diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config index 1bec159..d655bf7 100644 --- a/conf/pipeline/raredisease/hasta.config +++ b/conf/pipeline/raredisease/hasta.config @@ -10,13 +10,6 @@ process { withLabel:'sentieon' { 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') { 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 "'