Commit 84b4fbf2 authored by bow's avatar bow
Browse files

Set default config for CollectRnaSeqMetrics RefFlat value

parent 9d2bf4ea
......@@ -68,7 +68,7 @@ class CollectRnaSeqMetrics(val root: Configurable) extends Picard with Summariza
var stopAfter: Option[Long] = config("stop_after")
override def beforeGraph: Unit = {
require(refFlat != null, "RefFlat file must be supplied.")
if (refFlat == null) refFlat = config("refFlat")
val validFlags = StrandSpecificity.values.map(_.toString).toSet
strandSpecificity match {
case Some(s) => require(validFlags.contains(s),
......
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