Fixing markduplicate dependency

cb17d470 · Peter van 't Hof · b4cb9bd0 · cb17d470
Commit cb17d470 authored Apr 05, 2017 by Peter van 't Hof
--- a/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -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")