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Commit 0a530446 authored by ffinfo's avatar ffinfo
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Fixing syntax

parent 6acda157
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1 merge request!54Added alt post script
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bwa.wdl
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...@@ -20,8 +20,8 @@ task Mem { ...@@ -20,8 +20,8 @@ task Mem {
then "java -Xmx" + picardMemory + "G -jar " + picardJar then "java -Xmx" + picardMemory + "G -jar " + picardJar
else "picard -Xmx" + picardMemory + "G" else "picard -Xmx" + picardMemory + "G"
String altCommand = if (defined(bwaIndex.altIndex)) then "| bwa-postalt " + bwaIndex.altIndex+ " | \ String altCommand = if (defined(bwaIndex.altIndex)) then "| bwa-postalt " + bwaIndex.altIndex+ " | " +
" + picardCommand + " SetNmAndUqTags \ picardCommand + " SetNmAndUqTags \
INPUT=/dev/stdin OUTPUT=" + outputPath + " \ INPUT=/dev/stdin OUTPUT=" + outputPath + " \
CREATE_INDEX=true R=" + bwaIndex.fasta else "" CREATE_INDEX=true R=" + bwaIndex.fasta else ""
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