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@ -196,8 +196,8 @@ process {
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publishDir = [
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path: { "${params.outdir}/bowtie2/build" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_index,
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pattern: 'bowtie2'
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pattern: 'bowtie2',
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enabled: params.save_hostremoval_index
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]
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}
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@ -213,14 +213,14 @@ process {
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[
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path: { "${params.outdir}/bowtie2/align" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_bam,
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pattern: '*.bam'
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pattern: '*.bam',
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enabled: params.save_hostremoval_bam
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],
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[
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path: { "${params.outdir}/bowtie2/align" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_unmapped,
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pattern: '*.fastq.gz'
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pattern: '*.fastq.gz',
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enabled: params.save_hostremoval_unmapped
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]
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]
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}
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@ -230,8 +230,8 @@ process {
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publishDir = [
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path: { "${params.outdir}/minimap2/index" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_index,
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pattern: '*.mmi'
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pattern: '*.mmi',
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enabled: params.save_hostremoval_index
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]
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}
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@ -240,8 +240,8 @@ process {
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publishDir = [
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path: { "${params.outdir}/minimap2/align" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_bam,
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pattern: '*.bam'
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pattern: '*.bam',
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enabled: params.save_hostremoval_bam
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]
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}
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@ -255,8 +255,8 @@ process {
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publishDir = [
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path: { "${params.outdir}/samtools/bam2fq" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_unmapped,
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pattern: '*.fq.gz'
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pattern: '*.fq.gz',
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enabled: params.save_hostremoval_unmapped
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]
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}
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@ -446,13 +446,13 @@ process {
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}
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withName: CENTRIFUGE_CENTRIFUGE {
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.centrifuge" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.centrifuge" }
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publishDir = [
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path: { "${params.outdir}/centrifuge/${meta.db_name}/" },
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mode: params.publish_dir_mode,
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pattern: '*.{txt,sam,gz}'
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]
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.centrifuge" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.centrifuge" }
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}
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withName: CENTRIFUGE_KREPORT {
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@ -477,13 +477,13 @@ process {
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}
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withName: KAIJU_KAIJU {
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.kaiju" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.kaiju" }
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publishDir = [
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path: { "${params.outdir}/kaiju/${meta.db_name}/" },
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mode: params.publish_dir_mode,
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pattern: '*.tsv'
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]
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ext.args = { "${meta.db_params}" }
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}
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withName: 'KAIJU_KAIJU2TABLE_SINGLE' {
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