Commit dbccba19 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

General gatk

parent 7c5cd789
package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.Input
/**
* Created by pjvan_thof on 2/26/15.
*/
class Gatk(val root: Configurable) extends BiopetJavaCommandLineFunction {
override def subPath = "gatk" :: super.subPath
jarFile = config("gatk_jar")
override val defaultVmem = "5G"
@Input(required = true)
val reference: File = config("reference")
@Input(required = false)
val gatkKey: File = config("gatk_key")
//val intervals: List[File] = config("intervals")
}
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