Commit 7accfa72 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed traits

parent 00a7a89a
......@@ -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 {
......
......@@ -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)
......
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