Skip to content
Snippets Groups Projects
Commit 4841f1ce authored by pjvan_thof's avatar pjvan_thof
Browse files

Fixing picard executables

parent 691a6392
No related branches found
No related tags found
1 merge request!24Changes after testing
Hide whitespace changes
Inline Side-by-side
Showing
with 5 additions and 5 deletions
picard.wdl
+ 5
− 5
View file @ 4841f1ce
......@@ -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
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment