Commit 72a96f7e authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Adding Gears to summary output of Mapping

parent 3cd8150f
......@@ -19,18 +19,17 @@ import java.io.File
import java.util.Date
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.pipelines.gears.Gears
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.bwa.{ BwaAln, BwaMem, BwaSampe, BwaSamse }
import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, ReorderSam, SortSam }
import nl.lumc.sasc.biopet.extensions.tools.FastqSplitter
import nl.lumc.sasc.biopet.extensions.{ Gsnap, Tophat, _ }
import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import nl.lumc.sasc.biopet.pipelines.gears.Gears
import nl.lumc.sasc.biopet.pipelines.mapping.scripts.TophatRecondition
import nl.lumc.sasc.biopet.extensions.tools.FastqSplitter
import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
import scala.math._
......@@ -266,6 +265,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
gears.init()
gears.biopetScript()
addAll(gears.functions)
addSummaryQScript(gears)
}
if (config("generate_wig", default = false).asBoolean)
......
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