Fixing BIOPET-562

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala

@@ -112,21 +112,22 @@ class ShivaVariantcalling(val root: Configurable) extends QScript
         vtDecompose.inputVcf = vtNormalize.outputVcf
         vtDecompose.outputVcf = swapExt(caller.outputDir, vtNormalize.outputVcf, ".vcf.gz", ".decompose.vcf.gz")
         add(vtDecompose, Tabix(this, vtDecompose.outputVcf))
-        cv.variant :+= TaggedFile(vtDecompose.outputVcf, caller.name)
+        if (caller.mergeVcfResults) cv.variant :+= TaggedFile(vtDecompose.outputVcf, caller.name)
       } else if (normalize && !decompose) {
         vtNormalize.outputVcf = swapExt(caller.outputDir, caller.outputFile, ".vcf.gz", ".normalized.vcf.gz")
         add(vtNormalize, Tabix(this, vtNormalize.outputVcf))
-        cv.variant :+= TaggedFile(vtNormalize.outputVcf, caller.name)
+        if (caller.mergeVcfResults) cv.variant :+= TaggedFile(vtNormalize.outputVcf, caller.name)
       } else if (!normalize && decompose) {
         vtDecompose.inputVcf = caller.outputFile
         vtDecompose.outputVcf = swapExt(caller.outputDir, caller.outputFile, ".vcf.gz", ".decompose.vcf.gz")
         add(vtDecompose, Tabix(this, vtDecompose.outputVcf))
-        cv.variant :+= TaggedFile(vtDecompose.outputVcf, caller.name)
-      } else cv.variant :+= TaggedFile(caller.outputFile, caller.name)
+        if (caller.mergeVcfResults) cv.variant :+= TaggedFile(vtDecompose.outputVcf, caller.name)
+      } else if (caller.mergeVcfResults) cv.variant :+= TaggedFile(caller.outputFile, caller.name)
+    }
+    if (cv.variant.nonEmpty) {
+      add(cv)
+      addStats(finalFile, "final")
     }
-    add(cv)
-
-    addStats(finalFile, "final")
 
     addSummaryJobs()
   }

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Variantcaller.scala

@@ -27,6 +27,8 @@ trait Variantcaller extends QScript with BiopetQScript with Reference {
 
   var namePrefix: String = _
 
+  val mergeVcfResults: Boolean = config("merge_vcf_results", default = true)
+
   /**
    * Map of samplename -> (preprocessed) bam file
    */