Merge pull request #701 from mahesh-panchal/use_publishDir

Proposal: Use publishDir from config instead of current method
nf-core · Oct 29, 2021 · 0ecc9a1 · 0ecc9a1
2 parents a6882e8 + 0ad0307
commit 0ecc9a1
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Showing 111 changed files with 1,333 additions and 4,133 deletions.
diff --git a/conf/modules.config b/conf/modules.config
diff --git a/conf/test.config b/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"
+ // }
+ // }
+}
diff --git a/modules/local/bedtools_genomecov.nf b/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")
+ ${task.process.tokenize(':').last()}:
+ bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
  END_VERSIONS
  """
 }
diff --git a/modules/local/cat_additional_fasta.nf b/modules/local/cat_additional_fasta.nf
@@ -1,13 +1,5 @@
-// Import generic module functions
-include { saveFiles; getProcessName } from './functions'
-
-params.options = [:]
-
 process CAT_ADDITIONAL_FASTA {
  tag "$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
  """

diff --git a/modules/local/deseq2_qc.nf b/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

diff --git a/modules/local/dupradar.nf b/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

diff --git a/modules/local/functions.nf b/modules/local/functions.nf
diff --git a/modules/local/get_chrom_sizes.nf b/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
  """

diff --git a/modules/local/gtf2bed.nf b/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
  """

diff --git a/modules/local/gtf_gene_filter.nf b/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
  """

diff --git a/modules/local/multiqc.nf b/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" )
+ ${task.process.tokenize(':').last()}:
+ multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
  END_VERSIONS
  """
 }
diff --git a/modules/local/multiqc_custom_biotype.nf b/modules/local/multiqc_custom_biotype.nf
@@ -1,14 +1,5 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
 process MULTIQC_CUSTOM_BIOTYPE {
  tag "$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
  """