diff --git a/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala b/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
index 58b8f9a333cc02188ab1ab4df58497aa188bbe47..b33a964d0be86d00203e9e118df2ab1c1ef80d99 100644
--- a/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
+++ b/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
@@ -101,6 +101,9 @@ object WriteDependencies extends Logging with Configurable {
         file.addOutputJob(function)
         files += output -> file
       }
+      val file = files.getOrElse(function.jobOutputFile, QueueFile(function.jobOutputFile))
+      file.addOutputJob(function)
+      files += function.jobOutputFile -> file
     }
 
     val jobs = functionNames.par.map {