From 1885db3cc01cd42c4f75de44e7ff845c1bd2000c Mon Sep 17 00:00:00 2001
From: pjvan_thof <pjrvanthof@gmail.com>
Date: Wed, 13 Jun 2018 15:06:08 +0200
Subject: [PATCH] Update forgotten tool
---
gatk.wdl | 12 +++++++++---
1 file changed, 9 insertions(+), 3 deletions(-)
diff --git a/gatk.wdl b/gatk.wdl
index 0155703..5353d25 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -249,7 +249,6 @@ task HaplotypeCallerGvcf {
Float? memory
Float? memoryMultiplier
-
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(gatkJar)
@@ -289,17 +288,24 @@ task SplitNCigarReads {
File refFastaIndex
File refDict
String outputBam
- String gatkJar
+ String? gatkJar
Array[File]+ intervals
Float? memory
Float? memoryMultiplier
+ Float? memory
+ Float? memoryMultiplier
Int mem = ceil(select_first([memory, 4.0]))
+
+ String toolCommand = if defined(gatkJar)
+ then "java -Xmx" + mem + "G -jar " + gatkJar
+ else "gatk -Xmx" + mem + "G"
+
command {
set -e -o pipefail
${preCommand}
- java -Xms${mem}G -jar ${gatkJar} \
+ ${toolCommand} \
SplitNCigarReads \
-I ${inputBam} \
-R ${refFasta} \
--
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