Added centrifuge to report

gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp

@@ -10,11 +10,12 @@
 <%@ var libId: Option[String] = None %>
 <%@ var args: Map[String, Any] %>
 <%@ var outputDir: File %>
+<%@ var summaryTag: String = "krakenreport" %>
 
 <%
     val summaries = if (sampleId.isEmpty && libId.isEmpty) {
-        summary.getSampleValues("gearskraken", "stats", "krakenreport").map(x => x._1 -> x._2.get.asInstanceOf[Map[String, Any]])
-    } else summary.getValue(sampleId, libId, "gearskraken", "stats", "krakenreport").map(sampleId.get -> _.asInstanceOf[Map[String, Any]]).toList.toMap
+        summary.getSampleValues("gearskraken", "stats", summaryTag).map(x => x._1 -> x._2.get.asInstanceOf[Map[String, Any]])
+    } else summary.getValue(sampleId, libId, "gearskraken", "stats", summaryTag).map(sampleId.get -> _.asInstanceOf[Map[String, Any]]).toList.toMap
 
     val tempFile = File.createTempFile("krona.", ".xml")
     tempFile.deleteOnExit()

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala

@@ -44,7 +44,7 @@ class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScrip
     krakenReportJSON.output = new File(outputDir, s"$outputName.krkn.json")
     krakenReportJSON.skipNames = config("skipNames", default = false)
     add(krakenReportJSON)
-    addSummarizable(krakenReportJSON, "centrifugereport")
+    addSummarizable(krakenReportJSON, "centrifuge_report")
 
     addSummaryJobs()
   }

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala

@@ -38,13 +38,17 @@ object GearsReport extends MultisampleReportBuilder {
 
   def indexPage = {
     val krakenExecuted = summary.getSampleValues("gearskraken", "stats", "krakenreport").values.forall(_.isDefined)
+    val centrifugeExecuted = summary.getSampleValues("gearskraken", "stats", "centrifuge_report").values.forall(_.isDefined)
     val qiimeClosesOtuTable = summary.getValue("gears", "files", "pipeline", "qiime_closed_otu_table", "path")
       .map(x => new File(x.toString))
     val qiimeOpenOtuTable = summary.getValue("gears", "files", "pipeline", "qiime_open_otu_table", "path")
       .map(x => new File(x.toString))
 
     ReportPage(
-      (if (krakenExecuted) List("Kraken analysis" -> ReportPage(List(), List(
+      (if (centrifugeExecuted) List("Centriguge analysis" -> ReportPage(List(), List(
+        "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
+        )), Map("summaryTag" -> "centriguge_report")))
+      else Nil) ::: (if (krakenExecuted) List("Kraken analysis" -> ReportPage(List(), List(
         "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
         )), Map()))
       else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> ReportPage(List(), List(