diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala index ff4397af59bdd76f6ac80237b3de1149b4cb8005..67fb3e54b3aa7ba15ce8ad9c1b48cbe482f1ee4b 100644 --- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala +++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala @@ -20,8 +20,13 @@ object GearsReport extends MultisampleReportBuilder { .map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x)) def indexPage = { + val krakenExecuted = summary.getSampleValues("gearskraken", "stats", "krakenreport").values.forall(_.isDefined) + ReportPage( - List("Samples" -> generateSamplesPage(pageArgs)) ++ + (if (krakenExecuted) List("Kraken" -> ReportPage(List(), List( + "Kraken analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp" + )), Map())) + else Nil) ::: List("Samples" -> generateSamplesPage(pageArgs)) ++ Map( "Versions" -> ReportPage(List(), List( "Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp") @@ -41,7 +46,12 @@ object GearsReport extends MultisampleReportBuilder { /** Single sample page */ def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = { - ReportPage(List( + val krakenExecuted = summary.getValue(Some(sampleId), None, "gearskraken", "stats", "krakenreport").isDefined + + ReportPage((if (krakenExecuted) List("Kraken" -> ReportPage(List(), List( + "Kraken analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp" + )), Map())) + else Nil) ::: List( "Libraries" -> generateLibraryPage(args) ), List("QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"), "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp") @@ -53,7 +63,7 @@ object GearsReport extends MultisampleReportBuilder { val krakenExecuted = summary.getValue(Some(sampleId), Some(libId), "gearskraken", "stats", "krakenreport").isDefined ReportPage( - if (krakenExecuted) List("Gears - Metagenomics" -> ReportPage(List(), List( + if (krakenExecuted) List("Kraken" -> ReportPage(List(), List( "Kraken analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp" )), Map())) else Nil, List(