From c80402130bdb7471e8f37fece8cb643625a0df02 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Thu, 8 Jul 2021 09:58:51 +0200
Subject: [PATCH] fix Xmx in AnnotateInsertedSequence
---
gridss.wdl | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/gridss.wdl b/gridss.wdl
index 069d695..aedac9a 100644
--- a/gridss.wdl
+++ b/gridss.wdl
@@ -39,7 +39,9 @@ task AnnotateInsertedSequence {
}
command {
- AnnotateInsertedSequence -Xmx~{javaXmx} \
+ set -e
+ _JAVA_OPTIONS="${_JAVA_OPTIONS}:-Xmx~{javaXmx}"
+ AnnotateInsertedSequence \
REFERENCE_SEQUENCE=~{viralReference} \
INPUT=~{inputVcf} \
OUTPUT=~{outputPath} \
@@ -215,6 +217,7 @@ task Virusbreakend {
}
command {
+ set -e
mkdir virusbreakenddb
tar -xzvf ~{virusbreakendDB} -C virusbreakenddb --strip-components 1
virusbreakend \
--
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