Commit 997c7f15 authored by Sander Bollen's avatar Sander Bollen
Browse files

xhmm genotype wrapper

parent 3f5dd689
package nl.lumc.sasc.biopet.extensions.xhmm
import java.io.File
import nl.lumc.sasc.biopet.core.Reference
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Argument, Input, Output}
/**
* Created by Sander Bollen on 23-11-16.
*/
class XhmmGenotype(val root: Configurable) extends Xhmm with Reference {
@Input
var inputMatrix: File = _
@Input
var inputXcnv: File = _
@Output
var outputVcf: File = _
@Input
var r: File = _
@Argument
var discoverParamsFile: File = config("discover_params", namespace = "xhmm")
def cmdLine = {
executable + required("--genotype") +
required("-p", discoverParamsFile) +
required("-r", inputMatrix) +
required("-R", r) +
required("-g", inputXcnv) +
required("-F", referenceFasta()) +
required("-v", outputVcf)
}
}
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