TinyCap report base

public/TinyCap/src/main/resources/nl/lumc/sasc/biopet/pipleines/tinycap/tinycapFront.ssp

+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
+#import(nl.lumc.sasc.biopet.core.report.ReportPage)
+<%@ var summary: Summary %>
+<%@ var rootPath: String %>
+<%@ var pipeline: String %>
+
+<table class="table">
+<tbody>
+    <tr><th>Pipeline</th><td>${pipeline}</td></tr>
+    <tr><th>Version</th><td>${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(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>
+<br/>
+<div class="row">
+<div class="col-md-1"></div>
+<div class="col-md-6">
+    <p>
+        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.
+        Futhermore, you can view all versions of software tools used by selecting <em>Versions</em> from the top menu.
+    </p>
+
+    <p>
+        <small>Brought to you by <a href="https://sasc.lumc.nl" target="_blank"><abbr
+            title="Sequence Analysis Support Core">SASC</abbr></a> and <a
+        href="https://www.lumc.nl/org/klinische-genetica/" target="_blank"><abbr title="Clinical Genetics LUMC">KG</abbr></a>,
+        LUMC.
+        </small>
+    </p>
+</div>
+</div>
\ No newline at end of file

public/TinyCap/src/main/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCap.scala

 package nl.lumc.sasc.biopet.pipelines.tinycap
 
-import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference }
+import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
+import nl.lumc.sasc.biopet.core.{PipelineCommand, Reference}
 import nl.lumc.sasc.biopet.extensions.HtseqCount
 import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingTrait
 import nl.lumc.sasc.biopet.utils.config.Configurable
@@ -85,6 +86,13 @@ class TinyCap(val root: Configurable) extends QScript with MultisampleMappingTra
     "annotationGff" -> annotationGff
   )
 
+  override def reportClass: Option[ReportBuilderExtension] = {
+    val report = new TinyCapReport(this)
+    report.outputDir = new File(outputDir, "report")
+    report.summaryFile = summaryFile
+    Some(report)
+  }
+
   override def addMultiSampleJobs = {
     super.addMultiSampleJobs
   }

public/TinyCap/src/main/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapReport.scala

+package nl.lumc.sasc.biopet.pipelines.tinycap
+
+import nl.lumc.sasc.biopet.core.report.{ReportPage, ReportSection, ReportBuilderExtension}
+import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingReportTrait
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+/**
+  * Created by wyleung on 4-2-16.
+  */
+class TinyCapReport(val root: Configurable) extends ReportBuilderExtension {
+  def builder = TinyCapReport
+
+}
+
+object TinyCapReport extends MultisampleMappingReportTrait {
+  /** Name of the report */
+  def reportName = "TinyCap Report"
+
+  /** Front section for the report */
+  override def frontSection: ReportSection = ReportSection("/nl/lumc/sasc/biopet/pipelines/tinycap/tinycapFront.ssp")
+
+  override def pipelineName = "tinycap"
+
+
+  /** Root page for the carp report */
+  override def indexPage = {
+
+    val wgsExecuted = summary.getSampleValues("bammetrics", "stats", "wgs").values.exists(_.isDefined)
+    val rnaExecuted = summary.getSampleValues("bammetrics", "stats", "rna").values.exists(_.isDefined)
+
+    ReportPage(
+      List("Samples" -> generateSamplesPage(pageArgs)) ++
+        Map("Reference" -> ReportPage(List(), List(
+          "Reference" -> ReportSection("/nl/lumc/sasc/biopet/core/report/reference.ssp", Map("pipeline" -> pipelineName))
+        ), Map()),
+          "Files" -> filesPage,
+          "Versions" -> ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
+          )), Map())
+        ),
+      List(
+        "Report" -> frontSection,
+        "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
+          Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)
+        )) ++
+        (if (wgsExecuted) List("Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
+          Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)))
+        else Nil) ++
+        (if (rnaExecuted) List("Rna coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp",
+          Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)))
+        else Nil) ++
+        List("QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",
+          Map("showPlot" -> true, "showTable" -> false)),
+          "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
+            Map("showPlot" -> true, "showTable" -> false))
+        ),
+      pageArgs ++ Map("pipeline" -> pipelineName)
+    )
+  }
+
+
+
+}

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

@@ -6,7 +6,7 @@
 
 <table class="table">
 <tbody>
-    <tr><th>Pipeline</th><td>Shiva</td></tr>
+    <tr><th>Pipeline</th><td>${pipeline}</td></tr>
     <tr><th>Version</th><td>${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>