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Merge pull request #59 from nf-core/hostremoval-publish-fix

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Add finer control over for hostremoval saving
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James A. Fellows Yates 2022-04-21 12:57:09 +02:00 committed by GitHub
commit 47a34d4c7e
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3 changed files with 31 additions and 5 deletions
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20
conf/modules.config
View file

@ -133,20 +133,34 @@ process {
} }
withName: BOWTIE2_BUILD { withName: BOWTIE2_BUILD {
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [ publishDir = [
path: { "${params.outdir}/bowtie2/build" }, path: { "${params.outdir}/bowtie2/build" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
pattern: '*.bt2' enabled: params.save_hostremoval_index,
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: '*.{fastq.gz,bam}' pattern: '*.log'
],
[
path: { "${params.outdir}/bowtie2/align" },
mode: params.publish_dir_mode,
enabled: params.save_hostremoval_mapped,
pattern: '*.bam'
],
[
path: { "${params.outdir}/bowtie2/align" },
mode: params.publish_dir_mode,
enabled: params.save_hostremoval_unmapped,
pattern: '*.fastq.gz'
]
] ]
} }

7
nextflow.config
View file

@ -82,8 +82,11 @@ params {
// Host Removal // Host Removal
perform_shortread_hostremoval = false perform_shortread_hostremoval = false
shortread_hostremoval_reference = null shortread_hostremoval_reference = null
shortread_hostremoval_index = null shortread_hostremoval_index = null
save_hostremoval_index = false
save_hostremoval_mapped = false
save_hostremoval_unmapped = false
// MALT // MALT
run_malt = false run_malt = false

9
nextflow_schema.json
View file

@ -370,6 +370,15 @@
"type": "string", "type": "string",
"default": "None" "default": "None"
}, },
"save_hostremoval_index": {
"type": "boolean"
},
"save_hostremoval_mapped": {
"type": "boolean"
},
"save_hostremoval_unmapped": {
"type": "boolean"
},
"run_kaiju": { "run_kaiju": {
"type": "boolean" "type": "boolean"
}, },