Commit 8d9d194b authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files


parent 182c68fa
......@@ -447,7 +447,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
bowtie2.rg +:= ("PU:" + platformUnit)
bowtie2.rg +:= ("SM:" + sampleId.get)
bowtie2.R1 = R1
if (paired) bowtie2.R2 = Some(R2.get)
bowtie2.R2 = R2
val sortSam = new SortSam(this)
sortSam.output = output
val pipe = bowtie2 | sortSam
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