Adding missing argument

biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/RefflatStats.scala

@@ -49,7 +49,7 @@ class RefflatStats(val parent: Configurable) extends ToolCommandFunction with Re
     if (reference == null) reference = referenceFasta()
   }
 
-  override def cmdLine =
+  override def cmdLine: String =
     super.cmdLine +
       required("-a", refflatFile) +
       required("-R", reference) +

gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala

@@ -237,6 +237,8 @@ class Gentrap(val parent: Configurable)
       new File(outputDir, "expression_measures" + File.separator + "transcript.stats")
     refflatStats.exonOutput =
       new File(outputDir, "expression_measures" + File.separator + "exon.stats")
+    refflatStats.intronOutput =
+      new File(outputDir, "expression_measures" + File.separator + "intron.stats")
     refflatStats.jobOutputFile = new File(outputDir, ".reflatstats.out")
     add(refflatStats)