Implemented addMultisampleJobs method

protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala

@@ -41,7 +41,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
     var outputSnps: FastaOutput = _
 
     protected def addJobs(): Unit = {
-      addLibsJobs()
+      addPerLibJobs()
       output = addGenerateFasta(sampleId, sampleDir)
       outputSnps = addGenerateFasta(sampleId, sampleDir, snpsOnly = true)
     }
@@ -56,11 +56,13 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
     gatkPipeline.biopetScript
     addAll(gatkPipeline.functions)
 
+    addPerSampleJobs()
+  }
+
+  def addMultiSampleJobs(): Unit = {
     val refVariants = addGenerateFasta(null, outputDir + "reference/", outputName = "reference")
     val refVariantSnps = addGenerateFasta(null, outputDir + "reference/", outputName = "reference", snpsOnly = true)
 
-    addSamplesJobs()
-
     val catVariants = Cat(this, refVariants.variants :: samples.map(_._2.output.variants).toList, outputDir + "fastas/variant.fasta")
     add(catVariants)
     val catVariantsSnps = Cat(this, refVariantSnps.variants :: samples.map(_._2.outputSnps.variants).toList, outputDir + "fastas/variant.snps_only.fasta")
@@ -129,6 +131,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
 
     addTreeJobs(catVariantsSnps.output, catConsensusVariantsSnps.output, outputDir + "trees" + File.separator + "snps_only", "snps_only")
     addTreeJobs(catVariants.output, catConsensusVariants.output, outputDir + "trees" + File.separator + "snps_indels", "snps_indels")
+
   }
 
   def addGenerateFasta(sampleName: String, outputDir: String, outputName: String = null,

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala

@@ -127,7 +127,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
     gatkVariantcalling.outputDir = sampleDir + "/variantcalling/"
 
     protected def addJobs(): Unit = {
-      addLibsJobs()
+      addPerLibJobs()
       gatkVariantcalling.inputBams = libraries.map(_._2.mapping.finalBamFile).toList
       gatkVariantcalling.preProcesBams = false
       if (!singleSampleCalling) {
@@ -150,10 +150,11 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
     override def configPath: List[String] = super.configPath ::: "multisample" :: Nil
   }
 
-  def biopetScript() {
-    addSamplesJobs
+  def biopetScript(): Unit = {
+    addPerSampleJobs
+  }
 
-    //SampleWide jobs
+  def addMultiSampleJobs(): Unit = {
     val gvcfFiles: List[File] = if (mergeGvcfs && externalGvcfs.size + samples.size > 1) {
       val newFile = outputDir + "merged.gvcf.vcf.gz"
       add(CombineGVCFs(this, externalGvcfs ++ samples.map(_._2.gatkVariantcalling.scriptOutput.gvcfFile), newFile))

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala

@@ -37,6 +37,9 @@ class MultisamplePipelineTemplate(val root: Configurable) extends QScript with M
     }
   }
 
+  def addMultiSampleJobs(): Unit = {
+  }
+
   def init(): Unit = {
   }
 

public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala

@@ -67,7 +67,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript {
     val controls: List[String] = config("control", default = Nil)
 
     def addJobs(): Unit = {
-      addLibsJobs()
+      addPerLibJobs()
       val bamFiles = libraries.map(_._2.mapping.finalBamFile).toList
       if (bamFiles.length == 1) {
         add(Ln(qscript, bamFiles.head, bamFile))
@@ -102,8 +102,10 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript {
     // Third step is calling peaks on the bam files produced with the mapping pipeline, this will be done with MACS2
     logger.info("Starting CArP pipeline")
 
-    addSamplesJobs
+    addPerSampleJobs
+  }
 
+  def addMultiSampleJobs(): Unit = {
     for ((sampleId, sample) <- samples) {
       for (controlId <- sample.controls) {
         if (!samples.contains(controlId))

public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala

@@ -103,7 +103,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
     }
 
     protected def addJobs(): Unit = {
-      addLibsJobs()
+      addPerLibJobs()
       val libraryBamfiles = libraries.map(_._2.mapping.finalBamFile).toList
       val libraryFastqFiles = libraries.map(_._2.prefixFastq).toList
 
@@ -151,7 +151,10 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
       tagsLibrary = cdl.output
     }
 
-    addSamplesJobs
+    addPerSampleJobs
+  }
+
+  def addMultiSampleJobs(): Unit = {
   }
 
   def addBedtoolsCounts(bamFile: File, outputPrefix: String, outputDir: String) {