mirror of
https://github.com/MillironX/taxprofiler.git
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Merge pull request #192 from nf-core/publishing-fix
Fix publishing of log files of rpreprocessing steps
This commit is contained in:
James A. Fellows Yates
GitHub
commit
aa117e8af9
4 changed files with 125 additions and 50 deletions
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@ -33,7 +33,7 @@ process {
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}
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withName: FALCO {
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ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }
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ext.prefix = { "${meta.id}_${meta.run_accession}_raw_falco" }
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publishDir = [
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path: { "${params.outdir}/falco/raw" },
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mode: params.publish_dir_mode,
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@ -42,7 +42,7 @@ process {
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}
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withName: FALCO_PROCESSED {
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ext.prefix = { "${meta.id}_${meta.run_accession}_processed" }
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ext.prefix = { "${meta.id}_${meta.run_accession}_processed_falco" }
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publishDir = [
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path: { "${params.outdir}/falco/processed" },
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mode: params.publish_dir_mode,
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@ -61,10 +61,17 @@ process {
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].join(' ').trim()
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/fastp" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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[
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path: { "${params.outdir}/fastp" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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],
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[
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path: { "${params.outdir}/fastp" },
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mode: params.publish_dir_mode,
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pattern: '*.{log,html,json}'
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]
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]
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}
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@ -82,10 +89,17 @@ process {
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].join(' ').trim()
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/fastp" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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[
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path: { "${params.outdir}/fastp" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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],
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[
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path: { "${params.outdir}/fastp" },
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mode: params.publish_dir_mode,
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pattern: '*.{log,html,json}'
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]
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]
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}
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@ -98,10 +112,17 @@ process {
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].join(' ').trim()
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/adapterremoval" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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[
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path: { "${params.outdir}/adapterremoval" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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],
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[
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path: { "${params.outdir}/adapterremoval" },
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mode: params.publish_dir_mode,
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pattern: '*.settings'
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]
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]
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}
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@ -117,20 +138,34 @@ process {
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].join(' ').trim()
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/adapterremoval" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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[
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path: { "${params.outdir}/adapterremoval" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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],
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[
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path: { "${params.outdir}/adapterremoval" },
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mode: params.publish_dir_mode,
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pattern: '*.settings'
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]
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]
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}
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withName: PORECHOP_PORECHOP {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/porechop" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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[
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path: { "${params.outdir}/porechop" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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],
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[
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path: { "${params.outdir}/porechop" },
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mode: params.publish_dir_mode,
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pattern: '*.log'
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]
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]
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}
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@ -143,10 +178,17 @@ process {
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.join(' ').trim()
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ext.prefix = { "${meta.id}_${meta.run_accession}_filtered" }
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publishDir = [
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path: { "${params.outdir}/filtlong" },
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mode: params.publish_dir_mode,
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pattern: '*.{fastq.gz,log}',
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enabled: params.save_preprocessed_reads
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[
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path: { "${params.outdir}/filtlong" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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],
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[
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path: { "${params.outdir}/filtlong" },
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mode: params.publish_dir_mode,
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pattern: '*.log'
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]
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]
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}
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@ -163,21 +205,21 @@ process {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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[
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path: { "${params.outdir}/bowtie2/align" },
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mode: params.publish_dir_mode,
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pattern: '*.log'
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path: { "${params.outdir}/bowtie2/align" },
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mode: params.publish_dir_mode,
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pattern: '*.log'
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],
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[
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path: { "${params.outdir}/bowtie2/align" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_mapped,
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pattern: '*.bam'
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path: { "${params.outdir}/bowtie2/align" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_mapped,
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pattern: '*.bam'
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],
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[
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path: { "${params.outdir}/bowtie2/align" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_unmapped,
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pattern: '*.fastq.gz'
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path: { "${params.outdir}/bowtie2/align" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_unmapped,
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pattern: '*.fastq.gz'
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]
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]
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}
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@ -240,10 +282,17 @@ process {
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].join(' ').trim()
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ext.prefix = { "${meta.id}-${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/bbduk/" },
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mode: params.publish_dir_mode,
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pattern: '*.{fastq.gz,log}',
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enabled: params.save_complexityfiltered_reads
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[
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path: { "${params.outdir}/bbduk/" },
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mode: params.publish_dir_mode,
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pattern: '*.{fastq.gz,log}',
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enabled: params.save_complexityfiltered_reads
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],
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[
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path: { "${params.outdir}/bbduk/" },
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mode: params.publish_dir_mode,
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pattern: '*.log'
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]
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]
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}
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@ -255,10 +304,17 @@ process {
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].join(' ').trim()
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ext.prefix = { "${meta.id}-${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/prinseqplusplus/" },
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mode: params.publish_dir_mode,
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pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz,log}',
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enabled: params.save_complexityfiltered_reads
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[
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path: { "${params.outdir}/prinseqplusplus/" },
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mode: params.publish_dir_mode,
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pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz}',
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enabled: params.save_complexityfiltered_reads
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],
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[
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path: { "${params.outdir}/prinseqplusplus/" },
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mode: params.publish_dir_mode,
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pattern: '*.log'
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]
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]
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}
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@ -295,7 +351,7 @@ process {
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withName: KRAKEN2_KRAKEN2 {
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ext.args = params.kraken2_save_minimizers ? { "${meta.db_params} --report-minimizer-data" } : { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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ext.prefix = params.perform_runmerging ? { meta.tool == "bracken" ? "${meta.id}-${meta.db_name}.bracken" : "${meta.id}-${meta.db_name}" } : { meta.tool == "bracken" ? "${meta.id}-${meta.run_accession}-${meta.db_name}.bracken" : "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/kraken2/${meta.db_name}/" },
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mode: params.publish_dir_mode,
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@ -305,7 +361,7 @@ process {
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withName: BRACKEN_BRACKEN {
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errorStrategy = 'ignore'
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.bracken" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.bracken" }
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publishDir = [
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path: { "${params.outdir}/bracken/${meta.db_name}/" },
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mode: params.publish_dir_mode,
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@ -318,7 +374,7 @@ process {
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publishDir = [
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path: { "${params.outdir}/bracken/" },
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mode: params.publish_dir_mode,
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pattern: '*.{txt}'
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pattern: '*.txt'
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]
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}
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@ -73,7 +73,8 @@
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"falco": {
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"branch": "master",
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"git_sha": "fc959214036403ad83efe7a41d43d0606c445cda",
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"installed_by": ["modules"]
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"installed_by": ["modules"],
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"patch": "modules/nf-core/falco/falco.diff"
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},
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"fastp": {
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"branch": "master",
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16
modules/nf-core/falco/falco.diff
generated
Normal file
16
modules/nf-core/falco/falco.diff
generated
Normal file
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@ -0,0 +1,16 @@
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Changes in module 'nf-core/falco'
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--- modules/nf-core/falco/main.nf
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+++ modules/nf-core/falco/main.nf
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@@ -33,7 +33,9 @@
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"""
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} else {
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"""
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- falco $args --threads $task.cpus ${reads}
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+ [ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
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+ [ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
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+ falco $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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************************************************************
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4
modules/nf-core/falco/main.nf
generated
4
modules/nf-core/falco/main.nf
generated
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@ -33,7 +33,9 @@ process FALCO {
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"""
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} else {
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"""
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falco $args --threads $task.cpus ${reads}
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[ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
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[ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
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falco $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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