Commit e3fd97af authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix output file for tophat step

parent d91e8f6f
......@@ -380,7 +380,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
// merge with mapped file
val mergeSamFile = MergeSamFiles(this, List(tophat.outputAcceptedHits, sorter.output),
tophat.output_dir, "coordinate")
new File(tophat.output_dir, "fixed_merged.bam"), sortOrder = "coordinate")
mergeSamFile.createIndex = true
mergeSamFile.isIntermediate = true
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