diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala index d7029a5bc996cdce6e47e95f496ebb72ef405b30..fe830808034f0a1e34e6bfaacc7a53bb9dd8416f 100644 --- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala +++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala @@ -57,8 +57,11 @@ object ShivaReport extends MultisampleReportBuilder { var regionPages: Map[String, ReportPage] = Map() def createPage(name: String, amplicon: Boolean = false): ReportPage = { - //TODO: get target content - ReportPage(Map(), List("Coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp")), Map("target" -> name)) + ReportPage( + Map(), + List("Coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp")), + Map("target" -> name) + ) } amplicon match { @@ -72,8 +75,14 @@ object ShivaReport extends MultisampleReportBuilder { case _ => } - if (regionPages.nonEmpty) Some("Regions" -> ReportPage(regionPages.keys.toList.sorted.map(x => x -> regionPages(x)).toMap, List(), Map())) - else None + if (regionPages.nonEmpty) Some("Regions" -> ReportPage( + Map(), + regionPages.map(p => (p._1 -> ReportSection( + "/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp", + Map("target" -> p._1.stripSuffix(" (Amplicon)")) + ))).toList.sortBy(_._1), + Map()) + ) else None } def filesPage = ReportPage(Map(), List(