Passing gender information to shivavariantcalling

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

@@ -60,11 +60,13 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
       override def namePrefix = "multisample"
       override def configNamespace: String = "shivavariantcalling"
       override def configPath: List[String] = super.configPath ::: "multisample" :: Nil
+      genders = samples.map { case (sampleName, sample) => sampleName -> sample.gender }
     }
     else new ShivaVariantcalling(qscript) {
       override def configNamespace = "shivavariantcalling"
       sampleId = sample
       libId = library
+      genders = sample.map(x => x -> samples(x).gender).toMap
     }
   }
 

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

@@ -14,15 +14,16 @@
  */
 package nl.lumc.sasc.biopet.pipelines.shiva
 
-import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, SampleLibraryTag }
+import nl.lumc.sasc.biopet.core.{ MultiSampleQScript, PipelineCommand, Reference, SampleLibraryTag }
+import MultiSampleQScript.Gender
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.extensions.Tabix
 import nl.lumc.sasc.biopet.extensions.gatk.{ CombineVariants, GenotypeConcordance }
 import nl.lumc.sasc.biopet.extensions.tools.VcfStats
-import nl.lumc.sasc.biopet.extensions.vt.{ VtDecompose, VtNormalize }
+import nl.lumc.sasc.biopet.extensions.vt.{VtDecompose, VtNormalize}
 import nl.lumc.sasc.biopet.pipelines.bammetrics.TargetRegions
 import nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.{ VarscanCnsSingleSample, _ }
-import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }
+import nl.lumc.sasc.biopet.utils.{BamUtils, Logging}
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
@@ -48,9 +49,21 @@ class ShivaVariantcalling(val parent: Configurable) extends QScript
 
   var inputBqsrFiles: Map[String, File] = Map()
 
+  var genders: Map[String, Gender.Value] = _
+
   /** Executed before script */
   def init(): Unit = {
     if (inputBamsArg.nonEmpty) inputBams = BamUtils.sampleBamMap(inputBamsArg)
+    if (genders == null) genders = {
+      val samples: Map[String, Any] = config("genders")
+      samples.map { case (sampleName, gender) =>
+        sampleName -> (gender.toString.toLowerCase match {
+          case "male"   => Gender.Male
+          case "female" => Gender.Female
+          case _ => Gender.Unknown
+        })
+      }
+    }
   }
 
   var referenceVcf: Option[File] = config("reference_vcf")
@@ -100,6 +113,7 @@ class ShivaVariantcalling(val parent: Configurable) extends QScript
       caller.inputBqsrFiles = inputBqsrFiles
       caller.namePrefix = namePrefix
       caller.outputDir = new File(outputDir, caller.name)
+      caller.genders = genders
       add(caller)
       addStats(caller.outputFile, caller.name)
       val normalize: Boolean = config("execute_vt_normalize", default = false, namespace = caller.configNamespace)

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

@@ -14,6 +14,7 @@
  */
 package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
 
+import nl.lumc.sasc.biopet.core.MultiSampleQScript.Gender
 import nl.lumc.sasc.biopet.core.{ BiopetQScript, Reference }
 import org.broadinstitute.gatk.queue.QScript
 
@@ -27,6 +28,8 @@ trait Variantcaller extends QScript with BiopetQScript with Reference {
 
   var namePrefix: String = _
 
+  var genders: Map[String, Gender.Value] = _
+
   val mergeVcfResults: Boolean = config("merge_vcf_results", default = true)
 
   /**