Fixed traits

public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala → public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTrait.scala

@@ -8,6 +8,7 @@ import nl.lumc.sasc.biopet.extensions.Ln
 import nl.lumc.sasc.biopet.extensions.picard.{MarkDuplicates, MergeSamFiles, AddOrReplaceReadGroups, SamToFastq}
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
 import nl.lumc.sasc.biopet.utils.Logging
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 
 import MultisampleMapping.MergeStrategy
@@ -17,10 +18,8 @@ import scala.collection.JavaConversions._
 /**
   * Created by pjvanthof on 18/12/15.
   */
-trait MultisampleMapping extends QScript
-  with MultiSampleQScript
-  with Reference { qscript =>
-  //def this() = this(null)
+trait MultisampleMappingTrait extends MultiSampleQScript
+  with Reference { qscript: QScript =>
 
   def mergeStrategy: MergeStrategy.Value = {
     val value: String = config("merge_strategy", default = "preprocessmarkduplicates")
@@ -190,6 +189,9 @@ trait MultisampleMapping extends QScript
     }
   }
 }
+class MultisampleMapping(val root: Configurable) extends QScript with MultisampleMappingTrait {
+  def this() = this(null)
+}
 
 object MultisampleMapping extends PipelineCommand {
 

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

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.shiva
 
 import nl.lumc.sasc.biopet.core.Reference
 import nl.lumc.sasc.biopet.pipelines.bammetrics.TargetRegions
-import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMapping
+import nl.lumc.sasc.biopet.pipelines.mapping.{MultisampleMappingTrait}
 import nl.lumc.sasc.biopet.pipelines.toucan.Toucan
 import org.broadinstitute.gatk.queue.QScript
 
@@ -26,7 +26,7 @@ import org.broadinstitute.gatk.queue.QScript
  *
  * Created by pjvan_thof on 2/26/15.
  */
-trait ShivaTrait extends MultisampleMapping with Reference with TargetRegions { qscript: QScript =>
+trait ShivaTrait extends MultisampleMappingTrait with Reference with TargetRegions { qscript: QScript =>
 
   override def reportClass = {
     val shiva = new ShivaReport(this)