Added dummy sections for alignment

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

+#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.core.report.ReportPage)
+<%@ var summary: Summary %>
+<%@ var sampleId: Option[String] = None %>
+<%@ var libId: Option[String] = None %>
+<%@ var sampleLevel: Boolean = false %>
+<%@ var rootPath: String %>
+#{
+    val samples = sampleId match {
+    case Some(sample) => List(sample.toString)
+    case _ => summary.samples.toList
+    }
+}#
+<table>
+    <thead><tr>
+        <th>Sample</th>
+        #if (!sampleLevel) <th>Library</th> #end
+        <th>Total</th>
+        <th>Mapped</th>
+        <th>(%)</th>
+        <th>Duplicates</th>
+        <th>(%)</th>
+        <th>Insert size</th>
+    </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 total = summary.getValue((prefixPath ::: List("biopet_flagstat", "All")):_*).getOrElse(0L).asInstanceOf[Long]
+                    val mapped = summary.getValue((prefixPath ::: List("biopet_flagstat", "Mapped")):_*).getOrElse(0L).asInstanceOf[Long]
+                    val duplicates = summary.getValue((prefixPath ::: List("biopet_flagstat", "Duplicates")):_*).getOrElse(0L).asInstanceOf[Long]
+                    val insertsizeMean = summary.getValue((prefixPath ::: List("insert_size_metrics", "mean_insert_size")):_*)
+                }#
+                <td>${total}</td>
+                <td>${mapped}</td>
+                <td>${mapped.toDouble / total * 100}%</td>
+                <td>${duplicates}</td>
+                <td>${duplicates.toDouble / total * 100}%</td>
+                <td>${insertsizeMean}</td>
+                </tr>
+            #end
+        #end
+    </tbody>
+</table>
\ No newline at end of file

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

+#{ //TODO: Need content }#
+
+Todo
\ No newline at end of file

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

+#{ //TODO: Need content }#
+
+Todo
\ No newline at end of file

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

+#{ //TODO: Need content }#
+
+Todo
\ No newline at end of file

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

+#{ //TODO: Need content }#
+
+Todo
\ No newline at end of file

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

+package nl.lumc.sasc.biopet.pipelines.bammetrics
+
+import nl.lumc.sasc.biopet.core.report.{ReportBuilder, ReportPage, ReportSection}
+
+/**
+ * Created by pjvan_thof on 3/30/15.
+ */
+object BammetricsReport extends ReportBuilder {
+  val reportName = "Bam Metrics"
+
+  def indexPage = ReportPage(Map(
+    "Bam Metrics" -> bamMetricsPage
+  ), List(
+    "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp")
+  ),
+    Map()
+  )
+
+  def bamMetricsPage = ReportPage(
+    Map(),
+    List(
+      "Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
+      "Flagstat" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/flagstat.ssp"),
+      "Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp"),
+      "GC Bias" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/gcBias.ssp")
+  ),
+    Map()
+  )
+
+  // FIXME: Not yet finished
+}

public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp

@@ -3,6 +3,7 @@
 <%@ var summary: Summary %>
 <%@ var sampleId: Option[String] = None %>
 <%@ var libId: Option[String] = None %>
+<%@ var rootPath: String %>
 #{
     val samples = sampleId match {
         case Some(sample) => List(sample.toString)
@@ -31,11 +32,11 @@
                 libs.count(summary.getLibraryValue(sample, _, "flexiprep", "settings", "paired").getOrElse(false) == true)
             }
         }#
-        <tr><td rowspan="${sampleRowspan}">${sample}</td>
+        <tr><td rowspan="${sampleRowspan}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
         #for (libId <- libs)
             #if (libs.head != libId) <tr> #end
             #{ val paired = summary.getLibraryValue(sample, libId, "flexiprep", "settings", "paired").getOrElse(false) }#
-            <td #if (paired == true) rowspan="2" #end>${libId}</td>
+            <td #if (paired == true) rowspan="2" #end><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td>
             #{ val reads = if (paired == true) List("R1", "R2") else List("R1") }#
             #for (read <- reads)
                 #if (read == "R2") </tr><tr> #end

public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp

+#{ //TODO: Need content }#
+
+Todo
\ No newline at end of file

public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp

@@ -3,6 +3,7 @@
 <%@ var summary: Summary %>
 <%@ var sampleId: Option[String] = None %>
 <%@ var libId: Option[String] = None %>
+<%@ var rootPath: String %>
 #{
     val samples = sampleId match {
         case Some(sample) => List(sample.toString)
@@ -30,11 +31,11 @@
                 libs.count(summary.getLibraryValue(sample, _, "flexiprep", "settings", "paired").getOrElse(false) == true)
             }
         }#
-        <tr><td rowspan="${sampleRowspan}">${sample}</td>
+        <tr><td rowspan="${sampleRowspan}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
         #for (libId <- libs)
             #if (libs.head != libId) <tr> #end
             #{ val paired = summary.getLibraryValue(sample, libId, "flexiprep", "settings", "paired").getOrElse(false) }#
-            <td #if (paired == true) rowspan="2" #end>${libId}</td>
+            <td #if (paired == true) rowspan="2" #end><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td>
             #{ val reads = if (paired == true) List("R1", "R2") else List("R1") }#
             #for (read <- reads)
                 #if (read == "R2") </tr><tr> #end

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala

@@ -8,20 +8,30 @@ import nl.lumc.sasc.biopet.core.report.{ ReportSection, ReportPage, ReportBuilde
 object FlexiprepReport extends ReportBuilder {
   val reportName = "Flexiprep"
 
-  def indexPage = {
-    ReportPage(Map(), List(
-      "Read Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
-      "Base Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"),
-      fastqcPlotSection("Base quality", "plot_per_base_quality"),
-      fastqcPlotSection("Sequence quality", "plot_per_sequence_quality"),
-      fastqcPlotSection("Base GC content", "plot_per_base_gc_content"),
-      fastqcPlotSection("Sequence GC content", "plot_per_sequence_gc_content"),
-      fastqcPlotSection("Base seqeunce content", "plot_per_base_sequence_content"),
-      fastqcPlotSection("Duplication", "plot_duplication_levels"),
-      fastqcPlotSection("Kmers", "plot_kmer_profiles"),
-      fastqcPlotSection("Length distribution", "plot_sequence_length_distribution")
-    ), Map())
-  }
+  def indexPage = ReportPage(Map(
+    "QC" -> flexiprepPage
+  ), List(
+    "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp")
+  ),
+    Map()
+  )
+
+  def flexiprepPage = ReportPage(
+    Map(),
+    List(
+    "Read Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
+    "Base Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"),
+    fastqcPlotSection("Base quality", "plot_per_base_quality"),
+    fastqcPlotSection("Sequence quality", "plot_per_sequence_quality"),
+    fastqcPlotSection("Base GC content", "plot_per_base_gc_content"),
+    fastqcPlotSection("Sequence GC content", "plot_per_sequence_gc_content"),
+    fastqcPlotSection("Base seqeunce content", "plot_per_base_sequence_content"),
+    fastqcPlotSection("Duplication", "plot_duplication_levels"),
+    fastqcPlotSection("Kmers", "plot_kmer_profiles"),
+    fastqcPlotSection("Length distribution", "plot_sequence_length_distribution")
+  ),
+    Map()
+  )
 
   protected def fastqcPlotSection(name: String, tag: String) = {
     name -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastaqcPlot.ssp", Map("plot" -> tag))

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

@@ -2,6 +2,7 @@
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
 <%@ var summary: Summary %>
 <%@ var sampleId: Option[String] = None %>
+<%@ var rootPath: String %>
 #{
     val fields = List("Hom", "HomVar", "HomRef", "NoCall", "Variant", "NonInformative", "Total")
     val samples = sampleId match {
@@ -16,7 +17,7 @@
 </tr></thead>
 <tbody>
     #for (sample <- samples.toList.sorted)
-        <tr><td>${sample}</td>
+        <tr><td><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
         #for (field <- fields)
             <td>${summary.getSampleValue(sample, "shivavariantcalling", "stats", "multisample-vcfstats-final", "genotype", field)}</td>
         #end

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

@@ -6,6 +6,8 @@
 <table>
 <tbody>
     <tr><th>Pipeline</th><td>Shiva</td></tr>
-    <tr><th><a href="${rootPath}/Samples/index.html">Samples</a></th><td>${summary.samples.size}</td></tr>
 </tbody>
-</table>
\ No newline at end of file
+</table>
+
+#{//TODO: Add settings}#
+Todo: settings
\ No newline at end of file

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

 package nl.lumc.sasc.biopet.pipelines.shiva
 
 import nl.lumc.sasc.biopet.core.report.{ ReportSection, MultisampleReportBuilder, ReportPage }
+import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
 import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
 
 /**
@@ -9,20 +10,31 @@ import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
 object ShivaReport extends MultisampleReportBuilder {
   def indexPage = ReportPage(
     Map(
-      "General" -> ReportPage(Map(), List(
+      /*"General" -> ReportPage(Map(), List(
         "Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp"),
+        "Alignment" -> 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")
-      ), Map()),
+      ), Map()),*/
       "Samples" -> generateSamplesPage(pageArgs)
     ),
-    List("Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp")),
+    List(
+      "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp"),
+      "Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp"),
+      "Alignment" -> 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")
+    ),
     pageArgs
   )
 
   def samplePage(sampleId: String, args: Map[String, Any]) = {
-    ReportPage(Map("Libraries" -> generateLibraryPage(args)), List(
-      "Libraries" -> ReportSection("/nl/lumc/sasc/biopet/core/report/librariesList.ssp"),
+    ReportPage(Map(
+      "Libraries" -> generateLibraryPage(args),
+      "Alignment" -> BammetricsReport.bamMetricsPage
+    ), List(
+      "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
+      "Preprocessing" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp", Map("sampleLevel" -> true)),
       "Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp"),
       "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
       "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
@@ -30,13 +42,17 @@ object ShivaReport extends MultisampleReportBuilder {
   }
 
   def libraryPage(libId: String, args: Map[String, Any]) = {
-    ReportPage(Map("QC" -> FlexiprepReport.indexPage), List(
+    ReportPage(Map(
+      "Alignment" -> BammetricsReport.bamMetricsPage,
+      "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)
   }
 
-  def reportName = "Title Test"
+  def reportName = "Shiva Report"
 
   // FIXME: Not yet finished
 }