From 31ea0eee57d936385545973ec1ba058537bd4567 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 21 May 2014 14:39:36 +0200
Subject: [PATCH] - Fixed scattercounts
---
.../src/main/java/nl/lumc/sasc/biopet/wrappers/Star.scala | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Star.scala b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Star.scala
index b599fae78..f898b6676 100644
--- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Star.scala
+++ b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Star.scala
@@ -18,7 +18,7 @@ class Star(private var globalConfig: Config) extends CommandLineFunction {
@Input(doc="Fastq file R2", shortName="R2", required=false) var R2: File = _
@Argument(doc="Output Directory", shortName="outputDir") var outputDir: String = _
@Argument(doc="GenomeDir", required=false) var genomeDir: String = _
- if (genomeDir == null) genomeDir = config.getAsString("genomeDir", referenceFile.getParent + "/star/ref")
+ if (genomeDir == null) genomeDir = config.getAsString("genomeDir", referenceFile.getParent + "/star")
@Argument(doc="STAR runmode", shortName="runmode", required=false) var runmode: String = _
@@ -30,7 +30,7 @@ class Star(private var globalConfig: Config) extends CommandLineFunction {
if (threads > maxThreads) threads = maxThreads
nCoresRequest = Option(threads)
- @Output var outputSam: File = new File(outputDir + "/Aligned.out.sam")
+ @Output var outputSam: File = new File(outputDir + "/star_output.sam")
def commandLine : String= {
//init()
--
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