diff --git a/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala b/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala
index 0f59d8776017525c607f9e0d01e4b9a578639703..a2c02fa8fa1f85593e88d28488d3e83e456e6175 100644
--- a/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala
+++ b/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala
@@ -63,6 +63,7 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
         val fastaUris = genomeConfig.getOrElse("fasta_uri",
           throw new IllegalArgumentException(s"No fasta_uri found for $speciesName - $genomeName")) match {
             case a: Traversable[_] => a.map(_.toString).toArray
+            case a: util.ArrayList[_] => a.map(_.toString).toArray
             case a                 => Array(a.toString)
           }