Commit ba8bfc42 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added default to multisample mapping

parent 42de7719
......@@ -102,7 +102,12 @@ trait MultisampleMappingTrait extends MultiSampleQScript
lazy val correctReadgroups: Boolean = config("correct_readgroups", default = false)
lazy val mapping = if (inputR1.isDefined || (inputBam.isDefined && bamToFastq)) {
val m = new Mapping(qscript)
val m = new Mapping(qscript) {
override def configNamespace = "mapping"
override def defaults: Map[String, Any] = super.defaults ++
Map("keep_final_bamfile" -> !(samples(sampleId).libraries.size > 1 ||
preProcessBam.map(_ != bamFile).getOrElse(false)))
}
m.sampleId = Some(sampleId)
m.libId = Some(libId)
m.outputDir = libDir
......
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