Merge pull request #1 from mahesh-panchal/use_publishDir_nofunctions

Use publish dir but with no functions.nf
nf-core · Oct 12, 2021 · a06315a · a06315a
2 parents 35908e6 + 553705c
commit a06315a
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Showing 57 changed files with 132 additions and 315 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -13,7 +13,7 @@
 process {
 
     publishDir = [
-        path: { "${params.outdir}/${getSoftwareName(task.process)}" },
+        path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
         mode: params.publish_dir_mode,
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
@@ -22,7 +22,7 @@ process {
     withName: BEDTOOLS_GENOMECOV {
         ext.args   = '-split -du'
         publishDir = [
-            path: { "${params.outdir}/${getSoftwareName(task.process)}/${meta.id}" },
+            path: { "${params.outdir}/bedtools/${meta.id}" },
             enabled: false
         ]
     }
@@ -108,7 +108,7 @@ process {
         ext.args   = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
         publishDir = [
             path: { [
-                "${params.outdir}/${getSoftwareName(task.process)}",
+                "${params.outdir}/multiqc",
                 params.skip_alignment? '' : "/${params.aligner}"
                 ].join('') },
             mode: params.publish_dir_mode,
@@ -124,13 +124,13 @@ process {
     }
     withName: MULTIQC_TSV_FAIL_MAPPED {
         publishDir = [
-            path: { "${params.outdir}/${getSoftwareName(task.process)}" },
+            path: { "${params.outdir}/multiqc" },
             enabled: false
         ]
     }
     withName: MULTIQC_TSV_STRAND_CHECK {
         publishDir = [
-            path: { "${params.outdir}/${getSoftwareName(task.process)}" },
+            path: { "${params.outdir}/multiqc" },
             enabled: false
         ]
     }
@@ -180,7 +180,7 @@ process {
     }
     withName: HISAT2_EXTRACTSPLICESITES {
         publishDir = [
-            path: { "${params.outdir}/${getSoftwareName(task.process)}" },
+            path: { "${params.outdir}/hisat2" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: params.save_reference
@@ -347,7 +347,7 @@ process {
     // QUANTIFY_SALMON workflow
     withName: '.*:QUANTIFY_SALMON:SALMON_QUANT' {
         publishDir = [
-            path: { "${params.outdir}/${getSoftwareName(task.process)}" },
+            path: { "${params.outdir}/salmon" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
@@ -362,21 +362,21 @@ process {
     }
     withName: '.*:QUANTIFY_SALMON:SALMON_TXIMPORT' {
         publishDir = [
-            path: { "${params.outdir}/${getSoftwareName(task.process)}" },
+            path: { "${params.outdir}/salmon" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
     withName: '.*:QUANTIFY_SALMON:SALMON_MERGE_COUNTS' {
         publishDir = [
-            path: { "${params.outdir}/${getSoftwareName(task.process)}" },
+            path: { "${params.outdir}/salmon" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
     withName: '.*:QUANTIFY_SALMON:SALMON_SE_.*' {
         publishDir = [
-            path: { "${params.outdir}/${getSoftwareName(task.process)}" },
+            path: { "${params.outdir}/salmon" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
@@ -411,7 +411,7 @@ process {
         ext.args   = '-n'
         ext.suffix = '.umi_dedup.transcriptome'
         publishDir = [
-            path: { "${params.outdir}/${getSoftwareName(task.process)}" },
+            path: { "${params.outdir}/samtools" },
             enabled: false
         ]
     }
@@ -441,12 +441,12 @@ process {
         ext.args   = '--num_alignments 1 --fastx -v'
         publishDir = [
             [
-                path: { "${params.outdir}/${getSoftwareName(task.process)}" },
+                path: { "${params.outdir}/sortmerna" },
                 mode: params.publish_dir_mode,
                 pattern: "*.log"
             ],
             [
-                path: { "${params.outdir}/${getSoftwareName(task.process)}" },
+                path: { "${params.outdir}/sortmerna" },
                 mode: params.publish_dir_mode,
                 pattern: "*.fastq.gz",
                 enabled: params.save_non_ribo_reads
@@ -488,12 +488,12 @@ process {
             ].join(' ').trim()
         publishDir = [
             [
-                path: { "${params.outdir}/${getSoftwareName(task.process)}" },
+                path: { "${params.outdir}/umitools" },
                 mode: params.publish_dir_mode,
                 pattern: "*.log"
             ],
             [
-                path: { "${params.outdir}/${getSoftwareName(task.process)}" },
+                path: { "${params.outdir}/umitools" },
                 mode: params.publish_dir_mode,
                 pattern: "*.fastq.gz",
                 enabled: params.save_umi_intermeds
@@ -507,18 +507,18 @@ process {
         ].join(' ').trim()
         publishDir = [
             [
-                path: { "${params.outdir}/${getSoftwareName(task.process)}/fastqc" },
+                path: { "${params.outdir}/trimgalore/fastqc" },
                 mode: params.publish_dir_mode,
                 pattern: "*.{html,zip}"
             ],
             [
-                path: { "${params.outdir}/${getSoftwareName(task.process)}" },
+                path: { "${params.outdir}/trimgalore" },
                 mode: params.publish_dir_mode,
                 pattern: "*.fq.gz",
                 enabled: params.save_trimmed
             ],
             [
-                path: { "${params.outdir}/${getSoftwareName(task.process)}" },
+                path: { "${params.outdir}/trimgalore" },
                 mode: params.publish_dir_mode,
                 pattern: "*.txt"
             ]

diff --git a/lib/functions.nf b/lib/functions.nf
diff --git a/modules/local/bedtools_genomecov.nf b/modules/local/bedtools_genomecov.nf
@@ -1,6 +1,3 @@
-// Import generic module functions
-include { getSoftwareName; getProcessName } from "$projectDir/lib/functions"
-
 process BEDTOOLS_GENOMECOV {
     tag "$meta.id"
     label 'process_medium'
@@ -48,8 +45,8 @@ process BEDTOOLS_GENOMECOV {
         | bedtools sort > ${prefix_reverse}.bedGraph
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+    BEDTOOLS_GENOMECOV:
+        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
     END_VERSIONS
     """
 }
diff --git a/modules/local/cat_additional_fasta.nf b/modules/local/cat_additional_fasta.nf
@@ -1,6 +1,3 @@
-// Import generic module functions
-include { getSoftwareName; getProcessName } from "$projectDir/lib/functions"
-
 process CAT_ADDITIONAL_FASTA {
     tag "$add_fasta"
 
@@ -37,7 +34,7 @@ process CAT_ADDITIONAL_FASTA {
     cat $gtf ${add_fasta.baseName}.gtf > ${name}.gtf
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    CAT_ADDITIONAL_FASTA:
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """

diff --git a/modules/local/deseq2_qc.nf b/modules/local/deseq2_qc.nf
@@ -1,6 +1,3 @@
-// Import generic module functions
-include { getSoftwareName; getProcessName } from "$projectDir/lib/functions"
-
 params.multiqc_label = ''
 
 process DESEQ2_QC {
@@ -53,7 +50,7 @@ process DESEQ2_QC {
     fi
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    DESEQ2_QC:
         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
@@ -1,6 +1,3 @@
-// Import generic module functions
-include { getSoftwareName; getProcessName } from "$projectDir/lib/functions"
-
 process DUPRADAR {
     tag "$meta.id"
     label 'process_long'
@@ -42,7 +39,7 @@ process DUPRADAR {
         $task.cpus
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    DUPRADAR:
         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/get_chrom_sizes.nf b/modules/local/get_chrom_sizes.nf
@@ -1,6 +1,3 @@
-// Import generic module functions
-include { getSoftwareName; getProcessName } from "$projectDir/lib/functions"
-
 process GET_CHROM_SIZES {
     tag "$fasta"
 
@@ -28,7 +25,7 @@ process GET_CHROM_SIZES {
     cut -f 1,2 ${fasta}.fai > ${fasta}.sizes
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    GET_CHROM_SIZES:
         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
@@ -1,6 +1,3 @@
-// Import generic module functions
-include { getSoftwareName; getProcessName } from "$projectDir/lib/functions"
-
 process GTF2BED {
     tag "$gtf"
     label 'process_low'
@@ -26,7 +23,7 @@ process GTF2BED {
         > ${gtf.baseName}.bed
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    GTF2BED:
         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
@@ -1,6 +1,3 @@
-// Import generic module functions
-include { getSoftwareName; getProcessName } from "$projectDir/lib/functions"
-
 process GTF_GENE_FILTER {
     tag "$fasta"
 
@@ -27,7 +24,7 @@ process GTF_GENE_FILTER {
         -o ${fasta.baseName}_genes.gtf
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    GTF_GENE_FILTER:
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """

diff --git a/modules/local/multiqc.nf b/modules/local/multiqc.nf
@@ -1,6 +1,3 @@
-// Import generic module functions
-include { getSoftwareName; getProcessName } from "$projectDir/lib/functions"
-
 process MULTIQC {
     label 'process_medium'
 
@@ -63,8 +60,8 @@ process MULTIQC {
         .
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$( multiqc --version | sed -e "s/multiqc, version //g" )
+    MULTIQC:
+        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
     END_VERSIONS
     """
 }
diff --git a/modules/local/multiqc_custom_biotype.nf b/modules/local/multiqc_custom_biotype.nf
@@ -1,6 +1,3 @@
-// Import generic module functions
-include { getSoftwareName; getProcessName } from "$projectDir/lib/functions"
-
 process MULTIQC_CUSTOM_BIOTYPE {
     tag "$meta.id"
 
@@ -31,7 +28,7 @@ process MULTIQC_CUSTOM_BIOTYPE {
         -o ${prefix}.biotype_counts_rrna_mqc.tsv
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    MULTIQC_CUSTOM_BIOTYPE:
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """

diff --git a/modules/local/multiqc_tsv_from_list.nf b/modules/local/multiqc_tsv_from_list.nf
@@ -1,6 +1,3 @@
-// Import generic module functions
-include { getSoftwareName; getProcessName } from "$projectDir/lib/functions"
-
 process MULTIQC_TSV_FROM_LIST {
 
     memory 100.MB

diff --git a/modules/local/rsem_merge_counts.nf b/modules/local/rsem_merge_counts.nf
@@ -1,6 +1,3 @@
-// Import generic module functions
-include { getSoftwareName; getProcessName } from "$projectDir/lib/functions"
-
 process RSEM_MERGE_COUNTS {
     label "process_medium"
 
@@ -50,7 +47,7 @@ process RSEM_MERGE_COUNTS {
     paste transcript_ids.txt tmp/isoforms/*.tpm.txt > rsem.merged.transcript_tpm.tsv
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    RSEM_MERGE_COUNTS:
         sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
     END_VERSIONS
     """

diff --git a/modules/local/salmon_merge_counts.nf b/modules/local/salmon_merge_counts.nf
@@ -1,6 +1,3 @@
-// Import generic module functions
-include { getSoftwareName; getProcessName } from "$projectDir/lib/functions"
-
 process SALMON_MERGE_COUNTS {
     label "process_medium"
 
@@ -90,7 +87,7 @@ process SALMON_MERGE_COUNTS {
     paste transcript_ids.txt tmp/isoforms_tpm/* > salmon.merged.transcript_tpm.tsv
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    SALMON_MERGE_COUNTS:
         sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
     END_VERSIONS
     """

diff --git a/modules/local/salmon_summarizedexperiment.nf b/modules/local/salmon_summarizedexperiment.nf
@@ -1,6 +1,3 @@
-// Import generic module functions
-include { getSoftwareName; getProcessName } from "$projectDir/lib/functions"
-
 process SALMON_SUMMARIZEDEXPERIMENT {
     tag "$tx2gene"
     label "process_medium"
@@ -29,7 +26,7 @@ process SALMON_SUMMARIZEDEXPERIMENT {
         $tpm
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    SALMON_SUMMARIZEDEXPERIMENT:
         r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
         bioconductor-summarizedexperiment: \$(Rscript -e "library(SummarizedExperiment); cat(as.character(packageVersion('SummarizedExperiment')))")
     END_VERSIONS

diff --git a/modules/local/salmon_tx2gene.nf b/modules/local/salmon_tx2gene.nf
@@ -1,6 +1,3 @@
-// Import generic module functions
-include { getSoftwareName; getProcessName } from "$projectDir/lib/functions"
-
 process SALMON_TX2GENE {
     tag "$gtf"
     label "process_low"
@@ -30,7 +27,7 @@ process SALMON_TX2GENE {
         -o salmon_tx2gene.tsv
 
     cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+    SALMON_TX2GENE:
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """