Commit 9c297111 authored by Peter van 't Hof's avatar Peter van 't Hof

Added shiva report to Basty

parent d7ef6f44
......@@ -21,9 +21,10 @@ package nl.lumc.sasc.biopet.pipelines.basty
import java.io.File
import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import nl.lumc.sasc.biopet.core.{MultiSampleQScript, PipelineCommand}
import nl.lumc.sasc.biopet.extensions.{Cat, Raxml, RunGubbins}
import nl.lumc.sasc.biopet.pipelines.shiva.Shiva
import nl.lumc.sasc.biopet.pipelines.shiva.{Shiva, ShivaReport}
import nl.lumc.sasc.biopet.extensions.tools.BastyGenerateFasta
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
......@@ -51,6 +52,13 @@ class Basty(val parent: Configurable) extends QScript with MultiSampleQScript {
lazy val shiva = new Shiva(qscript)
override def reportClass: Option[ReportBuilderExtension] = {
val shiva = new ShivaReport(this)
shiva.outputDir = new File(outputDir, "report")
shiva.summaryDbFile = summaryDbFile
Some(shiva)
}
def summaryFiles: Map[String, File] = Map()
def summarySettings: Map[String, Any] = Map("boot_runs" -> numBoot)
......
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