Less errorprone approach of storing the path to outputfiles for the svcallers.

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

@@ -67,15 +67,20 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
     for ((sample, bamFile) <- inputBams) {
       var sampleVcfs: List[File] = List()
       callers.foreach { caller =>
-        sampleVcfs :+= caller.outputFiles(sample)
+        sampleVcfs :+= caller.outputVCF(sample).get
       }
       val mergeSVcalls = new Pysvtools(this)
       mergeSVcalls.input = sampleVcfs
       mergeSVcalls.output = new File(outputDir, sample + ".merged.vcf")
       add(mergeSVcalls)
-      outputFiles += (sample -> mergeSVcalls.output)
+      //      outputFiles += (sample -> mergeSVcalls.output)
     }
 
+    // merging the VCF calls by project
+    // basicly this will do all samples from this pipeline run
+    // group by "tags"
+    // sample tagging is however not available within this pipeline
+
     addSummaryJobs()
   }
 

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

@@ -19,7 +19,7 @@ class Breakdancer(val root: Configurable) extends SvCaller {
       val bdvcf = BreakdancerVCF(this, breakdancer.output, new File(breakdancerSampleDir, sample + ".breakdancer.vcf"))
       add(bdcfg, breakdancer, bdvcf)
 
-      outputFiles += (sample -> bdvcf.output)
+      addVCF(sample, bdvcf.output)
     }
   }
 }

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

@@ -14,7 +14,7 @@ class Clever(val root: Configurable) extends SvCaller {
       val clever = CleverCaller(this, bamFile, cleverDir)
       add(clever)
 
-      outputFiles += (sample -> clever.outputvcf)
+      addVCF(sample, clever.outputvcf)
     }
   }
 }

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

@@ -4,7 +4,7 @@ import nl.lumc.sasc.biopet.extensions.delly.DellyCaller
 import nl.lumc.sasc.biopet.extensions.gatk.CatVariants
 import nl.lumc.sasc.biopet.utils.config.Configurable
 
-/** Script for sv caler delly */
+/** Script for sv caller delly */
 class Delly(val root: Configurable) extends SvCaller {
   def name = "delly"
 
@@ -54,8 +54,7 @@ class Delly(val root: Configurable) extends SvCaller {
       }
 
       add(catVariants)
-
-      outputFiles += (sample -> catVariants.outputFile)
+      addVCF(sample, catVariants.outputFile)
     }
   }
 }

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

@@ -15,5 +15,15 @@ trait SvCaller extends QScript with BiopetQScript with Reference {
 
   var inputBams: Map[String, File] = _
 
+  def outputVCF(sample: String): Option[File] = {
+    outputVcfs.get(sample)
+  }
+
+  protected var outputVcfs: Map[String, File] = _
+
+  protected def addVCF(sampleId: String, outputVCF: File) = {
+    outputVcfs += (sampleId -> outputVCF)
+  }
+
   def init() = {}
 }