get gvcfs from shiva

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Grep.scala

@@ -7,8 +7,8 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
-  * Created by pjvanthof on 30/03/16.
-  */
+ * Created by pjvanthof on 30/03/16.
+ */
 class Grep(val root: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "Input file", required = true)
   var input: File = _

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

@@ -72,7 +72,7 @@ class ShivaVariantcalling(val root: Configurable) extends QScript
   /** Variantcallers requested by the config */
   protected val configCallers: Set[String] = config("variantcallers")
 
-  protected val callers: List[Variantcaller] = {
+  val callers: List[Variantcaller] = {
     (for (name <- configCallers) yield {
       if (!callersList.exists(_.name == name))
         Logging.addError(s"variantcaller '$name' does not exist, possible to use: " + callersList.map(_.name).mkString(", "))
@@ -80,6 +80,8 @@ class ShivaVariantcalling(val root: Configurable) extends QScript
     }).flatten.toList.sortBy(_.prio)
   }
 
+  callers.filter(_.isInstanceOf[HaplotypeCallerGvcf])
+
   /** This will add jobs for this pipeline */
   def biopetScript(): Unit = {
     require(inputBams.nonEmpty, "No input bams found")

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala

@@ -13,14 +13,21 @@ class HaplotypeCallerGvcf(val root: Configurable) extends Variantcaller {
   val name = "haplotypecaller_gvcf"
   protected def defaultPrio = 5
 
+  /**
+    *
+    */
+  protected var gVcfFiles: Map[String, File] = Map()
+
+  def getGvcfs = gVcfFiles
+
   def biopetScript() {
-    val gvcfFiles = for ((sample, inputBam) <- inputBams) yield {
+    gVcfFiles = for ((sample, inputBam) <- inputBams) yield {
       val hc = broad.HaplotypeCaller.gvcf(this, inputBam, new File(outputDir, sample + ".gvcf.vcf.gz"))
       add(hc)
-      hc.out
+      sample -> hc.out
     }
 
-    val genotypeGVCFs = broad.GenotypeGVCFs(this, gvcfFiles.toList, outputFile)
+    val genotypeGVCFs = broad.GenotypeGVCFs(this, gVcfFiles.values.toList, outputFile)
     add(genotypeGVCFs)
   }
 }

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Variantcaller.scala

@@ -28,6 +28,9 @@ trait Variantcaller extends QScript with BiopetQScript with Reference {
 
   var namePrefix: String = _
 
+  /**
+    * Map of samplename -> (preprocessed) bam file
+    */
   var inputBams: Map[String, File] = _
 
   def init() = {}