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Code Issues Releases Packages Activity

Make modules entries consistent

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This commit is contained in:
James Fellows Yates 2023-03-07 11:06:35 +01:00
parent d647e61a2f
commit b5a2983c5f
1 changed files with 15 additions and 15 deletions
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30
conf/modules.config
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@ -196,8 +196,8 @@ process {
publishDir = [ publishDir = [
path: { "${params.outdir}/bowtie2/build" }, path: { "${params.outdir}/bowtie2/build" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
enabled: params.save_hostremoval_index, pattern: 'bowtie2',
pattern: 'bowtie2' enabled: params.save_hostremoval_index
] ]
} }
@ -213,14 +213,14 @@ process {
[ [
path: { "${params.outdir}/bowtie2/align" }, path: { "${params.outdir}/bowtie2/align" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
enabled: params.save_hostremoval_bam, pattern: '*.bam',
pattern: '*.bam' enabled: params.save_hostremoval_bam
], ],
[ [
path: { "${params.outdir}/bowtie2/align" }, path: { "${params.outdir}/bowtie2/align" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
enabled: params.save_hostremoval_unmapped, pattern: '*.fastq.gz',
pattern: '*.fastq.gz' enabled: params.save_hostremoval_unmapped
] ]
] ]
} }
@ -230,8 +230,8 @@ process {
publishDir = [ publishDir = [
path: { "${params.outdir}/minimap2/index" }, path: { "${params.outdir}/minimap2/index" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
enabled: params.save_hostremoval_index, pattern: '*.mmi',
pattern: '*.mmi' enabled: params.save_hostremoval_index
] ]
} }
@ -240,8 +240,8 @@ process {
publishDir = [ publishDir = [
path: { "${params.outdir}/minimap2/align" }, path: { "${params.outdir}/minimap2/align" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
enabled: params.save_hostremoval_bam, pattern: '*.bam',
pattern: '*.bam' enabled: params.save_hostremoval_bam
] ]
} }
@ -255,8 +255,8 @@ process {
publishDir = [ publishDir = [
path: { "${params.outdir}/samtools/bam2fq" }, path: { "${params.outdir}/samtools/bam2fq" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
enabled: params.save_hostremoval_unmapped, pattern: '*.fq.gz',
pattern: '*.fq.gz' enabled: params.save_hostremoval_unmapped
] ]
} }
@ -446,13 +446,13 @@ process {
} }
withName: CENTRIFUGE_CENTRIFUGE { withName: CENTRIFUGE_CENTRIFUGE {
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.centrifuge" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.centrifuge" }
publishDir = [ publishDir = [
path: { "${params.outdir}/centrifuge/${meta.db_name}/" }, path: { "${params.outdir}/centrifuge/${meta.db_name}/" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
pattern: '*.{txt,sam,gz}' pattern: '*.{txt,sam,gz}'
] ]
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.centrifuge" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.centrifuge" }
} }
withName: CENTRIFUGE_KREPORT { withName: CENTRIFUGE_KREPORT {
@ -477,13 +477,13 @@ process {
} }
withName: KAIJU_KAIJU { withName: KAIJU_KAIJU {
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.kaiju" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.kaiju" } ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.kaiju" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.kaiju" }
publishDir = [ publishDir = [
path: { "${params.outdir}/kaiju/${meta.db_name}/" }, path: { "${params.outdir}/kaiju/${meta.db_name}/" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
pattern: '*.tsv' pattern: '*.tsv'
] ]
ext.args = { "${meta.db_params}" }
} }
withName: 'KAIJU_KAIJU2TABLE_SINGLE' { withName: 'KAIJU_KAIJU2TABLE_SINGLE' {