From 315f523052593225b04197aee28b1d6a515fe9ef Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 17 May 2016 11:47:54 +0200
Subject: [PATCH] Added gtf to star index generation
---
.../sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala | 1 +
1 file changed, 1 insertion(+)
diff --git 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
index 4acca6b83..f4a0e0406 100644
--- 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(
--
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