diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index a8a5825a5efab26f21228f39fd5efd6f0d857122..65a06dbf4a45cb97f8df16af608a23fa02f139bd 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -98,7 +98,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
     }
     val unzippedExt = "." + getExtension(unzippedFilename)
     (unzippedFilename, unzippedExt)
-  }
+  } ensuring(_._2.length > 1, "Flexiprep input files must have an extension when uncompressed.")
 
   /** Function that's need to be executed before the script is accessed */
   def init() {