showing sv counts also when only one sample is being displayed

shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFilesSv.ssp

@@ -2,9 +2,15 @@
 #import(nl.lumc.sasc.biopet.utils.summary.Summary)
 <%@ var summary: Summary %>
 <%@ var sampleId: Option[String] = None %>
-<%@ var libId: Option[String] = None %>
 <%@ var rootPath: String %>
 
+#{
+    val sampleNames: List[String] = sampleId match {
+        case Some(sampleName) => List(sampleName.toString)
+        case _ => summary.samples.toList.sorted
+    }
+}#
+
 <div class="panel-body">
 <!-- Table -->
 <table class="table">
@@ -14,20 +20,20 @@
         <th>MD5</th>
     </tr></thead>
     <tbody>
-        #if (summary.samples.size > 1)
+        #if (sampleNames.size > 1)
             <tr>
                 <td>Merged</td>
-                <td>${ShivaReport.formatVcfFilePath(summary.getValue(sampleId, libId, "shivasvcalling", "files", "pipeline", "final_mergedvcf", "path"))}</td>
-                <td>${summary.getValue(sampleId, libId, "shivasvcalling", "files", "pipeline", "final_mergedvcf", "md5")}</td>
+                <td>${ShivaReport.formatVcfFilePath(summary.getValue("shivasvcalling", "files", "pipeline", "final_mergedvcf", "path"))}</td>
+                <td>${summary.getValue("shivasvcalling", "files", "pipeline", "final_mergedvcf", "md5")}</td>
             </tr>
         #end
 
-        #for (sampleName <- summary.samples.toList.sorted)
+        #for (sampleName <- sampleNames)
             <tr>
             <tr>
                 <td><a href="${rootPath}Samples/${sampleName}/index.html">${sampleName}</a></td>
-                <td>${ShivaReport.formatVcfFilePath(summary.getValue(sampleId, libId, "shivasvcalling", "files", "pipeline", sampleName, "path"))}</td>
-                <td>${summary.getValue(sampleId, libId, "shivasvcalling", "files", "pipeline", sampleName, "md5")}</td>
+                <td>${ShivaReport.formatVcfFilePath(summary.getValue("shivasvcalling", "files", "pipeline", sampleName, "path"))}</td>
+                <td>${summary.getValue("shivasvcalling", "files", "pipeline", sampleName, "md5")}</td>
             </tr>
         #end
     </tbody>

shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariantsSv.ssp

@@ -2,13 +2,17 @@
 #import(java.io.File)
 <%@ var rootPath: String %>
 <%@ var outputDir: File %>
+<%@ var sampleId: Option[String] = None %>
 <%@ var summary: Summary %>
 <%@ var showPlot: Boolean = false %>
 <%@ var showTable: Boolean = true %>
 <%@ var showIntro: Boolean = true %>
 
 #{
-    val sampleNames: List[String] = summary.samples.toList.sorted
+    val sampleNames: List[String] = sampleId match {
+        case Some(sampleName) => List(sampleName.toString)
+        case _ => summary.samples.toList.sorted
+    }
 
     val counts: Map[String, Map[String, Array[Long]]] = ShivaSvCallingReport.parseSummaryForSvCounts(summary)
     val traCounts: Map[String, Long] = ShivaSvCallingReport.parseSummaryForTranslocations(summary)

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala

@@ -111,8 +111,8 @@ trait ShivaReportTrait extends MultisampleMappingReportTrait {
     if (!variantcallingExecuted && !svCallingExecuted) super.filesPage
     else {
       var sections: List[(String, ReportSection)] = List()
-      if (variantcallingExecuted) sections = sections :+ ("Result files from SNV calling", ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFiles.ssp", Map("sampleId" -> None)))
-      if (svCallingExecuted) sections = sections :+ ("Result files from SV calling", ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFilesSv.ssp"))
+      if (variantcallingExecuted) sections = sections :+ ("VCF files from SNV calling", ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFiles.ssp", Map("sampleId" -> None)))
+      if (svCallingExecuted) sections = sections :+ ("VCF files from SV calling", ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFilesSv.ssp"))
 
       val oldPage = super.filesPage
       oldPage.copy(sections = oldPage.sections ++ sections)
@@ -121,9 +121,10 @@ trait ShivaReportTrait extends MultisampleMappingReportTrait {
 
   /** Single sample page */
   override def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {
-    val variantcallingSection = if (variantcallingExecuted) List("Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp")) else Nil
+    val variantcallingSection = if (variantcallingExecuted) List("SNV Calling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp")) else Nil
+    val svSection = if (svCallingExecuted) List("SV Calling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariantsSv.ssp")) else Nil
     val oldPage = super.samplePage(sampleId, args)
-    oldPage.copy(sections = variantcallingSection ++ oldPage.sections)
+    oldPage.copy(sections = variantcallingSection ++ svSection ++ oldPage.sections)
   }
 
   /** Name of the report */