diff --git a/public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala b/public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala
index bfdd643445a653ee6ea1a621531131f0593e6b5c..9035928e825e79dd9a3ffa98cd24470d9e9fe5b6 100644
--- a/public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala
+++ b/public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala
@@ -88,7 +88,7 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
           contig -> cvChr.outputFile
       }
       add(cvTotal)
-      (cvTotal.outputFile, Map[String, File]())
+      (cvTotal.outputFile, chrGens)
     }
 
     val snpTests = BedRecordList.fromReference(referenceFasta())