Commit e4c45c85 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Add more options

parent 285e2e4d
......@@ -9,18 +9,35 @@ import org.broadinstitute.gatk.utils.commandline.Input
/**
* Created by pjvan_thof on 2/26/15.
*/
class Gatk(val root: Configurable) extends BiopetJavaCommandLineFunction {
abstract class Gatk extends BiopetJavaCommandLineFunction {
override def subPath = "gatk" :: super.subPath
jarFile = config("gatk_jar")
val analysisType: String
override val defaultVmem = "5G"
@Input(required = true)
val reference: File = config("reference")
var reference: File = config("reference")
@Input(required = false)
var gatkKey: File = config("gatk_key")
@Input(required = false)
val gatkKey: File = config("gatk_key")
var intervals: List[File] = config("intervals")
//val intervals: List[File] = config("intervals")
@Input(required = false)
var excludeIntervals: List[File] = config("exclude_intervals")
@Input(required = false)
var pedigree: List[File] = config("pedigree")
override def commandLine = super.commandLine +
required("-T", analysisType) +
required("-R", reference) +
optional("-K", gatkKey) +
repeat("-I", intervals) +
repeat("-XL", excludeIntervals) +
repeat("-ped", pedigree)
}
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