Adding stdout file back to outputs

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala

@@ -116,7 +116,7 @@ object WriteDependencies extends Logging with Configurable {
           "depends_on_intermediate" -> BiopetQScript.safeOutputs(f).getOrElse(Seq()).exists(files(_).isIntermediate),
           "depends_on_jobs" -> BiopetQScript.safeOutputs(f).getOrElse(Seq()).toList.flatMap(files(_).outputJobNames).distinct,
           "output_used_by_jobs" -> BiopetQScript.safeOutputs(f).getOrElse(Seq()).toList.flatMap(files(_).inputJobNames).distinct,
-          "outputs" -> BiopetQScript.safeOutputs(f).getOrElse(Seq()).toList,
+          "outputs" -> (f.jobOutputFile :: BiopetQScript.safeOutputs(f).getOrElse(Seq()).toList),
           "inputs" -> BiopetQScript.safeOutputs(f).getOrElse(Seq()).toList,
           "done_files" -> BiopetQScript.safeDoneFiles(f).getOrElse(Seq()).toList,
           "fail_files" -> BiopetQScript.safeFailFiles(f).getOrElse(Seq()).toList,