diff --git a/gffcompare.wdl b/gffcompare.wdl
index 8b135479a14a51ff073733b892c137f9c4e1e2d6..5c83ba9d9a0bc790d53b74fc0391e86b294e2dff 100644
--- a/gffcompare.wdl
+++ b/gffcompare.wdl
@@ -91,7 +91,7 @@ task GffCompare {
         else 0
     Int noInputFiles = length(inputGtfFiles)
     Boolean oneFile = (noFilesGtfList + noInputFiles) == 1
-    String annotatedName = if oneFile
+    String annotatedName = if oneFile && defined(referenceAnnotation)
         then "annotated"
         else "combined"