Commit f2db87ce authored by sajvanderzeeuw's avatar sajvanderzeeuw
Browse files

Added all Sickle Options

parent 4ddf34bf
......@@ -27,9 +27,13 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
var fastqc: Fastqc = _
executable = config("exe", default = "sickle")
executable = config("exe", default = "sickle", freeVar = false)
var qualityType: String = config("qualitytype")
var qualityThreshold: Option[Int] = config("qualityThreshold")
var lengthThreshold: Option[Int] = config("lengthThreshold")
var noFiveprime: Boolean = config("noFiveprime")
var discardN: Boolean = config("discardN")
var quiet: Boolean = config("quiet")
var defaultQualityType: String = config("defaultqualitytype", default = "sanger")
override val versionRegex = """sickle version (.*)""".r
override def versionCommand = executable + " --version"
......@@ -47,10 +51,14 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
required("-s", output_singles)
} else cmd += required("se")
cmd +
required("-f", input_R1) +
required("-f", input_R1) +
required("-t", qualityType) +
required("-o", output_R1) +
optional("-q", qualityThreshold) +
optional("-l", lengthThreshold) +
optional("-x", noFiveprime) +
optional("-n", discardN) +
optional("--quiet", quiet)
" > " + required(output_stats)
}
}
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