mirror of
https://github.com/MillironX/taxprofiler.git
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388 lines
14 KiB
Text
388 lines
14 KiB
Text
/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Config file for defining DSL2 per module options and publishing paths
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Available keys to override module options:
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ext.args = Additional arguments appended to command in module.
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ext.args2 = Second set of arguments appended to command in module (multi-tool modules).
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ext.args3 = Third set of arguments appended to command in module (multi-tool modules).
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ext.prefix = File name prefix for output files.
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----------------------------------------------------------------------------------------
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*/
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process {
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withName: SAMPLESHEET_CHECK {
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publishDir = [
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path: { "${params.outdir}/pipeline_info" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
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]
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}
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withName: DATABASE_CHECK {
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publishDir = [
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path: { "${params.outdir}/pipeline_info" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
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]
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}
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withName: FASTQC {
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ext.args = '--quiet'
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ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }
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publishDir = [
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path: { "${params.outdir}/fastqc/raw" },
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mode: params.publish_dir_mode,
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pattern: '*.html'
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]
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}
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withName: FASTQC_PROCESSED {
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ext.args = '--quiet'
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ext.prefix = { "${meta.id}_${meta.run_accession}_processed" }
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publishDir = [
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path: { "${params.outdir}/fastqc/processed" },
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mode: params.publish_dir_mode,
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pattern: '*.html'
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]
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}
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withName: FASTP_SINGLE {
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ext.args = [
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// trimming options
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params.shortread_qc_skipadaptertrim ? "--disable_adapter_trimming" : "",
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params.shortread_qc_adapter1 ? "--adapter_sequence ${params.shortread_qc_adapter1}" : "",
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// filtering options
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"--length_required ${params.shortread_qc_minlength}",
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(params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp') ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''
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].join(' ').trim()
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/fastp" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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]
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}
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withName: FASTP_PAIRED {
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ext.args = [
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// collapsing options - option to retain singletons
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params.shortread_qc_excludeunmerged ? '' : "--include_unmerged",
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// trimming options
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params.shortread_qc_skipadaptertrim ? "--disable_adapter_trimming" : "",
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params.shortread_qc_adapter1 ? "--adapter_sequence ${params.shortread_qc_adapter1}" : "",
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params.shortread_qc_adapter2 ? "--adapter_sequence_r2 ${params.shortread_qc_adapter2}" : "--detect_adapter_for_pe",
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// filtering options
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"--length_required ${params.shortread_qc_minlength}",
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params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp' ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''
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].join(' ').trim()
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/fastp" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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]
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}
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withName: ADAPTERREMOVAL_SINGLE {
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ext.args = [
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// trimming options
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params.shortread_qc_skipadaptertrim ? "--adapter1 '' --adapter2 ''" : "",
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params.shortread_qc_adapter1 ? "--adapter1 ${params.shortread_qc_adapter1}" : "",
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// filtering options
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"--minlength ${params.shortread_qc_minlength}"
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].join(' ').trim()
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/adapterremoval" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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]
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}
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withName: ADAPTERREMOVAL_PAIRED {
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ext.args = [
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// collapsing options
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params.shortread_qc_mergepairs ? "--collapse" : "",
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// trimming options
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params.shortread_qc_skipadaptertrim ? "--adapter1 '' --adapter2 ''" : "",
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params.shortread_qc_adapter1 ? "--adapter1 ${params.shortread_qc_adapter1}" : "",
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params.shortread_qc_adapter2 ? "--adapter2 ${params.shortread_qc_adapter2}" : "",
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// filtering options
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"--minlength ${params.shortread_qc_minlength}"
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].join(' ').trim()
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/adapterremoval" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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]
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}
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withName: PORECHOP {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/porechop" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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]
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}
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withName: FILTLONG {
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ext.args = [
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"--min_length ${params.longread_qc_minlength}",
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"--keep_percent ${params.longread_qc_keep_percent}",
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"--target_bases ${params.longread_qc_target_bases}"
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]
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.join(' ').trim()
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ext.prefix = { "${meta.id}_${meta.run_accession}_filtered" }
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publishDir = [
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path: { "${params.outdir}/filtlong" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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]
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}
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withName: BOWTIE2_BUILD {
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publishDir = [
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path: { "${params.outdir}/bowtie2/build" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_index,
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pattern: 'bowtie2'
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]
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}
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withName: BOWTIE2_ALIGN {
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ext.prefix = { "${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: '*.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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withName: MINIMAP2_INDEX {
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ext.args = '-x map-ont'
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publishDir = [
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path: { "${params.outdir}/minimap2/index" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_index,
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pattern: 'minimap2'
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]
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}
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withName: MINIMAP2_ALIGN {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/minimap2/align" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_mapped,
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pattern: '*.bam'
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]
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}
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withName: SAMTOOLS_VIEW {
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ext.args = '-f 4'
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ext.prefix = { "${meta.id}.mapped.sorted" }
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publishDir = [
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path: { "${params.outdir}/samtools/view" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_unmapped,
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pattern: '*.bam'
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]
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}
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withName: SAMTOOLS_BAM2FQ {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/samtools/bam2fq" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_unmapped,
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pattern: '*.fq.gz'
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]
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}
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withName: BBMAP_BBDUK {
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ext.args = [
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"entropy=${params.shortread_complexityfilter_entropy}",
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"entropywindow=${params.shortread_complexityfilter_bbduk_windowsize}",
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params.shortread_complexityfilter_bbduk_mask ? "entropymask=t" : "entropymask=f"
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].join(' ').trim()
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ext.prefix = { "${meta.id}-${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/bbduk/" },
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mode: params.publish_dir_mode,
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pattern: '*.{fastq.gz,log}',
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enabled: params.save_complexityfiltered_reads
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]
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}
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withName: PRINSEQPLUSPLUS {
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ext.args = [
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params.shortread_complexityfilter_prinseqplusplus_mode == 'dust' ? "-lc_dust=${params.shortread_complexityfilter_prinseqplusplus_dustscore}" : "-lc_entropy=${params.shortread_complexityfilter_entropy}",
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"-trim_qual_left=0 -trim_qual_left=0 -trim_qual_window=0 -trim_qual_step=0"
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].join(' ').trim()
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ext.prefix = { "${meta.id}-${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/prinseqplusplus/" },
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mode: params.publish_dir_mode,
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pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz,log}',
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enabled: params.save_complexityfiltered_reads
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]
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}
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withName: CAT_FASTQ {
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ext.prefix = { "${meta.id}" }
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publishDir = [
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path: { "${params.outdir}/run_merging/" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.save_runmerged_reads
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]
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}
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withName: MALT_RUN {
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ext.args = { "${meta.db_params}" }
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// one run with multiple samples, so fix ID to just db name to ensure clean log name
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ext.prefix = { "${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/malt/${meta.db_name}" },
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mode: params.publish_dir_mode,
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pattern: '*.{rma6,log,sam}'
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]
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}
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withName: MEGAN_RMA2INFO {
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ext.args = "-c2c Taxonomy"
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ext.prefix = { "${meta.id}" }
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publishDir = [
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path: { "${params.outdir}/malt/${meta.db_name}" },
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mode: params.publish_dir_mode,
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pattern: '*.{txt.gz,megan}'
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]
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}
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withName: KRAKEN2_KRAKEN2 {
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/kraken2/${meta.db_name}" },
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mode: params.publish_dir_mode,
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pattern: '*.{txt,report,fastq.gz}'
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]
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}
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withName: KRAKENTOOLS_KREPORT2KRONA {
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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}
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withName: KRONA_KRAKENCLEANUP {
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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}
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withName: KRONA_KTIMPORTTEXT {
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ext.prefix = { "${meta.tool}-${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/krona" },
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mode: params.publish_dir_mode,
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pattern: '*.{html}'
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]
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}
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withName: METAPHLAN3 {
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/metaphlan3/${meta.db_name}" },
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mode: params.publish_dir_mode,
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pattern: '*.{biom,txt}'
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]
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}
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withName: CENTRIFUGE_CENTRIFUGE {
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publishDir = [
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path: { "${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}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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}
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withName: CENTRIFUGE_KREPORT {
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/centrifuge/${meta.db_name}" },
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mode: params.publish_dir_mode,
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pattern: '*.{txt}'
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]
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}
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withName: KAIJU_KAIJU {
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publishDir = [
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path: { "${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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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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}
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withName: KAIJU_KAIJU2TABLE {
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/kaiju/${meta.db_name}" },
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mode: params.publish_dir_mode,
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pattern: '*.{txt}'
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]
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}
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withName: DIAMOND_BLASTX {
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/diamond/${meta.db_name}" },
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mode: params.publish_dir_mode,
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pattern: '*.{blast,xml,txt,daa,sam,tsv,paf}'
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]
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}
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withName: CUSTOM_DUMPSOFTWAREVERSIONS {
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publishDir = [
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path: { "${params.outdir}/pipeline_info" },
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mode: params.publish_dir_mode,
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pattern: '*_versions.yml'
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]
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}
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withName: MULTIQC {
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publishDir = [
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path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
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]
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}
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}
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