diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config index a076dbc..c31b940 100644 --- a/conf/pipeline/raredisease/hasta.config +++ b/conf/pipeline/raredisease/hasta.config @@ -7,7 +7,13 @@ process { cpus = { check_max( 16 * task.attempt, 'cpus' ) } memory = { check_max( 80.GB * task.attempt, 'memory' ) } } + + // Java memory fixes 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" : ''}" } + } + } \ No newline at end of file