From 8a1dfa17583049144129370ee008fe7c7816c5dc Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 2 Feb 2016 07:01:49 +0100
Subject: [PATCH] fixed output file of basecounter
---
.../nl/lumc/sasc/biopet/extensions/tools/BaseCounter.scala | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BaseCounter.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BaseCounter.scala
index 16348d31b..189525cf1 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BaseCounter.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BaseCounter.scala
@@ -77,7 +77,6 @@ class BaseCounter(val root: Configurable) extends ToolCommandFunction {
def strandedAntiSenseMetaExonCounts = new File(outputDir, s"$prefix.base.metaexons.stranded.antisense.counts")
override def beforeGraph(): Unit = {
- super.beforeGraph()
outputFiles ++= List(transcriptTotalCounts, transcriptTotalSenseCounts, transcriptTotalAntiSenseCounts,
transcriptExonicCounts, transcriptExonicSenseCounts, transcriptExonicAntiSenseCounts,
transcriptIntronicCounts, transcriptIntronicSenseCounts, transcriptIntronicAntiSenseCounts,
@@ -90,6 +89,9 @@ class BaseCounter(val root: Configurable) extends ToolCommandFunction {
mergeIntronCounts, mergeIntronSenseCounts, mergeIntronAntiSenseCounts,
nonStrandedMetaExonCounts,
strandedMetaExonCounts, strandedSenseMetaExonCounts, strandedAntiSenseMetaExonCounts)
+ jobOutputFile = new File(outputDir, s".$prefix.basecounter.out")
+ super.beforeGraph()
+
}
override def cmdLine = super.cmdLine +
--
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