Should address #164

public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala

@@ -42,7 +42,7 @@ trait BastyTrait extends MultiSampleQScript {
 
   lazy val shiva: ShivaTrait = new Shiva(qscript)
 
-  def summaryFile: File = new File(outputDir, "Sage.summary.json")
+  def summaryFile: File = new File(outputDir, "Basty.summary.json")
 
   //TODO: Add summary
   def summaryFiles: Map[String, File] = Map()

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

@@ -269,7 +269,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
     }
   }
 
-  lazy val variantcalling = if (config("multisample_sample_variantcalling", default = true).asBoolean) {
+  lazy val variantcalling = if (config("multisample__variantcalling", default = true).asBoolean) {
     Some(makeVariantcalling(multisample = true))
   } else None