Commit 5d9c7d3a authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added report

parent 84b0a9f7
package nl.lumc.sasc.biopet.pipelines.gears
import nl.lumc.sasc.biopet.core.{ PipelineCommand, MultiSampleQScript }
import nl.lumc.sasc.biopet.pipelines.shiva.ShivaReport
import nl.lumc.sasc.biopet.utils.Logging
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
......@@ -11,6 +12,13 @@ import org.broadinstitute.gatk.queue.QScript
class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qscript =>
def this() = this(null)
override def reportClass = {
val gearsReport = new GearsReport(this)
gearsReport.outputDir = new File(outputDir, "report")
gearsReport.summaryFile = summaryFile
Some(gearsReport)
}
/** Init for pipeline */
def init(): Unit = {
}
......
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