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Code Issues Releases Packages Activity

move errorStrategy to config

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This commit is contained in:
James Fellows Yates 2023-03-07 11:09:25 +01:00
parent b5a2983c5f
commit 8ca9fad3b1
2 changed files with 13 additions and 3 deletions
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13
conf/base.config
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@ -60,6 +60,19 @@ process {
withName:CUSTOM_DUMPSOFTWAREVERSIONS { withName:CUSTOM_DUMPSOFTWAREVERSIONS {
cache = false cache = false
} }
withName: BRACKEN_BRACKEN {
errorStrategy = 'ignore'
}
withName: CENTRIFUGE_KREPORT {
errorStrategy = {task.exitStatus == 255 ? 'ignore' : 'retry'}
}
withName: KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE {
errorStrategy = { task.exitStatus in [255,1] ? 'ignore' : 'retry' }
}
withName: MEGAN_RMA2INFO_TSV { withName: MEGAN_RMA2INFO_TSV {
cpus = { check_max( 1 , 'cpus' ) } cpus = { check_max( 1 , 'cpus' ) }
memory = { check_max( 6.GB * task.attempt, 'memory' ) } memory = { check_max( 6.GB * task.attempt, 'memory' ) }

3
conf/modules.config
View file

@ -354,7 +354,6 @@ process {
} }
withName: BRACKEN_BRACKEN { withName: BRACKEN_BRACKEN {
errorStrategy = 'ignore'
ext.args = { "${meta.db_params}" } ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.bracken" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.bracken" } ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.bracken" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.bracken" }
publishDir = [ publishDir = [
@ -456,7 +455,6 @@ process {
} }
withName: CENTRIFUGE_KREPORT { withName: CENTRIFUGE_KREPORT {
errorStrategy = {task.exitStatus == 255 ? 'ignore' : 'retry'}
ext.args = { "${meta.db_params}" } ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.centrifuge" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.centrifuge" } ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.centrifuge" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.centrifuge" }
publishDir = [ publishDir = [
@ -467,7 +465,6 @@ process {
} }
withName: KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE { withName: KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE {
errorStrategy = { task.exitStatus in [255,1] ? 'ignore' : 'retry' }
ext.prefix = { "centrifuge_${meta.id}_combined_reports" } ext.prefix = { "centrifuge_${meta.id}_combined_reports" }
publishDir = [ publishDir = [
path: { "${params.outdir}/centrifuge/" }, path: { "${params.outdir}/centrifuge/" },