Commit 3f5dd689 authored by Sander Bollen's avatar Sander Bollen
Browse files

xhmm discover wrapper

parent 6b51387d
package nl.lumc.sasc.biopet.extensions.xhmm
import java.io.File
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 XhmmDiscover(val root: Configurable) extends Xhmm {
@Input
var inputMatrix: File = _
@Output
var outputXcnv: File = _
@Input
var r: File = _
@Argument
var discoverParamsFile: File = config("discover_params", namespace = "xhmm")
private lazy val outputXcnvAuxFile: File = {
new File(outputXcnv.getAbsolutePath + ".aux")
}
@Argument
var xhmmAnalysisName: String = _
def cmdLine = {
executable + required("--discover") +
required("-r", inputMatrix) +
required("-R", r) +
required("-c", outputXcnv) +
required("-a", outputXcnvAuxFile) +
required("-s", xhmmAnalysisName)
}
}
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