Refactor local modules to nf-core standard and added topic channels

CHANGELOG.md

@@ -55,10 +55,9 @@ 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     |
-
-> **NB:** Dependency has been **updated** if both old and new version information is present.
-> **NB:** Dependency has been **added** if just the new version information is present.
-> **NB:** Dependency has been **removed** if version information isn't present.
+| python                      | 3.8.3       | 3.12.12     |
+| multiqc                     | 1.25.1      | 1.33        |
+|                             |             |             |
 
 ## [[2.1.0](https://github.com/nf-core/chipseq/releases/tag/2.1.0)] - 2024-10-07
 

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

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

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
     """
 }

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

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
     """
 }

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

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 -V:version | sed \"s/version='//; s/';//\""), 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
     """
 }

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

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
     """
 }

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

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
@@ -51,7 +52,8 @@ 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
 
     when:
     task.ext.when == null || task.ext.when
@@ -65,22 +67,12 @@ process MULTIQC {
         ${args} \\
         ${custom_config} \\
         .
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
-    END_VERSIONS
     """
 
     stub:
     """
     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
     """
 }

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

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
     """
 }

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

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
     """
 }

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

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
     """
 }

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 ]
 }