Commit e58842e5 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix args

parent bcfaa188
......@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.breakdancer
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.{Reference, BiopetQScript, PipelineCommand}
import nl.lumc.sasc.biopet.core.{ Reference, BiopetQScript, PipelineCommand }
import org.broadinstitute.gatk.queue.QScript
/// Breakdancer is actually a mini pipeline executing binaries from the breakdancer package
......@@ -47,7 +47,6 @@ class Breakdancer(val root: Configurable) extends QScript with BiopetQScript wit
}
override def init(): Unit = {
}
def biopetScript() {
......
......@@ -51,8 +51,8 @@ class BreakdancerCaller(val root: Configurable) extends BiopetCommandLineFunctio
var x: Option[Int] = config("x", default = 1000)
var b: Option[Int] = config("b", default = 100)
var t: Boolean = config("t", default = false)
var d: String = config("d")
var g: String = config("g")
var d: Option[String] = config("d")
var g: Option[String] = config("g")
var l: Boolean = config("l", default = false)
var a: Boolean = config("a", default = false)
var h: Boolean = config("h", default = false)
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment