Added initial version of gentrap report

public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/gentrapFront.ssp

+#import(nl.lumc.sasc.biopet.core.summary.Summary)
+<%@ var summary: Summary %>
+#{
+    println("blabla")
+}#
+<table class="table">
+<tbody>
+    <tr><th>Pipeline</th><td>Gentrap</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>
+</tbody>
+</table>
+<br/>
+<div class="row">
+<div class="col-md-1"></div>
+<div class="col-md-6">
+    <p>
+        Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc risus est, volutpat quis enim sit amet, lacinia posuere ante. Mauris eget massa efficitur, luctus nisl ut, placerat nibh. Pellentesque id nulla maximus, rutrum dui nec, lobortis odio. Fusce eu enim ac sem auctor congue. Ut ac ullamcorper quam, eget sollicitudin felis. Maecenas posuere sagittis blandit. Proin mollis magna lectus, id gravida est consectetur vitae. Nulla id risus at tellus laoreet finibus in id lacus. Duis lobortis commodo nisl viverra tempor. Curabitur sit amet pretium dui, sit amet tincidunt mauris. Duis volutpat eu purus ut molestie.
+    </p>
+</div>
+</div>
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public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapReport.scala

+package nl.lumc.sasc.biopet.pipelines.gentrap
+
+import nl.lumc.sasc.biopet.core.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
+
+/**
+ * Created by pjvanthof on 25/06/15.
+ */
+class GentrapReport(val root: Configurable) extends ReportBuilderExtension {
+  val builder = GentrapReport
+}
+
+object GentrapReport 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/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)
+  }
+
+  /** Name of the report */
+  def reportName = "Gentrap Report"
+}
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