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Code Issues Releases Packages Activity

Get build directory working

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This commit is contained in:
James Fellows Yates 2022-04-18 06:37:23 +02:00
parent b036ed5b73
commit 9880baa0b8
1 changed files with 9 additions and 7 deletions
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16
conf/modules.config
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@ -137,29 +137,31 @@ process {
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, enabled: params.save_hostremoval_index,
pattern: 'bowtie2/*' pattern: 'bowtie2'
] ]
} }
withName: BOWTIE2_ALIGN { withName: BOWTIE2_ALIGN {
ext.prefix = { "${meta.id}_${meta.run_accession}" } ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [[ publishDir = [
[
path: { "${params.outdir}/bowtie2/align" }, path: { "${params.outdir}/bowtie2/align" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
pattern: '*.log' pattern: '*.log'
], ],
[ [
path: { "${params.outdir}/bowtie2/align" }, path: { "${params.outdir}/bowtie2/align" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
enabled: params.save_hostremoval_mapped, enabled: params.save_hostremoval_mapped,
pattern: '*.bam' pattern: '*.bam'
], ],
publishDir = [ [
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, enabled: params.save_hostremoval_unmapped,
pattern: '*.fastq.gz' pattern: '*.fastq.gz'
]] ]
]
} }
withName: BBMAP_BBDUK { withName: BBMAP_BBDUK {