From 160ed6f2525aba0e673022beda11e24272ae4d31 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Thu, 25 Jun 2020 08:49:17 +0200
Subject: [PATCH] update picard
---
picard.wdl | 1 +
1 file changed, 1 insertion(+)
diff --git a/picard.wdl b/picard.wdl
index 85c07db..1028758 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.
--
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