From ced5696b6ea724d6ed3fd5d3687a7b1b03011298 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Mon, 18 Jun 2018 16:38:15 +0200
Subject: [PATCH] remove duplicate -Xmx and -jar
---
gatk.wdl | 2 --
1 file changed, 2 deletions(-)
diff --git a/gatk.wdl b/gatk.wdl
index d54277b..d591626 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -216,7 +216,6 @@ task GenotypeGVCFs {
${preCommand}
${toolCommand} \
- -Xmx${mem}G -jar ${gatkJar} \
GenotypeGVCFs \
-R ${refFasta} \
-O ${outputPath} \
@@ -267,7 +266,6 @@ task HaplotypeCallerGvcf {
set -e -o pipefail
${preCommand}
${toolCommand} \
- -Xmx${mem}G -jar ${gatkJar} \
HaplotypeCaller \
-R ${refFasta} \
-O ${gvcfPath} \
--
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