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fix: use parameter for publish mode everywhere

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This commit is contained in:
Moritz E. Beber 2022-04-05 12:16:26 +02:00
parent c40a9a0011
commit af12435fa5
1 changed files with 9 additions and 9 deletions
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18
conf/modules.config
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@ -43,7 +43,7 @@ process {
ext.prefix = { "${meta.id}_${meta.run_accession}_raw" } ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }
publishDir = [ publishDir = [
path: { "${params.outdir}/fastqc/raw" }, path: { "${params.outdir}/fastqc/raw" },
mode: 'copy', mode: params.publish_dir_mode,
pattern: '*.html' pattern: '*.html'
] ]
} }
@ -53,7 +53,7 @@ process {
ext.prefix = { "${meta.id}_${meta.run_accession}_processed" } ext.prefix = { "${meta.id}_${meta.run_accession}_processed" }
publishDir = [ publishDir = [
path: { "${params.outdir}/fastqc/processed" }, path: { "${params.outdir}/fastqc/processed" },
mode: 'copy', mode: params.publish_dir_mode,
pattern: '*.html' pattern: '*.html'
] ]
} }
@ -69,7 +69,7 @@ process {
ext.prefix = { "${meta.id}_${meta.run_accession}" } ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [ publishDir = [
path: { "${params.outdir}/fastp" }, path: { "${params.outdir}/fastp" },
mode: 'copy', mode: params.publish_dir_mode,
pattern: '*.fastq.gz' pattern: '*.fastq.gz'
] ]
} }
@ -88,7 +88,7 @@ process {
ext.prefix = { "${meta.id}_${meta.run_accession}" } ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [ publishDir = [
path: { "${params.outdir}/fastp" }, path: { "${params.outdir}/fastp" },
mode: 'copy', mode: params.publish_dir_mode,
pattern: '*.fastq.gz' pattern: '*.fastq.gz'
] ]
} }
@ -104,7 +104,7 @@ process {
ext.prefix = { "${meta.id}_${meta.run_accession}" } ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [ publishDir = [
path: { "${params.outdir}/adapterremoval" }, path: { "${params.outdir}/adapterremoval" },
mode: 'copy', mode: params.publish_dir_mode,
pattern: '*.fastq.gz' pattern: '*.fastq.gz'
] ]
} }
@ -123,7 +123,7 @@ process {
ext.prefix = { "${meta.id}_${meta.run_accession}" } ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [ publishDir = [
path: { "${params.outdir}/adapterremoval" }, path: { "${params.outdir}/adapterremoval" },
mode: 'copy', mode: params.publish_dir_mode,
pattern: '*.fastq.gz' pattern: '*.fastq.gz'
] ]
} }
@ -132,7 +132,7 @@ process {
ext.prefix = { "${meta.id}_${meta.run_accession}" } ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [ publishDir = [
path: { "${params.outdir}/porechop" }, path: { "${params.outdir}/porechop" },
mode: 'copy', mode: params.publish_dir_mode,
pattern: '*.fastq.gz' pattern: '*.fastq.gz'
] ]
} }
@ -169,7 +169,7 @@ process {
ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" } ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
publishDir = [ publishDir = [
path: { "${params.outdir}/malt/${meta.db_name}" }, path: { "${params.outdir}/malt/${meta.db_name}" },
mode: 'copy', mode: params.publish_dir_mode,
pattern: '*.{rma6,tab,text,sam,log}' pattern: '*.{rma6,tab,text,sam,log}'
] ]
} }
@ -179,7 +179,7 @@ process {
ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" } ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
publishDir = [ publishDir = [
path: { "${params.outdir}/kraken2/${meta.db_name}" }, path: { "${params.outdir}/kraken2/${meta.db_name}" },
mode: 'copy', mode: params.publish_dir_mode,
pattern: '*.{fastq.gz,txt}' pattern: '*.{fastq.gz,txt}'
] ]
} }