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Percentage_of_total.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Read_counts-1.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Read_counts-2.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Read_counts.yaml",
+                "multiqc/broad_peak/multiqc_data/samtools-flagstat-pct-table.yaml",
+                "multiqc/broad_peak/multiqc_data/samtools-flagstat-table.yaml",
                 "multiqc/broad_peak/multiqc_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1.yaml",
                 "multiqc/broad_peak/multiqc_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts-2.yaml",
                 "multiqc/broad_peak/multiqc_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.yaml",
@@ -570,12 +570,8 @@
                 "multiqc/broad_peak/multiqc_plots/pdf/read_distribution_profile.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/rsc_coefficient-cnt.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/rsc_coefficient-pct.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Percentage_of_total-1.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Percentage_of_total-2.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Read_counts-1.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Read_counts-2.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Read_counts.pdf",
+                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-pct-table.pdf",
+                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-table.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-log.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-2-cnt.pdf",
@@ -658,12 +654,8 @@
                 "multiqc/broad_peak/multiqc_plots/png/read_distribution_profile.png",
                 "multiqc/broad_peak/multiqc_plots/png/rsc_coefficient-cnt.png",
                 "multiqc/broad_peak/multiqc_plots/png/rsc_coefficient-pct.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Percentage_of_total-1.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Percentage_of_total-2.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Percentage_of_total.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Read_counts-1.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Read_counts-2.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Read_counts.png",
+                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-pct-table.png",
+                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-table.png",
                 "multiqc/broad_peak/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.png",
                 "multiqc/broad_peak/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-log.png",
                 "multiqc/broad_peak/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-2-cnt.png",
@@ -746,12 +738,8 @@
                 "multiqc/broad_peak/multiqc_plots/svg/read_distribution_profile.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/rsc_coefficient-cnt.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/rsc_coefficient-pct.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Percentage_of_total-1.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Percentage_of_total-2.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Read_counts-1.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Read_counts-2.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Read_counts.svg",
+                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-pct-table.svg",
+                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-table.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-log.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-2-cnt.svg",
@@ -872,108 +860,108 @@
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "cutadapt_filtered_reads_plot.yaml:md5,976fdb8049d847c977195863418e3655",
-                "cutadapt_trimmed_sequences_plot_3_Counts.yaml:md5,e6733f4ff773a27d0ab81564913b4b54",
-                "cutadapt_trimmed_sequences_plot_3_Obs_Exp.yaml:md5,9ffcfe37c02af14b8eddd4746066e56a",
+                "cutadapt_trimmed_sequences_plot_3_Counts.yaml:md5,1dba61b1d90518e1f020b71c4cfa04c4",
+                "cutadapt_trimmed_sequences_plot_3_Obs_Exp.yaml:md5,42335c2990d3a991e2bd0716f80b0515",
                 "fastqc-1-status-check-heatmap.yaml:md5,6c6e1591b5ff248c85446f9728a3dad4",
-                "fastqc-1_adapter_content_plot.yaml:md5,d78273a7e4ff36434bb91246fef01523",
-                "fastqc-1_per_base_n_content_plot.yaml:md5,3625446964b669ccff279aba54510462",
-                "fastqc-1_per_base_sequence_quality_plot.yaml:md5,1fb4d35d6b94fc4f41d5be1304844b95",
-                "fastqc-1_per_sequence_gc_content_plot_Counts.yaml:md5,101f11f9cebcc626755f32322b27ebd3",
-                "fastqc-1_per_sequence_gc_content_plot_Percentages.yaml:md5,0055f4bbded45434618259f47fe5fe85",
-                "fastqc-1_per_sequence_quality_scores_plot.yaml:md5,eed2628303916e49143ccf37300fb5de",
+                "fastqc-1_adapter_content_plot.yaml:md5,8acbcb9c6f3b5e42b19a7ab4bd1d607b",
+                "fastqc-1_per_base_n_content_plot.yaml:md5,24c7a2b7d290d797e7757adfd7b67175",
+                "fastqc-1_per_base_sequence_quality_plot.yaml:md5,ddaf5d8d0dad842c9e00a9cdde2a82c7",
+                "fastqc-1_per_sequence_gc_content_plot_Counts.yaml:md5,191d3d72a05700fa5b69854ff47b6e66",
+                "fastqc-1_per_sequence_gc_content_plot_Percentages.yaml:md5,f9cc6e0466e1791e9b3bd765ab3b9a57",
+                "fastqc-1_per_sequence_quality_scores_plot.yaml:md5,6bfed2114551676b4c60e897f12c6e12",
                 "fastqc-1_sequence_counts_plot.yaml:md5,6ca3a8cf8d258777e29b8e8731157d90",
-                "fastqc-1_sequence_duplication_levels_plot.yaml:md5,3e3622b7dd80be1db92ac06df8e3d056",
+                "fastqc-1_sequence_duplication_levels_plot.yaml:md5,fa8e5813c72d6366bf50d99c0eb20f56",
                 "fastqc-1_top_overrepresented_sequences_table.yaml:md5,a333a02f5313876cf1713d7b0168d5f3",
                 "fastqc-status-check-heatmap.yaml:md5,1e473e0f9140b718607d8c72cf3c0b45",
-                "fastqc_adapter_content_plot.yaml:md5,591991daf3e3c49873f4a51a3710b072",
-                "fastqc_per_base_n_content_plot.yaml:md5,c16a4af177b9ad9694a9535023906927",
-                "fastqc_per_base_sequence_quality_plot.yaml:md5,20fc07ce2bc8e369d5fdd18afc6e60e9",
-                "fastqc_per_sequence_gc_content_plot_Counts.yaml:md5,ab233171fb8fd4e717886b01868ebcf2",
-                "fastqc_per_sequence_gc_content_plot_Percentages.yaml:md5,db29d683777cc0742585d1c48e712bd3",
-                "fastqc_per_sequence_quality_scores_plot.yaml:md5,351b55974af5ee21294ebf5deb850d7c",
+                "fastqc_adapter_content_plot.yaml:md5,de00547c4d9e5920e0e5c5b1f47981f7",
+                "fastqc_per_base_n_content_plot.yaml:md5,a2ac6f6a3323630922fb494def39b5c1",
+                "fastqc_per_base_sequence_quality_plot.yaml:md5,b0a022b4a3db86cc799142779155f9ed",
+                "fastqc_per_sequence_gc_content_plot_Counts.yaml:md5,679a374990a8c3b7a87fc55afca4c5f8",
+                "fastqc_per_sequence_gc_content_plot_Percentages.yaml:md5,c7a1700b9f6987c5dea327799902204a",
+                "fastqc_per_sequence_quality_scores_plot.yaml:md5,d4a8f8ced23faa497edb023ac00d9632",
                 "fastqc_sequence_counts_plot.yaml:md5,5522b2b42f0b3753dd359aad1565d7c2",
-                "fastqc_sequence_duplication_levels_plot.yaml:md5,e883323380f2880c81ea36dc91ad8678",
-                "fastqc_sequence_length_distribution_plot.yaml:md5,d57678f16381986766d56b631c838106",
+                "fastqc_sequence_duplication_levels_plot.yaml:md5,e5532eac263c0b33ed3c024eca5fce94",
+                "fastqc_sequence_length_distribution_plot.yaml:md5,e701cb601de4693ab09473b849e4f110",
                 "fastqc_top_overrepresented_sequences_table.yaml:md5,443e161371f73cebf63c14f7a9f3580d",
                 "featureCounts_assignment_plot.yaml:md5,4da17bf822e2c2645d81610248f44db3",
+                "llms-full.txt:md5,77b52a1c7589b6f8af5e46de2fd0f1cc",
+                "multiqc.parquet:md5,99b4b02535b8a795ba8078ffd049b8a3",
                 "multiqc_citations.yaml:md5,fca5dc7cb20162434c714d26b11161f3",
                 "multiqc_fastqc.yaml:md5,30fe6d1a5e5c04695dda81294b828ec9",
-                "multiqc_fastqc_1.yaml:md5,cd4a85c27c3cf85f1d0612afce793186",
+                "multiqc_fastqc_fastqc-1.yaml:md5,cd4a85c27c3cf85f1d0612afce793186",
                 "multiqc_featurecounts.yaml:md5,344706a7a1f373f2710ef124f59284e5",
                 "multiqc_frip_score.yaml:md5,5ba89c150b7a147baa0ab0dcfce1f05d",
                 "multiqc_nsc_coefficient.yaml:md5,67e001b4585b8a393d0249b2e3afb4ae",
-                "multiqc_peak_annotation.yaml:md5,eed4fb1ce72c9dfcf28b33143a5f63c5",
-                "multiqc_peak_count.yaml:md5,b595892dcd65c4f233597c17b0d982f1",
+                "multiqc_peak_annotation.yaml:md5,78df87b99cb55116a35f13c5f7c1b681",
+                "multiqc_peak_count.yaml:md5,376125e8c6397578228b72646742beea",
                 "multiqc_phantompeakqualtools.yaml:md5,077cc1853cfcefb23550b48a9df5e986",
-                "multiqc_picard-1_AlignmentSummaryMetrics.yaml:md5,910c34a3121a7d4487bcf3cb55207384",
-                "multiqc_picard-1_insertSize.yaml:md5,16201c88fece186148c98254636fa9e6",
-                "multiqc_picard-1_quality_by_cycle.yaml:md5,526872757159b0bd6af9a5039177797a",
-                "multiqc_picard-1_quality_score_distribution.yaml:md5,79c9e54f68b9416e3126b06c1d105566",
-                "multiqc_picard_baseContent.yaml:md5,a0c1880f0f3c0e63e85787d76b74a429",
+                "multiqc_picard-1_AlignmentSummaryMetrics_picard-1.yaml:md5,910c34a3121a7d4487bcf3cb55207384",
+                "multiqc_picard-1_insertSize_picard-1.yaml:md5,16201c88fece186148c98254636fa9e6",
+                "multiqc_picard-1_quality_by_cycle_picard-1.yaml:md5,526872757159b0bd6af9a5039177797a",
+                "multiqc_picard-1_quality_score_distribution_picard-1.yaml:md5,79c9e54f68b9416e3126b06c1d105566",
+                "multiqc_picard_baseContent_picard-1.yaml:md5,a0c1880f0f3c0e63e85787d76b74a429",
                 "multiqc_picard_dups.yaml:md5,721d70bf8b989783143645ccb8d08455",
                 "multiqc_rsc_coefficient.yaml:md5,e8970cea6ccc4d0af17b5db285263280",
                 "multiqc_samtools_flagstat.yaml:md5,601b23aea7001ea7f5e0be6b6365e772",
-                "multiqc_samtools_flagstat_1.yaml:md5,15b7e81b7518c1864a6c505ccb32f2df",
-                "multiqc_samtools_flagstat_2.yaml:md5,e4304235970c0dfe9aeb2941a8a342ce",
+                "multiqc_samtools_flagstat_samtools-1.yaml:md5,15b7e81b7518c1864a6c505ccb32f2df",
+                "multiqc_samtools_flagstat_samtools-2.yaml:md5,e4304235970c0dfe9aeb2941a8a342ce",
                 "multiqc_samtools_idxstats.yaml:md5,9e6ecc522c159c111d41aabb9c798d0f",
-                "multiqc_samtools_idxstats_1.yaml:md5,2ff19f2ed79bae9facb5710773080004",
-                "multiqc_samtools_idxstats_2.yaml:md5,99aa2c5e1db7c750377f4495fa81f693",
-                "multiqc_samtools_stats.yaml:md5,fc38617b8f0b70f57bbc591fd77ee77c",
-                "multiqc_samtools_stats_1.yaml:md5,3f040ce9f37db47eb2e7193d52b05182",
-                "multiqc_samtools_stats_2.yaml:md5,15b13d9b289a574d79f79c24e4372721",
+                "multiqc_samtools_idxstats_samtools-1.yaml:md5,2ff19f2ed79bae9facb5710773080004",
+                "multiqc_samtools_idxstats_samtools-2.yaml:md5,99aa2c5e1db7c750377f4495fa81f693",
+                "multiqc_samtools_stats.yaml:md5,1e9f2bc66560aca36f392abdebc0b0e3",
+                "multiqc_samtools_stats_samtools-1.yaml:md5,5a6304bfc116c8b019bbe430a7dbfdf6",
+                "multiqc_samtools_stats_samtools-2.yaml:md5,9a4367fabfb6e76c55b1c0223654d537",
+                "picard-1_MarkIlluminaAdapters_histogram_picard-1.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard-1_MeanQualityByCycle_histogram_picard-1.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard-1_MeanQualityByCycle_histogram_picard-1_1.yaml:md5,526872757159b0bd6af9a5039177797a",
+                "picard-1_QualityScoreDistribution_histogram_picard-1.yaml:md5,79c9e54f68b9416e3126b06c1d105566",
                 "picard-1_alignment_readlength_plot.yaml:md5,c99d90a720884dfa66f477f7a13e681f",
                 "picard-1_alignment_summary_Aligned_Bases.yaml:md5,b14ee00e59f209cad52b1a07685c38d2",
                 "picard-1_alignment_summary_Aligned_Reads.yaml:md5,7d6c5677c692de58a6491c01367762be",
-                "picard-1_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
-                "picard-1_histogram_1.yaml:md5,526872757159b0bd6af9a5039177797a",
-                "picard-1_histogram_2.yaml:md5,79c9e54f68b9416e3126b06c1d105566",
-                "picard-1_insert_size_Counts.yaml:md5,f614c442b35ff8c27db4a1e6d0ab03ce",
-                "picard-1_insert_size_Percentages.yaml:md5,7db9e226a7a209c028565b264860fa0f",
-                "picard-1_quality_by_cycle.yaml:md5,cedb46311f7cc819c462a64b91e167f3",
-                "picard-1_quality_score_distribution.yaml:md5,4bf77c1d1b3e285c7890944354e9bcbd",
-                "picard_base_distribution_by_cycle__Adenine.yaml:md5,da07ea85f68ef4d99772b3e7216ec242",
-                "picard_base_distribution_by_cycle__Cytosine.yaml:md5,e2623d2c67a0f8abcc68f4b530031fc4",
-                "picard_base_distribution_by_cycle__Guanine.yaml:md5,a4629a62eba1d79deaf064195c5e5320",
-                "picard_base_distribution_by_cycle__Thymine.yaml:md5,1b58b1984ee58765915647627c3bfef2",
-                "picard_base_distribution_by_cycle__Undetermined.yaml:md5,01c9667b3d66ee80de71daf62b9c4a07",
+                "picard-1_insert_size_Counts.yaml:md5,2cee6b7abaf92e4670602022a5bf59d4",
+                "picard-1_insert_size_Percentages.yaml:md5,3f0d1d4b0bbfcdf4a80c1e6e1053dd7f",
+                "picard-1_quality_by_cycle.yaml:md5,00a4f81a30d81b9a40e685bbe2afbc8d",
+                "picard-1_quality_score_distribution.yaml:md5,60537e416243d36e080737bcc41b9983",
+                "picard_MarkIlluminaAdapters_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard_MeanQualityByCycle_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard_MeanQualityByCycle_histogram_1.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard_QualityScoreDistribution_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard_base_distribution_by_cycle__Adenine.yaml:md5,186d2c901e4d8c9c123160a746b70fdc",
+                "picard_base_distribution_by_cycle__Cytosine.yaml:md5,1654fe8abc0f6386b6ca89241c14a3a8",
+                "picard_base_distribution_by_cycle__Guanine.yaml:md5,25e8cf56ad7ec3167cc720ebdc3e4374",
+                "picard_base_distribution_by_cycle__Thymine.yaml:md5,8c75b21b4b54a6ee02f87724fbccda1c",
+                "picard_base_distribution_by_cycle__Undetermined.yaml:md5,071c74b4002e06e425d39052234cc859",
                 "picard_deduplication.yaml:md5,e02f8703f07c37f064568607d6321d24",
-                "picard_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
-                "picard_histogram_1.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
-                "picard_histogram_2.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
-                "samtools-flagstat-dp_Percentage_of_total-1.yaml:md5,7342b056780ccdac6db6df3a51f841aa",
-                "samtools-flagstat-dp_Percentage_of_total-2.yaml:md5,23d1562aa31479dd63736d6d4a46a4e6",
-                "samtools-flagstat-dp_Percentage_of_total.yaml:md5,d3cbbb549ccb8fb6038e872503396201",
-                "samtools-flagstat-dp_Read_counts-1.yaml:md5,7342afa5e7fee42d744baddfb29e9567",
-                "samtools-flagstat-dp_Read_counts-2.yaml:md5,024332a773c5f7ff529924014506e6a3",
-                "samtools-flagstat-dp_Read_counts.yaml:md5,e6b08e90403de66c56cfbafa2c4b778b",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-1.yaml:md5,5297ed41b97a41f257408f5229c7de63",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-2.yaml:md5,49a782c2b00fe0f09123614f99a9318d",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts.yaml:md5,1b262636bad8ed71e4ad1723e7f62867",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-1.yaml:md5,f7a719fcf29a52132bfa1a0559fbd712",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-2.yaml:md5,bf95aa0b14e75e843939cb10bfb5ebf7",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.yaml:md5,abc8f48da8bb3ed6ebd335f81bc52c4c",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts-1.yaml:md5,42353887cd98928c9a63099039260ab4",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts-2.yaml:md5,bc7e8f4b1f7cf4049e017ead3b36c6b8",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts.yaml:md5,c813c38035d8ecf0d15240893b7010f2",
+                "samtools-flagstat-pct-table.yaml:md5,23d1562aa31479dd63736d6d4a46a4e6",
+                "samtools-flagstat-table.yaml:md5,024332a773c5f7ff529924014506e6a3",
+                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-1.yaml:md5,b8f7652263656270f29bfbd384172bf4",
+                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-2.yaml:md5,6cabdb677d5fcf1614d20f65bb01b288",
+                "samtools-idxstats-mapped-reads-plot_Normalised_Counts.yaml:md5,c79b82e8dded6baebab4e1ed2609ee86",
+                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-1.yaml:md5,531c0e05ac422786a09ae7ce326cc961",
+                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-2.yaml:md5,ffaecbc2700366a6e041aed9b788a33a",
+                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.yaml:md5,c0027222ed89bbfb0773535fcf03f700",
+                "samtools-idxstats-mapped-reads-plot_Raw_Counts-1.yaml:md5,70e40bb677ff77f69d20e983466c4843",
+                "samtools-idxstats-mapped-reads-plot_Raw_Counts-2.yaml:md5,314284fdd2ac5ecb48677457e44e30a4",
+                "samtools-idxstats-mapped-reads-plot_Raw_Counts.yaml:md5,8778e6124881596800ecb0fabed676af",
                 "samtools-stats-dp.yaml:md5,37d2f4096a9e99c8680aa09dd2ec8f10",
                 "samtools_alignment_plot.yaml:md5,8f259411704feadcfda2158cebd64830",
                 "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384"
             ]
         ],
+        "timestamp": "2026-03-26T09:26:04.859632",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2026-03-20T22:36:57.512559418"
+            "nf-test": "0.9.4",
+            "nextflow": "25.04.0"
+        }
     },
     "bowtie2 with stub": {
         "content": [
             20
         ],
+        "timestamp": "2026-03-14T15:14:30.739354966",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
-        },
-        "timestamp": "2026-03-14T15:14:30.739354966"
+        }
     }
 }
\ No newline at end of file
diff --git a/tests/chromap.nf.test.snap b/tests/chromap.nf.test.snap
index 52444b86f..bc07778ed 100644
--- a/tests/chromap.nf.test.snap
+++ b/tests/chromap.nf.test.snap
@@ -29,8 +29,8 @@
                     "deeptools": "3.5.6"
                 },
                 "DESEQ2_QC": {
-                    "bioconductor-deseq2": "1.28.0",
-                    "r-base": "4.0.3"
+                    "DESeq2": "1.28.0",
+                    "R": "4.0.3"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -45,11 +45,8 @@
                 "GTF2BED": {
                     "perl": "5.26.2"
                 },
-                "HOMER_ANNOTATEPEAKS": {
-                    "homer": 4.11
-                },
                 "IGV": {
-                    "python": "3.8.3"
+                    "python": "3.12.12"
                 },
                 "MACS3_CALLPEAK": {
                     "macs3": "3.0.4"
@@ -61,6 +58,9 @@
                 "MULTIQC_CUSTOM_PEAKS": {
                     "sed": 4.7
                 },
+                "MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS": {
+                    "R": "4.5.3"
+                },
                 "PICARD_COLLECTMULTIPLEMETRICS": {
                     "picard": "3.4.0"
                 },
@@ -77,7 +77,7 @@
                     "R": "4.5.3"
                 },
                 "SAMPLESHEET_CHECK": {
-                    "python": "3.8.3"
+                    "python": "3.12.12"
                 },
                 "SAMTOOLS_FAIDX": {
                     "samtools": "1.22.1"
@@ -434,65 +434,65 @@
                 "multiqc/broad_peak/multiqc_data/fastqc_sequence_length_distribution_plot.yaml",
                 "multiqc/broad_peak/multiqc_data/fastqc_top_overrepresented_sequences_table.yaml",
                 "multiqc/broad_peak/multiqc_data/featureCounts_assignment_plot.yaml",
+                "multiqc/broad_peak/multiqc_data/llms-full.txt",
                 "multiqc/broad_peak/multiqc_data/multiqc.log",
+                "multiqc/broad_peak/multiqc_data/multiqc.parquet",
                 "multiqc/broad_peak/multiqc_data/multiqc_citations.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_cutadapt.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_data.json",
                 "multiqc/broad_peak/multiqc_data/multiqc_deseq2_clustering_1.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_deseq2_pca_1.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_fastqc.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_fastqc_1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_fastqc_fastqc-1.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_featurecounts.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_frip_score.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_nsc_coefficient.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_peak_annotation.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_peak_count.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_phantompeakqualtools.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_AlignmentSummaryMetrics.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_insertSize.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_quality_by_cycle.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_quality_score_distribution.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard_baseContent.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_AlignmentSummaryMetrics_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_insertSize_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_quality_by_cycle_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_quality_score_distribution_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard_baseContent_picard-1.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_picard_dups.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_rsc_coefficient.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat_1.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat_2.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat_samtools-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat_samtools-2.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats_1.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats_2.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats_samtools-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats_samtools-2.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats_1.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats_2.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats_samtools-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats_samtools-2.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_software_versions.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_sources.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_strand_shift_correlation.yaml",
+                "multiqc/broad_peak/multiqc_data/picard-1_MarkIlluminaAdapters_histogram_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/picard-1_MeanQualityByCycle_histogram_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/picard-1_MeanQualityByCycle_histogram_picard-1_1.yaml",
+                "multiqc/broad_peak/multiqc_data/picard-1_QualityScoreDistribution_histogram_picard-1.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_alignment_readlength_plot.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_alignment_summary_Aligned_Bases.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_alignment_summary_Aligned_Reads.yaml",
-                "multiqc/broad_peak/multiqc_data/picard-1_histogram.yaml",
-                "multiqc/broad_peak/multiqc_data/picard-1_histogram_1.yaml",
-                "multiqc/broad_peak/multiqc_data/picard-1_histogram_2.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_insert_size_Counts.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_insert_size_Percentages.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_quality_by_cycle.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_quality_score_distribution.yaml",
+                "multiqc/broad_peak/multiqc_data/picard_MarkIlluminaAdapters_histogram.yaml",
+                "multiqc/broad_peak/multiqc_data/picard_MeanQualityByCycle_histogram.yaml",
+                "multiqc/broad_peak/multiqc_data/picard_MeanQualityByCycle_histogram_1.yaml",
+                "multiqc/broad_peak/multiqc_data/picard_QualityScoreDistribution_histogram.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Adenine.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Cytosine.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Guanine.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Thymine.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Undetermined.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_deduplication.yaml",
-                "multiqc/broad_peak/multiqc_data/picard_histogram.yaml",
-                "multiqc/broad_peak/multiqc_data/picard_histogram_1.yaml",
-                "multiqc/broad_peak/multiqc_data/picard_histogram_2.yaml",
                 "multiqc/broad_peak/multiqc_data/read_distribution_profile.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Percentage_of_total-1.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Percentage_of_total-2.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Percentage_of_total.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Read_counts-1.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Read_counts-2.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Read_counts.yaml",
+                "multiqc/broad_peak/multiqc_data/samtools-flagstat-pct-table.yaml",
+                "multiqc/broad_peak/multiqc_data/samtools-flagstat-table.yaml",
                 "multiqc/broad_peak/multiqc_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1.yaml",
                 "multiqc/broad_peak/multiqc_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts-2.yaml",
                 "multiqc/broad_peak/multiqc_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.yaml",
@@ -565,12 +565,8 @@
                 "multiqc/broad_peak/multiqc_plots/pdf/read_distribution_profile.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/rsc_coefficient-cnt.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/rsc_coefficient-pct.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Percentage_of_total-1.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Percentage_of_total-2.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Read_counts-1.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Read_counts-2.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Read_counts.pdf",
+                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-pct-table.pdf",
+                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-table.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-log.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-2-cnt.pdf",
@@ -653,12 +649,8 @@
                 "multiqc/broad_peak/multiqc_plots/png/read_distribution_profile.png",
                 "multiqc/broad_peak/multiqc_plots/png/rsc_coefficient-cnt.png",
                 "multiqc/broad_peak/multiqc_plots/png/rsc_coefficient-pct.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Percentage_of_total-1.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Percentage_of_total-2.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Percentage_of_total.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Read_counts-1.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Read_counts-2.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Read_counts.png",
+                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-pct-table.png",
+                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-table.png",
                 "multiqc/broad_peak/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.png",
                 "multiqc/broad_peak/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-log.png",
                 "multiqc/broad_peak/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-2-cnt.png",
@@ -741,12 +733,8 @@
                 "multiqc/broad_peak/multiqc_plots/svg/read_distribution_profile.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/rsc_coefficient-cnt.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/rsc_coefficient-pct.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Percentage_of_total-1.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Percentage_of_total-2.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Read_counts-1.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Read_counts-2.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Read_counts.svg",
+                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-pct-table.svg",
+                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-table.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-log.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-2-cnt.svg",
@@ -868,108 +856,108 @@
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "genome.index:md5,377432ea6242989cae4dabb60859f6bd",
                 "cutadapt_filtered_reads_plot.yaml:md5,976fdb8049d847c977195863418e3655",
-                "cutadapt_trimmed_sequences_plot_3_Counts.yaml:md5,e6733f4ff773a27d0ab81564913b4b54",
-                "cutadapt_trimmed_sequences_plot_3_Obs_Exp.yaml:md5,9ffcfe37c02af14b8eddd4746066e56a",
+                "cutadapt_trimmed_sequences_plot_3_Counts.yaml:md5,1dba61b1d90518e1f020b71c4cfa04c4",
+                "cutadapt_trimmed_sequences_plot_3_Obs_Exp.yaml:md5,42335c2990d3a991e2bd0716f80b0515",
                 "fastqc-1-status-check-heatmap.yaml:md5,6c6e1591b5ff248c85446f9728a3dad4",
-                "fastqc-1_adapter_content_plot.yaml:md5,d78273a7e4ff36434bb91246fef01523",
-                "fastqc-1_per_base_n_content_plot.yaml:md5,3625446964b669ccff279aba54510462",
-                "fastqc-1_per_base_sequence_quality_plot.yaml:md5,1fb4d35d6b94fc4f41d5be1304844b95",
-                "fastqc-1_per_sequence_gc_content_plot_Counts.yaml:md5,101f11f9cebcc626755f32322b27ebd3",
-                "fastqc-1_per_sequence_gc_content_plot_Percentages.yaml:md5,0055f4bbded45434618259f47fe5fe85",
-                "fastqc-1_per_sequence_quality_scores_plot.yaml:md5,eed2628303916e49143ccf37300fb5de",
+                "fastqc-1_adapter_content_plot.yaml:md5,8acbcb9c6f3b5e42b19a7ab4bd1d607b",
+                "fastqc-1_per_base_n_content_plot.yaml:md5,24c7a2b7d290d797e7757adfd7b67175",
+                "fastqc-1_per_base_sequence_quality_plot.yaml:md5,ddaf5d8d0dad842c9e00a9cdde2a82c7",
+                "fastqc-1_per_sequence_gc_content_plot_Counts.yaml:md5,191d3d72a05700fa5b69854ff47b6e66",
+                "fastqc-1_per_sequence_gc_content_plot_Percentages.yaml:md5,f9cc6e0466e1791e9b3bd765ab3b9a57",
+                "fastqc-1_per_sequence_quality_scores_plot.yaml:md5,6bfed2114551676b4c60e897f12c6e12",
                 "fastqc-1_sequence_counts_plot.yaml:md5,6ca3a8cf8d258777e29b8e8731157d90",
-                "fastqc-1_sequence_duplication_levels_plot.yaml:md5,3e3622b7dd80be1db92ac06df8e3d056",
+                "fastqc-1_sequence_duplication_levels_plot.yaml:md5,fa8e5813c72d6366bf50d99c0eb20f56",
                 "fastqc-1_top_overrepresented_sequences_table.yaml:md5,a333a02f5313876cf1713d7b0168d5f3",
                 "fastqc-status-check-heatmap.yaml:md5,1e473e0f9140b718607d8c72cf3c0b45",
-                "fastqc_adapter_content_plot.yaml:md5,591991daf3e3c49873f4a51a3710b072",
-                "fastqc_per_base_n_content_plot.yaml:md5,c16a4af177b9ad9694a9535023906927",
-                "fastqc_per_base_sequence_quality_plot.yaml:md5,20fc07ce2bc8e369d5fdd18afc6e60e9",
-                "fastqc_per_sequence_gc_content_plot_Counts.yaml:md5,ab233171fb8fd4e717886b01868ebcf2",
-                "fastqc_per_sequence_gc_content_plot_Percentages.yaml:md5,db29d683777cc0742585d1c48e712bd3",
-                "fastqc_per_sequence_quality_scores_plot.yaml:md5,351b55974af5ee21294ebf5deb850d7c",
+                "fastqc_adapter_content_plot.yaml:md5,de00547c4d9e5920e0e5c5b1f47981f7",
+                "fastqc_per_base_n_content_plot.yaml:md5,a2ac6f6a3323630922fb494def39b5c1",
+                "fastqc_per_base_sequence_quality_plot.yaml:md5,b0a022b4a3db86cc799142779155f9ed",
+                "fastqc_per_sequence_gc_content_plot_Counts.yaml:md5,679a374990a8c3b7a87fc55afca4c5f8",
+                "fastqc_per_sequence_gc_content_plot_Percentages.yaml:md5,c7a1700b9f6987c5dea327799902204a",
+                "fastqc_per_sequence_quality_scores_plot.yaml:md5,d4a8f8ced23faa497edb023ac00d9632",
                 "fastqc_sequence_counts_plot.yaml:md5,5522b2b42f0b3753dd359aad1565d7c2",
-                "fastqc_sequence_duplication_levels_plot.yaml:md5,e883323380f2880c81ea36dc91ad8678",
-                "fastqc_sequence_length_distribution_plot.yaml:md5,d57678f16381986766d56b631c838106",
+                "fastqc_sequence_duplication_levels_plot.yaml:md5,e5532eac263c0b33ed3c024eca5fce94",
+                "fastqc_sequence_length_distribution_plot.yaml:md5,e701cb601de4693ab09473b849e4f110",
                 "fastqc_top_overrepresented_sequences_table.yaml:md5,443e161371f73cebf63c14f7a9f3580d",
                 "featureCounts_assignment_plot.yaml:md5,7ba9bc1659472a0859c527d0f8f10c8b",
+                "llms-full.txt:md5,a8e704a8a5f8f600f54cc4db24703e25",
+                "multiqc.parquet:md5,1021d6967e6855322d0c3915564cc061",
                 "multiqc_citations.yaml:md5,fca5dc7cb20162434c714d26b11161f3",
                 "multiqc_fastqc.yaml:md5,30fe6d1a5e5c04695dda81294b828ec9",
-                "multiqc_fastqc_1.yaml:md5,cd4a85c27c3cf85f1d0612afce793186",
+                "multiqc_fastqc_fastqc-1.yaml:md5,cd4a85c27c3cf85f1d0612afce793186",
                 "multiqc_featurecounts.yaml:md5,e8d7d07826b918b9de226607c83ebeab",
                 "multiqc_frip_score.yaml:md5,bb0959532068d1639a75c7d9c49d492b",
                 "multiqc_nsc_coefficient.yaml:md5,a19610ff8ca0d60834a3408e76f15c92",
-                "multiqc_peak_annotation.yaml:md5,9e16a9d6e5bcbf2e5bceee0ef7eec600",
-                "multiqc_peak_count.yaml:md5,395d6208b4e19a68666f9d22a770cfce",
+                "multiqc_peak_annotation.yaml:md5,e1125690706108b09f6faadd439d1bda",
+                "multiqc_peak_count.yaml:md5,1b843998281cbb51afac96ba2cfea8ea",
                 "multiqc_phantompeakqualtools.yaml:md5,a28abb9241ec87e4a0d077f29acf6669",
-                "multiqc_picard-1_AlignmentSummaryMetrics.yaml:md5,73dfc8dfa07e06633c66e12715ab2b18",
-                "multiqc_picard-1_insertSize.yaml:md5,3364ad42f23a53723388df3f0b13a25d",
-                "multiqc_picard-1_quality_by_cycle.yaml:md5,c3036e5c3626ca012a7345b3b578ad8f",
-                "multiqc_picard-1_quality_score_distribution.yaml:md5,37ef6ec1ee50f6816b703f3f7d4040c9",
-                "multiqc_picard_baseContent.yaml:md5,39b10e42d8b300d3b6dc2bb8d453c8e8",
+                "multiqc_picard-1_AlignmentSummaryMetrics_picard-1.yaml:md5,73dfc8dfa07e06633c66e12715ab2b18",
+                "multiqc_picard-1_insertSize_picard-1.yaml:md5,3364ad42f23a53723388df3f0b13a25d",
+                "multiqc_picard-1_quality_by_cycle_picard-1.yaml:md5,c3036e5c3626ca012a7345b3b578ad8f",
+                "multiqc_picard-1_quality_score_distribution_picard-1.yaml:md5,37ef6ec1ee50f6816b703f3f7d4040c9",
+                "multiqc_picard_baseContent_picard-1.yaml:md5,39b10e42d8b300d3b6dc2bb8d453c8e8",
                 "multiqc_picard_dups.yaml:md5,15a0c399e9eb03f96b6986897d28ee46",
                 "multiqc_rsc_coefficient.yaml:md5,4cdfd1cf61b780606ff79b3b7702e2d3",
                 "multiqc_samtools_flagstat.yaml:md5,b0602157e3b133c8c6a5ea0da373f95e",
-                "multiqc_samtools_flagstat_1.yaml:md5,3d34f85288be603b026182b3153d73b0",
-                "multiqc_samtools_flagstat_2.yaml:md5,e1ff04aa8821cea5669edc9e158c61f0",
+                "multiqc_samtools_flagstat_samtools-1.yaml:md5,3d34f85288be603b026182b3153d73b0",
+                "multiqc_samtools_flagstat_samtools-2.yaml:md5,e1ff04aa8821cea5669edc9e158c61f0",
                 "multiqc_samtools_idxstats.yaml:md5,ea5462b130dba17cc734b06fdffea98f",
-                "multiqc_samtools_idxstats_1.yaml:md5,ca00f0c2ad430266007ad46b39950976",
-                "multiqc_samtools_idxstats_2.yaml:md5,431ef2b34a7c7c9d6123b3ac5f49a9eb",
-                "multiqc_samtools_stats.yaml:md5,79c81250f7c13657d3a5410bfb2836cb",
-                "multiqc_samtools_stats_1.yaml:md5,5c197924c6282f82c5d7e154ea6c5dc7",
-                "multiqc_samtools_stats_2.yaml:md5,a08674e1272632fe61880e4aa6b8654c",
+                "multiqc_samtools_idxstats_samtools-1.yaml:md5,ca00f0c2ad430266007ad46b39950976",
+                "multiqc_samtools_idxstats_samtools-2.yaml:md5,431ef2b34a7c7c9d6123b3ac5f49a9eb",
+                "multiqc_samtools_stats.yaml:md5,a7808cb87393256d4b1f20d8ffa6d5ef",
+                "multiqc_samtools_stats_samtools-1.yaml:md5,aaa97e9703d0da10544c3c3f44facff4",
+                "multiqc_samtools_stats_samtools-2.yaml:md5,84c66e46d40774e0ef59aba7e4d25a2b",
+                "picard-1_MarkIlluminaAdapters_histogram_picard-1.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard-1_MeanQualityByCycle_histogram_picard-1.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard-1_MeanQualityByCycle_histogram_picard-1_1.yaml:md5,c3036e5c3626ca012a7345b3b578ad8f",
+                "picard-1_QualityScoreDistribution_histogram_picard-1.yaml:md5,37ef6ec1ee50f6816b703f3f7d4040c9",
                 "picard-1_alignment_readlength_plot.yaml:md5,654f00b7a14220482e4eab35dda2e2a4",
                 "picard-1_alignment_summary_Aligned_Bases.yaml:md5,890df66d27392114a8fff8b92062f884",
                 "picard-1_alignment_summary_Aligned_Reads.yaml:md5,41a9fd39fa4e4cf4874c74d9c3b1b36f",
-                "picard-1_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
-                "picard-1_histogram_1.yaml:md5,c3036e5c3626ca012a7345b3b578ad8f",
-                "picard-1_histogram_2.yaml:md5,37ef6ec1ee50f6816b703f3f7d4040c9",
-                "picard-1_insert_size_Counts.yaml:md5,6b5ec6e58c61e2b8c02dcc1079d4850b",
-                "picard-1_insert_size_Percentages.yaml:md5,78f9b07ed2216cc9f10edadc1d26b1e8",
-                "picard-1_quality_by_cycle.yaml:md5,cc12a6863a9e9fd351d5f368bbbf67fa",
-                "picard-1_quality_score_distribution.yaml:md5,f265abd4067a5efa88592f59c2285a74",
-                "picard_base_distribution_by_cycle__Adenine.yaml:md5,ce7a138e6e63261b2a9bbb0a1a893ad3",
-                "picard_base_distribution_by_cycle__Cytosine.yaml:md5,06b2ce4ae7426f37bebaf5f811afcd37",
-                "picard_base_distribution_by_cycle__Guanine.yaml:md5,f6558c8c952c62492ab48e2afbdfaf05",
-                "picard_base_distribution_by_cycle__Thymine.yaml:md5,fad99bf3733f7ba3b965473116a74fc3",
-                "picard_base_distribution_by_cycle__Undetermined.yaml:md5,77df6cbfd78cc0f8914e2663c349e2d3",
+                "picard-1_insert_size_Counts.yaml:md5,1d06f38b9904f9a43999cb3894d60d0b",
+                "picard-1_insert_size_Percentages.yaml:md5,8256d8f2b45d26bea3c011702c449799",
+                "picard-1_quality_by_cycle.yaml:md5,b119f1649c55b3d660817f236a94a496",
+                "picard-1_quality_score_distribution.yaml:md5,d38889b5767b074cb69d7efd13d87565",
+                "picard_MarkIlluminaAdapters_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard_MeanQualityByCycle_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard_MeanQualityByCycle_histogram_1.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard_QualityScoreDistribution_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard_base_distribution_by_cycle__Adenine.yaml:md5,a6d21988c39254c54cc9680820b97537",
+                "picard_base_distribution_by_cycle__Cytosine.yaml:md5,d1b9ded13f629f8f8392773bcfcc91ec",
+                "picard_base_distribution_by_cycle__Guanine.yaml:md5,5b703b51b4db9eac363b42bbe6f63c5d",
+                "picard_base_distribution_by_cycle__Thymine.yaml:md5,594c63ee377428fa414e2c9b90ff5f40",
+                "picard_base_distribution_by_cycle__Undetermined.yaml:md5,5fcdc8fd9bdc545986c9340a12723e73",
                 "picard_deduplication.yaml:md5,7ff4f04ead40ec4e9e5b7ba071848260",
-                "picard_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
-                "picard_histogram_1.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
-                "picard_histogram_2.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
-                "samtools-flagstat-dp_Percentage_of_total-1.yaml:md5,cf95e15f68492c3d28bd2f97a1e520fa",
-                "samtools-flagstat-dp_Percentage_of_total-2.yaml:md5,1b1eec5d19ddf1b345b133f2fda62036",
-                "samtools-flagstat-dp_Percentage_of_total.yaml:md5,da48ca14276999ee304433554ec71838",
-                "samtools-flagstat-dp_Read_counts-1.yaml:md5,2ae75ff402a33ed6860caeede16eb3ef",
-                "samtools-flagstat-dp_Read_counts-2.yaml:md5,838317f2e7734a94a078523723d32843",
-                "samtools-flagstat-dp_Read_counts.yaml:md5,eceac01ca34290c4db7fb6140d153be8",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-1.yaml:md5,5c933fa507dbf7596a605230111f0a64",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-2.yaml:md5,c1ddb17ae59d9165e87dad0c1f307798",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts.yaml:md5,1997cdb7d0d94607b4963db997448e30",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-1.yaml:md5,ccd6f471d40577dc0c3f41cabc4e4de3",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-2.yaml:md5,fa7b86a76db7dbcecf9f6d8aaef02548",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.yaml:md5,af595221614c392509298544209abb4b",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts-1.yaml:md5,2c93beb85d475bb55b7aafa2586e2711",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts-2.yaml:md5,09f96c565fcc0b81aec8f60a9ea2a0e3",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts.yaml:md5,9a9403f14725273c8b44d90937ef0aa6",
+                "samtools-flagstat-pct-table.yaml:md5,1b1eec5d19ddf1b345b133f2fda62036",
+                "samtools-flagstat-table.yaml:md5,838317f2e7734a94a078523723d32843",
+                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-1.yaml:md5,8f4fff3963b1ac99cea6d383f8643408",
+                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-2.yaml:md5,4e71bf6886f146683bd0de1ff5f252a9",
+                "samtools-idxstats-mapped-reads-plot_Normalised_Counts.yaml:md5,28798f61ef786d1121cd60535d8d8a12",
+                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-1.yaml:md5,f9d9ff9b3a48c80080f06224e369ed16",
+                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-2.yaml:md5,4e11d304039ec78f557e5cf36447d15a",
+                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.yaml:md5,2a969645b5bc2b45754706e026d30bc4",
+                "samtools-idxstats-mapped-reads-plot_Raw_Counts-1.yaml:md5,9c55f8f6fc48ccf9fdc1e056ea880b82",
+                "samtools-idxstats-mapped-reads-plot_Raw_Counts-2.yaml:md5,5f6e7048432cec03afda912db5052a12",
+                "samtools-idxstats-mapped-reads-plot_Raw_Counts.yaml:md5,89fd9a44ab2de47153f4ff077e90b074",
                 "samtools-stats-dp.yaml:md5,a6bf11b91c4d80c11d84fe7f5cab8cb7",
                 "samtools_alignment_plot.yaml:md5,861b787bfca0dac75cb2d9467ee21f36",
                 "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384"
             ]
         ],
+        "timestamp": "2026-03-26T09:39:17.499506",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2026-03-20T22:56:58.445163531"
+            "nf-test": "0.9.4",
+            "nextflow": "25.04.0"
+        }
     },
     "chromap with stub": {
         "content": [
             20
         ],
+        "timestamp": "2026-03-17T14:23:25.411753",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.04.0"
-        },
-        "timestamp": "2026-03-17T14:23:25.411753"
+        }
     }
 }
\ No newline at end of file
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index 35b71ed29..6db943e96 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -36,8 +36,8 @@
                     "deeptools": "3.5.6"
                 },
                 "DESEQ2_QC": {
-                    "bioconductor-deseq2": "1.28.0",
-                    "r-base": "4.0.3"
+                    "DESeq2": "1.28.0",
+                    "R": "4.0.3"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -52,11 +52,8 @@
                 "GTF2BED": {
                     "perl": "5.26.2"
                 },
-                "HOMER_ANNOTATEPEAKS": {
-                    "homer": 4.11
-                },
                 "IGV": {
-                    "python": "3.8.3"
+                    "python": "3.12.12"
                 },
                 "MACS3_CALLPEAK": {
                     "macs3": "3.0.4"
@@ -68,6 +65,9 @@
                 "MULTIQC_CUSTOM_PEAKS": {
                     "sed": 4.7
                 },
+                "MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS": {
+                    "R": "4.5.3"
+                },
                 "PICARD_COLLECTMULTIPLEMETRICS": {
                     "picard": "3.4.0"
                 },
@@ -84,7 +84,7 @@
                     "R": "4.5.3"
                 },
                 "SAMPLESHEET_CHECK": {
-                    "python": "3.8.3"
+                    "python": "3.12.12"
                 },
                 "SAMTOOLS_FAIDX": {
                     "samtools": "1.22.1"
@@ -438,65 +438,65 @@
                 "multiqc/broad_peak/multiqc_data/fastqc_sequence_length_distribution_plot.yaml",
                 "multiqc/broad_peak/multiqc_data/fastqc_top_overrepresented_sequences_table.yaml",
                 "multiqc/broad_peak/multiqc_data/featureCounts_assignment_plot.yaml",
+                "multiqc/broad_peak/multiqc_data/llms-full.txt",
                 "multiqc/broad_peak/multiqc_data/multiqc.log",
+                "multiqc/broad_peak/multiqc_data/multiqc.parquet",
                 "multiqc/broad_peak/multiqc_data/multiqc_citations.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_cutadapt.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_data.json",
                 "multiqc/broad_peak/multiqc_data/multiqc_deseq2_clustering_1.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_deseq2_pca_1.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_fastqc.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_fastqc_1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_fastqc_fastqc-1.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_featurecounts.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_frip_score.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_nsc_coefficient.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_peak_annotation.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_peak_count.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_phantompeakqualtools.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_AlignmentSummaryMetrics.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_insertSize.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_quality_by_cycle.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_quality_score_distribution.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard_baseContent.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_AlignmentSummaryMetrics_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_insertSize_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_quality_by_cycle_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_quality_score_distribution_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard_baseContent_picard-1.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_picard_dups.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_rsc_coefficient.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat_1.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat_2.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat_samtools-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat_samtools-2.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats_1.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats_2.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats_samtools-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats_samtools-2.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats_1.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats_2.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats_samtools-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats_samtools-2.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_software_versions.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_sources.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_strand_shift_correlation.yaml",
+                "multiqc/broad_peak/multiqc_data/picard-1_MarkIlluminaAdapters_histogram_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/picard-1_MeanQualityByCycle_histogram_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/picard-1_MeanQualityByCycle_histogram_picard-1_1.yaml",
+                "multiqc/broad_peak/multiqc_data/picard-1_QualityScoreDistribution_histogram_picard-1.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_alignment_readlength_plot.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_alignment_summary_Aligned_Bases.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_alignment_summary_Aligned_Reads.yaml",
-                "multiqc/broad_peak/multiqc_data/picard-1_histogram.yaml",
-                "multiqc/broad_peak/multiqc_data/picard-1_histogram_1.yaml",
-                "multiqc/broad_peak/multiqc_data/picard-1_histogram_2.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_insert_size_Counts.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_insert_size_Percentages.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_quality_by_cycle.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_quality_score_distribution.yaml",
+                "multiqc/broad_peak/multiqc_data/picard_MarkIlluminaAdapters_histogram.yaml",
+                "multiqc/broad_peak/multiqc_data/picard_MeanQualityByCycle_histogram.yaml",
+                "multiqc/broad_peak/multiqc_data/picard_MeanQualityByCycle_histogram_1.yaml",
+                "multiqc/broad_peak/multiqc_data/picard_QualityScoreDistribution_histogram.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Adenine.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Cytosine.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Guanine.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Thymine.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Undetermined.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_deduplication.yaml",
-                "multiqc/broad_peak/multiqc_data/picard_histogram.yaml",
-                "multiqc/broad_peak/multiqc_data/picard_histogram_1.yaml",
-                "multiqc/broad_peak/multiqc_data/picard_histogram_2.yaml",
                 "multiqc/broad_peak/multiqc_data/read_distribution_profile.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Percentage_of_total-1.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Percentage_of_total-2.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Percentage_of_total.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Read_counts-1.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Read_counts-2.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Read_counts.yaml",
+                "multiqc/broad_peak/multiqc_data/samtools-flagstat-pct-table.yaml",
+                "multiqc/broad_peak/multiqc_data/samtools-flagstat-table.yaml",
                 "multiqc/broad_peak/multiqc_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1.yaml",
                 "multiqc/broad_peak/multiqc_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts-2.yaml",
                 "multiqc/broad_peak/multiqc_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.yaml",
@@ -569,12 +569,8 @@
                 "multiqc/broad_peak/multiqc_plots/pdf/read_distribution_profile.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/rsc_coefficient-cnt.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/rsc_coefficient-pct.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Percentage_of_total-1.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Percentage_of_total-2.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Read_counts-1.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Read_counts-2.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Read_counts.pdf",
+                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-pct-table.pdf",
+                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-table.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-log.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-2-cnt.pdf",
@@ -657,12 +653,8 @@
                 "multiqc/broad_peak/multiqc_plots/png/read_distribution_profile.png",
                 "multiqc/broad_peak/multiqc_plots/png/rsc_coefficient-cnt.png",
                 "multiqc/broad_peak/multiqc_plots/png/rsc_coefficient-pct.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Percentage_of_total-1.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Percentage_of_total-2.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Percentage_of_total.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Read_counts-1.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Read_counts-2.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Read_counts.png",
+                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-pct-table.png",
+                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-table.png",
                 "multiqc/broad_peak/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.png",
                 "multiqc/broad_peak/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-log.png",
                 "multiqc/broad_peak/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-2-cnt.png",
@@ -745,12 +737,8 @@
                 "multiqc/broad_peak/multiqc_plots/svg/read_distribution_profile.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/rsc_coefficient-cnt.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/rsc_coefficient-pct.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Percentage_of_total-1.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Percentage_of_total-2.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Read_counts-1.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Read_counts-2.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Read_counts.svg",
+                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-pct-table.svg",
+                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-table.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-log.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-2-cnt.svg",
@@ -871,98 +859,98 @@
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "cutadapt_filtered_reads_plot.yaml:md5,976fdb8049d847c977195863418e3655",
-                "cutadapt_trimmed_sequences_plot_3_Counts.yaml:md5,e6733f4ff773a27d0ab81564913b4b54",
-                "cutadapt_trimmed_sequences_plot_3_Obs_Exp.yaml:md5,9ffcfe37c02af14b8eddd4746066e56a",
+                "cutadapt_trimmed_sequences_plot_3_Counts.yaml:md5,1dba61b1d90518e1f020b71c4cfa04c4",
+                "cutadapt_trimmed_sequences_plot_3_Obs_Exp.yaml:md5,42335c2990d3a991e2bd0716f80b0515",
                 "fastqc-1-status-check-heatmap.yaml:md5,6c6e1591b5ff248c85446f9728a3dad4",
-                "fastqc-1_adapter_content_plot.yaml:md5,d78273a7e4ff36434bb91246fef01523",
-                "fastqc-1_per_base_n_content_plot.yaml:md5,3625446964b669ccff279aba54510462",
-                "fastqc-1_per_base_sequence_quality_plot.yaml:md5,1fb4d35d6b94fc4f41d5be1304844b95",
-                "fastqc-1_per_sequence_gc_content_plot_Counts.yaml:md5,101f11f9cebcc626755f32322b27ebd3",
-                "fastqc-1_per_sequence_gc_content_plot_Percentages.yaml:md5,0055f4bbded45434618259f47fe5fe85",
-                "fastqc-1_per_sequence_quality_scores_plot.yaml:md5,eed2628303916e49143ccf37300fb5de",
+                "fastqc-1_adapter_content_plot.yaml:md5,8acbcb9c6f3b5e42b19a7ab4bd1d607b",
+                "fastqc-1_per_base_n_content_plot.yaml:md5,24c7a2b7d290d797e7757adfd7b67175",
+                "fastqc-1_per_base_sequence_quality_plot.yaml:md5,ddaf5d8d0dad842c9e00a9cdde2a82c7",
+                "fastqc-1_per_sequence_gc_content_plot_Counts.yaml:md5,191d3d72a05700fa5b69854ff47b6e66",
+                "fastqc-1_per_sequence_gc_content_plot_Percentages.yaml:md5,f9cc6e0466e1791e9b3bd765ab3b9a57",
+                "fastqc-1_per_sequence_quality_scores_plot.yaml:md5,6bfed2114551676b4c60e897f12c6e12",
                 "fastqc-1_sequence_counts_plot.yaml:md5,6ca3a8cf8d258777e29b8e8731157d90",
-                "fastqc-1_sequence_duplication_levels_plot.yaml:md5,3e3622b7dd80be1db92ac06df8e3d056",
+                "fastqc-1_sequence_duplication_levels_plot.yaml:md5,fa8e5813c72d6366bf50d99c0eb20f56",
                 "fastqc-1_top_overrepresented_sequences_table.yaml:md5,a333a02f5313876cf1713d7b0168d5f3",
                 "fastqc-status-check-heatmap.yaml:md5,1e473e0f9140b718607d8c72cf3c0b45",
-                "fastqc_adapter_content_plot.yaml:md5,591991daf3e3c49873f4a51a3710b072",
-                "fastqc_per_base_n_content_plot.yaml:md5,c16a4af177b9ad9694a9535023906927",
-                "fastqc_per_base_sequence_quality_plot.yaml:md5,20fc07ce2bc8e369d5fdd18afc6e60e9",
-                "fastqc_per_sequence_gc_content_plot_Counts.yaml:md5,ab233171fb8fd4e717886b01868ebcf2",
-                "fastqc_per_sequence_gc_content_plot_Percentages.yaml:md5,db29d683777cc0742585d1c48e712bd3",
-                "fastqc_per_sequence_quality_scores_plot.yaml:md5,351b55974af5ee21294ebf5deb850d7c",
+                "fastqc_adapter_content_plot.yaml:md5,de00547c4d9e5920e0e5c5b1f47981f7",
+                "fastqc_per_base_n_content_plot.yaml:md5,a2ac6f6a3323630922fb494def39b5c1",
+                "fastqc_per_base_sequence_quality_plot.yaml:md5,b0a022b4a3db86cc799142779155f9ed",
+                "fastqc_per_sequence_gc_content_plot_Counts.yaml:md5,679a374990a8c3b7a87fc55afca4c5f8",
+                "fastqc_per_sequence_gc_content_plot_Percentages.yaml:md5,c7a1700b9f6987c5dea327799902204a",
+                "fastqc_per_sequence_quality_scores_plot.yaml:md5,d4a8f8ced23faa497edb023ac00d9632",
                 "fastqc_sequence_counts_plot.yaml:md5,5522b2b42f0b3753dd359aad1565d7c2",
-                "fastqc_sequence_duplication_levels_plot.yaml:md5,e883323380f2880c81ea36dc91ad8678",
-                "fastqc_sequence_length_distribution_plot.yaml:md5,d57678f16381986766d56b631c838106",
+                "fastqc_sequence_duplication_levels_plot.yaml:md5,e5532eac263c0b33ed3c024eca5fce94",
+                "fastqc_sequence_length_distribution_plot.yaml:md5,e701cb601de4693ab09473b849e4f110",
                 "fastqc_top_overrepresented_sequences_table.yaml:md5,443e161371f73cebf63c14f7a9f3580d",
                 "featureCounts_assignment_plot.yaml:md5,9ebb47589533f668f7b2b4e59d5231c5",
+                "llms-full.txt:md5,b5b5f6cc68b1770ed707020d9561edc3",
+                "multiqc.parquet:md5,d51dc50a673f5237e5d75acf3ef806b8",
                 "multiqc_citations.yaml:md5,fca5dc7cb20162434c714d26b11161f3",
                 "multiqc_fastqc.yaml:md5,30fe6d1a5e5c04695dda81294b828ec9",
-                "multiqc_fastqc_1.yaml:md5,cd4a85c27c3cf85f1d0612afce793186",
+                "multiqc_fastqc_fastqc-1.yaml:md5,cd4a85c27c3cf85f1d0612afce793186",
                 "multiqc_featurecounts.yaml:md5,6af47474530327a6254a44f1f833ab1c",
                 "multiqc_frip_score.yaml:md5,a12e53352fb861b27e22fada20d4a352",
                 "multiqc_nsc_coefficient.yaml:md5,2f98bade263dddff526bc627bd956f94",
-                "multiqc_peak_annotation.yaml:md5,807711a8de90b96350cdb704713f377c",
-                "multiqc_peak_count.yaml:md5,9febb685e0995e635c0d34644aef1c22",
+                "multiqc_peak_annotation.yaml:md5,af9465db4191ab2a1bc5b0c2edf34448",
+                "multiqc_peak_count.yaml:md5,059422f241221e925b026cbdfbe1625d",
                 "multiqc_phantompeakqualtools.yaml:md5,e9b072da0ce783d5b7ec217d83a15987",
-                "multiqc_picard-1_AlignmentSummaryMetrics.yaml:md5,3127f1885c9d22281d5e853478833a70",
-                "multiqc_picard-1_insertSize.yaml:md5,43486e24b88a3712442e891968bd2ce0",
-                "multiqc_picard-1_quality_by_cycle.yaml:md5,e3132d7e118d112e819c781db8b68f23",
-                "multiqc_picard-1_quality_score_distribution.yaml:md5,ae43cc721ebb096df6dc36c2b077c288",
-                "multiqc_picard_baseContent.yaml:md5,01c7596a92f3884c4972c987745c96ec",
+                "multiqc_picard-1_AlignmentSummaryMetrics_picard-1.yaml:md5,3127f1885c9d22281d5e853478833a70",
+                "multiqc_picard-1_insertSize_picard-1.yaml:md5,43486e24b88a3712442e891968bd2ce0",
+                "multiqc_picard-1_quality_by_cycle_picard-1.yaml:md5,e3132d7e118d112e819c781db8b68f23",
+                "multiqc_picard-1_quality_score_distribution_picard-1.yaml:md5,ae43cc721ebb096df6dc36c2b077c288",
+                "multiqc_picard_baseContent_picard-1.yaml:md5,01c7596a92f3884c4972c987745c96ec",
                 "multiqc_picard_dups.yaml:md5,9bf99a105d35807fc4645086d72998e0",
                 "multiqc_rsc_coefficient.yaml:md5,e5c7d53b2b9b12bb55690838915820ae",
                 "multiqc_samtools_flagstat.yaml:md5,f1f82442834faeea1e3393b91faa3f38",
-                "multiqc_samtools_flagstat_1.yaml:md5,7ae591bb360acba0858ccc9177245a44",
-                "multiqc_samtools_flagstat_2.yaml:md5,89c5fd1d7975ad6bfe9dbbeefcaa2a4b",
+                "multiqc_samtools_flagstat_samtools-1.yaml:md5,7ae591bb360acba0858ccc9177245a44",
+                "multiqc_samtools_flagstat_samtools-2.yaml:md5,89c5fd1d7975ad6bfe9dbbeefcaa2a4b",
                 "multiqc_samtools_idxstats.yaml:md5,48c253ff301403f97b6973603784b25a",
-                "multiqc_samtools_idxstats_1.yaml:md5,684841cb92622bdd9aebfcc6e08aa03f",
-                "multiqc_samtools_idxstats_2.yaml:md5,f81be62ac233142a9923a8d724c99802",
-                "multiqc_samtools_stats.yaml:md5,533bfee2bf752b47276e14a3b108f1b2",
-                "multiqc_samtools_stats_1.yaml:md5,ff3a9d5854cf0471c96fa52ec3579066",
-                "multiqc_samtools_stats_2.yaml:md5,be2d5080821f867bf05b87a84c83b864",
+                "multiqc_samtools_idxstats_samtools-1.yaml:md5,684841cb92622bdd9aebfcc6e08aa03f",
+                "multiqc_samtools_idxstats_samtools-2.yaml:md5,f81be62ac233142a9923a8d724c99802",
+                "multiqc_samtools_stats.yaml:md5,d5f7a98962e1eb5dfd9472ec758a1db5",
+                "multiqc_samtools_stats_samtools-1.yaml:md5,377a378a5991eea6989f28ca1643193c",
+                "multiqc_samtools_stats_samtools-2.yaml:md5,3099c37b6a7c44064732eaabdc1c817b",
+                "picard-1_MarkIlluminaAdapters_histogram_picard-1.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard-1_MeanQualityByCycle_histogram_picard-1.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard-1_MeanQualityByCycle_histogram_picard-1_1.yaml:md5,e3132d7e118d112e819c781db8b68f23",
+                "picard-1_QualityScoreDistribution_histogram_picard-1.yaml:md5,ae43cc721ebb096df6dc36c2b077c288",
                 "picard-1_alignment_readlength_plot.yaml:md5,3edd8c54cbfad9c32847a94ba80008e3",
                 "picard-1_alignment_summary_Aligned_Bases.yaml:md5,9477ebe92f7bf9a1b667aff6f9efe845",
                 "picard-1_alignment_summary_Aligned_Reads.yaml:md5,9d19a860ec8c799d7b229b47c76d383c",
-                "picard-1_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
-                "picard-1_histogram_1.yaml:md5,e3132d7e118d112e819c781db8b68f23",
-                "picard-1_histogram_2.yaml:md5,ae43cc721ebb096df6dc36c2b077c288",
-                "picard-1_insert_size_Counts.yaml:md5,653f4829a5e9a98bbb21b2fba99ad672",
-                "picard-1_insert_size_Percentages.yaml:md5,364de79ac1c04ba383d66b7a1d71541d",
-                "picard-1_quality_by_cycle.yaml:md5,04479bcef32a5ea65ce55f6772373c60",
-                "picard-1_quality_score_distribution.yaml:md5,6bdb95104cc7ea521d2db72896da9272",
-                "picard_base_distribution_by_cycle__Adenine.yaml:md5,1452490858309fc8dd9f308045790a8b",
-                "picard_base_distribution_by_cycle__Cytosine.yaml:md5,a88f7594290117503637336e33629751",
-                "picard_base_distribution_by_cycle__Guanine.yaml:md5,b0f4ecff965c1da1eda2dfa80b0723f7",
-                "picard_base_distribution_by_cycle__Thymine.yaml:md5,bff14a87ef525cce731dbe42bf463ea8",
-                "picard_base_distribution_by_cycle__Undetermined.yaml:md5,7772113ed25a6d2951a4e6100c30932b",
+                "picard-1_insert_size_Counts.yaml:md5,c047df94604200060a4c873c75f7922d",
+                "picard-1_insert_size_Percentages.yaml:md5,460fa96e94211dbeece20d3ccef400fe",
+                "picard-1_quality_by_cycle.yaml:md5,612f7b69b152122c504f8afa219a24e3",
+                "picard-1_quality_score_distribution.yaml:md5,80afa74f39b48b02236546bc0b235bc4",
+                "picard_MarkIlluminaAdapters_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard_MeanQualityByCycle_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard_MeanQualityByCycle_histogram_1.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard_QualityScoreDistribution_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard_base_distribution_by_cycle__Adenine.yaml:md5,d5739dbfa20e1e60010312ec44e31655",
+                "picard_base_distribution_by_cycle__Cytosine.yaml:md5,fc40672c06220ba9c67a6b5541220428",
+                "picard_base_distribution_by_cycle__Guanine.yaml:md5,e4658e2ec03376e4848248c8609c1291",
+                "picard_base_distribution_by_cycle__Thymine.yaml:md5,606e88cb102b3cd1568e032039edc045",
+                "picard_base_distribution_by_cycle__Undetermined.yaml:md5,0ac8d0fc8ce7093f1f8158365546aa18",
                 "picard_deduplication.yaml:md5,c5d69579294e7592e5e28277e01c278e",
-                "picard_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
-                "picard_histogram_1.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
-                "picard_histogram_2.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
-                "samtools-flagstat-dp_Percentage_of_total-1.yaml:md5,09bb5ef391631b8845e3f3fe212f8048",
-                "samtools-flagstat-dp_Percentage_of_total-2.yaml:md5,96d661539b95863c30e181e5b64e46ca",
-                "samtools-flagstat-dp_Percentage_of_total.yaml:md5,cc9d1b338f526d4bab4bfa867c5dcd21",
-                "samtools-flagstat-dp_Read_counts-1.yaml:md5,ca690a967e8e0f699d27f38e864e2fce",
-                "samtools-flagstat-dp_Read_counts-2.yaml:md5,46debe080c753b6ba45501ea268e5d95",
-                "samtools-flagstat-dp_Read_counts.yaml:md5,2a3cbb23287d2123c29cfa1a3454a72a",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-1.yaml:md5,ac2602eede7202f9c0348760eb0b8bb6",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-2.yaml:md5,b1fe44cbd1cda8d4727a232c8c8bd513",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts.yaml:md5,ac1c7fc1c35a6719c962993d9bf5471e",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-1.yaml:md5,80c5b4f9cc0400799be48ef05aa6c410",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-2.yaml:md5,62d984dcdceba150863dd1e72c93f245",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.yaml:md5,989f82110113d8855a3f0cfa996cbdc6",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts-1.yaml:md5,94ddd17f7b9d15e547be9294e872e193",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts-2.yaml:md5,b8204d3b4480d3e9eec09d1289e52637",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts.yaml:md5,c944d25812a73c4ce9de9834943e6732",
+                "samtools-flagstat-pct-table.yaml:md5,96d661539b95863c30e181e5b64e46ca",
+                "samtools-flagstat-table.yaml:md5,46debe080c753b6ba45501ea268e5d95",
+                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-1.yaml:md5,ff73ac12f1542f46e1e61ef489c3c8e3",
+                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-2.yaml:md5,59851fa41690f7e7878e75ed9a6d31e7",
+                "samtools-idxstats-mapped-reads-plot_Normalised_Counts.yaml:md5,9eb530fdcb78b2740a2e26cc72112a32",
+                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-1.yaml:md5,e958aaff27c81aa1f197d491ff4bc0d2",
+                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-2.yaml:md5,e28a272081d679b36d3e1e31a5db1b02",
+                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.yaml:md5,a702f17e2426770da83f10037cb77e76",
+                "samtools-idxstats-mapped-reads-plot_Raw_Counts-1.yaml:md5,12a4d0294e7844b66ac8a434e5505268",
+                "samtools-idxstats-mapped-reads-plot_Raw_Counts-2.yaml:md5,42395713ecc6263c85e11416a126613d",
+                "samtools-idxstats-mapped-reads-plot_Raw_Counts.yaml:md5,4d58d9f278bd63548788dd0b9edff741",
                 "samtools-stats-dp.yaml:md5,ba5ad95c00d0bcef0d7aa32f941a813d",
                 "samtools_alignment_plot.yaml:md5,c1b5b60c3c83928275df7f720c5b1697",
                 "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384"
             ]
         ],
+        "timestamp": "2026-03-26T09:52:21.465107",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2026-03-20T22:58:38.10424597"
+            "nf-test": "0.9.4",
+            "nextflow": "25.04.0"
+        }
     }
 }
\ No newline at end of file
diff --git a/tests/skip_consensus_peaks.nf.test.snap b/tests/skip_consensus_peaks.nf.test.snap
index 3995c5e3f..916f94e7e 100644
--- a/tests/skip_consensus_peaks.nf.test.snap
+++ b/tests/skip_consensus_peaks.nf.test.snap
@@ -3,11 +3,11 @@
         "content": [
             20
         ],
+        "timestamp": "2026-03-17T14:29:41.990841",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.04.0"
-        },
-        "timestamp": "2026-03-17T14:29:41.990841"
+        }
     },
     "skip_consensus_peaks": {
         "content": [
@@ -55,11 +55,8 @@
                 "GTF2BED": {
                     "perl": "5.26.2"
                 },
-                "HOMER_ANNOTATEPEAKS": {
-                    "homer": 4.11
-                },
                 "IGV": {
-                    "python": "3.8.3"
+                    "python": "3.12.12"
                 },
                 "MACS3_CALLPEAK": {
                     "macs3": "3.0.4"
@@ -67,6 +64,9 @@
                 "MULTIQC_CUSTOM_PEAKS": {
                     "sed": 4.7
                 },
+                "MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS": {
+                    "R": "4.5.3"
+                },
                 "PICARD_COLLECTMULTIPLEMETRICS": {
                     "picard": "3.4.0"
                 },
@@ -83,7 +83,7 @@
                     "R": "4.5.3"
                 },
                 "SAMPLESHEET_CHECK": {
-                    "python": "3.8.3"
+                    "python": "3.12.12"
                 },
                 "SAMTOOLS_FAIDX": {
                     "samtools": "1.22.1"
@@ -406,62 +406,62 @@
                 "multiqc/broad_peak/multiqc_data/fastqc_sequence_duplication_levels_plot.yaml",
                 "multiqc/broad_peak/multiqc_data/fastqc_sequence_length_distribution_plot.yaml",
                 "multiqc/broad_peak/multiqc_data/fastqc_top_overrepresented_sequences_table.yaml",
+                "multiqc/broad_peak/multiqc_data/llms-full.txt",
                 "multiqc/broad_peak/multiqc_data/multiqc.log",
+                "multiqc/broad_peak/multiqc_data/multiqc.parquet",
                 "multiqc/broad_peak/multiqc_data/multiqc_citations.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_cutadapt.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_data.json",
                 "multiqc/broad_peak/multiqc_data/multiqc_fastqc.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_fastqc_1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_fastqc_fastqc-1.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_frip_score.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_nsc_coefficient.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_peak_annotation.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_peak_count.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_phantompeakqualtools.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_AlignmentSummaryMetrics.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_insertSize.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_quality_by_cycle.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_quality_score_distribution.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard_baseContent.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_AlignmentSummaryMetrics_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_insertSize_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_quality_by_cycle_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_quality_score_distribution_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard_baseContent_picard-1.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_picard_dups.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_rsc_coefficient.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat_1.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat_2.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat_samtools-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat_samtools-2.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats_1.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats_2.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats_samtools-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats_samtools-2.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats_1.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats_2.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats_samtools-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats_samtools-2.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_software_versions.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_sources.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_strand_shift_correlation.yaml",
+                "multiqc/broad_peak/multiqc_data/picard-1_MarkIlluminaAdapters_histogram_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/picard-1_MeanQualityByCycle_histogram_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/picard-1_MeanQualityByCycle_histogram_picard-1_1.yaml",
+                "multiqc/broad_peak/multiqc_data/picard-1_QualityScoreDistribution_histogram_picard-1.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_alignment_readlength_plot.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_alignment_summary_Aligned_Bases.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_alignment_summary_Aligned_Reads.yaml",
-                "multiqc/broad_peak/multiqc_data/picard-1_histogram.yaml",
-                "multiqc/broad_peak/multiqc_data/picard-1_histogram_1.yaml",
-                "multiqc/broad_peak/multiqc_data/picard-1_histogram_2.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_insert_size_Counts.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_insert_size_Percentages.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_quality_by_cycle.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_quality_score_distribution.yaml",
+                "multiqc/broad_peak/multiqc_data/picard_MarkIlluminaAdapters_histogram.yaml",
+                "multiqc/broad_peak/multiqc_data/picard_MeanQualityByCycle_histogram.yaml",
+                "multiqc/broad_peak/multiqc_data/picard_MeanQualityByCycle_histogram_1.yaml",
+                "multiqc/broad_peak/multiqc_data/picard_QualityScoreDistribution_histogram.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Adenine.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Cytosine.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Guanine.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Thymine.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Undetermined.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_deduplication.yaml",
-                "multiqc/broad_peak/multiqc_data/picard_histogram.yaml",
-                "multiqc/broad_peak/multiqc_data/picard_histogram_1.yaml",
-                "multiqc/broad_peak/multiqc_data/picard_histogram_2.yaml",
                 "multiqc/broad_peak/multiqc_data/read_distribution_profile.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Percentage_of_total-1.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Percentage_of_total-2.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Percentage_of_total.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Read_counts-1.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Read_counts-2.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Read_counts.yaml",
+                "multiqc/broad_peak/multiqc_data/samtools-flagstat-pct-table.yaml",
+                "multiqc/broad_peak/multiqc_data/samtools-flagstat-table.yaml",
                 "multiqc/broad_peak/multiqc_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1.yaml",
                 "multiqc/broad_peak/multiqc_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts-2.yaml",
                 "multiqc/broad_peak/multiqc_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.yaml",
@@ -530,12 +530,8 @@
                 "multiqc/broad_peak/multiqc_plots/pdf/read_distribution_profile.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/rsc_coefficient-cnt.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/rsc_coefficient-pct.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Percentage_of_total-1.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Percentage_of_total-2.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Read_counts-1.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Read_counts-2.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Read_counts.pdf",
+                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-pct-table.pdf",
+                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-table.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-log.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-2-cnt.pdf",
@@ -614,12 +610,8 @@
                 "multiqc/broad_peak/multiqc_plots/png/read_distribution_profile.png",
                 "multiqc/broad_peak/multiqc_plots/png/rsc_coefficient-cnt.png",
                 "multiqc/broad_peak/multiqc_plots/png/rsc_coefficient-pct.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Percentage_of_total-1.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Percentage_of_total-2.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Percentage_of_total.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Read_counts-1.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Read_counts-2.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Read_counts.png",
+                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-pct-table.png",
+                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-table.png",
                 "multiqc/broad_peak/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.png",
                 "multiqc/broad_peak/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-log.png",
                 "multiqc/broad_peak/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-2-cnt.png",
@@ -698,12 +690,8 @@
                 "multiqc/broad_peak/multiqc_plots/svg/read_distribution_profile.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/rsc_coefficient-cnt.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/rsc_coefficient-pct.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Percentage_of_total-1.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Percentage_of_total-2.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Read_counts-1.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Read_counts-2.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Read_counts.svg",
+                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-pct-table.svg",
+                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-table.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-log.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-2-cnt.svg",
@@ -814,96 +802,96 @@
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "cutadapt_filtered_reads_plot.yaml:md5,976fdb8049d847c977195863418e3655",
-                "cutadapt_trimmed_sequences_plot_3_Counts.yaml:md5,e6733f4ff773a27d0ab81564913b4b54",
-                "cutadapt_trimmed_sequences_plot_3_Obs_Exp.yaml:md5,9ffcfe37c02af14b8eddd4746066e56a",
+                "cutadapt_trimmed_sequences_plot_3_Counts.yaml:md5,1dba61b1d90518e1f020b71c4cfa04c4",
+                "cutadapt_trimmed_sequences_plot_3_Obs_Exp.yaml:md5,42335c2990d3a991e2bd0716f80b0515",
                 "fastqc-1-status-check-heatmap.yaml:md5,6c6e1591b5ff248c85446f9728a3dad4",
-                "fastqc-1_adapter_content_plot.yaml:md5,d78273a7e4ff36434bb91246fef01523",
-                "fastqc-1_per_base_n_content_plot.yaml:md5,3625446964b669ccff279aba54510462",
-                "fastqc-1_per_base_sequence_quality_plot.yaml:md5,1fb4d35d6b94fc4f41d5be1304844b95",
-                "fastqc-1_per_sequence_gc_content_plot_Counts.yaml:md5,101f11f9cebcc626755f32322b27ebd3",
-                "fastqc-1_per_sequence_gc_content_plot_Percentages.yaml:md5,0055f4bbded45434618259f47fe5fe85",
-                "fastqc-1_per_sequence_quality_scores_plot.yaml:md5,eed2628303916e49143ccf37300fb5de",
+                "fastqc-1_adapter_content_plot.yaml:md5,8acbcb9c6f3b5e42b19a7ab4bd1d607b",
+                "fastqc-1_per_base_n_content_plot.yaml:md5,24c7a2b7d290d797e7757adfd7b67175",
+                "fastqc-1_per_base_sequence_quality_plot.yaml:md5,ddaf5d8d0dad842c9e00a9cdde2a82c7",
+                "fastqc-1_per_sequence_gc_content_plot_Counts.yaml:md5,191d3d72a05700fa5b69854ff47b6e66",
+                "fastqc-1_per_sequence_gc_content_plot_Percentages.yaml:md5,f9cc6e0466e1791e9b3bd765ab3b9a57",
+                "fastqc-1_per_sequence_quality_scores_plot.yaml:md5,6bfed2114551676b4c60e897f12c6e12",
                 "fastqc-1_sequence_counts_plot.yaml:md5,6ca3a8cf8d258777e29b8e8731157d90",
-                "fastqc-1_sequence_duplication_levels_plot.yaml:md5,3e3622b7dd80be1db92ac06df8e3d056",
+                "fastqc-1_sequence_duplication_levels_plot.yaml:md5,fa8e5813c72d6366bf50d99c0eb20f56",
                 "fastqc-1_top_overrepresented_sequences_table.yaml:md5,a333a02f5313876cf1713d7b0168d5f3",
                 "fastqc-status-check-heatmap.yaml:md5,1e473e0f9140b718607d8c72cf3c0b45",
-                "fastqc_adapter_content_plot.yaml:md5,591991daf3e3c49873f4a51a3710b072",
-                "fastqc_per_base_n_content_plot.yaml:md5,c16a4af177b9ad9694a9535023906927",
-                "fastqc_per_base_sequence_quality_plot.yaml:md5,20fc07ce2bc8e369d5fdd18afc6e60e9",
-                "fastqc_per_sequence_gc_content_plot_Counts.yaml:md5,ab233171fb8fd4e717886b01868ebcf2",
-                "fastqc_per_sequence_gc_content_plot_Percentages.yaml:md5,db29d683777cc0742585d1c48e712bd3",
-                "fastqc_per_sequence_quality_scores_plot.yaml:md5,351b55974af5ee21294ebf5deb850d7c",
+                "fastqc_adapter_content_plot.yaml:md5,de00547c4d9e5920e0e5c5b1f47981f7",
+                "fastqc_per_base_n_content_plot.yaml:md5,a2ac6f6a3323630922fb494def39b5c1",
+                "fastqc_per_base_sequence_quality_plot.yaml:md5,b0a022b4a3db86cc799142779155f9ed",
+                "fastqc_per_sequence_gc_content_plot_Counts.yaml:md5,679a374990a8c3b7a87fc55afca4c5f8",
+                "fastqc_per_sequence_gc_content_plot_Percentages.yaml:md5,c7a1700b9f6987c5dea327799902204a",
+                "fastqc_per_sequence_quality_scores_plot.yaml:md5,d4a8f8ced23faa497edb023ac00d9632",
                 "fastqc_sequence_counts_plot.yaml:md5,5522b2b42f0b3753dd359aad1565d7c2",
-                "fastqc_sequence_duplication_levels_plot.yaml:md5,e883323380f2880c81ea36dc91ad8678",
-                "fastqc_sequence_length_distribution_plot.yaml:md5,d57678f16381986766d56b631c838106",
+                "fastqc_sequence_duplication_levels_plot.yaml:md5,e5532eac263c0b33ed3c024eca5fce94",
+                "fastqc_sequence_length_distribution_plot.yaml:md5,e701cb601de4693ab09473b849e4f110",
                 "fastqc_top_overrepresented_sequences_table.yaml:md5,443e161371f73cebf63c14f7a9f3580d",
+                "llms-full.txt:md5,d4acf16d6ba49180502b0019bcd2d6c9",
+                "multiqc.parquet:md5,97238dcfd7d08cf243e3dca203123076",
                 "multiqc_citations.yaml:md5,c4cdebc20cfc52eb2eee741a36323b3e",
                 "multiqc_fastqc.yaml:md5,30fe6d1a5e5c04695dda81294b828ec9",
-                "multiqc_fastqc_1.yaml:md5,cd4a85c27c3cf85f1d0612afce793186",
+                "multiqc_fastqc_fastqc-1.yaml:md5,cd4a85c27c3cf85f1d0612afce793186",
                 "multiqc_frip_score.yaml:md5,a12e53352fb861b27e22fada20d4a352",
                 "multiqc_nsc_coefficient.yaml:md5,2f98bade263dddff526bc627bd956f94",
-                "multiqc_peak_annotation.yaml:md5,807711a8de90b96350cdb704713f377c",
-                "multiqc_peak_count.yaml:md5,9febb685e0995e635c0d34644aef1c22",
+                "multiqc_peak_annotation.yaml:md5,af9465db4191ab2a1bc5b0c2edf34448",
+                "multiqc_peak_count.yaml:md5,059422f241221e925b026cbdfbe1625d",
                 "multiqc_phantompeakqualtools.yaml:md5,e9b072da0ce783d5b7ec217d83a15987",
-                "multiqc_picard-1_AlignmentSummaryMetrics.yaml:md5,3127f1885c9d22281d5e853478833a70",
-                "multiqc_picard-1_insertSize.yaml:md5,43486e24b88a3712442e891968bd2ce0",
-                "multiqc_picard-1_quality_by_cycle.yaml:md5,e3132d7e118d112e819c781db8b68f23",
-                "multiqc_picard-1_quality_score_distribution.yaml:md5,ae43cc721ebb096df6dc36c2b077c288",
-                "multiqc_picard_baseContent.yaml:md5,01c7596a92f3884c4972c987745c96ec",
+                "multiqc_picard-1_AlignmentSummaryMetrics_picard-1.yaml:md5,3127f1885c9d22281d5e853478833a70",
+                "multiqc_picard-1_insertSize_picard-1.yaml:md5,43486e24b88a3712442e891968bd2ce0",
+                "multiqc_picard-1_quality_by_cycle_picard-1.yaml:md5,e3132d7e118d112e819c781db8b68f23",
+                "multiqc_picard-1_quality_score_distribution_picard-1.yaml:md5,ae43cc721ebb096df6dc36c2b077c288",
+                "multiqc_picard_baseContent_picard-1.yaml:md5,01c7596a92f3884c4972c987745c96ec",
                 "multiqc_picard_dups.yaml:md5,9bf99a105d35807fc4645086d72998e0",
                 "multiqc_rsc_coefficient.yaml:md5,e5c7d53b2b9b12bb55690838915820ae",
                 "multiqc_samtools_flagstat.yaml:md5,f1f82442834faeea1e3393b91faa3f38",
-                "multiqc_samtools_flagstat_1.yaml:md5,7ae591bb360acba0858ccc9177245a44",
-                "multiqc_samtools_flagstat_2.yaml:md5,89c5fd1d7975ad6bfe9dbbeefcaa2a4b",
+                "multiqc_samtools_flagstat_samtools-1.yaml:md5,7ae591bb360acba0858ccc9177245a44",
+                "multiqc_samtools_flagstat_samtools-2.yaml:md5,89c5fd1d7975ad6bfe9dbbeefcaa2a4b",
                 "multiqc_samtools_idxstats.yaml:md5,48c253ff301403f97b6973603784b25a",
-                "multiqc_samtools_idxstats_1.yaml:md5,684841cb92622bdd9aebfcc6e08aa03f",
-                "multiqc_samtools_idxstats_2.yaml:md5,f81be62ac233142a9923a8d724c99802",
-                "multiqc_samtools_stats.yaml:md5,533bfee2bf752b47276e14a3b108f1b2",
-                "multiqc_samtools_stats_1.yaml:md5,ff3a9d5854cf0471c96fa52ec3579066",
-                "multiqc_samtools_stats_2.yaml:md5,be2d5080821f867bf05b87a84c83b864",
+                "multiqc_samtools_idxstats_samtools-1.yaml:md5,684841cb92622bdd9aebfcc6e08aa03f",
+                "multiqc_samtools_idxstats_samtools-2.yaml:md5,f81be62ac233142a9923a8d724c99802",
+                "multiqc_samtools_stats.yaml:md5,d5f7a98962e1eb5dfd9472ec758a1db5",
+                "multiqc_samtools_stats_samtools-1.yaml:md5,377a378a5991eea6989f28ca1643193c",
+                "multiqc_samtools_stats_samtools-2.yaml:md5,3099c37b6a7c44064732eaabdc1c817b",
+                "picard-1_MarkIlluminaAdapters_histogram_picard-1.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard-1_MeanQualityByCycle_histogram_picard-1.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard-1_MeanQualityByCycle_histogram_picard-1_1.yaml:md5,e3132d7e118d112e819c781db8b68f23",
+                "picard-1_QualityScoreDistribution_histogram_picard-1.yaml:md5,ae43cc721ebb096df6dc36c2b077c288",
                 "picard-1_alignment_readlength_plot.yaml:md5,3edd8c54cbfad9c32847a94ba80008e3",
                 "picard-1_alignment_summary_Aligned_Bases.yaml:md5,9477ebe92f7bf9a1b667aff6f9efe845",
                 "picard-1_alignment_summary_Aligned_Reads.yaml:md5,9d19a860ec8c799d7b229b47c76d383c",
-                "picard-1_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
-                "picard-1_histogram_1.yaml:md5,e3132d7e118d112e819c781db8b68f23",
-                "picard-1_histogram_2.yaml:md5,ae43cc721ebb096df6dc36c2b077c288",
-                "picard-1_insert_size_Counts.yaml:md5,653f4829a5e9a98bbb21b2fba99ad672",
-                "picard-1_insert_size_Percentages.yaml:md5,364de79ac1c04ba383d66b7a1d71541d",
-                "picard-1_quality_by_cycle.yaml:md5,04479bcef32a5ea65ce55f6772373c60",
-                "picard-1_quality_score_distribution.yaml:md5,6bdb95104cc7ea521d2db72896da9272",
-                "picard_base_distribution_by_cycle__Adenine.yaml:md5,1452490858309fc8dd9f308045790a8b",
-                "picard_base_distribution_by_cycle__Cytosine.yaml:md5,a88f7594290117503637336e33629751",
-                "picard_base_distribution_by_cycle__Guanine.yaml:md5,b0f4ecff965c1da1eda2dfa80b0723f7",
-                "picard_base_distribution_by_cycle__Thymine.yaml:md5,bff14a87ef525cce731dbe42bf463ea8",
-                "picard_base_distribution_by_cycle__Undetermined.yaml:md5,7772113ed25a6d2951a4e6100c30932b",
+                "picard-1_insert_size_Counts.yaml:md5,c047df94604200060a4c873c75f7922d",
+                "picard-1_insert_size_Percentages.yaml:md5,460fa96e94211dbeece20d3ccef400fe",
+                "picard-1_quality_by_cycle.yaml:md5,612f7b69b152122c504f8afa219a24e3",
+                "picard-1_quality_score_distribution.yaml:md5,80afa74f39b48b02236546bc0b235bc4",
+                "picard_MarkIlluminaAdapters_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard_MeanQualityByCycle_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard_MeanQualityByCycle_histogram_1.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard_QualityScoreDistribution_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard_base_distribution_by_cycle__Adenine.yaml:md5,d5739dbfa20e1e60010312ec44e31655",
+                "picard_base_distribution_by_cycle__Cytosine.yaml:md5,fc40672c06220ba9c67a6b5541220428",
+                "picard_base_distribution_by_cycle__Guanine.yaml:md5,e4658e2ec03376e4848248c8609c1291",
+                "picard_base_distribution_by_cycle__Thymine.yaml:md5,606e88cb102b3cd1568e032039edc045",
+                "picard_base_distribution_by_cycle__Undetermined.yaml:md5,0ac8d0fc8ce7093f1f8158365546aa18",
                 "picard_deduplication.yaml:md5,c5d69579294e7592e5e28277e01c278e",
-                "picard_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
-                "picard_histogram_1.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
-                "picard_histogram_2.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
-                "samtools-flagstat-dp_Percentage_of_total-1.yaml:md5,09bb5ef391631b8845e3f3fe212f8048",
-                "samtools-flagstat-dp_Percentage_of_total-2.yaml:md5,96d661539b95863c30e181e5b64e46ca",
-                "samtools-flagstat-dp_Percentage_of_total.yaml:md5,cc9d1b338f526d4bab4bfa867c5dcd21",
-                "samtools-flagstat-dp_Read_counts-1.yaml:md5,ca690a967e8e0f699d27f38e864e2fce",
-                "samtools-flagstat-dp_Read_counts-2.yaml:md5,46debe080c753b6ba45501ea268e5d95",
-                "samtools-flagstat-dp_Read_counts.yaml:md5,2a3cbb23287d2123c29cfa1a3454a72a",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-1.yaml:md5,ac2602eede7202f9c0348760eb0b8bb6",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-2.yaml:md5,b1fe44cbd1cda8d4727a232c8c8bd513",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts.yaml:md5,ac1c7fc1c35a6719c962993d9bf5471e",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-1.yaml:md5,80c5b4f9cc0400799be48ef05aa6c410",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-2.yaml:md5,62d984dcdceba150863dd1e72c93f245",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.yaml:md5,989f82110113d8855a3f0cfa996cbdc6",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts-1.yaml:md5,94ddd17f7b9d15e547be9294e872e193",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts-2.yaml:md5,b8204d3b4480d3e9eec09d1289e52637",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts.yaml:md5,c944d25812a73c4ce9de9834943e6732",
+                "samtools-flagstat-pct-table.yaml:md5,96d661539b95863c30e181e5b64e46ca",
+                "samtools-flagstat-table.yaml:md5,46debe080c753b6ba45501ea268e5d95",
+                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-1.yaml:md5,ff73ac12f1542f46e1e61ef489c3c8e3",
+                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-2.yaml:md5,59851fa41690f7e7878e75ed9a6d31e7",
+                "samtools-idxstats-mapped-reads-plot_Normalised_Counts.yaml:md5,9eb530fdcb78b2740a2e26cc72112a32",
+                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-1.yaml:md5,e958aaff27c81aa1f197d491ff4bc0d2",
+                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-2.yaml:md5,e28a272081d679b36d3e1e31a5db1b02",
+                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.yaml:md5,a702f17e2426770da83f10037cb77e76",
+                "samtools-idxstats-mapped-reads-plot_Raw_Counts-1.yaml:md5,12a4d0294e7844b66ac8a434e5505268",
+                "samtools-idxstats-mapped-reads-plot_Raw_Counts-2.yaml:md5,42395713ecc6263c85e11416a126613d",
+                "samtools-idxstats-mapped-reads-plot_Raw_Counts.yaml:md5,4d58d9f278bd63548788dd0b9edff741",
                 "samtools-stats-dp.yaml:md5,ba5ad95c00d0bcef0d7aa32f941a813d",
                 "samtools_alignment_plot.yaml:md5,c1b5b60c3c83928275df7f720c5b1697",
                 "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384"
             ]
         ],
+        "timestamp": "2026-03-26T10:03:56.500035",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2026-03-20T23:11:22.404678758"
+            "nf-test": "0.9.4",
+            "nextflow": "25.04.0"
+        }
     }
 }
\ No newline at end of file
diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap
index addcf3020..cdbea53ce 100644
--- a/tests/skip_trimming.nf.test.snap
+++ b/tests/skip_trimming.nf.test.snap
@@ -36,8 +36,8 @@
                     "deeptools": "3.5.6"
                 },
                 "DESEQ2_QC": {
-                    "bioconductor-deseq2": "1.28.0",
-                    "r-base": "4.0.3"
+                    "DESeq2": "1.28.0",
+                    "R": "4.0.3"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -52,11 +52,8 @@
                 "GTF2BED": {
                     "perl": "5.26.2"
                 },
-                "HOMER_ANNOTATEPEAKS": {
-                    "homer": 4.11
-                },
                 "IGV": {
-                    "python": "3.8.3"
+                    "python": "3.12.12"
                 },
                 "MACS3_CALLPEAK": {
                     "macs3": "3.0.4"
@@ -68,6 +65,9 @@
                 "MULTIQC_CUSTOM_PEAKS": {
                     "sed": 4.7
                 },
+                "MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS": {
+                    "R": "4.5.3"
+                },
                 "PICARD_COLLECTMULTIPLEMETRICS": {
                     "picard": "3.4.0"
                 },
@@ -84,7 +84,7 @@
                     "R": "4.5.3"
                 },
                 "SAMPLESHEET_CHECK": {
-                    "python": "3.8.3"
+                    "python": "3.12.12"
                 },
                 "SAMTOOLS_FAIDX": {
                     "samtools": "1.22.1"
@@ -421,7 +421,9 @@
                 "multiqc/broad_peak/multiqc_data/fastqc_sequence_duplication_levels_plot.yaml",
                 "multiqc/broad_peak/multiqc_data/fastqc_top_overrepresented_sequences_table.yaml",
                 "multiqc/broad_peak/multiqc_data/featureCounts_assignment_plot.yaml",
+                "multiqc/broad_peak/multiqc_data/llms-full.txt",
                 "multiqc/broad_peak/multiqc_data/multiqc.log",
+                "multiqc/broad_peak/multiqc_data/multiqc.parquet",
                 "multiqc/broad_peak/multiqc_data/multiqc_citations.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_data.json",
                 "multiqc/broad_peak/multiqc_data/multiqc_deseq2_clustering_1.yaml",
@@ -433,51 +435,49 @@
                 "multiqc/broad_peak/multiqc_data/multiqc_peak_annotation.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_peak_count.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_phantompeakqualtools.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_AlignmentSummaryMetrics.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_insertSize.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_quality_by_cycle.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_quality_score_distribution.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard_baseContent.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_AlignmentSummaryMetrics_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_insertSize_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_quality_by_cycle_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_quality_score_distribution_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard_baseContent_picard-1.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_picard_dups.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_rsc_coefficient.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat_1.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat_2.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat_samtools-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat_samtools-2.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats_1.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats_2.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats_samtools-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats_samtools-2.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats_1.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats_2.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats_samtools-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats_samtools-2.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_software_versions.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_sources.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_strand_shift_correlation.yaml",
+                "multiqc/broad_peak/multiqc_data/picard-1_MarkIlluminaAdapters_histogram_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/picard-1_MeanQualityByCycle_histogram_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/picard-1_MeanQualityByCycle_histogram_picard-1_1.yaml",
+                "multiqc/broad_peak/multiqc_data/picard-1_QualityScoreDistribution_histogram_picard-1.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_alignment_readlength_plot.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_alignment_summary_Aligned_Bases.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_alignment_summary_Aligned_Reads.yaml",
-                "multiqc/broad_peak/multiqc_data/picard-1_histogram.yaml",
-                "multiqc/broad_peak/multiqc_data/picard-1_histogram_1.yaml",
-                "multiqc/broad_peak/multiqc_data/picard-1_histogram_2.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_insert_size_Counts.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_insert_size_Percentages.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_quality_by_cycle.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_quality_score_distribution.yaml",
+                "multiqc/broad_peak/multiqc_data/picard_MarkIlluminaAdapters_histogram.yaml",
+                "multiqc/broad_peak/multiqc_data/picard_MeanQualityByCycle_histogram.yaml",
+                "multiqc/broad_peak/multiqc_data/picard_MeanQualityByCycle_histogram_1.yaml",
+                "multiqc/broad_peak/multiqc_data/picard_QualityScoreDistribution_histogram.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Adenine.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Cytosine.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Guanine.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Thymine.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Undetermined.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_deduplication.yaml",
-                "multiqc/broad_peak/multiqc_data/picard_histogram.yaml",
-                "multiqc/broad_peak/multiqc_data/picard_histogram_1.yaml",
-                "multiqc/broad_peak/multiqc_data/picard_histogram_2.yaml",
                 "multiqc/broad_peak/multiqc_data/read_distribution_profile.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Percentage_of_total-1.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Percentage_of_total-2.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Percentage_of_total.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Read_counts-1.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Read_counts-2.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Read_counts.yaml",
+                "multiqc/broad_peak/multiqc_data/samtools-flagstat-pct-table.yaml",
+                "multiqc/broad_peak/multiqc_data/samtools-flagstat-table.yaml",
                 "multiqc/broad_peak/multiqc_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1.yaml",
                 "multiqc/broad_peak/multiqc_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts-2.yaml",
                 "multiqc/broad_peak/multiqc_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.yaml",
@@ -534,12 +534,8 @@
                 "multiqc/broad_peak/multiqc_plots/pdf/read_distribution_profile.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/rsc_coefficient-cnt.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/rsc_coefficient-pct.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Percentage_of_total-1.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Percentage_of_total-2.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Read_counts-1.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Read_counts-2.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Read_counts.pdf",
+                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-pct-table.pdf",
+                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-table.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-log.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-2-cnt.pdf",
@@ -606,12 +602,8 @@
                 "multiqc/broad_peak/multiqc_plots/png/read_distribution_profile.png",
                 "multiqc/broad_peak/multiqc_plots/png/rsc_coefficient-cnt.png",
                 "multiqc/broad_peak/multiqc_plots/png/rsc_coefficient-pct.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Percentage_of_total-1.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Percentage_of_total-2.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Percentage_of_total.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Read_counts-1.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Read_counts-2.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Read_counts.png",
+                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-pct-table.png",
+                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-table.png",
                 "multiqc/broad_peak/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.png",
                 "multiqc/broad_peak/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-log.png",
                 "multiqc/broad_peak/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-2-cnt.png",
@@ -678,12 +670,8 @@
                 "multiqc/broad_peak/multiqc_plots/svg/read_distribution_profile.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/rsc_coefficient-cnt.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/rsc_coefficient-pct.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Percentage_of_total-1.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Percentage_of_total-2.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Read_counts-1.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Read_counts-2.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Read_counts.svg",
+                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-pct-table.svg",
+                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-table.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-log.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-2-cnt.svg",
@@ -764,93 +752,93 @@
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "fastqc-status-check-heatmap.yaml:md5,1e473e0f9140b718607d8c72cf3c0b45",
-                "fastqc_adapter_content_plot.yaml:md5,591991daf3e3c49873f4a51a3710b072",
-                "fastqc_per_base_n_content_plot.yaml:md5,c16a4af177b9ad9694a9535023906927",
-                "fastqc_per_base_sequence_quality_plot.yaml:md5,20fc07ce2bc8e369d5fdd18afc6e60e9",
-                "fastqc_per_sequence_gc_content_plot_Counts.yaml:md5,ab233171fb8fd4e717886b01868ebcf2",
-                "fastqc_per_sequence_gc_content_plot_Percentages.yaml:md5,db29d683777cc0742585d1c48e712bd3",
-                "fastqc_per_sequence_quality_scores_plot.yaml:md5,351b55974af5ee21294ebf5deb850d7c",
+                "fastqc_adapter_content_plot.yaml:md5,de00547c4d9e5920e0e5c5b1f47981f7",
+                "fastqc_per_base_n_content_plot.yaml:md5,a2ac6f6a3323630922fb494def39b5c1",
+                "fastqc_per_base_sequence_quality_plot.yaml:md5,b0a022b4a3db86cc799142779155f9ed",
+                "fastqc_per_sequence_gc_content_plot_Counts.yaml:md5,679a374990a8c3b7a87fc55afca4c5f8",
+                "fastqc_per_sequence_gc_content_plot_Percentages.yaml:md5,c7a1700b9f6987c5dea327799902204a",
+                "fastqc_per_sequence_quality_scores_plot.yaml:md5,d4a8f8ced23faa497edb023ac00d9632",
                 "fastqc_sequence_counts_plot.yaml:md5,5522b2b42f0b3753dd359aad1565d7c2",
-                "fastqc_sequence_duplication_levels_plot.yaml:md5,e883323380f2880c81ea36dc91ad8678",
+                "fastqc_sequence_duplication_levels_plot.yaml:md5,e5532eac263c0b33ed3c024eca5fce94",
                 "fastqc_top_overrepresented_sequences_table.yaml:md5,443e161371f73cebf63c14f7a9f3580d",
                 "featureCounts_assignment_plot.yaml:md5,7d46061ca4ab9c393806d9dc2190d469",
+                "llms-full.txt:md5,9aa6b17d18a6fb44643b563cf281ace7",
+                "multiqc.parquet:md5,bef5f76bb83b79a3c56be2298b2f3f8f",
                 "multiqc_citations.yaml:md5,fa96797dbe164da76c4006ba9a9aa1e2",
                 "multiqc_fastqc.yaml:md5,30fe6d1a5e5c04695dda81294b828ec9",
                 "multiqc_featurecounts.yaml:md5,80609145666915fc888987e28628ec87",
                 "multiqc_frip_score.yaml:md5,68a0bf27565f380e121d4861fd35ed67",
                 "multiqc_nsc_coefficient.yaml:md5,167f8d2ff0b5c54265ef70e727257348",
-                "multiqc_peak_annotation.yaml:md5,91cbb7d9660d47c3de8771deb1ee5192",
-                "multiqc_peak_count.yaml:md5,a90be51b16c07f36278cc0a5948159a1",
+                "multiqc_peak_annotation.yaml:md5,16fa0c6cd67454ee116fd0db95483b4b",
+                "multiqc_peak_count.yaml:md5,812155a102b674566b29d2845b745483",
                 "multiqc_phantompeakqualtools.yaml:md5,4acbd2e598839f94376040108a6ff2b7",
-                "multiqc_picard-1_AlignmentSummaryMetrics.yaml:md5,99a15cd2e0477f4338a2f31713c58681",
-                "multiqc_picard-1_insertSize.yaml:md5,4468b6ca00b3be89426b1319b309bc62",
-                "multiqc_picard-1_quality_by_cycle.yaml:md5,5cb2257bf0ad79b5ae628c7cdf9c4e46",
-                "multiqc_picard-1_quality_score_distribution.yaml:md5,4012d180f127ee70efe233a816cbb97f",
-                "multiqc_picard_baseContent.yaml:md5,5ad8bb85fe50da94430bed46337305c8",
+                "multiqc_picard-1_AlignmentSummaryMetrics_picard-1.yaml:md5,99a15cd2e0477f4338a2f31713c58681",
+                "multiqc_picard-1_insertSize_picard-1.yaml:md5,4468b6ca00b3be89426b1319b309bc62",
+                "multiqc_picard-1_quality_by_cycle_picard-1.yaml:md5,5cb2257bf0ad79b5ae628c7cdf9c4e46",
+                "multiqc_picard-1_quality_score_distribution_picard-1.yaml:md5,4012d180f127ee70efe233a816cbb97f",
+                "multiqc_picard_baseContent_picard-1.yaml:md5,5ad8bb85fe50da94430bed46337305c8",
                 "multiqc_picard_dups.yaml:md5,c56ed89e6fca1ddb83d8072c462ae9ff",
                 "multiqc_rsc_coefficient.yaml:md5,717c1a82cf31984a5e0ee82e0c01026b",
                 "multiqc_samtools_flagstat.yaml:md5,06aa81950bf78bd0bad8099096653560",
-                "multiqc_samtools_flagstat_1.yaml:md5,5e1b0386799c0a3123858e145219615a",
-                "multiqc_samtools_flagstat_2.yaml:md5,61dd8be96d7009afcabe717a7a52d11a",
+                "multiqc_samtools_flagstat_samtools-1.yaml:md5,5e1b0386799c0a3123858e145219615a",
+                "multiqc_samtools_flagstat_samtools-2.yaml:md5,61dd8be96d7009afcabe717a7a52d11a",
                 "multiqc_samtools_idxstats.yaml:md5,dc6b87d84aeef0439da6077b67501cc3",
-                "multiqc_samtools_idxstats_1.yaml:md5,d7a1a6d14cfb88aa868784024f9b208e",
-                "multiqc_samtools_idxstats_2.yaml:md5,0a34ea933b55ee8ec1882cb22b0a097d",
-                "multiqc_samtools_stats.yaml:md5,4f6b2c1a2c66f3dc383608132776aafd",
-                "multiqc_samtools_stats_1.yaml:md5,572342726058b8bec39ab26180d94b92",
-                "multiqc_samtools_stats_2.yaml:md5,e29f10b3ac3cd08a2a96eb72d06bfaf1",
+                "multiqc_samtools_idxstats_samtools-1.yaml:md5,d7a1a6d14cfb88aa868784024f9b208e",
+                "multiqc_samtools_idxstats_samtools-2.yaml:md5,0a34ea933b55ee8ec1882cb22b0a097d",
+                "multiqc_samtools_stats.yaml:md5,eefe4770ca5885f4bb4cd83224c4cd11",
+                "multiqc_samtools_stats_samtools-1.yaml:md5,74c9138c91053d4cc9cc9bb315427613",
+                "multiqc_samtools_stats_samtools-2.yaml:md5,127dad3350641f8a1f8dc2d311947e5f",
+                "picard-1_MarkIlluminaAdapters_histogram_picard-1.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard-1_MeanQualityByCycle_histogram_picard-1.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard-1_MeanQualityByCycle_histogram_picard-1_1.yaml:md5,5cb2257bf0ad79b5ae628c7cdf9c4e46",
+                "picard-1_QualityScoreDistribution_histogram_picard-1.yaml:md5,4012d180f127ee70efe233a816cbb97f",
                 "picard-1_alignment_readlength_plot.yaml:md5,cd5131a2c38d9dc8072c39ee191d7e0b",
                 "picard-1_alignment_summary_Aligned_Bases.yaml:md5,86717ca1bbeef507046dee670543c763",
                 "picard-1_alignment_summary_Aligned_Reads.yaml:md5,c8559ff41529868f4e419cd22c41ba6f",
-                "picard-1_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
-                "picard-1_histogram_1.yaml:md5,5cb2257bf0ad79b5ae628c7cdf9c4e46",
-                "picard-1_histogram_2.yaml:md5,4012d180f127ee70efe233a816cbb97f",
-                "picard-1_insert_size_Counts.yaml:md5,465abea2c884be140e89c8cf3ad309c3",
-                "picard-1_insert_size_Percentages.yaml:md5,fb6c20e3a3f3020c209b5f806904082f",
-                "picard-1_quality_by_cycle.yaml:md5,fb474b70c11f8fe81f72369c08b8054c",
-                "picard-1_quality_score_distribution.yaml:md5,903baf5e71843524678485a8705c6617",
-                "picard_base_distribution_by_cycle__Adenine.yaml:md5,42d1afd748eae02fa3e752d324e6a374",
-                "picard_base_distribution_by_cycle__Cytosine.yaml:md5,54924614f53ea4cd0869f6c778b69999",
-                "picard_base_distribution_by_cycle__Guanine.yaml:md5,dd0dde5afd7b5b921adb9649ea138ceb",
-                "picard_base_distribution_by_cycle__Thymine.yaml:md5,fa6581e44811ce0cb14a34a89541ce15",
-                "picard_base_distribution_by_cycle__Undetermined.yaml:md5,4139649de017250f52cf86e4a9b44e00",
+                "picard-1_insert_size_Counts.yaml:md5,45f4c14ea212a1b7c4a0a1082be0cc6a",
+                "picard-1_insert_size_Percentages.yaml:md5,50244bb7b53dbbcb6732cf24eaa77757",
+                "picard-1_quality_by_cycle.yaml:md5,1838715577db38e8c3be9615405683f9",
+                "picard-1_quality_score_distribution.yaml:md5,799573490cf48ea17c2e0f727875152f",
+                "picard_MarkIlluminaAdapters_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard_MeanQualityByCycle_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard_MeanQualityByCycle_histogram_1.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard_QualityScoreDistribution_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard_base_distribution_by_cycle__Adenine.yaml:md5,84f8ccd787d62847ad25ed8d06c2cbcc",
+                "picard_base_distribution_by_cycle__Cytosine.yaml:md5,4b90cd4680fffa4524ec5c692026dbe4",
+                "picard_base_distribution_by_cycle__Guanine.yaml:md5,f85075ad0d2e8b5a836a30572a4138e9",
+                "picard_base_distribution_by_cycle__Thymine.yaml:md5,bf7bc4fcdb8b7d04c51dc0bcee45125b",
+                "picard_base_distribution_by_cycle__Undetermined.yaml:md5,1250c439077870950c015c3420cca8a0",
                 "picard_deduplication.yaml:md5,3b3298251d41828d79d76eb75188d368",
-                "picard_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
-                "picard_histogram_1.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
-                "picard_histogram_2.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
-                "samtools-flagstat-dp_Percentage_of_total-1.yaml:md5,0c14d9c586f29e6b576ad273032eea58",
-                "samtools-flagstat-dp_Percentage_of_total-2.yaml:md5,0c814013444b7866198be9f3a421475d",
-                "samtools-flagstat-dp_Percentage_of_total.yaml:md5,78b526c2c4712e47690c336a5b0980ed",
-                "samtools-flagstat-dp_Read_counts-1.yaml:md5,2368c79bd7b994ac9055dc7b62fd5c17",
-                "samtools-flagstat-dp_Read_counts-2.yaml:md5,fb0e11473916f2cd1d7ec502f57f39ff",
-                "samtools-flagstat-dp_Read_counts.yaml:md5,a20c997bdd2aff3e21e12aca5dd43c61",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-1.yaml:md5,48a345c40ec8f84e90b2a4a5aaf3db7c",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-2.yaml:md5,1fcc4a8f8aa7de6e54ec1f3ea610ed4b",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts.yaml:md5,4692f35c7b651a040aae2cf92744a1ea",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-1.yaml:md5,1f4e1d615529ad05be46adbfd13ad6a0",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-2.yaml:md5,af055d9f7409215eaf77b090ca57413b",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.yaml:md5,78f10a87fd257421174bad50cfe72412",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts-1.yaml:md5,972b5bd2f63137965c322ed8c5b6e245",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts-2.yaml:md5,35f42b24afe3b25a093c78d8610cd732",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts.yaml:md5,c035319353bb52655028940619e48afd",
+                "samtools-flagstat-pct-table.yaml:md5,0c814013444b7866198be9f3a421475d",
+                "samtools-flagstat-table.yaml:md5,fb0e11473916f2cd1d7ec502f57f39ff",
+                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-1.yaml:md5,87eb19cf6f8d2394b739c6ff371c39a9",
+                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-2.yaml:md5,ec4a3930a35575b9099d0bfd4a6b6ec0",
+                "samtools-idxstats-mapped-reads-plot_Normalised_Counts.yaml:md5,f25c2b68b2a00eb0b668df0491c564b4",
+                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-1.yaml:md5,9c4f7c545cc306ebaf6910b2128ab609",
+                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-2.yaml:md5,ae6817cbbcf8a99e881d6829e21382f9",
+                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.yaml:md5,5ef7780eff7f0dc70ca782745e41fd3a",
+                "samtools-idxstats-mapped-reads-plot_Raw_Counts-1.yaml:md5,3e6f8318e123ee0741735c95a61813ba",
+                "samtools-idxstats-mapped-reads-plot_Raw_Counts-2.yaml:md5,77a20ca5d2d63701bda9139cea5b217b",
+                "samtools-idxstats-mapped-reads-plot_Raw_Counts.yaml:md5,6e147564ac1255add4fb8f87fbeef984",
                 "samtools-stats-dp.yaml:md5,b1858c8488f3c506498726af69965dd6",
                 "samtools_alignment_plot.yaml:md5,a33df285c13ab5b360d9eb5282471908",
                 "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384"
             ]
         ],
+        "timestamp": "2026-03-26T10:16:50.220349",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2026-03-20T23:25:33.477057646"
+            "nf-test": "0.9.4",
+            "nextflow": "25.04.0"
+        }
     },
     "skip_trimming with stub": {
         "content": [
             190
         ],
+        "timestamp": "2026-03-17T14:36:41.411257",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.04.0"
-        },
-        "timestamp": "2026-03-17T14:36:41.411257"
+        }
     }
 }
\ No newline at end of file
diff --git a/tests/star.nf.test.snap b/tests/star.nf.test.snap
index 7e862b009..61b1ddf22 100644
--- a/tests/star.nf.test.snap
+++ b/tests/star.nf.test.snap
@@ -29,8 +29,8 @@
                     "deeptools": "3.5.6"
                 },
                 "DESEQ2_QC": {
-                    "bioconductor-deseq2": "1.28.0",
-                    "r-base": "4.0.3"
+                    "DESeq2": "1.28.0",
+                    "R": "4.0.3"
                 },
                 "FASTQC": {
                     "fastqc": "0.12.1"
@@ -45,11 +45,8 @@
                 "GTF2BED": {
                     "perl": "5.26.2"
                 },
-                "HOMER_ANNOTATEPEAKS": {
-                    "homer": 4.11
-                },
                 "IGV": {
-                    "python": "3.8.3"
+                    "python": "3.12.12"
                 },
                 "MACS3_CALLPEAK": {
                     "macs3": "3.0.4"
@@ -61,6 +58,9 @@
                 "MULTIQC_CUSTOM_PEAKS": {
                     "sed": 4.7
                 },
+                "MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS": {
+                    "R": "4.5.3"
+                },
                 "PICARD_COLLECTMULTIPLEMETRICS": {
                     "picard": "3.4.0"
                 },
@@ -77,7 +77,7 @@
                     "R": "4.5.3"
                 },
                 "SAMPLESHEET_CHECK": {
-                    "python": "3.8.3"
+                    "python": "3.12.12"
                 },
                 "SAMTOOLS_FAIDX": {
                     "samtools": "1.22.1"
@@ -183,65 +183,65 @@
                 "multiqc/broad_peak/multiqc_data/fastqc_sequence_length_distribution_plot.yaml",
                 "multiqc/broad_peak/multiqc_data/fastqc_top_overrepresented_sequences_table.yaml",
                 "multiqc/broad_peak/multiqc_data/featureCounts_assignment_plot.yaml",
+                "multiqc/broad_peak/multiqc_data/llms-full.txt",
                 "multiqc/broad_peak/multiqc_data/multiqc.log",
+                "multiqc/broad_peak/multiqc_data/multiqc.parquet",
                 "multiqc/broad_peak/multiqc_data/multiqc_citations.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_cutadapt.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_data.json",
                 "multiqc/broad_peak/multiqc_data/multiqc_deseq2_clustering_1.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_deseq2_pca_1.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_fastqc.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_fastqc_1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_fastqc_fastqc-1.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_featurecounts.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_frip_score.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_nsc_coefficient.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_peak_annotation.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_peak_count.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_phantompeakqualtools.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_AlignmentSummaryMetrics.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_insertSize.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_quality_by_cycle.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_quality_score_distribution.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_picard_baseContent.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_AlignmentSummaryMetrics_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_insertSize_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_quality_by_cycle_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard-1_quality_score_distribution_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_picard_baseContent_picard-1.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_picard_dups.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_rsc_coefficient.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat_1.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat_2.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat_samtools-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat_samtools-2.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats_1.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats_2.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats_samtools-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats_samtools-2.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats_1.yaml",
-                "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats_2.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats_samtools-1.yaml",
+                "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats_samtools-2.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_software_versions.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_sources.yaml",
                 "multiqc/broad_peak/multiqc_data/multiqc_strand_shift_correlation.yaml",
+                "multiqc/broad_peak/multiqc_data/picard-1_MarkIlluminaAdapters_histogram_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/picard-1_MeanQualityByCycle_histogram_picard-1.yaml",
+                "multiqc/broad_peak/multiqc_data/picard-1_MeanQualityByCycle_histogram_picard-1_1.yaml",
+                "multiqc/broad_peak/multiqc_data/picard-1_QualityScoreDistribution_histogram_picard-1.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_alignment_readlength_plot.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_alignment_summary_Aligned_Bases.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_alignment_summary_Aligned_Reads.yaml",
-                "multiqc/broad_peak/multiqc_data/picard-1_histogram.yaml",
-                "multiqc/broad_peak/multiqc_data/picard-1_histogram_1.yaml",
-                "multiqc/broad_peak/multiqc_data/picard-1_histogram_2.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_insert_size_Counts.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_insert_size_Percentages.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_quality_by_cycle.yaml",
                 "multiqc/broad_peak/multiqc_data/picard-1_quality_score_distribution.yaml",
+                "multiqc/broad_peak/multiqc_data/picard_MarkIlluminaAdapters_histogram.yaml",
+                "multiqc/broad_peak/multiqc_data/picard_MeanQualityByCycle_histogram.yaml",
+                "multiqc/broad_peak/multiqc_data/picard_MeanQualityByCycle_histogram_1.yaml",
+                "multiqc/broad_peak/multiqc_data/picard_QualityScoreDistribution_histogram.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Adenine.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Cytosine.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Guanine.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Thymine.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Undetermined.yaml",
                 "multiqc/broad_peak/multiqc_data/picard_deduplication.yaml",
-                "multiqc/broad_peak/multiqc_data/picard_histogram.yaml",
-                "multiqc/broad_peak/multiqc_data/picard_histogram_1.yaml",
-                "multiqc/broad_peak/multiqc_data/picard_histogram_2.yaml",
                 "multiqc/broad_peak/multiqc_data/read_distribution_profile.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Percentage_of_total-1.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Percentage_of_total-2.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Percentage_of_total.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Read_counts-1.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Read_counts-2.yaml",
-                "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Read_counts.yaml",
+                "multiqc/broad_peak/multiqc_data/samtools-flagstat-pct-table.yaml",
+                "multiqc/broad_peak/multiqc_data/samtools-flagstat-table.yaml",
                 "multiqc/broad_peak/multiqc_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1.yaml",
                 "multiqc/broad_peak/multiqc_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts-2.yaml",
                 "multiqc/broad_peak/multiqc_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.yaml",
@@ -314,12 +314,8 @@
                 "multiqc/broad_peak/multiqc_plots/pdf/read_distribution_profile.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/rsc_coefficient-cnt.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/rsc_coefficient-pct.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Percentage_of_total-1.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Percentage_of_total-2.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Read_counts-1.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Read_counts-2.pdf",
-                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-dp_Read_counts.pdf",
+                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-pct-table.pdf",
+                "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-table.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-log.pdf",
                 "multiqc/broad_peak/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-2-cnt.pdf",
@@ -402,12 +398,8 @@
                 "multiqc/broad_peak/multiqc_plots/png/read_distribution_profile.png",
                 "multiqc/broad_peak/multiqc_plots/png/rsc_coefficient-cnt.png",
                 "multiqc/broad_peak/multiqc_plots/png/rsc_coefficient-pct.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Percentage_of_total-1.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Percentage_of_total-2.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Percentage_of_total.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Read_counts-1.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Read_counts-2.png",
-                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-dp_Read_counts.png",
+                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-pct-table.png",
+                "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-table.png",
                 "multiqc/broad_peak/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.png",
                 "multiqc/broad_peak/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-log.png",
                 "multiqc/broad_peak/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-2-cnt.png",
@@ -490,12 +482,8 @@
                 "multiqc/broad_peak/multiqc_plots/svg/read_distribution_profile.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/rsc_coefficient-cnt.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/rsc_coefficient-pct.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Percentage_of_total-1.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Percentage_of_total-2.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Read_counts-1.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Read_counts-2.svg",
-                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-dp_Read_counts.svg",
+                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-pct-table.svg",
+                "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-table.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-log.svg",
                 "multiqc/broad_peak/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-2-cnt.svg",
@@ -849,89 +837,89 @@
                 "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
                 "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc",
                 "cutadapt_filtered_reads_plot.yaml:md5,976fdb8049d847c977195863418e3655",
-                "cutadapt_trimmed_sequences_plot_3_Counts.yaml:md5,e6733f4ff773a27d0ab81564913b4b54",
-                "cutadapt_trimmed_sequences_plot_3_Obs_Exp.yaml:md5,9ffcfe37c02af14b8eddd4746066e56a",
+                "cutadapt_trimmed_sequences_plot_3_Counts.yaml:md5,1dba61b1d90518e1f020b71c4cfa04c4",
+                "cutadapt_trimmed_sequences_plot_3_Obs_Exp.yaml:md5,42335c2990d3a991e2bd0716f80b0515",
                 "fastqc-1-status-check-heatmap.yaml:md5,6c6e1591b5ff248c85446f9728a3dad4",
-                "fastqc-1_adapter_content_plot.yaml:md5,d78273a7e4ff36434bb91246fef01523",
-                "fastqc-1_per_base_n_content_plot.yaml:md5,3625446964b669ccff279aba54510462",
-                "fastqc-1_per_base_sequence_quality_plot.yaml:md5,1fb4d35d6b94fc4f41d5be1304844b95",
-                "fastqc-1_per_sequence_gc_content_plot_Counts.yaml:md5,101f11f9cebcc626755f32322b27ebd3",
-                "fastqc-1_per_sequence_gc_content_plot_Percentages.yaml:md5,0055f4bbded45434618259f47fe5fe85",
-                "fastqc-1_per_sequence_quality_scores_plot.yaml:md5,eed2628303916e49143ccf37300fb5de",
+                "fastqc-1_adapter_content_plot.yaml:md5,8acbcb9c6f3b5e42b19a7ab4bd1d607b",
+                "fastqc-1_per_base_n_content_plot.yaml:md5,24c7a2b7d290d797e7757adfd7b67175",
+                "fastqc-1_per_base_sequence_quality_plot.yaml:md5,ddaf5d8d0dad842c9e00a9cdde2a82c7",
+                "fastqc-1_per_sequence_gc_content_plot_Counts.yaml:md5,191d3d72a05700fa5b69854ff47b6e66",
+                "fastqc-1_per_sequence_gc_content_plot_Percentages.yaml:md5,f9cc6e0466e1791e9b3bd765ab3b9a57",
+                "fastqc-1_per_sequence_quality_scores_plot.yaml:md5,6bfed2114551676b4c60e897f12c6e12",
                 "fastqc-1_sequence_counts_plot.yaml:md5,6ca3a8cf8d258777e29b8e8731157d90",
-                "fastqc-1_sequence_duplication_levels_plot.yaml:md5,3e3622b7dd80be1db92ac06df8e3d056",
+                "fastqc-1_sequence_duplication_levels_plot.yaml:md5,fa8e5813c72d6366bf50d99c0eb20f56",
                 "fastqc-1_top_overrepresented_sequences_table.yaml:md5,a333a02f5313876cf1713d7b0168d5f3",
                 "fastqc-status-check-heatmap.yaml:md5,1e473e0f9140b718607d8c72cf3c0b45",
-                "fastqc_adapter_content_plot.yaml:md5,591991daf3e3c49873f4a51a3710b072",
-                "fastqc_per_base_n_content_plot.yaml:md5,c16a4af177b9ad9694a9535023906927",
-                "fastqc_per_base_sequence_quality_plot.yaml:md5,20fc07ce2bc8e369d5fdd18afc6e60e9",
-                "fastqc_per_sequence_gc_content_plot_Counts.yaml:md5,ab233171fb8fd4e717886b01868ebcf2",
-                "fastqc_per_sequence_gc_content_plot_Percentages.yaml:md5,db29d683777cc0742585d1c48e712bd3",
-                "fastqc_per_sequence_quality_scores_plot.yaml:md5,351b55974af5ee21294ebf5deb850d7c",
+                "fastqc_adapter_content_plot.yaml:md5,de00547c4d9e5920e0e5c5b1f47981f7",
+                "fastqc_per_base_n_content_plot.yaml:md5,a2ac6f6a3323630922fb494def39b5c1",
+                "fastqc_per_base_sequence_quality_plot.yaml:md5,b0a022b4a3db86cc799142779155f9ed",
+                "fastqc_per_sequence_gc_content_plot_Counts.yaml:md5,679a374990a8c3b7a87fc55afca4c5f8",
+                "fastqc_per_sequence_gc_content_plot_Percentages.yaml:md5,c7a1700b9f6987c5dea327799902204a",
+                "fastqc_per_sequence_quality_scores_plot.yaml:md5,d4a8f8ced23faa497edb023ac00d9632",
                 "fastqc_sequence_counts_plot.yaml:md5,5522b2b42f0b3753dd359aad1565d7c2",
-                "fastqc_sequence_duplication_levels_plot.yaml:md5,e883323380f2880c81ea36dc91ad8678",
-                "fastqc_sequence_length_distribution_plot.yaml:md5,d57678f16381986766d56b631c838106",
+                "fastqc_sequence_duplication_levels_plot.yaml:md5,e5532eac263c0b33ed3c024eca5fce94",
+                "fastqc_sequence_length_distribution_plot.yaml:md5,e701cb601de4693ab09473b849e4f110",
                 "fastqc_top_overrepresented_sequences_table.yaml:md5,443e161371f73cebf63c14f7a9f3580d",
                 "featureCounts_assignment_plot.yaml:md5,af828a63e428826fc5d3ff32647ce0c0",
+                "llms-full.txt:md5,cf1a888e785c555f81ae929eb1f86296",
+                "multiqc.parquet:md5,6eafc65636c9eade9616e16f5f279c69",
                 "multiqc_citations.yaml:md5,fca5dc7cb20162434c714d26b11161f3",
                 "multiqc_fastqc.yaml:md5,30fe6d1a5e5c04695dda81294b828ec9",
-                "multiqc_fastqc_1.yaml:md5,cd4a85c27c3cf85f1d0612afce793186",
+                "multiqc_fastqc_fastqc-1.yaml:md5,cd4a85c27c3cf85f1d0612afce793186",
                 "multiqc_featurecounts.yaml:md5,f69f606ff89c226af76a314ef8d5c570",
                 "multiqc_frip_score.yaml:md5,36436376e2c9a22a938134a7622f1329",
                 "multiqc_nsc_coefficient.yaml:md5,db4bf467647aaa58aa24f9c2a84baeed",
-                "multiqc_peak_annotation.yaml:md5,a2d85e81922d57a1881bbf4ff4c22d7f",
-                "multiqc_peak_count.yaml:md5,90357ad171d18834bfa94d2ca8f3627a",
+                "multiqc_peak_annotation.yaml:md5,9fcdf450e744f8e9939eefbc3328addc",
+                "multiqc_peak_count.yaml:md5,36fff5b98ab269eaf389ba9e92e90720",
                 "multiqc_phantompeakqualtools.yaml:md5,41ee3c7cb346e8edd6bfa1840dbb3148",
-                "multiqc_picard-1_AlignmentSummaryMetrics.yaml:md5,a08a48e002fbc010d987f067bccf9d21",
-                "multiqc_picard-1_insertSize.yaml:md5,d5752d2971e46bdb039b26e13975e0a8",
-                "multiqc_picard-1_quality_by_cycle.yaml:md5,274510d9d5ebd92855c91575d689f23c",
-                "multiqc_picard-1_quality_score_distribution.yaml:md5,7181c6520952202b6f6c4c59a79e2f9f",
-                "multiqc_picard_baseContent.yaml:md5,afeae1015f2202d6860a463f74f2dfb2",
+                "multiqc_picard-1_AlignmentSummaryMetrics_picard-1.yaml:md5,a08a48e002fbc010d987f067bccf9d21",
+                "multiqc_picard-1_insertSize_picard-1.yaml:md5,d5752d2971e46bdb039b26e13975e0a8",
+                "multiqc_picard-1_quality_by_cycle_picard-1.yaml:md5,274510d9d5ebd92855c91575d689f23c",
+                "multiqc_picard-1_quality_score_distribution_picard-1.yaml:md5,7181c6520952202b6f6c4c59a79e2f9f",
+                "multiqc_picard_baseContent_picard-1.yaml:md5,afeae1015f2202d6860a463f74f2dfb2",
                 "multiqc_picard_dups.yaml:md5,12a480fb4ec36fadd7de6b79d6646f77",
                 "multiqc_rsc_coefficient.yaml:md5,fd55f3f1c4324f4fcfa5222d846b894a",
                 "multiqc_samtools_flagstat.yaml:md5,052425f0d7c1b6b685ff13eddd1f7c3d",
-                "multiqc_samtools_flagstat_1.yaml:md5,68cc882c81e39977e7ee7e11f480c7a3",
-                "multiqc_samtools_flagstat_2.yaml:md5,24b7467f1c4958f748fbef7b5cb90b2e",
+                "multiqc_samtools_flagstat_samtools-1.yaml:md5,68cc882c81e39977e7ee7e11f480c7a3",
+                "multiqc_samtools_flagstat_samtools-2.yaml:md5,24b7467f1c4958f748fbef7b5cb90b2e",
                 "multiqc_samtools_idxstats.yaml:md5,161755a5da0e2f64d009b29db7caf3ee",
-                "multiqc_samtools_idxstats_1.yaml:md5,46ecc1660878d96d3c8ec4a5d7241032",
-                "multiqc_samtools_idxstats_2.yaml:md5,aee859edcc202e01934b40ca15c1e4f7",
-                "multiqc_samtools_stats.yaml:md5,8a995db38967f0b5c339078425ac70f9",
-                "multiqc_samtools_stats_1.yaml:md5,255695d4d6ca87b1bc2bb46dee0856fb",
-                "multiqc_samtools_stats_2.yaml:md5,d17c8c8a0c62973f443db09e458a3f30",
+                "multiqc_samtools_idxstats_samtools-1.yaml:md5,46ecc1660878d96d3c8ec4a5d7241032",
+                "multiqc_samtools_idxstats_samtools-2.yaml:md5,aee859edcc202e01934b40ca15c1e4f7",
+                "multiqc_samtools_stats.yaml:md5,54cd4858dcc218d7a863fa4cd6011b5b",
+                "multiqc_samtools_stats_samtools-1.yaml:md5,1c9ab92b301b6d0128eb73defdbf5979",
+                "multiqc_samtools_stats_samtools-2.yaml:md5,f0d498cb924131664569a56c90c389c4",
+                "picard-1_MarkIlluminaAdapters_histogram_picard-1.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard-1_MeanQualityByCycle_histogram_picard-1.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard-1_MeanQualityByCycle_histogram_picard-1_1.yaml:md5,274510d9d5ebd92855c91575d689f23c",
+                "picard-1_QualityScoreDistribution_histogram_picard-1.yaml:md5,7181c6520952202b6f6c4c59a79e2f9f",
                 "picard-1_alignment_readlength_plot.yaml:md5,43006423c38f9dacc54308a545ce27d6",
                 "picard-1_alignment_summary_Aligned_Bases.yaml:md5,1bfcb93e21b3630f3dba984a190b5c67",
                 "picard-1_alignment_summary_Aligned_Reads.yaml:md5,364411d722c2569b232d8d1f306270f6",
-                "picard-1_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
-                "picard-1_histogram_1.yaml:md5,274510d9d5ebd92855c91575d689f23c",
-                "picard-1_histogram_2.yaml:md5,7181c6520952202b6f6c4c59a79e2f9f",
-                "picard-1_insert_size_Counts.yaml:md5,3394bb38c3b2674fc8596cea504c2a35",
-                "picard-1_insert_size_Percentages.yaml:md5,101e18eff7487218d0bc0435d7cb3edd",
-                "picard-1_quality_by_cycle.yaml:md5,ac1570fa2fbb774d045b8063a38ea475",
-                "picard-1_quality_score_distribution.yaml:md5,54504c0c85ab893fa9bef8c5594b3fe8",
-                "picard_base_distribution_by_cycle__Adenine.yaml:md5,ea5539035066d55f9ce0cce3092e9b71",
-                "picard_base_distribution_by_cycle__Cytosine.yaml:md5,1ff0d8fa67bdac5bf12eeef76034ba35",
-                "picard_base_distribution_by_cycle__Guanine.yaml:md5,cf13ddf5eb118b54a2e7bae98ad82df4",
-                "picard_base_distribution_by_cycle__Thymine.yaml:md5,65f4fddb8f37c79751b3be001316ed91",
-                "picard_base_distribution_by_cycle__Undetermined.yaml:md5,fb60eee4ab17148525395d5ac03c45ff",
+                "picard-1_insert_size_Counts.yaml:md5,80a275af8db5394c70cee179aee54667",
+                "picard-1_insert_size_Percentages.yaml:md5,0a34c1f50d67f6ffc9b87641fcbf67a3",
+                "picard-1_quality_by_cycle.yaml:md5,61d735699fb066ec16341ee84a0b7b0a",
+                "picard-1_quality_score_distribution.yaml:md5,f9fa9aea9ebe0b26ab3dccb14da54d48",
+                "picard_MarkIlluminaAdapters_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard_MeanQualityByCycle_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard_MeanQualityByCycle_histogram_1.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard_QualityScoreDistribution_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
+                "picard_base_distribution_by_cycle__Adenine.yaml:md5,c987ceed3cfaa9d9bf483c1e38aae674",
+                "picard_base_distribution_by_cycle__Cytosine.yaml:md5,edf33d12cbae5b8aa218f0102f2f80ec",
+                "picard_base_distribution_by_cycle__Guanine.yaml:md5,bce2a947fe124c078a1b28bf5367658a",
+                "picard_base_distribution_by_cycle__Thymine.yaml:md5,344abd38aa71f1c83d6279c44f2c36cd",
+                "picard_base_distribution_by_cycle__Undetermined.yaml:md5,80f34d5f6817fd82ad33b2c9c8d85a3c",
                 "picard_deduplication.yaml:md5,2e601aca787c042f3217006177626c54",
-                "picard_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
-                "picard_histogram_1.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
-                "picard_histogram_2.yaml:md5,8a80554c91d9fca8acb82f023de02f11",
-                "samtools-flagstat-dp_Percentage_of_total-1.yaml:md5,7f5f29d5237dcf009f8da7ac51def174",
-                "samtools-flagstat-dp_Percentage_of_total-2.yaml:md5,1a17e60308156cb05bacdc4450aeb373",
-                "samtools-flagstat-dp_Percentage_of_total.yaml:md5,362d2193e88b87cecdb3684ac53b4950",
-                "samtools-flagstat-dp_Read_counts-1.yaml:md5,7eebf2653486a02db5860bb3ab5830ba",
-                "samtools-flagstat-dp_Read_counts-2.yaml:md5,84527e9fcc6cd9af3a5a1b04a90e3f99",
-                "samtools-flagstat-dp_Read_counts.yaml:md5,5a571810f75b695928faf1e0821f203a",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-1.yaml:md5,51652ae5862b748b78913cfd45db5027",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-2.yaml:md5,a61c13ea19f6eda57775ade3b6287b06",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts.yaml:md5,7f15d71423400784ac33c0378b8c01e5",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-1.yaml:md5,56e2a1bcd41156dff07d4a16083bb62e",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-2.yaml:md5,b88cf377100b36f0583a7d4cf94e82cf",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.yaml:md5,d4346380ce382d04ff2b32e0db262425",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts-1.yaml:md5,c5c5eb07c5bd898f02f8e45c1405f363",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts-2.yaml:md5,569910952bbfc4525972fe3431cf5165",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts.yaml:md5,419fc35bbb01e2a35f66f2abdb4b8d49",
+                "samtools-flagstat-pct-table.yaml:md5,1a17e60308156cb05bacdc4450aeb373",
+                "samtools-flagstat-table.yaml:md5,84527e9fcc6cd9af3a5a1b04a90e3f99",
+                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-1.yaml:md5,e4482329fe0cc9a766ff77da5364edbb",
+                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-2.yaml:md5,7a74c5b9073cf1f5ecf8121e227b60f3",
+                "samtools-idxstats-mapped-reads-plot_Normalised_Counts.yaml:md5,f97f198e1eccd9de2fd6ded1f3cccfcb",
+                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-1.yaml:md5,97ed83a1bcc418a5ed85e3127fd3e122",
+                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-2.yaml:md5,6cdd0622ae66e61630fa2dcd26575961",
+                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.yaml:md5,6761453407279a97cb9cc3ca1137c97f",
+                "samtools-idxstats-mapped-reads-plot_Raw_Counts-1.yaml:md5,d180edd0ff8240b3e185b600478ac562",
+                "samtools-idxstats-mapped-reads-plot_Raw_Counts-2.yaml:md5,29cc7b62046ca2a50b552060d76bbf2c",
+                "samtools-idxstats-mapped-reads-plot_Raw_Counts.yaml:md5,928f43f5e3249d4fa62672d82fc8f7b3",
                 "samtools-stats-dp.yaml:md5,3334c53a05a1f70ee4bd06226479a1a5",
                 "samtools_alignment_plot.yaml:md5,e78658bf88e7d795367a1c1323d96b62",
                 "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384",
@@ -991,20 +979,20 @@
                 "SPT5_T15_REP2.mLb.clN.sorted.bam.idxstats:md5,aa2db2bcb3aa876cfbfe24b49d98aabd"
             ]
         ],
+        "timestamp": "2026-03-26T10:33:51.882819",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2026-03-20T23:47:55.56498065"
+            "nf-test": "0.9.4",
+            "nextflow": "25.04.0"
+        }
     },
     "star with stub": {
         "content": [
             20
         ],
+        "timestamp": "2026-03-17T16:23:46.465421",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.04.0"
-        },
-        "timestamp": "2026-03-17T16:23:46.465421"
+        }
     }
 }
\ No newline at end of file

From adbd05b71de67100972ff3c66250d86fdae0971d Mon Sep 17 00:00:00 2001
From: Kevin-Brockers <kevin.brockers@yahoo.de>
Date: Thu, 26 Mar 2026 11:07:37 +0100
Subject: [PATCH 16/20] fixed formatting

---
 modules/local/gtf2bed/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/gtf2bed/main.nf b/modules/local/gtf2bed/main.nf
index 1248e978b..883834a9c 100644
--- a/modules/local/gtf2bed/main.nf
+++ b/modules/local/gtf2bed/main.nf
@@ -13,7 +13,7 @@ process GTF2BED {
     output:
     path '*.bed'       , emit: bed
     tuple val({"${task.process}"}), val('perl'), eval("perl -V:version | sed \"s/version='//; s/';//\""), topic:versions, emit: versions_perl
-                                                      
+
 
     when:
     task.ext.when == null || task.ext.when

From 0a631f1271068594671bc73c91d6bb6a9f56e42d Mon Sep 17 00:00:00 2001
From: Kevin-Brockers <kevin.brockers@yahoo.de>
Date: Thu, 26 Mar 2026 12:56:02 +0100
Subject: [PATCH 17/20] Added unstable multiqc outputs

---
 tests/.nftignore | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tests/.nftignore b/tests/.nftignore
index 35e0cf606..028688516 100644
--- a/tests/.nftignore
+++ b/tests/.nftignore
@@ -16,6 +16,8 @@ multiqc/multiqc_data/BETA-multiqc.parquet
 **/multiqc_software_versions.yaml
 multiqc/multiqc_data/multiqc_sources.txt
 multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
+**/multiqc_data/llms-full.txt
+**/multiqc_data/multiqc.parquet
 
 # === QC TOOL OUTPUTS ===
 fastqc/*_fastqc.{html,zip}

From cb5f0135ca5acea44b650e7d1744c4a647bdcdaa Mon Sep 17 00:00:00 2001
From: Kevin-Brockers <kevin.brockers@yahoo.de>
Date: Thu, 26 Mar 2026 14:43:06 +0100
Subject: [PATCH 18/20] ignore some multiqc outputs

---
 tests/bowtie2.nf.test.snap              | 4 +---
 tests/chromap.nf.test.snap              | 4 +---
 tests/default.nf.test.snap              | 4 +---
 tests/skip_consensus_peaks.nf.test.snap | 4 +---
 tests/skip_trimming.nf.test.snap        | 4 +---
 tests/star.nf.test.snap                 | 4 +---
 6 files changed, 6 insertions(+), 18 deletions(-)

diff --git a/tests/bowtie2.nf.test.snap b/tests/bowtie2.nf.test.snap
index fb78b3a3d..b201e9786 100644
--- a/tests/bowtie2.nf.test.snap
+++ b/tests/bowtie2.nf.test.snap
@@ -884,8 +884,6 @@
                 "fastqc_sequence_length_distribution_plot.yaml:md5,e701cb601de4693ab09473b849e4f110",
                 "fastqc_top_overrepresented_sequences_table.yaml:md5,443e161371f73cebf63c14f7a9f3580d",
                 "featureCounts_assignment_plot.yaml:md5,4da17bf822e2c2645d81610248f44db3",
-                "llms-full.txt:md5,77b52a1c7589b6f8af5e46de2fd0f1cc",
-                "multiqc.parquet:md5,99b4b02535b8a795ba8078ffd049b8a3",
                 "multiqc_citations.yaml:md5,fca5dc7cb20162434c714d26b11161f3",
                 "multiqc_fastqc.yaml:md5,30fe6d1a5e5c04695dda81294b828ec9",
                 "multiqc_fastqc_fastqc-1.yaml:md5,cd4a85c27c3cf85f1d0612afce793186",
@@ -948,7 +946,7 @@
                 "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384"
             ]
         ],
-        "timestamp": "2026-03-26T09:26:04.859632",
+        "timestamp": "2026-03-26T13:38:56.98274",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.04.0"
diff --git a/tests/chromap.nf.test.snap b/tests/chromap.nf.test.snap
index bc07778ed..cb1b94ffe 100644
--- a/tests/chromap.nf.test.snap
+++ b/tests/chromap.nf.test.snap
@@ -880,8 +880,6 @@
                 "fastqc_sequence_length_distribution_plot.yaml:md5,e701cb601de4693ab09473b849e4f110",
                 "fastqc_top_overrepresented_sequences_table.yaml:md5,443e161371f73cebf63c14f7a9f3580d",
                 "featureCounts_assignment_plot.yaml:md5,7ba9bc1659472a0859c527d0f8f10c8b",
-                "llms-full.txt:md5,a8e704a8a5f8f600f54cc4db24703e25",
-                "multiqc.parquet:md5,1021d6967e6855322d0c3915564cc061",
                 "multiqc_citations.yaml:md5,fca5dc7cb20162434c714d26b11161f3",
                 "multiqc_fastqc.yaml:md5,30fe6d1a5e5c04695dda81294b828ec9",
                 "multiqc_fastqc_fastqc-1.yaml:md5,cd4a85c27c3cf85f1d0612afce793186",
@@ -944,7 +942,7 @@
                 "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384"
             ]
         ],
-        "timestamp": "2026-03-26T09:39:17.499506",
+        "timestamp": "2026-03-26T13:48:17.847211",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.04.0"
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index 6db943e96..b65c99a20 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -883,8 +883,6 @@
                 "fastqc_sequence_length_distribution_plot.yaml:md5,e701cb601de4693ab09473b849e4f110",
                 "fastqc_top_overrepresented_sequences_table.yaml:md5,443e161371f73cebf63c14f7a9f3580d",
                 "featureCounts_assignment_plot.yaml:md5,9ebb47589533f668f7b2b4e59d5231c5",
-                "llms-full.txt:md5,b5b5f6cc68b1770ed707020d9561edc3",
-                "multiqc.parquet:md5,d51dc50a673f5237e5d75acf3ef806b8",
                 "multiqc_citations.yaml:md5,fca5dc7cb20162434c714d26b11161f3",
                 "multiqc_fastqc.yaml:md5,30fe6d1a5e5c04695dda81294b828ec9",
                 "multiqc_fastqc_fastqc-1.yaml:md5,cd4a85c27c3cf85f1d0612afce793186",
@@ -947,7 +945,7 @@
                 "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384"
             ]
         ],
-        "timestamp": "2026-03-26T09:52:21.465107",
+        "timestamp": "2026-03-26T13:57:56.16437",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.04.0"
diff --git a/tests/skip_consensus_peaks.nf.test.snap b/tests/skip_consensus_peaks.nf.test.snap
index 916f94e7e..977ee3f4c 100644
--- a/tests/skip_consensus_peaks.nf.test.snap
+++ b/tests/skip_consensus_peaks.nf.test.snap
@@ -825,8 +825,6 @@
                 "fastqc_sequence_duplication_levels_plot.yaml:md5,e5532eac263c0b33ed3c024eca5fce94",
                 "fastqc_sequence_length_distribution_plot.yaml:md5,e701cb601de4693ab09473b849e4f110",
                 "fastqc_top_overrepresented_sequences_table.yaml:md5,443e161371f73cebf63c14f7a9f3580d",
-                "llms-full.txt:md5,d4acf16d6ba49180502b0019bcd2d6c9",
-                "multiqc.parquet:md5,97238dcfd7d08cf243e3dca203123076",
                 "multiqc_citations.yaml:md5,c4cdebc20cfc52eb2eee741a36323b3e",
                 "multiqc_fastqc.yaml:md5,30fe6d1a5e5c04695dda81294b828ec9",
                 "multiqc_fastqc_fastqc-1.yaml:md5,cd4a85c27c3cf85f1d0612afce793186",
@@ -888,7 +886,7 @@
                 "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384"
             ]
         ],
-        "timestamp": "2026-03-26T10:03:56.500035",
+        "timestamp": "2026-03-26T14:06:46.726058",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.04.0"
diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap
index cdbea53ce..78b20cd57 100644
--- a/tests/skip_trimming.nf.test.snap
+++ b/tests/skip_trimming.nf.test.snap
@@ -762,8 +762,6 @@
                 "fastqc_sequence_duplication_levels_plot.yaml:md5,e5532eac263c0b33ed3c024eca5fce94",
                 "fastqc_top_overrepresented_sequences_table.yaml:md5,443e161371f73cebf63c14f7a9f3580d",
                 "featureCounts_assignment_plot.yaml:md5,7d46061ca4ab9c393806d9dc2190d469",
-                "llms-full.txt:md5,9aa6b17d18a6fb44643b563cf281ace7",
-                "multiqc.parquet:md5,bef5f76bb83b79a3c56be2298b2f3f8f",
                 "multiqc_citations.yaml:md5,fa96797dbe164da76c4006ba9a9aa1e2",
                 "multiqc_fastqc.yaml:md5,30fe6d1a5e5c04695dda81294b828ec9",
                 "multiqc_featurecounts.yaml:md5,80609145666915fc888987e28628ec87",
@@ -825,7 +823,7 @@
                 "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384"
             ]
         ],
-        "timestamp": "2026-03-26T10:16:50.220349",
+        "timestamp": "2026-03-26T14:16:04.604869",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.04.0"
diff --git a/tests/star.nf.test.snap b/tests/star.nf.test.snap
index 61b1ddf22..a139cab12 100644
--- a/tests/star.nf.test.snap
+++ b/tests/star.nf.test.snap
@@ -861,8 +861,6 @@
                 "fastqc_sequence_length_distribution_plot.yaml:md5,e701cb601de4693ab09473b849e4f110",
                 "fastqc_top_overrepresented_sequences_table.yaml:md5,443e161371f73cebf63c14f7a9f3580d",
                 "featureCounts_assignment_plot.yaml:md5,af828a63e428826fc5d3ff32647ce0c0",
-                "llms-full.txt:md5,cf1a888e785c555f81ae929eb1f86296",
-                "multiqc.parquet:md5,6eafc65636c9eade9616e16f5f279c69",
                 "multiqc_citations.yaml:md5,fca5dc7cb20162434c714d26b11161f3",
                 "multiqc_fastqc.yaml:md5,30fe6d1a5e5c04695dda81294b828ec9",
                 "multiqc_fastqc_fastqc-1.yaml:md5,cd4a85c27c3cf85f1d0612afce793186",
@@ -979,7 +977,7 @@
                 "SPT5_T15_REP2.mLb.clN.sorted.bam.idxstats:md5,aa2db2bcb3aa876cfbfe24b49d98aabd"
             ]
         ],
-        "timestamp": "2026-03-26T10:33:51.882819",
+        "timestamp": "2026-03-26T14:28:39.102565",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.04.0"

From 77ca9a4c3a2ca29848f9fa2bf763f2c41af89696 Mon Sep 17 00:00:00 2001
From: Kevin-Brockers <kevin.brockers@yahoo.de>
Date: Sat, 28 Mar 2026 10:01:59 +0100
Subject: [PATCH 19/20] Implemented Joses PR review suggestions

---
 modules/local/gtf2bed/main.nf                                  | 3 +--
 modules/local/multiqc_custom_phantompeakqualtools/main.nf      | 2 +-
 .../local/bam_peaks_call_qc_annotate_macs3_homer/main.nf       | 1 +
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/local/gtf2bed/main.nf b/modules/local/gtf2bed/main.nf
index 883834a9c..2109420a8 100644
--- a/modules/local/gtf2bed/main.nf
+++ b/modules/local/gtf2bed/main.nf
@@ -12,8 +12,7 @@ process GTF2BED {
 
     output:
     path '*.bed'       , emit: bed
-    tuple val({"${task.process}"}), val('perl'), eval("perl -V:version | sed \"s/version='//; s/';//\""), topic:versions, emit: versions_perl
-
+    tuple val("${task.process}"), val('perl'), eval("perl -V:version | sed \"s/version='//; s/';//\""), topic:versions, emit: versions_perl
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/local/multiqc_custom_phantompeakqualtools/main.nf b/modules/local/multiqc_custom_phantompeakqualtools/main.nf
index 368281e72..d6782b5db 100644
--- a/modules/local/multiqc_custom_phantompeakqualtools/main.nf
+++ b/modules/local/multiqc_custom_phantompeakqualtools/main.nf
@@ -1,6 +1,6 @@
 process MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS {
     tag "$meta.id"
-    conda "conda-forge::r-base=4.3.3"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c7/c73daa0b0040137fbea15fc8ee54c9bf4e0a9c5e9412cc7c13f7b38cc9c8bbd9/data':
         'community.wave.seqera.io/library/r-base:4.5.3--6814a4ccafc04d08' }"
diff --git a/subworkflows/local/bam_peaks_call_qc_annotate_macs3_homer/main.nf b/subworkflows/local/bam_peaks_call_qc_annotate_macs3_homer/main.nf
index e1d2fa85f..e2f56948c 100644
--- a/subworkflows/local/bam_peaks_call_qc_annotate_macs3_homer/main.nf
+++ b/subworkflows/local/bam_peaks_call_qc_annotate_macs3_homer/main.nf
@@ -98,6 +98,7 @@ workflow BAM_PEAKS_CALL_QC_ANNOTATE_MACS3_HOMER {
             ch_gtf
         )
         ch_homer_annotatepeaks = HOMER_ANNOTATEPEAKS.out.txt
+        ch_versions = ch_versions.mix(HOMER_ANNOTATEPEAKS.out.versions.first())
 
         if (!skip_peak_qc) {
             //

From 9eb4de03f6a658cc018e979898c23481b5e6fb11 Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Sun, 29 Mar 2026 23:29:57 +0200
Subject: [PATCH 20/20] Update changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e9641d847..a8cdd3497 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -18,6 +18,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#484](https://github.com/nf-core/chipseq/issues/484)] - Bulk, updated of modules and subworkflows.
 - [[#489](https://github.com/nf-core/chipseq/issues/489)] - Replace deprecated `CUSTOM_GETCHROMSIZES` with `SAMTOOLS_FAIDX`.
 - [[PR #493](https://github.com/nf-core/chipseq/pull/493)] - Follow up to #487.
+- [[PR #493](https://github.com/nf-core/chipseq/pull/493)] - Follow up to #487.
+- [[#492](https://github.com/nf-core/chipseq/issues/492), [#417](https://github.com/nf-core/chipseq/issues/417)] - Refactor local modules to nf-core standard.
 
 ### Parameters