Commit afa1608d authored by Peter van 't Hof's avatar Peter van 't Hof

Make it possible to disable gubbins

parent 9c297111
......@@ -45,6 +45,8 @@ class Basty(val parent: Configurable) extends QScript with MultiSampleQScript {
val numBoot: Int = config("boot_runs", default = 100, namespace = "raxml").asInt
val executeGubbins: Boolean = config("execute_gubbins", default = true)
override def defaults = Map(
"ploidy" -> 1,
"variantcallers" -> variantcallers
......@@ -192,11 +194,13 @@ class Basty(val parent: Configurable) extends QScript with MultiSampleQScript {
raxmlBi.w = dirSufixRaxml
add(raxmlBi)
val gubbins = new RunGubbins(this)
gubbins.fastafile = concensusVariants
gubbins.startingTree = raxmlBi.getBipartitionsFile
gubbins.outputDirectory = dirSufixGubbins
add(gubbins)
if (executeGubbins) {
val gubbins = new RunGubbins(this)
gubbins.fastafile = concensusVariants
gubbins.startingTree = raxmlBi.getBipartitionsFile
gubbins.outputDirectory = dirSufixGubbins
add(gubbins)
}
}
addTreeJobs(catVariantsSnps.output,
......
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