diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
index ab60204ac46d012856de51c6f3d179f36255eb66..a53409bee2ea8cd3a050a0fdea471a4b8a5da06f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
@@ -71,7 +71,7 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction with Refere
     super.beforeGraph()
     if (reference == null) reference = referenceFasta()
     if (outFileNamePrefix != null && !outFileNamePrefix.endsWith(".")) outFileNamePrefix += "."
-    val prefix = if (outFileNamePrefix != null) outputDir + outFileNamePrefix else outputDir
+    val prefix = if (outFileNamePrefix != null) outputDir + File.separator + outFileNamePrefix else outputDir
     if (runmode == null) {
       outputSam = new File(prefix + "Aligned.out.sam")
       outputTab = new File(prefix + "SJ.out.tab")