diff --git a/picard.wdl b/picard.wdl index 85c07dbadb8f0f0eccfde481d9e17556228d4edf..102875835bfb2760e650b11cb4b568e5e9212c07 100644 --- a/picard.wdl +++ b/picard.wdl @@ -662,6 +662,7 @@ task SortSam { # Default ram of 4 GB. Using 125001.0 to prevent an answer of # 4.000000001 which gets rounded to 5. + # GATK Best practices uses 75000 here: https://github.com/gatk-workflows/broad-prod-wgs-germline-snps-indels/blob/d2934ed656ade44801f9cfe1c0e78d4f80684b7b/PairedEndSingleSampleWf-fc-hg38.wdl#L778 Int XmxGb = ceil(maxRecordsInRam / 125001.0) Int timeMinutes = 1 + ceil(size(inputBam, "G") * 2) # A mulled container is needed to have both picard and bwa in one container.