Add gatk variantcalling with haplotypecaller

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

@@ -3,15 +3,27 @@ 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.ShivaTrait
+import nl.lumc.sasc.biopet.pipelines.shiva.{ShivaVariantcallingTrait, ShivaVariantcalling, ShivaTrait}
 import org.broadinstitute.gatk.queue.QScript
 
 /**
  * Created by pjvan_thof on 2/26/15.
  */
 class ShivaGatk(val root: Configurable) extends QScript with ShivaTrait {
+  qscript =>
   def this() = this(null)
 
+  override def makeVariantcalling(multisample: Boolean = false): ShivaVariantcallingTrait = {
+    if (multisample) new ShivaVariantcallingGatk(qscript) {
+      override def namePrefix = "multisample."
+      override def configName = "shivavariantcalling"
+      override def configPath: List[String] = super.configPath ::: "multisample" :: Nil
+    }
+    else new ShivaVariantcallingGatk(qscript) {
+      override def configName = "shivavariantcalling"
+    }
+  }
+
   override def makeSample(id: String) = new this.Sample(id)
   class Sample(sampleId: String) extends super.Sample(sampleId) {
     override def makeLibrary(id: String) = new this.Library(id)

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

+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
+
+/**
+ * Created by pjvan_thof on 2/26/15.
+ */
+class ShivaVariantcallingGatk(val root: Configurable) extends QScript with ShivaVariantcallingTrait {
+  qscript =>
+  def this() = this(null)
+
+  override def callers = new Haplotypecaller :: super.callers
+
+  class Haplotypecaller extends Variantcaller {
+    val name = "haplotypecaller"
+    protected val defaultPrio = 1
+    protected val defaultUse = true
+
+    def outputFile = new File(outputDir, namePrefix + "haplotypecaller.vcf.gz")
+
+    def addJobs() {
+      val hc = new HaplotypeCaller(qscript)
+      hc.input_file = inputBams
+      hc.out = outputFile
+      add(hc)
+    }
+  }
+}
+
+object ShivaVariantcallingGatk extends PipelineCommand
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public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala

@@ -26,7 +26,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
     addSummaryJobs
   }
 
-  def makeVariantcalling(multisample: Boolean = false) = {
+  def makeVariantcalling(multisample: Boolean = false): ShivaVariantcallingTrait = {
     if (multisample) new ShivaVariantcalling(qscript) {
       override def namePrefix = "multisample."
       override def configName = "shivavariantcalling"

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

@@ -29,13 +29,15 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
   }
 
   def init: Unit = {
-    if (!namePrefix.isEmpty && !namePrefix.endsWith(".")) namePrefix += "."
   }
 
+  def finalFile = new File(outputDir, namePrefix + "final.vcf.gz")
+
   def biopetScript: Unit = {
     val cv = new CombineVariants(qscript)
-    cv.outputFile = new File(outputDir, namePrefix + ".final.vcf.gz")
-    for (caller <- callers) {
+    cv.outputFile = finalFile
+    cv.setKey = "VariantCaller"
+    for (caller <- usedCallers) {
       caller.addJobs()
       cv.addInput(caller.outputFile, caller.name)
     }
@@ -44,7 +46,9 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
     addSummaryJobs
   }
 
-  def callers = List(new RawVcf).filter(_.use)
+  def callers: List[Variantcaller] = List(new RawVcf)
+
+  def usedCallers: List[Variantcaller] = callers.filter(_.use)
 
   trait Variantcaller {
     val name: String
@@ -96,5 +100,5 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
 
   def summarySettings = Map()
 
-  def summaryFiles = Map()
+  def summaryFiles: Map[String, File] = usedCallers.map(x => (x.name -> x.outputFile)).toMap + ("final" -> finalFile)
 }
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