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Commit d085b42f authored by Cats's avatar Cats
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fix vardict memory?

parent 8b0d6891
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1 merge request!45Changes for somatic variantcalling
...@@ -22,18 +22,19 @@ task VarDict { ...@@ -22,18 +22,19 @@ task VarDict {
Int geneColumn = 4 Int geneColumn = 4
String? preCommand String? preCommand
Int memory = 4 Int memory = 8
Float memoryMultiplier = 2.0 Float memoryMultiplier = 2.0
} }
String toolCommand = if defined(installDir) String toolCommand = if defined(installDir)
then installDir + "/VarDict" then installDir + "/VarDict"
else if useJavaVersion else if useJavaVersion
then "vardict-java -Xmx${memory}" then "vardict-java"
else "vardict" else "vardict"
command { command {
set -e -o pipefail set -e -o pipefail
export JAVA_OPTS="-Xmx~{memory}G"
~{preCommand} ~{preCommand}
~{toolCommand} \ ~{toolCommand} \
-G ~{refFasta} \ -G ~{refFasta} \
......
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