diff --git a/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp b/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp index a57d62ebb7b922ed0a8d9bc1e569c8486ea777c8..8ef51a20f1c6332294654343015c0d03acd0d50b 100644 --- a/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp +++ b/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp @@ -12,13 +12,13 @@ <%@ var outputDir: File %> <% - val bla = if (sampleId.isEmpty && libId.isEmpty) { + val summaries = if (sampleId.isEmpty && libId.isEmpty) { summary.getSampleValues("gearskraken", "stats", "krakenreport").map(x => x._1 -> x._2.get.asInstanceOf[Map[String, Any]]) } else summary.getValue(sampleId, libId, "gearskraken", "stats", "krakenreport").map(sampleId.get -> _.asInstanceOf[Map[String, Any]]).toList.toMap val tempFile = File.createTempFile("krona.", ".xml") tempFile.deleteOnExit() - GearsKraken.convertKrakenSummariesToKronaXml(bla, tempFile) + GearsKraken.convertKrakenSummariesToKronaXml(summaries, tempFile) val output = ReportBuilder.renderTemplate("/nl/lumc/sasc/biopet/core/report/krona.ssp", args ++ Map("kronaXml" -> tempFile))