Commit aeb3c024 authored by Peter van 't Hof's avatar Peter van 't Hof

Remove outputDir from arguments

parent c05ab685
......@@ -29,11 +29,10 @@ trait BiopetQScript extends Configurable with GatkLogging {
@Argument(doc = "JSON config file(s)", fullName = "config_file", shortName = "config", required = false)
val configfiles: List[File] = Nil
@Argument(doc = "Output directory", fullName = "output_directory", shortName = "outDir", required = true)
var outputDir: String = _
@Argument(doc = "Disable all scatters", shortName = "DSC", required = false)
var disableScatterDefault: Boolean = false
var disableScatter: Boolean = false
var outputFiles: Map[String, File] = Map()
......@@ -45,11 +44,12 @@ trait BiopetQScript extends Configurable with GatkLogging {
var functions: Seq[QFunction]
final def script() {
outputDir = config("output_dir", required = true)
if (!outputDir.endsWith("/")) outputDir += "/"
init
biopetScript
if (disableScatterDefault) for (function <- functions) function match {
if (disableScatter) for (function <- functions) function match {
case f: ScatterGatherableFunction => f.scatterCount = 1
case _ =>
}
......
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