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Adds generic fix for java memory issue on slurm

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This commit is contained in:
Emil Bertilsson 2022-06-09 10:28:20 +02:00
parent 8453f6b41a
commit 72e995f326
1 changed files with 7 additions and 1 deletions
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8
conf/pipeline/raredisease/hasta.config
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@ -7,7 +7,13 @@ process {
cpus = { check_max( 16 * task.attempt, 'cpus' ) } cpus = { check_max( 16 * task.attempt, 'cpus' ) }
memory = { check_max( 80.GB * task.attempt, 'memory' ) } memory = { check_max( 80.GB * task.attempt, 'memory' ) }
} }
// Java memory fixes
withName:'QUALIMAP_BAMQC' { withName:'QUALIMAP_BAMQC' {
ext.args = { "--java-mem-size=${task.memory.giga / 1.15 as long}G" } clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''} ${task.memory ? "--mem ${task.memory.mega * 1.15 as long}M" : ''}" }
} }
withName:'PICARD_MARKDUPLICATES' {
clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''} ${task.memory ? "--mem ${task.memory.mega * 1.15 as long}M" : ''}" }
}
} }