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Add error strategy for centrifuge/kreport

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sofstam 2022-07-28 08:54:32 +02:00
parent 9bc45a3f24
commit 71cf32cc6a
1 changed files with 2 additions and 1 deletions
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3
conf/modules.config
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@ -145,7 +145,7 @@ process {
publishDir = [ publishDir = [
path: { "${params.outdir}/filtlong" }, path: { "${params.outdir}/filtlong" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
pattern: '*.fastq.gz', pattern: '*.{fastq.gz,log}',
enabled: params.save_preprocessed_reads enabled: params.save_preprocessed_reads
] ]
} }
@ -347,6 +347,7 @@ 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}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" } ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
publishDir = [ publishDir = [