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Reduce ConcatVCF resources to sane levels #488

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maxulysse merged 2 commits into from
Oct 27, 2017
Merged

Reduce ConcatVCF resources to sane levels #488

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1bd8727
Reduce ConcatVCF resources to sane levels
marcelm Oct 19, 2017
f362185
Retry ConcatVCF if it fails with SIGPIPE
marcelm Oct 19, 2017
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6 changes: 4 additions & 2 deletions configuration/uppmax-localhost.config
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Original file line number Diff line number Diff line change
Expand Up @@ -57,8 +57,10 @@ process {
// These processes are defined in main.nf

$ConcatVCF {
cpus = 16
memory = {params.totalMemory}
cpus = 8
// For unknown reasons, ConcatVCF sometimes fails with SIGPIPE
// (exit code 141). Rerunning the process will usually work.
errorStrategy = {task.exitStatus == 141 ? 'retry' : 'terminate'}
}
$CreateRecalibrationTable {
cpus = 16
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