From 975ef9a2e8c703e0f3c6dcba260bf80ae2b742ad Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 24 Dec 2015 17:52:55 +0100
Subject: [PATCH] Adding summary to qiime closed
---
.../biopet/pipelines/gears/GearsQiimeClosed.scala | 14 ++++++++++++--
1 file changed, 12 insertions(+), 2 deletions(-)
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 e1c3aa269..9a61907fa 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 {
--
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