Added gtf to star index generation

315f5230 · Peter van 't Hof · 53cc5101 · 315f5230
Commit 315f5230 authored May 17, 2016 by Peter van 't Hof
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generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala ...sc/biopet/pipelines/generateindexes/GenerateIndexes.scala +1 -0

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--- a/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala
+++ b/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala
@@ -238,6 +238,7 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
        starIndex.outputDir = starDir
        starIndex.reference = createLinks(starDir)
        starIndex.runmode = "genomeGenerate"
+        starIndex.sjdbGTFfile = gtfFile
        add(starIndex)
        configDeps :+= starIndex.jobOutputFile
        outputConfig += "star" -> Map(