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Merge pull request #59 from nf-core/hostremoval-publish-fix
Add finer control over for hostremoval saving
This commit is contained in:
commit
47a34d4c7e
3 changed files with 31 additions and 5 deletions
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@ -133,20 +133,34 @@ process {
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}
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withName: BOWTIE2_BUILD {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/bowtie2/build" },
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mode: params.publish_dir_mode,
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pattern: '*.bt2'
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enabled: params.save_hostremoval_index,
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pattern: 'bowtie2'
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]
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}
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withName: BOWTIE2_ALIGN {
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ext.prefix = { "${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: '*.{fastq.gz,bam}'
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pattern: '*.log'
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],
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[
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path: { "${params.outdir}/bowtie2/align" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_mapped,
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pattern: '*.bam'
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],
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[
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path: { "${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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]
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]
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}
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@ -84,6 +84,9 @@ params {
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perform_shortread_hostremoval = false
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shortread_hostremoval_reference = null
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shortread_hostremoval_index = null
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save_hostremoval_index = false
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save_hostremoval_mapped = false
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save_hostremoval_unmapped = false
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// MALT
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run_malt = false
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@ -370,6 +370,15 @@
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"type": "string",
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"default": "None"
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},
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"save_hostremoval_index": {
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"type": "boolean"
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},
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"save_hostremoval_mapped": {
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"type": "boolean"
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},
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"save_hostremoval_unmapped": {
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"type": "boolean"
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},
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"run_kaiju": {
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"type": "boolean"
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},
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