Commit 589d229b authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix outputdirs

parent d5b3661d
......@@ -46,12 +46,12 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
val mapping = new Mapping(qscript)
mapping.sampleId = sampleId
mapping.libId = libId
mapping.outputDir = new File(libDir, "variantcalling/")
mapping.outputDir = libDir
/** Library variantcalling */
val gatkVariantcalling = new GatkVariantcalling(qscript)
gatkVariantcalling.sampleID = sampleId
gatkVariantcalling.outputDir = libDir
gatkVariantcalling.outputDir = new File(libDir, "variantcalling")
protected def addJobs(): Unit = {
val bamFile: Option[File] = if (config.contains("R1")) {
......
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