From d085b42fcf4e1b9d9be79e025bc8403b3fcbe2f7 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Fri, 10 Aug 2018 11:50:38 +0200
Subject: [PATCH] fix vardict memory?
---
vardict.wdl | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/vardict.wdl b/vardict.wdl
index 1cd35d5..c79a768 100644
--- a/vardict.wdl
+++ b/vardict.wdl
@@ -22,18 +22,19 @@ task VarDict {
Int geneColumn = 4
String? preCommand
- Int memory = 4
+ Int memory = 8
Float memoryMultiplier = 2.0
}
String toolCommand = if defined(installDir)
then installDir + "/VarDict"
else if useJavaVersion
- then "vardict-java -Xmx${memory}"
+ then "vardict-java"
else "vardict"
command {
set -e -o pipefail
+ export JAVA_OPTS="-Xmx~{memory}G"
~{preCommand}
~{toolCommand} \
-G ~{refFasta} \
--
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