Merge branch 'feature-gentrap_report' into 'develop'

Feature basic gentrap report

Part of #223 

This only contains basic stats, no gentrap specific stats added.

See merge request !302

public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp

+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
+#import(nl.lumc.sasc.biopet.core.report.ReportPage)
+#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
+#import(java.io.File)
+#import(org.apache.commons.io.FileUtils)
+<%@ var summary: Summary %>
+<%@ var sampleId: Option[String] = None %>
+<%@ var libId: Option[String] = None %>
+<%@ var rootPath: String %>
+<%@ var metricsTag: String = "bammetrics" %>
+<%@ var sampleLevel: Boolean = false %>
+<%@ var outputDir: File %>
+<%@ var fields: List[String] = List("PF_ALIGNED_BASES", "MEDIAN_5PRIME_BIAS", "MEDIAN_3PRIME_BIAS", "MEDIAN_5PRIME_TO_3PRIME_BIAS")%>
+<%@ var showPlot: Boolean = false %>
+<%@ var showTable: Boolean = true %>
+<%@ var showIntro: Boolean = true%>
+#{
+    val samples = sampleId match {
+    case Some(sample) => {
+    List(sample.toString)
+    }
+    case _ => summary.samples.toList
+    }
+}#
+
+#if (showIntro)
+    <br/>
+    <div class="row">
+    <div class="col-md-1"></div>
+    <div class="col-md-6">
+        <p>
+            This Show the relative coverage for all transcripts. De data here is generated by picard CollectRnaMetrics
+        </p>
+    </div>
+    </div>
+#end
+
+#if (showPlot)
+    #{ BammetricsReport.rnaHistogramPlot(outputDir, "rna", summary, !sampleLevel, sampleId = sampleId, libId = libId) }#
+
+    <div class="panel-body">
+    <img src="rna.png" class="img-responsive" />
+    </div>
+    <div class="panel-footer">
+        #if (showTable)
+            <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#rnaTable">Hide table</button>
+        #else
+            <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#rnaTable">Show table</button>
+        #end
+        <i class="glyphicon glyphicon-file"></i> <a href="rna.tsv">tsv file</a>
+    </div>
+#end
+
+<div class="panel-body collapse #if (showTable)in#end" id="rnaTable">
+<!-- Table -->
+<table class="table sortable-theme-bootstrap" data-sortable>
+    <thead><tr>
+        <th data-sorted="true" data-sorted-direction="ascending">Sample</th>
+        #if (!sampleLevel) <th>Library</th> #end
+        #for (field <- fields)
+            <th>${field.replaceAll("_", " ")}</th>
+        #end
+    </tr></thead>
+    <tbody>
+        #for (sample <- samples.toList.sorted)
+            #{
+                val libs = (libId, sampleLevel) match {
+                case (_, true) => List("")
+                case (Some(libId), _) => List(libId.toString)
+                case _ => summary.libraries(sample).toList
+                }
+            }#
+            <tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
+            #for (libId <- libs)
+                #if (libs.head != libId) <tr> #end
+                    #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td> #end
+                    #{
+                        val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List("bammetrics", "stats")
+
+                        val fieldValues = for (field <- fields) yield {
+                            summary.getValue((prefixPath ::: List("rna", "metrics", field.toUpperCase)):_*).getOrElse(prefixPath ::: metricsTag :: Nil)
+                        }
+                    }#
+                    #for (value <- fieldValues)
+                        <td>${value}</td>
+                    #end
+                </tr>
+            #end
+        #end
+    </tbody>
+</table>
+
+</div>

public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala

@@ -57,9 +57,13 @@ object BammetricsReport extends ReportBuilder {
                      sampleId: Option[String],
                      libId: Option[String],
                      metricsTag: String = "bammetrics") = {
+
+    val wgsExecuted = summary.getValue(sampleId, libId, metricsTag, "stats", "wgs").isDefined
+    val rnaExecuted = summary.getValue(sampleId, libId, metricsTag, "stats", "rna").isDefined
+
     val targets = (
-      summary.getValue(sampleId, libId, "bammetrics", "settings", "amplicon_name"),
-      summary.getValue(sampleId, libId, "bammetrics", "settings", "roi_name")
+      summary.getValue(sampleId, libId, metricsTag, "settings", "amplicon_name"),
+      summary.getValue(sampleId, libId, metricsTag, "settings", "roi_name")
     ) match {
         case (Some(amplicon: String), Some(roi: List[_])) => amplicon :: roi.map(_.toString)
         case (_, Some(roi: List[_])) => roi.map(_.toString)
@@ -74,9 +78,13 @@ object BammetricsReport extends ReportBuilder {
         Map())),
       List(
         "Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
-        "Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp", Map("showPlot" -> true)),
-        "Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp", Map("showPlot" -> true))
-      ),
+        "Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp", Map("showPlot" -> true))
+      ) ++ (if (wgsExecuted) List("Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
+          Map("showPlot" -> true)))
+        else Nil) ++
+        (if (rnaExecuted) List("Rna coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp",
+          Map("showPlot" -> true)))
+        else Nil),
       Map("metricsTag" -> metricsTag)
     )
   }
@@ -321,4 +329,94 @@ object BammetricsReport extends ReportBuilder {
     plot.title = Some("Whole genome coverage")
     plot.runLocal()
   }
+
+  /**
+   * Generate a line plot for rna coverage
+   * @param outputDir OutputDir for the tsv and png file
+   * @param prefix Prefix of the tsv and png file
+   * @param summary Summary class
+   * @param libraryLevel Default false, when set true plot will be based on library stats instead of sample stats
+   * @param sampleId Default it selects all sampples, when sample is giving it limits to selected sample
+   */
+  def rnaHistogramPlot(outputDir: File,
+                       prefix: String,
+                       summary: Summary,
+                       libraryLevel: Boolean = false,
+                       sampleId: Option[String] = None,
+                       libId: Option[String] = None): Unit = {
+    val tsvFile = new File(outputDir, prefix + ".tsv")
+    val pngFile = new File(outputDir, prefix + ".png")
+    val tsvWriter = new PrintWriter(tsvFile)
+    if (libraryLevel) {
+      tsvWriter.println((for (
+        sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample;
+        lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib
+      ) yield s"$sample-$lib")
+        .mkString("library\t", "\t", ""))
+    } else {
+      sampleId match {
+        case Some(sample) => tsvWriter.println("\t" + sample)
+        case _            => tsvWriter.println(summary.samples.mkString("Sample\t", "\t", ""))
+      }
+    }
+
+    var map: Map[Int, Map[String, Double]] = Map()
+
+    def fill(sample: String, lib: Option[String]): Unit = {
+
+      val insertSize = new SummaryValue(List("bammetrics", "stats", "rna", "histogram", "normalized_position"),
+        summary, Some(sample), lib).value.getOrElse(List())
+      val counts = new SummaryValue(List("bammetrics", "stats", "rna", "histogram", "All_Reads.normalized_coverage"),
+        summary, Some(sample), lib).value.getOrElse(List())
+
+      (insertSize, counts) match {
+        case (l: List[_], l2: List[_]) =>
+          l.zip(l2).foreach(i => {
+            val insertSize = i._1.toString.toInt
+            val count = i._2.toString.toDouble
+            val old = map.getOrElse(insertSize, Map())
+            if (libraryLevel) map += insertSize -> (old + ((s"$sample-" + lib.get) -> count))
+            else map += insertSize -> (old + (sample -> count))
+          })
+        case _ => throw new IllegalStateException("Must be a list")
+      }
+    }
+
+    if (libraryLevel) {
+      for (
+        sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample;
+        lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib
+      ) fill(sample, Some(lib))
+    } else if (sampleId.isDefined) fill(sampleId.get, None)
+    else summary.samples.foreach(fill(_, None))
+
+    for ((insertSize, counts) <- map) {
+      tsvWriter.print(insertSize)
+      if (libraryLevel) {
+        for (
+          sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample;
+          lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib
+        ) {
+          tsvWriter.print("\t" + counts.getOrElse(s"$sample-$lib", "0"))
+        }
+      } else {
+        for (sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample) {
+          tsvWriter.print("\t" + counts.getOrElse(sample, "0"))
+        }
+      }
+      tsvWriter.println()
+    }
+
+    tsvWriter.close()
+
+    val plot = new LinePlot(null)
+    plot.input = tsvFile
+    plot.output = pngFile
+    plot.xlabel = Some("Reletive position")
+    plot.ylabel = Some("Coverage")
+    plot.width = Some(1200)
+    plot.removeZero = true
+    plot.title = Some("Rna coverage")
+    plot.runLocal()
+  }
 }

public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala

@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.carp
 import java.io.File
 
 import nl.lumc.sasc.biopet.core._
+import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
 import nl.lumc.sasc.biopet.extensions.macs2.Macs2CallPeak
 import nl.lumc.sasc.biopet.extensions.picard.BuildBamIndex
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
@@ -95,7 +96,7 @@ class Carp(val root: Configurable) extends QScript with MultisampleMappingTrait
     }
   }
 
-  override def reportClass = {
+  override def reportClass: Option[ReportBuilderExtension] = {
     val carp = new CarpReport(this)
     carp.outputDir = new File(outputDir, "report")
     carp.summaryFile = summaryFile

public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpReport.scala

@@ -15,10 +15,9 @@
  */
 package nl.lumc.sasc.biopet.pipelines.carp
 
+import nl.lumc.sasc.biopet.core.report.{ ReportSection, ReportBuilderExtension }
+import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingReportTrait
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportSection, ReportPage, MultisampleReportBuilder }
-import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
-import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
 
 /**
  * Class for report for CArp
@@ -29,71 +28,10 @@ class CarpReport(val root: Configurable) extends ReportBuilderExtension {
   def builder = CarpReport
 }
 
-object CarpReport extends MultisampleReportBuilder {
-
-  /** Root page for the carp report */
-  def indexPage = {
-    //Source.fromInputStream(getClass.getResourceAsStream("/nl/lumc/sasc/biopet/pipelines/carp/carpFont.ssp")).foreach(print(_))
-    ReportPage(
-      List("Samples" -> generateSamplesPage(pageArgs)) ++
-        Map("Files" -> filesPage,
-          "Versions" -> ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
-          )), Map())
-        ),
-      List(
-        "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/carp/carpFront.ssp"),
-        "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
-          Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)
-        ),
-        "Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
-          Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)),
-        "Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
-          Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)),
-        "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
-    )
-  }
-
-  /** Files page, can be used general or at sample level */
-  def filesPage: ReportPage = ReportPage(List(), List(
-    "Input fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp"),
-    "After QC fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp"),
-    "Bam files per lib" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp", Map("sampleLevel" -> false)) //,
-  //"Preprocessed bam files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp",
-  //  Map("pipelineName" -> "shiva", "fileTag" -> "preProcessBam"))
-  ), Map())
-
-  /** Single sample page */
-  def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {
-    ReportPage(List(
-      "Libraries" -> generateLibraryPage(args),
-      "Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), None),
-      "Files" -> filesPage
-    ), List(
-      "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
-        if (summary.libraries(sampleId).size > 1) Map("showPlot" -> true) else Map()),
-      "Merged" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp", Map("sampleLevel" -> true)),
-      "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
-      "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
-    ), args)
-  }
-
-  /** Library page */
-  def libraryPage(sampleId: String, libId: String, args: Map[String, Any]): ReportPage = {
-    ReportPage(List(
-      "Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId)),
-      "QC" -> FlexiprepReport.flexiprepPage
-    ), List(
-      "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
-      "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
-      "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
-    ), args)
-  }
-
+object CarpReport extends MultisampleMappingReportTrait {
   /** Name of the report */
   def reportName = "Carp Report"
+  override def frontSection = ReportSection("/nl/lumc/sasc/biopet/pipelines/carp/carpFront.ssp")
+
+  override def pipelineName = "carp"
 }
\ No newline at end of file

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala

@@ -19,6 +19,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.FullVersion
 import nl.lumc.sasc.biopet.core._
+import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
 import nl.lumc.sasc.biopet.extensions.picard.{ MergeSamFiles, SortSam }
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
 import nl.lumc.sasc.biopet.extensions.tools.{ MergeTables, WipeReads }
@@ -53,6 +54,13 @@ class Gentrap(val root: Configurable) extends QScript
   // alternative constructor for initialization with empty configuration
   def this() = this(null)
 
+  override def reportClass: Option[ReportBuilderExtension] = {
+    val report = new GentrapReport(this)
+    report.outputDir = new File(outputDir, "report")
+    report.summaryFile = summaryFile
+    Some(report)
+  }
+
   /** Split aligner to use */
   var aligner: String = config("aligner", default = "gsnap")
 
@@ -124,8 +132,7 @@ class Gentrap(val root: Configurable) extends QScript
     ),
     // disable markduplicates since it may not play well with all aligners (this can still be overriden via config)
     "mapping" -> Map(
-      "skip_markduplicates" -> true,
-      "skip_metrics" -> true
+      "skip_markduplicates" -> true
     )
   )
 

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapReport.scala

@@ -15,10 +15,9 @@
  */
 package nl.lumc.sasc.biopet.pipelines.gentrap
 
+import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportSection }
+import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingReportTrait
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportSection, ReportPage, MultisampleReportBuilder }
-import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
-import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
 
 /**
  * Class to generate report for [[Gentrap]]
@@ -29,69 +28,12 @@ class GentrapReport(val root: Configurable) extends ReportBuilderExtension {
   def builder = GentrapReport
 }
 
-object GentrapReport extends MultisampleReportBuilder {
+object GentrapReport extends MultisampleMappingReportTrait {
 
-  /** Root page for the carp report */
-  def indexPage = {
-    //Source.fromInputStream(getClass.getResourceAsStream("/nl/lumc/sasc/biopet/pipelines/carp/carpFont.ssp")).foreach(print(_))
-    ReportPage(
-      List("Samples" -> generateSamplesPage(pageArgs)) ++
-        Map("Files" -> filesPage,
-          "Versions" -> ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
-          )), Map())
-        ),
-      List(
-        "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gentrap/gentrapFront.ssp"),
-        "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
-          Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)
-        ),
-        "Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
-          Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)),
-        "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
-    )
-  }
-
-  /** Files page, can be used general or at sample level */
-  def filesPage: ReportPage = ReportPage(List(), List(
-    "Input fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp"),
-    "After QC fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp"),
-    "Bam files per lib" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp", Map("sampleLevel" -> false)) //,
-  //"Preprocessed bam files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp",
-  //  Map("pipelineName" -> "shiva", "fileTag" -> "preProcessBam"))
-  ), Map())
-
-  /** Single sample page */
-  def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {
-    ReportPage(List(
-      "Libraries" -> generateLibraryPage(args),
-      "Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), None),
-      "Files" -> filesPage
-    ), List(
-      "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
-        if (summary.libraries(sampleId).size > 1) Map("showPlot" -> true) else Map()),
-      "Preprocessing" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp", Map("sampleLevel" -> true)),
-      "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
-      "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
-    ), args)
-  }
-
-  /** Library page */
-  def libraryPage(sampleId: String, libId: String, args: Map[String, Any]): ReportPage = {
-    ReportPage(List(
-      "Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId)),
-      "QC" -> FlexiprepReport.flexiprepPage
-    ), List(
-      "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
-      "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
-      "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
-    ), args)
-  }
+  override def frontSection = ReportSection("/nl/lumc/sasc/biopet/pipelines/gentrap/gentrapFront.ssp")
 
   /** Name of the report */
   def reportName = "Gentrap Report"
+
+  override def pipelineName = "gentrap"
 }
\ No newline at end of file

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

+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
+#import(nl.lumc.sasc.biopet.core.report.ReportPage)
+<%@ var summary: Summary %>
+<%@ var rootPath: String %>
+
+<table class="table">
+<tbody>
+    <tr><th>Pipeline</th><td>Shiva</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("shiva", "settings", "reference", "species")} - ${summary.getValue("shiva", "settings", "reference", "name")}</td></tr>
+    <tr><th>Number of samples</th><td>${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>Shiva</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/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala

+package nl.lumc.sasc.biopet.pipelines.mapping
+
+import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportSection, ReportPage, MultisampleReportBuilder }
+import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
+import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+/**
+ * Created by pjvanthof on 11/01/16.
+ */
+class MultisampleMappingReport(val root: Configurable) extends ReportBuilderExtension {
+  def builder = MultisampleMappingReport
+}
+
+object MultisampleMappingReport extends MultisampleMappingReportTrait {
+  /** Name of the report */
+  def reportName = "Mapping Report"
+}
+
+trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
+  /** Front section for the report */
+  def frontSection: ReportSection = ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/multisampleMappingFront.ssp")
+
+  def pipelineName = "multisamplemapping"
+
+  /** Root page for the carp report */
+  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)
+        ),
+        "Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.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
+    )
+  }
+
+  /** Files page, can be used general or at sample level */
+  def filesPage: ReportPage = ReportPage(List(), List(
+    "Input fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp"),
+    "After QC fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp"),
+    "Bam files per lib" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp", Map("sampleLevel" -> false)),
+    "Preprocessed bam files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp",
+      Map("pipelineName" -> pipelineName, "fileTag" -> "preProcessBam"))), Map())
+
+  /** Single sample page */
+  def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {
+    ReportPage(List(
+      "Libraries" -> generateLibraryPage(args),
+      "Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), None),
+      "Files" -> filesPage
+    ), List(
+      "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",