adding carp report to the pipeline

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

@@ -40,7 +40,10 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
   def this() = this(null)
 
   override def defaults = ConfigUtils.mergeMaps(Map(
-    "mapping" -> Map("skip_markduplicates" -> true, "aligner" -> "bwa-mem")
+    "mapping" -> Map(
+      "skip_markduplicates" -> true,
+      "aligner" -> "bwa-mem"
+    )
   ), super.defaults)
 
   def summaryFile = new File(outputDir, "Carp.summary.json")
@@ -117,6 +120,13 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
     }
   }
 
+  override def reportClass = {
+    val carp = new CarpReport(this)
+    carp.outputDir = new File(outputDir, "report")
+    carp.summaryFile = summaryFile
+    Some(carp)
+  }
+
   def init() = {
     // ensure that no samples are called 'control' since that is our reserved keyword
     require(!sampleIds.contains("control"),

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

 package nl.lumc.sasc.biopet.pipelines.carp
 
-import nl.lumc.sasc.biopet.core.report.{ ReportSection, ReportPage, MultisampleReportBuilder }
+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
 
-import scala.io.Source
-
 /**
  * Created by pjvanthof on 25/06/15.
  */
-class CarpReport {
-
+class CarpReport(val root: Configurable) extends ReportBuilderExtension {
+  val builder = CarpReport
 }
 
 object CarpReport extends MultisampleReportBuilder {