Commit 2387d560 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Remove intermediate

parent e40baa30
......@@ -333,7 +333,6 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
if (paired) bwaCommand.R2 = R2.get
bwaCommand.deps = deps
bwaCommand.R = Some(getReadGroupBwa)
bwaCommand.isIntermediate = true
val sortSam = new SortSam(this)
sortSam.output = output
add(bwaCommand | sortSam, chunking || !skipMarkduplicates)
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