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Start adding conditions in modules.conf - non-cat not working
This commit is contained in:
James Fellows Yates
parent
74bc6b7dd3
commit
3b90064ba4
3 changed files with 111 additions and 49 deletions
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@ -71,6 +71,12 @@ process {
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path: { "${params.outdir}/fastp" },
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mode: params.publish_dir_mode,
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pattern: '*.{log,html,json}'
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],
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[
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path: { "${params.outdir}/analysis_ready_reads" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.shortread_complexityfilter_tool && !params.perform_shortread_qc && params.save_analysis_ready_reads
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]
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]
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}
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@ -99,6 +105,12 @@ process {
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path: { "${params.outdir}/fastp" },
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mode: params.publish_dir_mode,
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pattern: '*.{log,html,json}'
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],
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[
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path: { "${params.outdir}/analysis_ready_reads" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.shortread_complexityfilter_tool && !params.perform_shortread_qc && params.save_analysis_ready_reads
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]
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]
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}
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@ -122,6 +134,12 @@ process {
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path: { "${params.outdir}/adapterremoval" },
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mode: params.publish_dir_mode,
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pattern: '*.settings'
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],
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[
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path: { "${params.outdir}/analysis_ready_reads" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.shortread_complexityfilter_tool && !params.perform_shortread_qc && params.save_analysis_ready_reads
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]
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]
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}
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@ -148,6 +166,12 @@ process {
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path: { "${params.outdir}/adapterremoval" },
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mode: params.publish_dir_mode,
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pattern: '*.settings'
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],
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[
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path: { "${params.outdir}/analysis_ready_reads" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.shortread_complexityfilter_tool && !params.perform_shortread_qc && params.save_analysis_ready_reads
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]
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]
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}
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@ -166,6 +190,7 @@ process {
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mode: params.publish_dir_mode,
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pattern: '*.log'
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]
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// TODO ANALYSIS READY
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]
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}
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@ -190,14 +215,78 @@ process {
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pattern: '*.log'
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]
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]
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// TODO ANALYSIS READY
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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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[
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path: { "${params.outdir}/bbduk/" },
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mode: params.publish_dir_mode,
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pattern: '*.{fastq.gz,log}',
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enabled: params.save_complexityfiltered_reads
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],
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[
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path: { "${params.outdir}/bbduk/" },
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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: { "${params.outdir}/analysis_ready_reads" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && params.shortread_complexityfilter_tool && params.save_analysis_ready_reads
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]
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]
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}
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withName: PRINSEQPLUSPLUS {
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ext.args = [
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params.shortread_complexityfilter_prinseqplusplus_mode == 'dust' ? "-lc_dust=${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}_${meta.run_accession}" }
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publishDir = [
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[
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path: { "${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}',
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enabled: params.save_complexityfiltered_reads
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],
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[
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path: { "${params.outdir}/prinseqplusplus/" },
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mode: params.publish_dir_mode,
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pattern: '*.log'
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],
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[
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path: { "${params.outdir}/analysis_ready_reads" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && params.shortread_complexityfilter_tool && params.save_analysis_ready_reads
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]
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]
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}
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withName: BOWTIE2_BUILD {
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publishDir = [
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[
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path: { "${params.outdir}/bowtie2/build" },
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mode: params.publish_dir_mode,
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pattern: 'bowtie2',
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enabled: params.save_hostremoval_index
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],
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[
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path: { "${params.outdir}/analysis_ready_reads" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.shortread_complexityfilter_tool && !params.perform_shortread_qc && params.save_analysis_ready_reads
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]
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]
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}
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@ -221,6 +310,12 @@ process {
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mode: params.publish_dir_mode,
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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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path: { "${params.outdir}/analysis_ready_reads" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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saveAs: { (( !params.perform_runmerging | params.perform_runmerging && !${meta.is_multirun} ) && params.perform_shortread_hostremoval && params.save_analysis_ready_reads ) ? it : null }
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]
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]
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}
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@ -243,6 +338,7 @@ process {
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pattern: '*.bam',
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enabled: params.save_hostremoval_bam
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]
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// TODO ANALYSIS READY READS
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}
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withName: SAMTOOLS_VIEW {
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@ -269,56 +365,21 @@ process {
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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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[
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path: { "${params.outdir}/bbduk/" },
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mode: params.publish_dir_mode,
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pattern: '*.{fastq.gz,log}',
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enabled: params.save_complexityfiltered_reads
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],
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[
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path: { "${params.outdir}/bbduk/" },
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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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}
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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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[
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path: { "${params.outdir}/prinseqplusplus/" },
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mode: params.publish_dir_mode,
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pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz}',
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enabled: params.save_complexityfiltered_reads
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],
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[
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path: { "${params.outdir}/prinseqplusplus/" },
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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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}
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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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path: { "${params.outdir}/run_merging/" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.save_runmerged_reads
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],
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[
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path: { "${params.outdir}/analysis_ready_reads" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.perform_runmerging && params.save_analysis_ready_reads
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]
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]
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}
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@ -105,6 +105,8 @@ params {
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save_hostremoval_bam = false
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save_hostremoval_unmapped = false
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// Publishing final reads going into profiling
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save_analysis_ready_reads = false
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// MALT
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run_malt = false
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@ -10,7 +10,7 @@ workflow INPUT_CHECK {
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main:
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// Table to list, group per sample, detect if sample has multi-run,
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// Table to list, group per sample, detect if sample has multi-run,
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// then spread back to per-run rows but with multi-run info added to meta
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ch_split_samplesheet = SAMPLESHEET_CHECK ( samplesheet )
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.csv
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@ -43,7 +43,6 @@ workflow INPUT_CHECK {
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// Channel generation
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ch_fastq = ch_parsed_samplesheet.fastq
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.map { create_fastq_channel(it) }
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.dump(tag: "boop")
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ch_nanopore = ch_parsed_samplesheet.nanopore
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.map { create_fastq_channel(it) }
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