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Reinstated maxRetries and increased memory for GATK4_MARKDUPLICATES in sbc_sharc.config for sarek

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lquayle88 2022-10-01 07:43:46 +01:00
parent 8103718389
commit dbb3b3b44b
1 changed files with 2 additions and 2 deletions
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4
conf/pipeline/sarek/sbc_sharc.config
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@ -18,7 +18,7 @@ process {
// error and retry handling // error and retry handling
errorStrategy = { task.exitStatus in [143,137,104,134,139,140,247] ? 'retry' : 'finish' } errorStrategy = { task.exitStatus in [143,137,104,134,139,140,247] ? 'retry' : 'finish' }
maxRetries = 1 maxRetries = 2
// process labels // process labels
@ -75,7 +75,7 @@ process {
} }
withName:'GATK4_MARKDUPLICATES' { withName:'GATK4_MARKDUPLICATES' {
memory = { check_max( 16.GB * task.attempt, 'memory' ) } memory = { check_max( 20.GB * task.attempt, 'memory' ) }
} }
withName:'FREEBAYES|SAMTOOLS_STATS|SAMTOOLS_INDEX|UNZIP' { withName:'FREEBAYES|SAMTOOLS_STATS|SAMTOOLS_INDEX|UNZIP' {