Commit cb17d470 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixing markduplicate dependency

parent b4cb9bd0
......@@ -271,7 +271,7 @@ class Mapping(val parent: Configurable) extends QScript with SummaryQScript with
if (!skipMarkduplicates) {
bamFile = new File(outputDir, outputName + ".dedup.bam")
val md = MarkDuplicates(this, bamFiles, finalBamFile)
val md = MarkDuplicates(this, mergedBamFile :: Nil, finalBamFile)
md.isIntermediate = !keepFinalBamFile
add(md)
addSummarizable(md, "mark_duplicates")
......
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