diff --git a/picard.wdl b/picard.wdl index adba2cf6762223322efe23c20c2fbc3b0da510e1..66916efa9ffb874617e1effea459e3dbb1b0c099 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