From 4841f1ce503fad8baacf9f5c69c9841b9b661f2f Mon Sep 17 00:00:00 2001
From: pjvan_thof <pjrvanthof@gmail.com>
Date: Thu, 14 Jun 2018 11:58:15 +0200
Subject: [PATCH] Fixing picard executables
---
picard.wdl | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/picard.wdl b/picard.wdl
index adba2cf..66916ef 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -11,7 +11,7 @@ task ScatterIntervalList {
String toolCommand = if defined(picardJar)
then "java -Xmx" + mem + "G -jar " + picardJar
- else "gatk -Xmx" + mem + "G"
+ else "picard -Xmx" + mem + "G"
command {
set -e -o pipefail
@@ -52,7 +52,7 @@ task GatherBamFiles {
String toolCommand = if defined(picardJar)
then "java -Xmx" + mem + "G -jar " + picardJar
- else "gatk -Xmx" + mem + "G"
+ else "picard -Xmx" + mem + "G"
command {
set -e -o pipefail
@@ -100,7 +100,7 @@ task MarkDuplicates {
String toolCommand = if defined(picardJar)
then "java -Xmx" + mem + "G -jar " + picardJar
- else "gatk -Xmx" + mem + "G"
+ else "picard -Xmx" + mem + "G"
command {
set -e -o pipefail
@@ -148,7 +148,7 @@ task MergeVCFs {
String toolCommand = if defined(picardJar)
then "java -Xmx" + mem + "G -jar " + picardJar
- else "gatk -Xmx" + mem + "G"
+ else "picard -Xmx" + mem + "G"
command {
set -e -o pipefail
@@ -182,7 +182,7 @@ task SamToFastq {
String toolCommand = if defined(picardJar)
then "java -Xmx" + mem + "G -jar " + picardJar
- else "gatk -Xmx" + mem + "G"
+ else "picard -Xmx" + mem + "G"
command {
set -e -o pipefail
--
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