Commit 8e606123 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding toucan to shiva

parent d7efc98b
......@@ -40,6 +40,11 @@
<artifactId>Mapping</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Toucan</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
......
......@@ -24,6 +24,7 @@ import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, MarkDuplicates, SamToFastq }
import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
import nl.lumc.sasc.biopet.pipelines.toucan.Toucan
import scala.collection.JavaConversions._
......@@ -292,6 +293,16 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
vc.biopetScript()
addAll(vc.functions)
addSummaryQScript(vc)
if (config("annotation", default = true).asBoolean) {
val toucan = new Toucan(this)
toucan.outputDir = new File(outputDir, "annotation")
toucan.inputVCF = vc.finalFile
toucan.init()
toucan.biopetScript()
addAll(toucan.functions)
addSummaryQScript(toucan)
}
})
svCalling.foreach(sv => {
......
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