Commit ee69910c authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added scala docs

parent 3e44feaf
......@@ -21,6 +21,11 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/**
* Extension for gubbins
* See; https://github.com/sanger-pathogens/gubbins
* No version known
*/
class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Contaminants", required = false)
......@@ -47,6 +52,7 @@ class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
var verbose: Boolean = config("verbose", default = false)
var noCleanup: Boolean = config("no_cleanup", default = false)
/** Set correct output files */
override def beforeGraph: Unit = {
super.beforeGraph
require(outputDirectory != null)
......@@ -63,6 +69,7 @@ class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
for (t <- out) outputFiles ::= new File(outputDirectory + File.separator + prefix.getOrElse("gubbins") + t)
}
/** Return command to execute */
def cmdLine = required("cd", outputDirectory) + " && " + required(executable) +
optional("--outgroup", outgroup) +
optional("--starting_tree", startingTree) +
......
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