From 4f41ec07bbb1bbbafd70985ecb812d64c0444f53 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 6 Jul 2020 10:55:35 +0200
Subject: [PATCH] add forgotten M
---
gatk.wdl | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/gatk.wdl b/gatk.wdl
index 0d36e44..939513d 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -734,7 +734,7 @@ task GatherBqsrReports {
command {
set -e
mkdir -p "$(dirname ~{outputReportPath})"
- gatk --java-options '-Xmx~{javaXmxMb} -XX:ParallelGCThreads=1' \
+ gatk --java-options '-Xmx~{javaXmxMb}M -XX:ParallelGCThreads=1' \
GatherBQSRReports \
-I ~{sep=' -I ' inputBQSRreports} \
-O ~{outputReportPath}
--
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