Commit f35b7861 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added gubbins to the pipeline

parent b32bc6cc
......@@ -4,8 +4,7 @@ import
import nl.lumc.sasc.biopet.core.MultiSampleQScript
import nl.lumc.sasc.biopet.core.PipelineCommand
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.Cat
import nl.lumc.sasc.biopet.extensions.Raxml
import nl.lumc.sasc.biopet.extensions.{ RunGubbins, Cat, Raxml }
import nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline
import org.broadinstitute.gatk.queue.QScript
......@@ -96,6 +95,12 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
raxmlBi.n = outputName + "_bi"
raxmlBi.w = outputDir
val gubbins = new RunGubbins(this)
gubbins.fastafile = input
gubbins.startingTree = raxmlBi.getBipartitionsFile
gubbins.outputDirectory = outputDir + "/gubbins/"
addRaxml(catVariantsSnps.output, outputDir + "raxml", "snps")
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