Commit 20504318 authored by Sander Bollen's avatar Sander Bollen

add missing extension for newref

parent 5adb9eea
package nl.lumc.sasc.biopet.extensions.wisecondor
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.Input
/**
* Created by Sander Bollen on 22-3-17.
*/
class WisecondorNewRef(val root: Configurable) extends Wisecondor {
@Input
var inputBeds: List[File] = Nil
var nNeighbourBins: Option[Int] = config("n_neighbour_bins", namespace = "wisecondor", default = None)
def cmdLine = {
executable + required("newref") +
repeat("-I", inputBeds) +
required("-O", output) +
required("-R", referenceFasta()) +
binCommand +
optional("-n", nNeighbourBins)
}
}
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