From 36568da026dbd86bfe9be2452f2d999a32c695f1 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Sun, 8 Mar 2015 11:12:55 +0100
Subject: [PATCH] Use correct alignment file for per-sample
CollectRnaSeqMetrics job
---
.../scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
index 8bdd6ede1..37ee728e6 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
@@ -619,7 +619,7 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
/** Picard CollectRnaSeqMetrics job */
private def collectRnaSeqMetricsJob: CollectRnaSeqMetrics = {
val job = new CollectRnaSeqMetrics(qscript)
- job.input = alnFileDirty
+ job.input = alnFile
job.output = createFile(".rna_metrics")
job.refFlat = annotationRefFlat
job.chartOutput = Option(createFile(".coverage_bias.pdf"))
--
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