Merge pull request #28 from biopet/fix-BIOPET-585

Fix biopet 585

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

@@ -69,6 +69,7 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
 
     // merge VCF by sample
     for ((sample, bamFile) <- inputBams) {
+      if (callers.size > 1) {
         var sampleVCFS: List[Option[File]] = List.empty
         callers.foreach { caller =>
           sampleVCFS ::= caller.outputVCF(sample)
@@ -78,14 +79,18 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
         mergeSVcalls.output = new File(outputDir, sample + ".merged.vcf")
         add(mergeSVcalls)
         outputMergedVCFbySample += (sample -> mergeSVcalls.output)
+      } else {
+        outputMergedVCFbySample += (sample -> callers.head.outputVCF(sample).get)
+      }
     }
 
+    if (inputBams.size > 1) {
       // merge all files from all samples in project
       val mergeSVcallsProject = new Pysvtools(this)
       mergeSVcallsProject.input = outputMergedVCFbySample.values.toList
       mergeSVcallsProject.output = outputMergedVCF
       add(mergeSVcallsProject)
-
+    }
     // merging the VCF calls by project
     // basicly this will do all samples from this pipeline run
     // group by "tags"
@@ -104,7 +109,7 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
   def summarySettings = Map("sv_callers" -> configCallers.toList)
 
   /** Files for the summary */
-  def summaryFiles: Map[String, File] = Map("final_mergedvcf" -> outputMergedVCF)
+  def summaryFiles: Map[String, File] = Map("final_mergedvcf" -> (if (inputBams.size > 1) outputMergedVCF else outputMergedVCFbySample.values.head))
 }
 
 object ShivaSvCalling extends PipelineCommand
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