Merge pull request #701 from mahesh-panchal/use_publishDir

Proposal: Use publishDir from config instead of current method

conf/test.config

@@ -40,10 +40,16 @@ params {
     pseudo_aligner      = 'salmon'
     umitools_bc_pattern = 'NNNN'
 
-    // When using RSEM, remove warning from STAR whilst building tiny indices
-    modules {
-        'rsem_preparereference' {
-            args2 = "--genomeSAindexNbases 7"
-        }
-    }
 }
+
+// When using RSEM, remove warning from STAR whilst building tiny indices
+process {
+    withName: 'RSEM_PREPAREREFERENCE' {
+        ext.args2 = "--genomeSAindexNbases 7"
+    }
+    // modules {
+    //     'rsem_preparereference' {
+    //         args2 = "--genomeSAindexNbases 7"
+    //     }
+    // }
+}

modules/local/bedtools_genomecov.nf

@@ -1,15 +1,6 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process BEDTOOLS_GENOMECOV {
     tag "$meta.id"
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
@@ -27,7 +18,8 @@ process BEDTOOLS_GENOMECOV {
     path "versions.yml"                        , emit: versions
 
     script:
-    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
+    def args   = task.ext.args ?: ''
 
     def prefix_forward = "${prefix}.forward"
     def prefix_reverse = "${prefix}.reverse"
@@ -41,20 +33,20 @@ process BEDTOOLS_GENOMECOV {
         -ibam $bam \\
         -bg \\
         -strand + \\
-        $options.args \\
+        $args \\
         | bedtools sort > ${prefix_forward}.bedGraph
 
     bedtools \\
         genomecov \\
         -ibam $bam \\
         -bg \\
         -strand - \\
-        $options.args \\
+        $args \\
         | bedtools sort > ${prefix_reverse}.bedGraph
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+    ${task.process.tokenize(':').last()}:
+        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
     END_VERSIONS
     """
 }

modules/local/cat_additional_fasta.nf

@@ -1,13 +1,5 @@
-// Import generic module functions
-include { saveFiles; getProcessName } from './functions'
-
-params.options = [:]
-
 process CAT_ADDITIONAL_FASTA {
     tag "$add_fasta"
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'genome', meta:[:], publish_by_meta:[]) }
 
     conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
@@ -42,7 +34,7 @@ process CAT_ADDITIONAL_FASTA {
     cat $gtf ${add_fasta.baseName}.gtf > ${name}.gtf
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    ${task.process.tokenize(':').last()}:
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """

modules/local/deseq2_qc.nf

@@ -1,15 +1,7 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options       = [:]
 params.multiqc_label = ''
-options              = initOptions(params.options)
 
 process DESEQ2_QC {
     label "process_medium"
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
     // (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
@@ -39,12 +31,13 @@ process DESEQ2_QC {
     script:
     def label_lower = params.multiqc_label.toLowerCase()
     def label_upper = params.multiqc_label.toUpperCase()
+    def args        = task.ext.args?: ''
     """
     deseq2_qc.r \\
         --count_file $counts \\
         --outdir ./ \\
         --cores $task.cpus \\
-        $options.args
+        $args
 
     if [ -f "R_sessionInfo.log" ]; then
         sed "s/deseq2_pca/${label_lower}_deseq2_pca/g" <$pca_header_multiqc >tmp.txt
@@ -57,7 +50,7 @@ process DESEQ2_QC {
     fi
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    ${task.process.tokenize(':').last()}:
         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/dupradar.nf

@@ -1,15 +1,6 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process DUPRADAR {
     tag "$meta.id"
     label 'process_long'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::bioconductor-dupradar=1.18.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
@@ -29,7 +20,7 @@ process DUPRADAR {
     path "versions.yml"               , emit: versions
 
     script: // This script is bundled with the pipeline, in nf-core/rnaseq/bin/
-    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
 
     def strandedness = 0
     if (meta.strandedness == 'forward') {
@@ -48,7 +39,7 @@ process DUPRADAR {
         $task.cpus
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    ${task.process.tokenize(':').last()}:
         r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
         bioconductor-dupradar: \$(Rscript -e "library(dupRadar); cat(as.character(packageVersion('dupRadar')))")
     END_VERSIONS

modules/local/get_chrom_sizes.nf

@@ -1,13 +1,5 @@
-// Import generic module functions
-include { saveFiles; getProcessName } from './functions'
-
-params.options = [:]
-
 process GET_CHROM_SIZES {
     tag "$fasta"
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'genome', meta:[:], publish_by_meta:[]) }
 
     conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
@@ -33,7 +25,7 @@ process GET_CHROM_SIZES {
     cut -f 1,2 ${fasta}.fai > ${fasta}.sizes
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    ${task.process.tokenize(':').last()}:
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """

modules/local/gtf2bed.nf

@@ -1,14 +1,6 @@
-// Import generic module functions
-include { saveFiles; getProcessName } from './functions'
-
-params.options = [:]
-
 process GTF2BED {
     tag "$gtf"
     label 'process_low'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'genome', meta:[:], publish_by_meta:[]) }
 
     conda (params.enable_conda ? "conda-forge::perl=5.26.2" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
@@ -31,7 +23,7 @@ process GTF2BED {
         > ${gtf.baseName}.bed
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    ${task.process.tokenize(':').last()}:
         perl: \$(echo \$(perl --version 2>&1) | sed 's/.*v\\(.*\\)) built.*/\\1/')
     END_VERSIONS
     """

modules/local/gtf_gene_filter.nf

@@ -1,13 +1,5 @@
-// Import generic module functions
-include { saveFiles; getProcessName } from './functions'
-
-params.options = [:]
-
 process GTF_GENE_FILTER {
     tag "$fasta"
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'genome', meta:[:], publish_by_meta:[]) }
 
     conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
@@ -32,7 +24,7 @@ process GTF_GENE_FILTER {
         -o ${fasta.baseName}_genes.gtf
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    ${task.process.tokenize(':').last()}:
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """

modules/local/multiqc.nf

@@ -1,14 +1,5 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process MULTIQC {
     label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
     conda (params.enable_conda ? "bioconda::multiqc=1.10.1" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
@@ -60,16 +51,17 @@ process MULTIQC {
 
     script:
     def custom_config = params.multiqc_config ? "--config $multiqc_custom_config" : ''
+    def args          = task.ext.args?: ''
     """
     multiqc \\
         -f \\
-        $options.args \\
+        $args \\
         $custom_config \\
         .
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$( multiqc --version | sed -e "s/multiqc, version //g" )
+    ${task.process.tokenize(':').last()}:
+        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
     END_VERSIONS
     """
 }

modules/local/multiqc_custom_biotype.nf

@@ -1,14 +1,5 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process MULTIQC_CUSTOM_BIOTYPE {
     tag "$meta.id"
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
@@ -26,7 +17,7 @@ process MULTIQC_CUSTOM_BIOTYPE {
     path "versions.yml"           , emit: versions
 
     script:
-    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
     """
     cut -f 1,7 $count | tail -n +3 | cat $header - >> ${prefix}.biotype_counts_mqc.tsv
 
@@ -37,7 +28,7 @@ process MULTIQC_CUSTOM_BIOTYPE {
         -o ${prefix}.biotype_counts_rrna_mqc.tsv
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    ${task.process.tokenize(':').last()}:
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """