Report update, sorting order (display)

public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp

@@ -15,7 +15,7 @@
             buffer.append("<ul class=\"dropdown-menu\">")
         }
 
-        for (subPage <- page.subPages) {
+        for (subPage <- page.subPages.sortBy(_._1)) {
             val href: String = {
                 if (path.isEmpty) rootPath + subPage._1 + "/index.html"
                 else rootPath + path.mkString("","/","/") + subPage._1 + "/index.html"

public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/reference.ssp

@@ -5,7 +5,7 @@
 <%@ var pipeline: String %>
 
 #{
-    val contigs = summary.getValue(pipeline, "settings", "reference", "contigs").get.asInstanceOf[Map[String, Map[String, Any]]]
+    val contigs = summary.getValue(pipeline, "settings", "reference", "contigs").getOrElse(Map.empty).asInstanceOf[Map[String, Map[String, Any]]]
 }#
 
 <table class="table">

public/mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/multisampleMappingFront.ssp

@@ -2,6 +2,7 @@
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
 <%@ var summary: Summary %>
 <%@ var rootPath: String %>
+<%@ var pipeline: String %>
 
 <table class="table">
 <tbody>
@@ -9,7 +10,7 @@
     <tr><th>Version</th><td>${summary.getValue("meta", "pipeline_version")}</td></tr>
     <tr><th>Last commit hash</th><td>${summary.getValue("meta", "last_commit_hash")}</td></tr>
     <tr><th>Output directory</th><td>${summary.getValue("meta", "output_dir")}</td></tr>
-    <tr><th>Reference</th><td>${summary.getValue("shiva", "settings", "reference", "species")} - ${summary.getValue("shiva", "settings", "reference", "name")}</td></tr>
+    <tr><th>Reference</th><td>${summary.getValue(pipeline, "settings", "reference", "species")} - ${summary.getValue(pipeline, "settings", "reference", "name")}</td></tr>
     <tr><th>Number of samples</th><td>${summary.samples.size}</td></tr>
 </tbody>
 </table>
@@ -18,7 +19,7 @@
     <div class="col-md-1"></div>
     <div class="col-md-6">
     <p>
-    In this web document you can find your <em>Shiva</em> pipeline report.
+    In this web document you can find your <em>${pipeline}</em> pipeline report.
     Different categories of data can be found in the left-side menu.
     Statistics per sample and library can be accessed through the top-level menu.
     Some statistics for target regions can be found in the regions tab.

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

@@ -56,7 +56,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
           "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
             Map("showPlot" -> true, "showTable" -> false))
         ),
-      pageArgs
+      pageArgs ++ Map("pipeline" -> pipelineName)
     )
   }