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Add error strategy for centrifuge/kreport
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1 changed files with 2 additions and 1 deletions
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@ -145,7 +145,7 @@ process {
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publishDir = [
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path: { "${params.outdir}/filtlong" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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pattern: '*.{fastq.gz,log}',
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enabled: params.save_preprocessed_reads
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]
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}
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@ -347,6 +347,7 @@ process {
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}
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withName: CENTRIFUGE_KREPORT {
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errorStrategy = {task.exitStatus == 255 ? 'ignore' : 'retry'}
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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