diff --git a/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp b/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp index bc3a405a7fdc8e0fce434deed3a68590f01a2fc7..eb19b30d62138980acf7b61b52477eacc8bff7e3 100644 --- a/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp +++ b/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp @@ -10,12 +10,13 @@ <%@ var libId: Option[String] = None %> <%@ var args: Map[String, Any] %> <%@ var outputDir: File %> -<%@ var summaryTag: String = "krakenreport" %> +<%@ var summaryStatsTag: String = "krakenreport" %> +<%@ var summaryModuleTag: String = "gearskraken" %> <% val summaries = if (sampleId.isEmpty && libId.isEmpty) { - summary.getSampleValues("gearskraken", "stats", summaryTag).map(x => x._1 -> x._2.get.asInstanceOf[Map[String, Any]]) - } else summary.getValue(sampleId, libId, "gearskraken", "stats", summaryTag).map(sampleId.get -> _.asInstanceOf[Map[String, Any]]).toList.toMap + summary.getSampleValues(summaryModuleTag, "stats", summaryStatsTag).map(x => x._1 -> x._2.get.asInstanceOf[Map[String, Any]]) + } else summary.getValue(sampleId, libId, summaryModuleTag, "stats", summaryStatsTag).map(sampleId.get -> _.asInstanceOf[Map[String, Any]]).toList.toMap val tempFile = File.createTempFile("krona.", ".xml") tempFile.deleteOnExit() diff --git a/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala b/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala index dde2a67eb62fac174990dcb2cb0c1954a143b464..bc38c3f329698ee53fa9a4d6b4d4fa64a25a31a3 100644 --- a/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala +++ b/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala @@ -47,7 +47,7 @@ object GearsReport extends MultisampleReportBuilder { ReportPage( (if (centrifugeExecuted) List("Centriguge analysis" -> ReportPage(List(), List( "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp" - )), Map("summaryTag" -> "centriguge_report"))) + )), Map("summaryStatsTag" -> "centrifuge_report", "summaryModuleTag" -> "gearscentrifuge"))) else Nil) ::: (if (krakenExecuted) List("Kraken analysis" -> ReportPage(List(), List( "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp" )), Map()))