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move errorStrategy to config
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parent
b5a2983c5f
commit
8ca9fad3b1
2 changed files with 13 additions and 3 deletions
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@ -60,6 +60,19 @@ process {
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withName:CUSTOM_DUMPSOFTWAREVERSIONS {
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cache = false
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}
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withName: BRACKEN_BRACKEN {
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errorStrategy = 'ignore'
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}
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withName: CENTRIFUGE_KREPORT {
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errorStrategy = {task.exitStatus == 255 ? 'ignore' : 'retry'}
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}
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withName: KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE {
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errorStrategy = { task.exitStatus in [255,1] ? 'ignore' : 'retry' }
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}
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withName: MEGAN_RMA2INFO_TSV {
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cpus = { check_max( 1 , 'cpus' ) }
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memory = { check_max( 6.GB * task.attempt, 'memory' ) }
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@ -354,7 +354,6 @@ process {
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}
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withName: BRACKEN_BRACKEN {
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errorStrategy = 'ignore'
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.bracken" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.bracken" }
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publishDir = [
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@ -456,7 +455,6 @@ process {
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}
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withName: CENTRIFUGE_KREPORT {
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errorStrategy = {task.exitStatus == 255 ? 'ignore' : 'retry'}
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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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publishDir = [
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@ -467,7 +465,6 @@ process {
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}
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withName: KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE {
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errorStrategy = { task.exitStatus in [255,1] ? 'ignore' : 'retry' }
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ext.prefix = { "centrifuge_${meta.id}_combined_reports" }
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publishDir = [
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path: { "${params.outdir}/centrifuge/" },
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