Added unassigned reads to krona plot for centrifuge

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala

@@ -120,7 +120,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
       val className = if (f.getClass.isAnonymousClass) f.getClass.getSuperclass.getSimpleName else f.getClass.getSimpleName
       BiopetQScript.safeOutputs(f) match {
         case Some(o) => f.jobOutputFile = new File(o.head.getAbsoluteFile.getParent, "." + f.firstOutput.getName + "." + className + ".out")
-        case _ => f.jobOutputFile = new File("./stdout") // Line is here for test backup
+        case _       => f.jobOutputFile = new File("./stdout") // Line is here for test backup
       }
     })
 

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

@@ -10,17 +10,23 @@
 <%@ var libId: Option[String] = None %>
 <%@ var args: Map[String, Any] %>
 <%@ var outputDir: File %>
+<%@ var centrifugeTag: Option[String] = None %>
 <%@ var summaryStatsTag: String = "krakenreport" %>
 <%@ var summaryModuleTag: String = "gearskraken" %>
 
 <%
-    val summaries = if (sampleId.isEmpty && libId.isEmpty) {
+    val summaries = if (sampleId.isEmpty) {
         summary.getSampleValues(summaryModuleTag, "stats", summaryStatsTag).map(x => x._1 -> x._2.get.asInstanceOf[Map[String, Any]])
     } else summary.getValue(sampleId, libId, summaryModuleTag, "stats", summaryStatsTag).map(sampleId.get -> _.asInstanceOf[Map[String, Any]]).toList.toMap
 
+    val totalReads = if (sampleId.isEmpty) {
+        centrifugeTag.map {tag => summary.getSampleValues(summaryModuleTag, "stats", tag, "metrics", "Read").map(x => x._1 -> x._2.getOrElse(0L).toString.toLong) }
+    } else centrifugeTag.flatMap(tag => summary.getValue(sampleId, libId, summaryModuleTag, "stats", tag, "metrics", "Read"))
+      .map(value => Map(sampleId.get -> value.toString.toLong))
+
     val tempFile = File.createTempFile("krona.", ".xml")
     tempFile.deleteOnExit()
-    GearsKraken.convertKrakenSummariesToKronaXml(summaries, tempFile)
+    GearsKraken.convertKrakenSummariesToKronaXml(summaries, tempFile, totalReads)
 
     val output = ReportBuilder.renderTemplate("/nl/lumc/sasc/biopet/core/report/krona.ssp",
     args ++ Map("kronaXml" -> tempFile))

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

@@ -120,7 +120,7 @@ object GearsKraken {
     convertKrakenSummariesToKronaXml(summaries, outputFile)
   }
 
-  def convertKrakenSummariesToKronaXml(summaries: Map[String, Map[String, Any]], outputFile: File): Unit = {
+  def convertKrakenSummariesToKronaXml(summaries: Map[String, Map[String, Any]], outputFile: File, totalReads: Option[Map[String, Long]] = None): Unit = {
 
     val samples = summaries.keys.toList.sorted
 
@@ -156,7 +156,7 @@ object GearsKraken {
             if (k == "root") {
               val unclassified = summaries(sample)("unclassified").asInstanceOf[Map[String, Any]]("size").asInstanceOf[Long]
               <val>
-                { getValue(sample, (path ::: k :: Nil).tail, "size").getOrElse(0).toString.toLong + unclassified }
+                { totalReads.flatMap(_.get(sample)).getOrElse(getValue(sample, (path ::: k :: Nil).tail, "size").getOrElse(0).toString.toLong + unclassified) }
               </val>
             } else {
               <val>

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

@@ -50,7 +50,7 @@ object GearsReport extends MultisampleReportBuilder {
       )), Map())), List(
         "Unique mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
           Map("summaryStatsTag" -> "centrifuge_unique_report")
-        )), Map("summaryModuleTag" -> "gearscentrifuge")))
+        )), Map("summaryModuleTag" -> "gearscentrifuge", "centrifugeTag" -> Some("centrifuge"))))
       else Nil) ::: (if (krakenExecuted) List("Kraken analysis" -> ReportPage(List(), List(
         "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
         )), Map()))
@@ -92,7 +92,7 @@ object GearsReport extends MultisampleReportBuilder {
     )), Map())), List(
       "Unique mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
         Map("summaryStatsTag" -> "centrifuge_unique_report")
-      )), Map("summaryModuleTag" -> "gearscentrifuge")))
+      )), Map("summaryModuleTag" -> "gearscentrifuge", "centrifugeTag" -> Some("centrifuge"))))
     else Nil) ::: (if (krakenExecuted) List("Kraken analysis" -> ReportPage(List(), List(
       "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
       )), Map()))
@@ -126,7 +126,7 @@ object GearsReport extends MultisampleReportBuilder {
       )), Map())), List(
         "Unique mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
           Map("summaryStatsTag" -> "centrifuge_unique_report")
-        )), Map("summaryModuleTag" -> "gearscentrifuge")))
+        )), Map("summaryModuleTag" -> "gearscentrifuge", "centrifugeTag" -> Some("centrifuge"))))
       else Nil) ::: (if (krakenExecuted) List("Kraken analysis" -> ReportPage(List(), List(
         "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
         )), Map()))

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

@@ -41,7 +41,7 @@ object GearsSingleReport extends ReportBuilder {
         else Nil) ++
         (if (centrifugeExecuted) List("Centrifuge analysis" ->
           ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
-            Map("summaryModuleTag" -> "gearscentrifuge", "summaryStatsTag" -> "centrifuge_unique_report")))
+            Map("summaryModuleTag" -> "gearscentrifuge", "summaryStatsTag" -> "centrifuge_unique_report", "centrifugeTag" -> Some("centrifuge"))))
         else Nil),
       pageArgs
     )

mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala

@@ -65,7 +65,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
         )), Map())), List(
           "Unique mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
             Map("summaryStatsTag" -> "centrifuge_unique_report")
-          )), Map("summaryModuleTag" -> "gearscentrifuge")))
+          )), Map("summaryModuleTag" -> "gearscentrifuge", "centrifugeTag" -> Some("centrifuge"))))
         else Nil) ++
         List("Reference" -> ReportPage(List(), List(
           "Reference" -> ReportSection("/nl/lumc/sasc/biopet/core/report/reference.ssp", Map("pipeline" -> pipelineName))
@@ -128,7 +128,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
       "Libraries" -> generateLibraryPage(args),
       "Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), None)) ++
       (if (centrifugeExecuted) List("Centriguge analysis" -> ReportPage(List("Non-unique" -> ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
-        Map("summaryStatsTag" -> "centrifuge_report")
+        Map("summaryStatsTag" -> "centrifuge_report", "centrifugeTag" -> Some("centrifuge"))
       )), Map())), List(
         "Unique mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
           Map("summaryStatsTag" -> "centrifuge_unique_report")
@@ -162,7 +162,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
         )), Map())), List(
           "Unique mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
             Map("summaryStatsTag" -> "centrifuge_unique_report")
-          )), Map("summaryModuleTag" -> "gearscentrifuge")))
+          )), Map("summaryModuleTag" -> "gearscentrifuge", "centrifugeTag" -> Some("centrifuge"))))
         else Nil) ::: (if (krakenExecuted) List("Dustbin analysis" -> ReportPage(List(), List(
           "Krona Plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
           )), Map()))