Fixed report types

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

@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.carp
 import java.io.File
 
 import nl.lumc.sasc.biopet.core._
+import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
 import nl.lumc.sasc.biopet.extensions.macs2.Macs2CallPeak
 import nl.lumc.sasc.biopet.extensions.picard.BuildBamIndex
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
@@ -95,7 +96,7 @@ class Carp(val root: Configurable) extends QScript with MultisampleMappingTrait
     }
   }
 
-  override def reportClass = {
+  override def reportClass: Option[ReportBuilderExtension] = {
     val carp = new CarpReport(this)
     carp.outputDir = new File(outputDir, "report")
     carp.summaryFile = summaryFile

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

@@ -15,7 +15,7 @@
  */
 package nl.lumc.sasc.biopet.pipelines.carp
 
-import nl.lumc.sasc.biopet.core.report.{ReportSection, ReportBuilderExtension}
+import nl.lumc.sasc.biopet.core.report.{ ReportSection, ReportBuilderExtension }
 import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingReportTrait
 import nl.lumc.sasc.biopet.utils.config.Configurable
 

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapReport.scala

@@ -15,7 +15,7 @@
  */
 package nl.lumc.sasc.biopet.pipelines.gentrap
 
-import nl.lumc.sasc.biopet.core.report.{ReportBuilderExtension, ReportSection}
+import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportSection }
 import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingReportTrait
 import nl.lumc.sasc.biopet.utils.config.Configurable
 

public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala

 package nl.lumc.sasc.biopet.pipelines.mapping
 
-import nl.lumc.sasc.biopet.core.report.{ReportBuilderExtension, ReportSection, ReportPage, MultisampleReportBuilder}
+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 nl.lumc.sasc.biopet.utils.config.Configurable
 
 /**
-  * Created by pjvanthof on 11/01/16.
-  */
+ * Created by pjvanthof on 11/01/16.
+ */
 class MultisampleMappingReport(val root: Configurable) extends ReportBuilderExtension {
   def builder = MultisampleMappingReport
 }
@@ -57,8 +57,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
     "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())
+      Map("pipelineName" -> "shiva", "fileTag" -> "preProcessBam"))), Map())
 
   /** Single sample page */
   def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {

public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTrait.scala

@@ -3,6 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.mapping
 import java.io.File
 
 import htsjdk.samtools.SamReaderFactory
+import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
 import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, MultiSampleQScript }
 import nl.lumc.sasc.biopet.extensions.Ln
 import nl.lumc.sasc.biopet.extensions.picard.{ MarkDuplicates, MergeSamFiles, AddOrReplaceReadGroups, SamToFastq }
@@ -37,7 +38,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
     addSummaryJobs()
   }
 
-  override def reportClass = {
+  override def reportClass: Option[ReportBuilderExtension] = {
     val report = new MultisampleMappingReport(this)
     report.outputDir = new File(outputDir, "report")
     report.summaryFile = summaryFile

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

@@ -15,13 +15,13 @@
  */
 package nl.lumc.sasc.biopet.pipelines.shiva
 
-import java.io.{File, PrintWriter}
+import java.io.{ File, PrintWriter }
 
 import nl.lumc.sasc.biopet.core.report._
 import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingReportTrait
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.utils.rscript.StackedBarPlot
-import nl.lumc.sasc.biopet.utils.summary.{Summary, SummaryValue}
+import nl.lumc.sasc.biopet.utils.summary.{ Summary, SummaryValue }
 
 /**
  * With this extension the report is executed within a pipeline
@@ -100,7 +100,8 @@ object ShivaReport extends MultisampleMappingReportTrait {
   /** Files page, can be used general or at sample level */
   override def filesPage: ReportPage = {
     val vcfFilesSection = if (variantcallingExecuted) List("VCF files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFiles.ssp",
-      Map("sampleId" -> None))) else Nil
+      Map("sampleId" -> None)))
+    else Nil
     val oldPage = super.filesPage
     oldPage.copy(sections = oldPage.sections ++ vcfFilesSection)
   }

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

@@ -16,8 +16,9 @@
 package nl.lumc.sasc.biopet.pipelines.shiva
 
 import nl.lumc.sasc.biopet.core.Reference
+import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
 import nl.lumc.sasc.biopet.pipelines.bammetrics.TargetRegions
-import nl.lumc.sasc.biopet.pipelines.mapping.{ MultisampleMappingTrait }
+import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingTrait
 import nl.lumc.sasc.biopet.pipelines.toucan.Toucan
 import org.broadinstitute.gatk.queue.QScript
 
@@ -28,7 +29,7 @@ import org.broadinstitute.gatk.queue.QScript
  */
 trait ShivaTrait extends MultisampleMappingTrait with Reference with TargetRegions { qscript: QScript =>
 
-  override def reportClass = {
+  override def reportClass: Option[ReportBuilderExtension] = {
     val shiva = new ShivaReport(this)
     shiva.outputDir = new File(outputDir, "report")
     shiva.summaryFile = summaryFile