Commit 6c15d952 authored by Peter van 't Hof's avatar Peter van 't Hof

Added cnv calling to shiva

parent b500ee16
......@@ -40,6 +40,11 @@
<artifactId>Mapping</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Kopisu</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Toucan</artifactId>
......
......@@ -15,10 +15,11 @@
*/
package nl.lumc.sasc.biopet.pipelines.shiva
import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference }
import nl.lumc.sasc.biopet.core.{PipelineCommand, Reference}
import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import nl.lumc.sasc.biopet.extensions.gatk._
import nl.lumc.sasc.biopet.pipelines.bammetrics.TargetRegions
import nl.lumc.sasc.biopet.pipelines.kopisu.Kopisu
import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingTrait
import nl.lumc.sasc.biopet.pipelines.toucan.Toucan
import nl.lumc.sasc.biopet.utils.config.Configurable
......@@ -162,6 +163,10 @@ class Shiva(val root: Configurable) extends QScript with MultisampleMappingTrait
Some(new ShivaSvCalling(this))
} else None
lazy val cnvCalling = if (config("cnv_calling", default = false).asBoolean) {
Some(new Kopisu()(this))
} else None
lazy val annotation = if (multisampleVariantCalling.isDefined &&
config("annotation", default = false).asBoolean) {
Some(new Toucan(this))
......@@ -183,11 +188,17 @@ class Shiva(val root: Configurable) extends QScript with MultisampleMappingTrait
}
})
svCalling.foreach(sv => {
svCalling.foreach { sv =>
sv.outputDir = new File(outputDir, "sv_calling")
sv.inputBams = samples.flatMap { case (sampleId, sample) => sample.preProcessBam.map(sampleId -> _) }
add(sv)
})
}
cnvCalling.foreach { cnv =>
cnv.outputDir = new File(outputDir, "cnv_calling")
cnv.inputBams = samples.flatMap { case (sampleId, sample) => sample.preProcessBam.map(sampleId -> _) }
add(cnv)
}
}
/** Location of summary file */
......
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