diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config index fb4d94a..1bec159 100644 --- a/conf/pipeline/raredisease/hasta.config +++ b/conf/pipeline/raredisease/hasta.config @@ -8,7 +8,14 @@ process { memory = { check_max( 80.GB * task.attempt, 'memory' ) } } withLabel:'sentieon' { - beforeScript = { "export PATH=\$PATH:\$SENTIEON_INSTALL_DIR/sentieon-genomics-202010.02/bin" } + beforeScript = { "export PATH=\$PATH:\$SENTIEON_INSTALL_DIR/sentieon-genomics-202112.02/bin" } + } + // Java memory fixes + withName:'QUALIMAP_BAMQC' { + 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" : ''}" } } withName: BCFTOOLS_VIEW { if (params.genome == 'GRCh37') {