mirror of
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100 lines
3.2 KiB
Text
100 lines
3.2 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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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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withName: SAMPLESHEET_CHECK {
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publishDir = [
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path: { "${params.outdir}/pipeline_info" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
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]
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}
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withName: FASTQC {
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ext.args = '--quiet'
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ext.prefix = { "${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: 'copy',
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pattern: '*.html'
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]
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}
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withName: FASTP {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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// TODO also include option to NOT merge
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ext.args = [
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{ ${meta.single_end} } == 0 ? "-m" : '',
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params.fastp_exclude_unmerged ? '' : "--include_unmerged"
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].join(' ').trim()
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publishDir = [
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path: { "${params.outdir}/fastp" },
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mode: 'copy',
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pattern: '*.fastq.gz'
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]
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}
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withName: FASTQC_POST {
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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: { "${params.outdir}/fastqc/processed" },
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mode: 'copy',
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pattern: '*.html'
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]
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}
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withName: CAT_FASTQ {
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publishDir = [
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path: { "${params.outdir}/prepared_sequences" },
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mode: 'copy',
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pattern: '*.fastq.gz'
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]
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}
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withName: MALT_RUN {
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publishDir = [
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path: { "${params.outdir}/malt/${meta.db_name}" },
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mode: 'copy',
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pattern: '*.{rma6,tab,text,sam,log}'
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]
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ext.args = { "${meta.db_params}" }
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ext.when = params.run_malt
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}
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withName: KRAKEN2_KRAKEN2 {
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publishDir = [
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path: { "${params.outdir}/kraken2/${meta.db_name}" },
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mode: 'copy',
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pattern: '.{fastq.gz,txt}'
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]
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ext.args = { "${meta.db_params}" }
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ext.when = params.run_kraken2
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ext.prefix = { "${meta.id}-${meta.db_name}" }
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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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}
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