Added start for Flexiprep report

public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepSummary.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 %>
+#{
+    val samples = sampleId match {
+        case Some(sample) => List(sample.toString)
+        case _ => summary.samples.toList
+    }
+}#
+<table>
+<thead><tr>
+    <th>Sample</th>
+    <th>Library</th>
+    <th>Read</th>
+    <th>Reads before QC</th>
+    <th>Bases before QC</th>
+    <th>Reads after QC</th>
+    <th>Bases after QC</th>
+</tr></thead>
+<tbody>
+    #for (sample <- samples.toList.sorted)
+        #{
+            val libs = libId match {
+                case Some(libId) => List(libId.toString)
+                case _ => summary.libraries(sample).toList
+            }
+
+            val sampleRowspan = {
+                libs.size +
+                libs.count(summary.getLibraryValue(sample, _, "flexiprep", "settings", "paired").getOrElse(false) == true)
+            }
+        }#
+        <tr><td rowspan="${sampleRowspan}">${sample}</td>
+        #for (libId <- summary.libraries(sample))
+            #{ val paired = summary.getLibraryValue(sample, libId, "flexiprep", "settings", "paired").getOrElse(false) }#
+            <td #if (paired == true) rowspan="2" #end>${libId}</td>
+            <td>R1</td>
+            <td>${summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_R1", "reads", "num_total")} </td>
+            <td> ${summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_R1", "bases", "num_total")}
+            </td>
+            <td>${summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_R1_after", "reads", "num_total")}</td>
+            <td> ${summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_R1_after", "bases", "num_total")}</td>
+            #if (paired == true)
+            </tr><tr>
+            <td>R2</td>
+            <td>${summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_R2", "reads", "num_total")}</td>
+            <td> ${summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_R2", "bases", "num_total")}</td>
+            <td>${summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_R2_after", "reads", "num_total")} </td>
+            <td> ${summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_R2_after", "bases", "num_total")}</td>
+            #end
+
+        #end
+        </tr>
+    #end
+</tbody>
+</table>
\ No newline at end of file

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

+package nl.lumc.sasc.biopet.pipelines.flexiprep
+
+import nl.lumc.sasc.biopet.core.report.{ ReportPage, ReportBuilder }
+
+/**
+ * Created by pjvan_thof on 3/30/15.
+ */
+object FlexiprepReport extends ReportBuilder {
+  val reportName = "Flexiprep"
+
+  def indexPage = {
+    ReportPage(Map(), Map("Summary" -> "/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepSummary.ssp"), Map())
+  }
+
+  // FIXME: Not yet finished
+}