Fixed outputDirs

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala

@@ -57,7 +57,10 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
     require(inputBams.nonEmpty, "No input bams found")
     require(callers.nonEmpty, "must select at least 1 SV caller, choices are: " + callersList.map(_.name).mkString(", "))
 
-    callers.foreach(add)
+    callers.foreach { caller =>
+      caller.outputDir = new File(outputDir, caller.name)
+      add(caller)
+    }
 
     addSummaryJobs()
   }

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala

@@ -87,6 +87,7 @@ trait ShivaVariantcallingTrait extends SummaryQScript
     for (caller <- callers) {
       caller.inputBams = inputBams
       caller.namePrefix = namePrefix
+      caller.outputDir = new File(outputDir, caller.name)
       add(caller)
       addStats(caller.outputFile, caller.name)
       val normalize: Boolean = config("execute_vt_normalize", default = false, submodule = caller.configName)