From 30fe43b745fb2f82961e423aaede2c762b2fe6af Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 21 May 2014 15:29:37 +0200
Subject: [PATCH] - Fixed output file for star
---
.../sasc/biopet/pipelines/mapping/Mapping.scala | 14 +++++++-------
1 file changed, 7 insertions(+), 7 deletions(-)
diff --git a/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index 2e07f081b..3825a8736 100644
--- a/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -88,7 +88,7 @@ class Mapping(private var globalConfig: Config) extends QScript {
bamFile = addSortSam(List(bwaCommand.output), swapExt(outputDir,bwaCommand.output,".sam",".bam"), outputDir)
} else if (aligner == "star") {
val starCommand = new Star(config) { R1 = fastq_R1; if (paired) R2 = fastq_R2; this.outputDir = qscript.outputDir + "star/" ;
- outputSam = new File(this.outputDir + "/star_output.sam") }
+ outputSam = new File(this.outputDir + "/Aligned.out.sam") }
add(starCommand)
bamFile = addAddOrReplaceReadGroups(List(starCommand.outputSam), swapExt(outputDir,starCommand.outputSam,".sam",".bam"), outputDir)
}
@@ -98,12 +98,12 @@ class Mapping(private var globalConfig: Config) extends QScript {
def addSortSam(inputSam:List[File], outputFile:File, dir:String) : File = {
val sortSam = new SortSam {
- input = inputSam
- createIndex = true
- output = outputFile
- memoryLimit = 2
- nCoresRequest = 2
- jobResourceRequests :+= "h_vmem=4G"
+ this.input = inputSam
+ this.createIndex = true
+ this.output = outputFile
+ this.memoryLimit = 2
+ this.nCoresRequest = 2
+ this.jobResourceRequests :+= "h_vmem=4G"
}
add(sortSam)
--
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