diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
index 82332de297f12df794fa3d770c3dcc22da04f57a..35d39691d25855699d63cae765c6f3e08a668750 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
@@ -17,14 +17,14 @@ package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.{Reference, BiopetCommandLineFunction}
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 
 /**
  * Extension for Tophat
  */
-class Tophat(val root: Configurable) extends BiopetCommandLineFunction {
+class Tophat(val root: Configurable) extends BiopetCommandLineFunction with Reference {
 
   executable = config("exe", default = "tophat", freeVar = false)