diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala index e1c3aa2694e5cedee5414bcbc2d4fc07748fe782..9a61907fa68644513108d0a55ee349dc1c84aafa 100644 --- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala +++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala @@ -2,7 +2,8 @@ package nl.lumc.sasc.biopet.pipelines.gears import java.io.{ File, PrintWriter } -import nl.lumc.sasc.biopet.core.{ BiopetQScript, SampleLibraryTag } +import nl.lumc.sasc.biopet.core.summary.SummaryQScript +import nl.lumc.sasc.biopet.core.SampleLibraryTag import nl.lumc.sasc.biopet.extensions.Flash import nl.lumc.sasc.biopet.extensions.qiime._ import nl.lumc.sasc.biopet.utils.ConfigUtils @@ -16,7 +17,7 @@ import scala.xml.{ PrettyPrinter, Elem } /** * Created by pjvan_thof on 12/4/15. */ -class GearsQiimeClosed(val root: Configurable) extends QScript with BiopetQScript with SampleLibraryTag { +class GearsQiimeClosed(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag { var fastqR1: File = _ @@ -64,6 +65,15 @@ class GearsQiimeClosed(val root: Configurable) extends QScript with BiopetQScrip _otuMap = closedReference.otuMap _otuTable = closedReference.otuTable } + + /** Must return a map with used settings for this pipeline */ + def summarySettings: Map[String, Any] = Map() + + /** File to put in the summary for thie pipeline */ + def summaryFiles: Map[String, File] = Map("otu_table" -> otuTable,"otu_map" -> otuMap) + + /** Name of summary output file */ + def summaryFile: File = new File(outputDir, "summary.closed_reference.json") } object GearsQiimeClosed {