Fixed tests

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala

@@ -33,7 +33,6 @@ class CollectRnaSeqMetrics(val root: Configurable) extends Picard with Summariza
 
   @Input(doc = "Gene annotations in refFlat form", required = true)
   var refFlat: File = config("refFlat")
-  //TODO: RefFlat could break gentrap, needs to be checked
 
   @Input(doc = "Location of rRNA sequences in interval list format", required = false)
   var ribosomalIntervals: Option[File] = config("ribosomal_intervals")

public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala

@@ -189,6 +189,7 @@ object GentrapTest {
   val executables = Map(
     "reference" -> "test",
     "dict" -> "test",
+    "refFlat" -> "test",
     "annotation_gtf" -> "test",
     "annotation_bed" -> "test",
     "annotation_refflat" -> "test",