Added bammetrics report to pipeline

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

@@ -56,6 +56,17 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
   def summarySettings = Map("amplicon_name" -> ampliconBedFile.collect { case x => x.getName.stripSuffix(".bed") },
     "roi_name" -> roiBedFiles.map(_.getName.stripSuffix(".bed")))
 
+  override def reportClass = {
+    val bammetricsReport = new BammetricsReport(this)
+    bammetricsReport.outputDir = new File(outputDir, "report")
+    bammetricsReport.summaryFile = summaryFile
+    bammetricsReport.args = if (libId.isDefined) Map(
+      "sampleId" -> sampleId.getOrElse("."),
+      "libId" -> libId.getOrElse("."))
+      else Map("sampleId" -> sampleId.getOrElse("."))
+    Some(bammetricsReport)
+  }
+
   /** executed before script */
   def init() {
   }

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

@@ -2,11 +2,14 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics
 
 import java.io.{ PrintWriter, File }
 
-import nl.lumc.sasc.biopet.core.report.{ ReportBuilder, ReportPage, ReportSection }
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.report.{ReportBuilderExtension, ReportBuilder, ReportPage, ReportSection}
 import nl.lumc.sasc.biopet.core.summary.{ SummaryValue, Summary }
 import nl.lumc.sasc.biopet.extensions.rscript.{ XYPlot, StackedBarPlot }
 
-//TODO: Add basic report to BamMetrics as single pipeline
+class BammetricsReport(val root: Configurable) extends ReportBuilderExtension {
+  val builder = BammetricsReport
+}
 
 /**
  * Created by pjvan_thof on 3/30/15.
@@ -54,7 +57,8 @@ 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))
+        "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))
       ),
       Map("metricsTag" -> metricsTag)
     )