From d0fa5d55ea19592263e5466e57ecd2f9d1749e0c Mon Sep 17 00:00:00 2001
From: pjvan_thof <pjrvanthof@gmail.com>
Date: Thu, 14 Jun 2018 12:06:03 +0200
Subject: [PATCH] fixing gatk mem option
---
gatk.wdl | 14 +++++++-------
1 file changed, 7 insertions(+), 7 deletions(-)
diff --git a/gatk.wdl b/gatk.wdl
index 78c53b8..d54277b 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -19,7 +19,7 @@ task ApplyBQSR {
String toolCommand = if defined(gatkJar)
then "java -Xmx" + mem + "G -jar " + gatkJar
- else "gatk -Xmx" + mem + "G"
+ else "gatk --java-options -Xmx" + mem + "G"
command {
set -e -o pipefail
@@ -74,7 +74,7 @@ task BaseRecalibrator {
String toolCommand = if defined(gatkJar)
then "java -Xmx" + mem + "G -jar " + gatkJar
- else "gatk -Xmx" + mem + "G"
+ else "gatk --java-options -Xmx" + mem + "G"
command {
set -e -o pipefail
@@ -120,7 +120,7 @@ task CombineGVCFs {
String toolCommand = if defined(gatkJar)
then "java -Xmx" + mem + "G -jar " + gatkJar
- else "gatk -Xmx" + mem + "G"
+ else "gatk --java-options -Xmx" + mem + "G"
command {
set -e -o pipefail
@@ -164,7 +164,7 @@ task GatherBqsrReports {
String toolCommand = if defined(gatkJar)
then "java -Xmx" + mem + "G -jar " + gatkJar
- else "gatk -Xmx" + mem + "G"
+ else "gatk --java-options -Xmx" + mem + "G"
command {
set -e -o pipefail
@@ -209,7 +209,7 @@ task GenotypeGVCFs {
String toolCommand = if defined(gatkJar)
then "java -Xmx" + mem + "G -jar " + gatkJar
- else "gatk -Xmx" + mem + "G"
+ else "gatk --java-options -Xmx" + mem + "G"
command {
set -e -o pipefail
@@ -261,7 +261,7 @@ task HaplotypeCallerGvcf {
String toolCommand = if defined(gatkJar)
then "java -Xmx" + mem + "G -jar " + gatkJar
- else "gatk -Xmx" + mem + "G"
+ else "gatk --java-options -Xmx" + mem + "G"
command {
set -e -o pipefail
@@ -306,7 +306,7 @@ task SplitNCigarReads {
String toolCommand = if defined(gatkJar)
then "java -Xmx" + mem + "G -jar " + gatkJar
- else "gatk -Xmx" + mem + "G"
+ else "gatk --java-options -Xmx" + mem + "G"
command {
set -e -o pipefail
--
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