diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config index 0b6d878..4c4d15e 100644 --- a/conf/pipeline/raredisease/hasta.config +++ b/conf/pipeline/raredisease/hasta.config @@ -10,7 +10,7 @@ process { withLabel:'sentieon' { beforeScript = { "export PATH=\$PATH:\$SENTIEON_INSTALL_DIR/sentieon-genomics-202112.02/bin" } } - withName: BCFTOOLS_VIEW { + withName: 'BCFTOOLS_VIEW' { if (params.genome == 'GRCh37') { ext.args = '--output-type z --apply-filters PASS --exclude "INFO/clinical_genomics_mipAF > 0.40 | INFO/swegenAF > 0.40 | INFO/clingen_ngiAF > 0.40 | INFO/gnomad_svAF > 0.40 "' } else if (params.genome == 'GRCh38') { @@ -20,7 +20,13 @@ process { enabled: false, ] } + + // 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" : ''}" } + } + }