diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
index dc5972ab488caf26cedc51f8362071d6e36cbd90..62c8292db9070616c16f24a6c37d502e67797221 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
@@ -155,7 +155,7 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
         "fastqc_data" -> "fastqc_data.txt")
         .map {
           case (name, relPath) =>
-            name -> Map("path" -> (outputDir + relPath))
+            name -> Map("path" -> (outputDir + File.pathSeparator + relPath))
         }
 
     ConfigUtils.mapToJson(outputMap)