Commit a90b06da authored by bow's avatar bow

Update base BiopetQScript command line argument names

parent c0598153
......@@ -8,10 +8,11 @@ import org.broadinstitute.gatk.queue.QSettings
import org.broadinstitute.gatk.queue.function.QFunction
trait BiopetQScript extends Configurable {
@Argument(doc = "Config Json file", shortName = "config", required = false)
@Argument(doc = "JSON config file(s)", fullName = "config_file", shortName = "conf", required = false)
val configfiles: List[File] = Nil
@Argument(doc = "Output directory", shortName = "outputDir", required = true)
@Argument(doc = "Output directory", fullName = "output_directory", shortName = "outDir", required = true)
var outputDir: String = _
var outputFiles: Map[String, File] = Map()
......
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