Commit 9098847e authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

deps not required

parent bfc2617e
......@@ -22,7 +22,7 @@ class Sickle(val globalConfig: Config) extends CommandLineFunction {
@Output(doc="stats output") var output_stats: File = null
@Input(doc="qualityType file", required=false) var qualityTypeFile: File = null
@Argument(doc="Quality Type", required=false) var qualityType: String = config.getAsString("qualitytype", null)
@Input(doc="deps") var deps: List[File] = Nil
@Input(doc="deps", required=false) var deps: List[File] = Nil
var defaultQualityType: String = config.getAsString("defaultqualitytype", "sanger")
......@@ -59,22 +59,7 @@ class Sickle(val globalConfig: Config) extends CommandLineFunction {
} else logger.warn("File : " + qualityTypeFile + " does not exist")
}
}
// private var version: String = _
// def getVersion : String = {
// val REG = """sickle version (.*)""".r
// if (version == null) for (line <- (sickle_exe + " --version").!!.split("\n")) {
// line match {
// case REG(m) => {
// version = m
// return version
// }
// case _ =>
// }
// }
// return version
// }
private var version: String = _
var versionCommand = sickle_exe + " --version"
var versionRegex = """sickle version (.*)"""
......
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