Merge branch 'fix-gvcfs-extract' into 'develop'

Fix gvcfs extract



See merge request !389

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala

@@ -106,16 +106,12 @@ class GenotypeGVCFs(val root: Configurable) extends CommandLineGATK with Scatter
   @Gather(enabled = false)
   private var outputIndex: File = _
 
-  @Output
-  @Gather(enabled = false)
-  private var dbsnpIndex: File = _
-
   override def beforeGraph() {
     super.beforeGraph()
     deps ++= variant.filter(orig => orig != null && (!orig.getName.endsWith(".list"))).map(orig => VcfUtils.getVcfIndexFile(orig))
     if (out != null && !org.broadinstitute.gatk.utils.io.IOUtils.isSpecialFile(out))
       outputIndex = VcfUtils.getVcfIndexFile(out)
-    dbsnp.foreach(x => dbsnpIndex = VcfUtils.getVcfIndexFile(x))
+    dbsnp.foreach(x => deps :+= VcfUtils.getVcfIndexFile(x))
   }
 
   override def cmdLine = super.cmdLine +

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

@@ -73,7 +73,7 @@ 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(", "))

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
 
+  /**
+   * Map of sample name -> gvcf. May be empty.
+   */
+  protected var gVcfFiles: Map[String, File] = Map()
+
+  def getGvcfs = gVcfFiles
+
   def biopetScript() {
     val gvcfFiles = for ((sample, inputBam) <- inputBams) yield {
       val hc = gatk.HaplotypeCaller.gvcf(this, inputBam, new File(outputDir, sample + ".gvcf.vcf.gz"))
       add(hc)
-      hc.out
+      sample -> hc.out
     }
 
-    val genotypeGVCFs = gatk.GenotypeGVCFs(this, gvcfFiles.toList, outputFile)
+    val genotypeGVCFs = gatk.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() = {}