Commit 657d8684 authored by bow's avatar bow
Browse files

Use absolute path for tophat fix output

parent a0e4262d
......@@ -368,12 +368,12 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
val fixedUnmapped = new File(tophat.output_dir, "unmapped_fixup.sam")
val fixer = new TophatRecondition(this)
fixer.inputBam = tophat.outputAcceptedHits
fixer.outputSam = fixedUnmapped
fixer.outputSam = fixedUnmapped.getAbsoluteFile
fixer.isIntermediate = true
add(fixer)
// sort fixed SAM file
val sorter = SortSam(this, fixer.outputSam, swapExt(fixer.outputSam, ".sam", ".sorted.bam"))
val sorter = SortSam(this, fixer.outputSam, new File(tophat.output_dir, "unmapped_fixup.sorted.bam"))
sorter.sortOrder = "coordinate"
sorter.isIntermediate = true
add(sorter)
......
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