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Simplify params which control host removal publish
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parent
5b7b214156
commit
d94534e8ac
3 changed files with 5 additions and 25 deletions
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@ -169,7 +169,7 @@ process {
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publishDir = [
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path: { "${params.outdir}/minimap2/index" },
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mode: params.publish_dir_mode,
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enabled: params.save_minimap2_hostremoval_index,
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enabled: params.save_hostremoval_index,
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pattern: 'minimap2'
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]
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}
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@ -179,7 +179,7 @@ process {
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publishDir = [
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path: { "${params.outdir}/minimap2/align" },
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mode: params.publish_dir_mode,
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enabled: params.save_minimap2_hostremoval_mapped,
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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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@ -190,7 +190,7 @@ process {
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publishDir = [
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path: { "${params.outdir}/samtools/view" },
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mode: params.publish_dir_mode,
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enabled: params.save_samtools_unmapped_bam,
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enabled: params.save_hostremoval_unmapped,
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pattern: '*.bam'
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]
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}
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@ -200,7 +200,7 @@ process {
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publishDir = [
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path: { "${params.outdir}/samtools/bam2fq" },
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mode: params.publish_dir_mode,
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enabled: params.save_minimap2_unmapped_fq,
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enabled: params.save_hostremoval_unmapped,
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pattern: '*.fq.gz'
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]
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}
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@ -84,14 +84,10 @@ 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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longread_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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longread_hostremoval_index = null
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save_minimap2_hostremoval_index = false
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save_minimap2_hostremoval_mapped = false
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save_samtools_unmapped_bam = false
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save_minimap2_unmapped_fq = false
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// MALT
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@ -401,22 +401,6 @@
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"longread_hostremoval_index": {
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"type": "string",
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"default": "None"
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},
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"save_minimap2_hostremoval_index": {
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"type": "boolean",
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"description": "Flag for publishing minimap2 host removal index"
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},
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"save_minimap2_hostremoval_mapped": {
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"type": "boolean",
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"description": "Flag for publishinig bam file with all long reads mapped to a reference"
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},
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"save_samtools_unmapped_bam": {
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"type": "boolean",
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"description": "Flag for publishing bam for reads that did not map to the host reference"
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},
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"save_minimap2_unmapped_fq": {
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"type": "boolean",
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"description": "Flag for publishing fastq files for reads that did not map to the host reference"
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}
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}
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}
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