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Commit 39ca1721 authored by pjvan_thof's avatar pjvan_thof
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Merge remote-tracking branch 'origin/BIOWDL-36' into BIOWDL-36

parents 86aebe5b ced5696b
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1 merge request!24Changes after testing
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...@@ -215,7 +215,6 @@ task GenotypeGVCFs { ...@@ -215,7 +215,6 @@ task GenotypeGVCFs {
${preCommand} ${preCommand}
${toolCommand} \ ${toolCommand} \
-Xmx${mem}G -jar ${gatkJar} \
GenotypeGVCFs \ GenotypeGVCFs \
-R ${refFasta} \ -R ${refFasta} \
-O ${outputPath} \ -O ${outputPath} \
...@@ -266,7 +265,6 @@ task HaplotypeCallerGvcf { ...@@ -266,7 +265,6 @@ task HaplotypeCallerGvcf {
set -e -o pipefail set -e -o pipefail
${preCommand} ${preCommand}
${toolCommand} \ ${toolCommand} \
-Xmx${mem}G -jar ${gatkJar} \
HaplotypeCaller \ HaplotypeCaller \
-R ${refFasta} \ -R ${refFasta} \
-O ${gvcfPath} \ -O ${gvcfPath} \
......
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