Adding UnifiedGenotyper

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

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
 import nl.lumc.sasc.biopet.core.PipelineCommand
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.extensions.gatk.broad._
-import nl.lumc.sasc.biopet.pipelines.shiva.{ShivaVariantcallingTrait, ShivaVariantcalling, ShivaTrait}
+import nl.lumc.sasc.biopet.pipelines.shiva.{ ShivaVariantcallingTrait, ShivaVariantcalling, ShivaTrait }
 import org.broadinstitute.gatk.queue.QScript
 
 /**

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

@@ -2,7 +2,6 @@ package nl.lumc.sasc.biopet.pipelines.gatk
 
 import nl.lumc.sasc.biopet.core.PipelineCommand
 import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.gatk.broad.HaplotypeCaller
 import nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcallingTrait
 import org.broadinstitute.gatk.queue.QScript
 
@@ -13,9 +12,9 @@ class ShivaVariantcallingGatk(val root: Configurable) extends QScript with Shiva
   qscript =>
   def this() = this(null)
 
-  override def callers = new Haplotypecaller :: super.callers
+  override def callers = new UnifiedGenotyper :: new HaplotypeCaller :: super.callers
 
-  class Haplotypecaller extends Variantcaller {
+  class HaplotypeCaller extends Variantcaller {
     val name = "haplotypecaller"
     protected val defaultPrio = 1
     protected val defaultUse = true
@@ -23,7 +22,22 @@ class ShivaVariantcallingGatk(val root: Configurable) extends QScript with Shiva
     def outputFile = new File(outputDir, namePrefix + "haplotypecaller.vcf.gz")
 
     def addJobs() {
-      val hc = new HaplotypeCaller(qscript)
+      val hc = new nl.lumc.sasc.biopet.extensions.gatk.broad.HaplotypeCaller(qscript)
+      hc.input_file = inputBams
+      hc.out = outputFile
+      add(hc)
+    }
+  }
+
+  class UnifiedGenotyper extends Variantcaller {
+    val name = "unifiedgenotyper"
+    protected val defaultPrio = 20
+    protected val defaultUse = false
+
+    def outputFile = new File(outputDir, namePrefix + "unifiedgenotyper.vcf.gz")
+
+    def addJobs() {
+      val hc = new nl.lumc.sasc.biopet.extensions.gatk.broad.UnifiedGenotyper(qscript)
       hc.input_file = inputBams
       hc.out = outputFile
       add(hc)

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

@@ -23,8 +23,8 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
   def namePrefix: String = {
     (sampleId, libId) match {
       case (Some(sampleId), Some(libId)) => sampleId + "-" + libId + "."
-      case (Some(sampleId), _) => sampleId + "."
-      case _ => ""
+      case (Some(sampleId), _)           => sampleId + "."
+      case _                             => ""
     }
   }