Commit 31ea0eee authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

- Fixed scattercounts

parent 630092d5
......@@ -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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