Commit d70e8930 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix some config values

parent 36641e26
......@@ -54,9 +54,9 @@ class Stampy(val root: Configurable) extends BiopetCommandLineFunction {
var sensitive: Boolean = config("sensitive", default = false)
var fast: Boolean = config("fast", default = false)
var readgroup: String = config("readgroup")
var readgroup: String = null
var verbosity: Option[Int] = config("verbosity", default = 2)
var logfile: String = config("logfile")
var logfile: Option[String] = config("logfile")
executable = config("exe", default = "stampy.py", freeVar = false)
override val versionRegex = """stampy v(.*) \(.*\), .*""".r
......@@ -68,6 +68,11 @@ class Stampy(val root: Configurable) extends BiopetCommandLineFunction {
override def versionCommand = executable + " --help"
override def beforeGraph: Unit = {
super.beforeGraph
require(readgroup != null)
}
def cmdLine: String = {
var cmd: String = required(executable) +
optional("-t", nCoresRequest) +
......
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