mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-10 23:03:10 +00:00
Standardise file names using only underscore
This commit is contained in:
parent
480248bcfd
commit
92dff9b453
2 changed files with 17 additions and 14 deletions
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@ -336,3 +336,6 @@ extra_fn_clean_exts:
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- ".unmapped"
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- ".unmapped"
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- "_filtered"
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- "_filtered"
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- "_processed"
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- "_processed"
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section_comments:
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general_stats: "By default, all read count columns are displayed as millions (M) of reads."
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@ -280,7 +280,7 @@ process {
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"entropywindow=${params.shortread_complexityfilter_bbduk_windowsize}",
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"entropywindow=${params.shortread_complexityfilter_bbduk_windowsize}",
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params.shortread_complexityfilter_bbduk_mask ? "entropymask=t" : "entropymask=f"
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params.shortread_complexityfilter_bbduk_mask ? "entropymask=t" : "entropymask=f"
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].join(' ').trim()
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].join(' ').trim()
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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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[
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[
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path: { "${params.outdir}/bbduk/" },
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path: { "${params.outdir}/bbduk/" },
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@ -301,7 +301,7 @@ process {
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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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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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"-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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].join(' ').trim()
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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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[
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[
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path: { "${params.outdir}/prinseqplusplus/" },
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path: { "${params.outdir}/prinseqplusplus/" },
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@ -350,7 +350,7 @@ process {
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withName: KRAKEN2_KRAKEN2 {
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withName: KRAKEN2_KRAKEN2 {
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ext.args = params.kraken2_save_minimizers ? { "${meta.db_params} --report-minimizer-data" } : { "${meta.db_params}" }
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ext.args = params.kraken2_save_minimizers ? { "${meta.db_params} --report-minimizer-data" } : { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { meta.tool == "bracken" ? "${meta.id}-${meta.db_name}.bracken" : "${meta.id}-${meta.db_name}.kraken" } : { meta.tool == "bracken" ? "${meta.id}-${meta.run_accession}-${meta.db_name}.bracken" : "${meta.id}-${meta.run_accession}-${meta.db_name}.kraken" }
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ext.prefix = params.perform_runmerging ? { meta.tool == "bracken" ? "${meta.id}_${meta.db_name}.bracken" : "${meta.id}_${meta.db_name}.kraken" } : { meta.tool == "bracken" ? "${meta.id}_${meta.run_accession}_${meta.db_name}.bracken" : "${meta.id}_${meta.run_accession}_${meta.db_name}.kraken" }
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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: params.publish_dir_mode,
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mode: params.publish_dir_mode,
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@ -360,7 +360,7 @@ process {
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withName: BRACKEN_BRACKEN {
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withName: BRACKEN_BRACKEN {
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errorStrategy = 'ignore'
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errorStrategy = 'ignore'
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.bracken" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.bracken" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.bracken" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.bracken" }
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publishDir = [
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publishDir = [
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path: { "${params.outdir}/bracken/${meta.db_name}/" },
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path: { "${params.outdir}/bracken/${meta.db_name}/" },
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mode: params.publish_dir_mode,
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mode: params.publish_dir_mode,
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@ -398,7 +398,7 @@ process {
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}
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}
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withName: KRONA_CLEANUP {
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withName: KRONA_CLEANUP {
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}" }
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publishDir = [
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publishDir = [
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path: { "${params.outdir}/krona/" },
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path: { "${params.outdir}/krona/" },
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mode: params.publish_dir_mode,
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mode: params.publish_dir_mode,
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@ -407,7 +407,7 @@ process {
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}
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}
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withName: KRONA_KTIMPORTTEXT {
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withName: KRONA_KTIMPORTTEXT {
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ext.prefix = { "${meta.tool}-${meta.id}" }
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ext.prefix = { "${meta.tool}_${meta.id}" }
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publishDir = [
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publishDir = [
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path: { "${params.outdir}/krona/" },
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path: { "${params.outdir}/krona/" },
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mode: params.publish_dir_mode,
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mode: params.publish_dir_mode,
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@ -417,12 +417,12 @@ process {
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withName: 'MEGAN_RMA2INFO_KRONA' {
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withName: 'MEGAN_RMA2INFO_KRONA' {
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ext.args = { "--read2class Taxonomy" }
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ext.args = { "--read2class Taxonomy" }
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ext.prefix = { "${meta.id}-${meta.db_name}" }
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ext.prefix = { "${meta.id}_${meta.db_name}" }
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}
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}
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withName: KRONA_KTIMPORTTAXONOMY {
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withName: KRONA_KTIMPORTTAXONOMY {
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ext.args = "-i"
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ext.args = "-i"
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ext.prefix = { "${meta.tool}-${meta.id}" }
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ext.prefix = { "${meta.tool}_${meta.id}" }
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publishDir = [
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publishDir = [
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path: { "${params.outdir}/krona/" },
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path: { "${params.outdir}/krona/" },
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mode: params.publish_dir_mode,
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mode: params.publish_dir_mode,
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@ -432,7 +432,7 @@ process {
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withName: METAPHLAN3_METAPHLAN3 {
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withName: METAPHLAN3_METAPHLAN3 {
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ext.args = { "${meta.db_params}" }
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.metaphlan3" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.metaphlan3" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.metaphlan3" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.metaphlan3" }
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publishDir = [
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publishDir = [
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path: { "${params.outdir}/metaphlan3/${meta.db_name}/" },
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path: { "${params.outdir}/metaphlan3/${meta.db_name}/" },
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mode: params.publish_dir_mode,
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mode: params.publish_dir_mode,
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@ -456,13 +456,13 @@ process {
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pattern: '*.{txt,sam,gz}'
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pattern: '*.{txt,sam,gz}'
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]
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]
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ext.args = { "${meta.db_params}" }
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.centrifuge" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.centrifuge" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.centrifuge" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.centrifuge" }
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}
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}
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withName: CENTRIFUGE_KREPORT {
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withName: CENTRIFUGE_KREPORT {
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errorStrategy = {task.exitStatus == 255 ? 'ignore' : 'retry'}
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errorStrategy = {task.exitStatus == 255 ? 'ignore' : 'retry'}
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ext.args = { "${meta.db_params}" }
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.centrifuge" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.centrifuge" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.centrifuge" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.centrifuge" }
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publishDir = [
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publishDir = [
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path: { "${params.outdir}/centrifuge/${meta.db_name}/" },
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path: { "${params.outdir}/centrifuge/${meta.db_name}/" },
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mode: params.publish_dir_mode,
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mode: params.publish_dir_mode,
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@ -480,7 +480,7 @@ process {
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}
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}
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withName: KAIJU_KAIJU {
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withName: KAIJU_KAIJU {
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.kaiju" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.kaiju" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.kaiju" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.kaiju" }
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publishDir = [
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publishDir = [
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path: { "${params.outdir}/kaiju/${meta.db_name}/" },
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path: { "${params.outdir}/kaiju/${meta.db_name}/" },
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mode: params.publish_dir_mode,
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mode: params.publish_dir_mode,
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@ -504,7 +504,7 @@ process {
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withName: DIAMOND_BLASTX {
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withName: DIAMOND_BLASTX {
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ext.args = { "${meta.db_params}" }
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.diamond" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.diamond" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.diamond" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.diamond" }
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publishDir = [
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publishDir = [
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path: { "${params.outdir}/diamond/${meta.db_name}/" },
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path: { "${params.outdir}/diamond/${meta.db_name}/" },
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mode: params.publish_dir_mode,
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mode: params.publish_dir_mode,
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@ -520,7 +520,7 @@ process {
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params.motus_save_mgc_read_counts ? "-M ${task.ext.prefix}.mgc" : ""
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params.motus_save_mgc_read_counts ? "-M ${task.ext.prefix}.mgc" : ""
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].join(',').replaceAll(','," ")
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].join(',').replaceAll(','," ")
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}
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}
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}" }
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publishDir = [
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publishDir = [
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path: { "${params.outdir}/motus/${meta.db_name}/" },
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path: { "${params.outdir}/motus/${meta.db_name}/" },
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mode: params.publish_dir_mode
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mode: params.publish_dir_mode
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