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 3825a87364760db8310e022b0dd83b2f98609fce..2e07f081bcc7ef02f8c8afdcb57f441ea69dd921 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 + "/Aligned.out.sam") } + outputSam = new File(this.outputDir + "/star_output.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 { - this.input = inputSam - this.createIndex = true - this.output = outputFile - this.memoryLimit = 2 - this.nCoresRequest = 2 - this.jobResourceRequests :+= "h_vmem=4G" + input = inputSam + createIndex = true + output = outputFile + memoryLimit = 2 + nCoresRequest = 2 + jobResourceRequests :+= "h_vmem=4G" } add(sortSam)