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Code Issues Releases Packages Activity

Add tool names to end of prefix files for easier distinguishing in general stats

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James Fellows Yates 2023-01-16 14:49:44 +01:00
parent d6fa45b500
commit c8f6d713a3
1 changed files with 5 additions and 5 deletions
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10
conf/modules.config
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@ -350,7 +350,7 @@ process {
withName: KRAKEN2_KRAKEN2 { withName: KRAKEN2_KRAKEN2 {
ext.args = params.kraken2_save_minimizers ? { "${meta.db_params} --report-minimizer-data" } : { "${meta.db_params}" } ext.args = params.kraken2_save_minimizers ? { "${meta.db_params} --report-minimizer-data" } : { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { meta.tool == "bracken" ? "${meta.id}-${meta.db_name}.bracken" : "${meta.id}-${meta.db_name}" } : { meta.tool == "bracken" ? "${meta.id}-${meta.run_accession}-${meta.db_name}.bracken" : "${meta.id}-${meta.run_accession}-${meta.db_name}" } 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" }
publishDir = [ publishDir = [
path: { "${params.outdir}/kraken2/${meta.db_name}/" }, path: { "${params.outdir}/kraken2/${meta.db_name}/" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
@ -389,7 +389,7 @@ process {
withName: KRAKENUNIQ_PRELOADEDKRAKENUNIQ { withName: KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
ext.args = { "${meta.db_params}" } ext.args = { "${meta.db_params}" }
// one run with multiple samples, so fix ID to just db name to ensure clean log name // one run with multiple samples, so fix ID to just db name to ensure clean log name
ext.prefix = { "${meta.db_name}" } ext.prefix = { "${meta.db_name}.krakenuniq" }
publishDir = [ publishDir = [
path: { "${params.outdir}/krakenuniq/${meta.db_name}/" }, path: { "${params.outdir}/krakenuniq/${meta.db_name}/" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
@ -432,7 +432,7 @@ process {
withName: METAPHLAN3_METAPHLAN3 { withName: METAPHLAN3_METAPHLAN3 {
ext.args = { "${meta.db_params}" } ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" } ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.metaphlan3" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.metaphlan3" }
publishDir = [ publishDir = [
path: { "${params.outdir}/metaphlan3/${meta.db_name}/" }, path: { "${params.outdir}/metaphlan3/${meta.db_name}/" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
@ -480,7 +480,7 @@ process {
} }
withName: KAIJU_KAIJU { withName: KAIJU_KAIJU {
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" } ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.kaiju" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.kaiju" }
publishDir = [ publishDir = [
path: { "${params.outdir}/kaiju/${meta.db_name}/" }, path: { "${params.outdir}/kaiju/${meta.db_name}/" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
@ -504,7 +504,7 @@ process {
withName: DIAMOND_BLASTX { withName: DIAMOND_BLASTX {
ext.args = { "${meta.db_params}" } ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" } ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.diamond" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.diamond" }
publishDir = [ publishDir = [
path: { "${params.outdir}/diamond/${meta.db_name}/" }, path: { "${params.outdir}/diamond/${meta.db_name}/" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,