mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-11 00:43:10 +00:00
commit
4c4475c316
3 changed files with 33 additions and 30 deletions
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@ -12,12 +12,6 @@
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process {
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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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withName: SAMPLESHEET_CHECK {
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publishDir = [
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publishDir = [
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path: { "${params.outdir}/pipeline_info" },
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path: { "${params.outdir}/pipeline_info" },
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@ -34,20 +28,12 @@ process {
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]
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]
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}
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}
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withName: UNTAR {
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publishDir = [
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path: { "${params.outdir}/databases" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
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]
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}
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withName: FASTQC {
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withName: FASTQC {
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ext.args = '--quiet'
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ext.args = '--quiet'
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ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }
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ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }
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publishDir = [
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publishDir = [
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path: { "${params.outdir}/fastqc/raw" },
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path: { "${params.outdir}/fastqc/raw" },
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mode: 'copy',
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mode: params.publish_dir_mode,
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pattern: '*.html'
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pattern: '*.html'
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]
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]
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}
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}
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@ -57,7 +43,7 @@ process {
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ext.prefix = { "${meta.id}_${meta.run_accession}_processed" }
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ext.prefix = { "${meta.id}_${meta.run_accession}_processed" }
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publishDir = [
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publishDir = [
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path: { "${params.outdir}/fastqc/processed" },
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path: { "${params.outdir}/fastqc/processed" },
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mode: 'copy',
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mode: params.publish_dir_mode,
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pattern: '*.html'
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pattern: '*.html'
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]
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]
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}
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}
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@ -73,8 +59,9 @@ process {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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publishDir = [
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path: { "${params.outdir}/fastp" },
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path: { "${params.outdir}/fastp" },
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mode: 'copy',
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz'
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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]
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]
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}
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}
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@ -92,8 +79,9 @@ process {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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publishDir = [
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path: { "${params.outdir}/fastp" },
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path: { "${params.outdir}/fastp" },
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mode: 'copy',
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz'
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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]
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]
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}
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}
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@ -108,8 +96,9 @@ process {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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publishDir = [
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path: { "${params.outdir}/adapterremoval" },
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path: { "${params.outdir}/adapterremoval" },
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mode: 'copy',
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz'
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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]
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]
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}
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}
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@ -127,8 +116,9 @@ process {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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publishDir = [
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path: { "${params.outdir}/adapterremoval" },
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path: { "${params.outdir}/adapterremoval" },
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mode: 'copy',
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz'
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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]
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]
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}
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}
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@ -136,8 +126,9 @@ process {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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publishDir = [
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path: { "${params.outdir}/porechop" },
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path: { "${params.outdir}/porechop" },
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mode: 'copy',
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz'
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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]
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]
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}
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}
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@ -151,7 +142,8 @@ process {
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publishDir = [
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publishDir = [
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path: { "${params.outdir}/bbduk/" },
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path: { "${params.outdir}/bbduk/" },
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mode: params.publish_dir_mode,
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mode: params.publish_dir_mode,
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pattern: '*.{fastq.gz,log}'
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pattern: '*.{fastq.gz,log}',
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enabled: params.save_complexityfiltered_reads
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]
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]
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}
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}
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@ -164,7 +156,8 @@ process {
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publishDir = [
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publishDir = [
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path: { "${params.outdir}/prinseqplusplus/" },
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path: { "${params.outdir}/prinseqplusplus/" },
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mode: params.publish_dir_mode,
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mode: params.publish_dir_mode,
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pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz,log}'
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pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz,log}',
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enabled: params.save_complexityfiltered_reads
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]
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]
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}
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}
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@ -173,7 +166,7 @@ process {
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ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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publishDir = [
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path: { "${params.outdir}/malt/${meta.db_name}" },
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path: { "${params.outdir}/malt/${meta.db_name}" },
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mode: 'copy',
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mode: params.publish_dir_mode,
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pattern: '*.{rma6,tab,text,sam,log}'
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pattern: '*.{rma6,tab,text,sam,log}'
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]
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]
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}
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}
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@ -183,7 +176,7 @@ process {
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ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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publishDir = [
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path: { "${params.outdir}/kraken2/${meta.db_name}" },
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path: { "${params.outdir}/kraken2/${meta.db_name}" },
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mode: 'copy',
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mode: params.publish_dir_mode,
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pattern: '*.{fastq.gz,txt}'
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pattern: '*.{fastq.gz,txt}'
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]
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]
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}
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}
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@ -64,6 +64,7 @@ params {
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shortread_clipmerge_adapter2 = null
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shortread_clipmerge_adapter2 = null
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shortread_clipmerge_minlength = 15
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shortread_clipmerge_minlength = 15
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longread_clip = false
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longread_clip = false
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save_preprocessed_reads = false
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// Complexity filtering
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// Complexity filtering
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shortread_complexityfilter = false
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shortread_complexityfilter = false
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@ -73,6 +74,7 @@ params {
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shortread_complexityfilter_bbduk_mask = false
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shortread_complexityfilter_bbduk_mask = false
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shortread_complexityfilter_prinseqplusplus_mode = 'entropy'
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shortread_complexityfilter_prinseqplusplus_mode = 'entropy'
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shortread_complexityfilter_prinseqplusplus_dustscore = 0.5
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shortread_complexityfilter_prinseqplusplus_dustscore = 0.5
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save_complexityfiltered_reads = false
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// MALT
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// MALT
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"type": "integer",
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"type": "integer",
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"default": 15
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"default": 15
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},
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},
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"save_preprocessed_reads": {
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"type": "boolean",
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"default": false
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},
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"shortread_complexityfilter_tool": {
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"shortread_complexityfilter_tool": {
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"type": "string",
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"type": "string",
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"default": "bbduk"
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"default": "bbduk"
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@ -334,6 +338,10 @@
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"shortread_complexityfilter_prinseqplusplus_dustscore": {
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"shortread_complexityfilter_prinseqplusplus_dustscore": {
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"type": "number",
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"type": "number",
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"default": 0.5
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"default": 0.5
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},
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"save_complexityfiltered_reads": {
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"type": "boolean",
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"default": false
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}
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}
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}
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}
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}
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}
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