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https://github.com/MillironX/taxprofiler.git
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fix: use parameter for publish mode everywhere
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parent
c40a9a0011
commit
af12435fa5
1 changed files with 9 additions and 9 deletions
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@ -43,7 +43,7 @@ process {
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ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }
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publishDir = [
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path: { "${params.outdir}/fastqc/raw" },
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mode: 'copy',
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mode: params.publish_dir_mode,
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pattern: '*.html'
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]
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}
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@ -53,7 +53,7 @@ process {
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ext.prefix = { "${meta.id}_${meta.run_accession}_processed" }
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publishDir = [
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path: { "${params.outdir}/fastqc/processed" },
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mode: 'copy',
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mode: params.publish_dir_mode,
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pattern: '*.html'
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]
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}
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@ -69,7 +69,7 @@ process {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/fastp" },
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mode: 'copy',
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz'
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]
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}
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@ -88,7 +88,7 @@ process {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/fastp" },
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mode: 'copy',
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz'
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]
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}
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@ -104,7 +104,7 @@ process {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/adapterremoval" },
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mode: 'copy',
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz'
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]
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}
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@ -123,7 +123,7 @@ process {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/adapterremoval" },
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mode: 'copy',
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz'
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]
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}
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@ -132,7 +132,7 @@ process {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/porechop" },
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mode: 'copy',
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz'
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]
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}
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@ -169,7 +169,7 @@ process {
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ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/malt/${meta.db_name}" },
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mode: 'copy',
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mode: params.publish_dir_mode,
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pattern: '*.{rma6,tab,text,sam,log}'
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]
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}
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@ -179,7 +179,7 @@ process {
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ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/kraken2/${meta.db_name}" },
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mode: 'copy',
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mode: params.publish_dir_mode,
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pattern: '*.{fastq.gz,txt}'
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]
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}
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