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Commit d0fa5d55 authored by pjvan_thof's avatar pjvan_thof
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fixing gatk mem option

parent 4841f1ce
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with 7 additions and 7 deletions
gatk.wdl
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...@@ -19,7 +19,7 @@ task ApplyBQSR { ...@@ -19,7 +19,7 @@ task ApplyBQSR {
String toolCommand = if defined(gatkJar) String toolCommand = if defined(gatkJar)
then "java -Xmx" + mem + "G -jar " + gatkJar then "java -Xmx" + mem + "G -jar " + gatkJar
else "gatk -Xmx" + mem + "G" else "gatk --java-options -Xmx" + mem + "G"
command { command {
set -e -o pipefail set -e -o pipefail
...@@ -74,7 +74,7 @@ task BaseRecalibrator { ...@@ -74,7 +74,7 @@ task BaseRecalibrator {
String toolCommand = if defined(gatkJar) String toolCommand = if defined(gatkJar)
then "java -Xmx" + mem + "G -jar " + gatkJar then "java -Xmx" + mem + "G -jar " + gatkJar
else "gatk -Xmx" + mem + "G" else "gatk --java-options -Xmx" + mem + "G"
command { command {
set -e -o pipefail set -e -o pipefail
...@@ -120,7 +120,7 @@ task CombineGVCFs { ...@@ -120,7 +120,7 @@ task CombineGVCFs {
String toolCommand = if defined(gatkJar) String toolCommand = if defined(gatkJar)
then "java -Xmx" + mem + "G -jar " + gatkJar then "java -Xmx" + mem + "G -jar " + gatkJar
else "gatk -Xmx" + mem + "G" else "gatk --java-options -Xmx" + mem + "G"
command { command {
set -e -o pipefail set -e -o pipefail
...@@ -164,7 +164,7 @@ task GatherBqsrReports { ...@@ -164,7 +164,7 @@ task GatherBqsrReports {
String toolCommand = if defined(gatkJar) String toolCommand = if defined(gatkJar)
then "java -Xmx" + mem + "G -jar " + gatkJar then "java -Xmx" + mem + "G -jar " + gatkJar
else "gatk -Xmx" + mem + "G" else "gatk --java-options -Xmx" + mem + "G"
command { command {
set -e -o pipefail set -e -o pipefail
...@@ -209,7 +209,7 @@ task GenotypeGVCFs { ...@@ -209,7 +209,7 @@ task GenotypeGVCFs {
String toolCommand = if defined(gatkJar) String toolCommand = if defined(gatkJar)
then "java -Xmx" + mem + "G -jar " + gatkJar then "java -Xmx" + mem + "G -jar " + gatkJar
else "gatk -Xmx" + mem + "G" else "gatk --java-options -Xmx" + mem + "G"
command { command {
set -e -o pipefail set -e -o pipefail
...@@ -261,7 +261,7 @@ task HaplotypeCallerGvcf { ...@@ -261,7 +261,7 @@ task HaplotypeCallerGvcf {
String toolCommand = if defined(gatkJar) String toolCommand = if defined(gatkJar)
then "java -Xmx" + mem + "G -jar " + gatkJar then "java -Xmx" + mem + "G -jar " + gatkJar
else "gatk -Xmx" + mem + "G" else "gatk --java-options -Xmx" + mem + "G"
command { command {
set -e -o pipefail set -e -o pipefail
...@@ -306,7 +306,7 @@ task SplitNCigarReads { ...@@ -306,7 +306,7 @@ task SplitNCigarReads {
String toolCommand = if defined(gatkJar) String toolCommand = if defined(gatkJar)
then "java -Xmx" + mem + "G -jar " + gatkJar then "java -Xmx" + mem + "G -jar " + gatkJar
else "gatk -Xmx" + mem + "G" else "gatk --java-options -Xmx" + mem + "G"
command { command {
set -e -o pipefail set -e -o pipefail
......
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