Commit d6fcf3f9 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed files

parent ab7420cc
......@@ -474,11 +474,11 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
val zcatR1 = extractIfNeeded(R1, output.getParentFile)
val zcatR2 = if (paired) Some(extractIfNeeded(R2.get, output.getParentFile)) else None
val starCommand = Star(this, zcatR1._2,, outputDir, isIntermediate = true)
val ar = addAddOrReplaceReadGroups(starCommand.outputSam, output)
val ar = addAddOrReplaceReadGroups(starCommand.outputSam, swapExt(outputDir, output, ".bam", ".addAddOrReplaceReadGroups.bam"))
val reorderSam = new ReorderSam(this)
reorderSam.input = ar._2
reorderSam.output = swapExt(ar._2.getParentFile, output, ".bam", ".reordered.bam")
reorderSam.output = output
val pipe = new BiopetFifoPipe(this, (zcatR1._1 :: (if (paired) zcatR2.get._1 else None) ::
Some(starCommand) :: Some(ar._1) :: Some(reorderSam) :: Nil).flatten)
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