Commit 975ef9a2 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding summary to qiime closed

parent e270ea9d
......@@ -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 {
......
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