Commit 0d7fce54 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Add ShiveGatk

parent 492b1223
......@@ -39,5 +39,10 @@
<artifactId>Mapping</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Shiva</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
</project>
package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.core.PipelineCommand
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.pipelines.shiva.{ShivaTrait, Shiva}
import org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvan_thof on 2/26/15.
*/
class ShivaGatk(val root: Configurable) extends QScript with ShivaTrait {
def this() = this(null)
override def makeSample(id: String) = new this.Sample(id)
class Sample(sampleId: String) extends super.Sample(sampleId) {
override def makeLibrary(id: String) = new this.Library(id)
class Library(libId: String) extends super.Library(libId) {
override def preProcess(input:File): Option[File] = {
//TODO: add preproces
None
}
}
override def doublePreProcess(input: List[File], isIntermediate: Boolean = false): Option[File] = {
if (input.size <= 1) super.doublePreProcess(input)
else {
super.doublePreProcess(input)
//TODO: Add indel realignment
}
}
}
}
object ShivaGatk extends PipelineCommand
\ No newline at end of file
......@@ -12,6 +12,7 @@ object BiopetExecutableProtected extends BiopetExecutable {
nl.lumc.sasc.biopet.pipelines.gatk.GatkVariantcalling,
nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline,
nl.lumc.sasc.biopet.pipelines.gatk.GatkVariantRecalibration,
nl.lumc.sasc.biopet.pipelines.gatk.ShivaGatk,
nl.lumc.sasc.biopet.pipelines.basty.Basty)
def tools = BiopetExecutablePublic.tools
......
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