Commit 00b8265b authored by sajvanderzeeuw's avatar sajvanderzeeuw
Browse files

Changed one option in BWA.scala so mapping had to be changed as well

parent f2db87ce
......@@ -188,7 +188,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
bwaCommand.R1 = R1
if (paired) bwaCommand.R2 = R2
bwaCommand.deps = deps
bwaCommand.RG = getReadGroup
bwaCommand.R = getReadGroup
bwaCommand.output = new File(chunkDir + outputName + ".sam")
add(bwaCommand, isIntermediate = true)
bamFiles :+= addSortSam(List(bwaCommand.output), swapExt(chunkDir, bwaCommand.output, ".sam", ".bam"), chunkDir)
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