diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala index eb52e5ab931c516333c4582f3373787d9922408e..c56a48b2d5628493765f79a45d7d85f1f2d6c1ca 100644 --- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala +++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala @@ -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)