Commit 03af79a2 authored by Sander Bollen's avatar Sander Bollen
Browse files

mergegatkdepths wrapper

parent c79918d9
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.{Input, Output}
/**
* Created by Sander Bollen on 23-11-16.
*/
class XhmmMergeGatkDepths(val root: Configurable) extends Xhmm {
@Input(doc = "List of input depths files")
var gatkDepthsFiles: List[File] = Nil
@Output(doc = "Merged output file in XHMM format")
var output: File = _
def cmdLine = {
executable + repeat("--GATKdepths", gatkDepthsFiles) + required("-o", output)
}
}
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