Commit 36f14bb5 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixed report

parent 96137126
...@@ -10,12 +10,13 @@ ...@@ -10,12 +10,13 @@
<%@ var libId: Option[String] = None %> <%@ var libId: Option[String] = None %>
<%@ var args: Map[String, Any] %> <%@ var args: Map[String, Any] %>
<%@ var outputDir: File %> <%@ var outputDir: File %>
<%@ var summaryTag: String = "krakenreport" %> <%@ var summaryStatsTag: String = "krakenreport" %>
<%@ var summaryModuleTag: String = "gearskraken" %>
<% <%
val summaries = if (sampleId.isEmpty && libId.isEmpty) { val summaries = if (sampleId.isEmpty && libId.isEmpty) {
summary.getSampleValues("gearskraken", "stats", summaryTag).map(x => x._1 -> x._2.get.asInstanceOf[Map[String, Any]]) summary.getSampleValues(summaryModuleTag, "stats", summaryStatsTag).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 } else summary.getValue(sampleId, libId, summaryModuleTag, "stats", summaryStatsTag).map(sampleId.get -> _.asInstanceOf[Map[String, Any]]).toList.toMap
val tempFile = File.createTempFile("krona.", ".xml") val tempFile = File.createTempFile("krona.", ".xml")
tempFile.deleteOnExit() tempFile.deleteOnExit()
......
...@@ -47,7 +47,7 @@ object GearsReport extends MultisampleReportBuilder { ...@@ -47,7 +47,7 @@ object GearsReport extends MultisampleReportBuilder {
ReportPage( ReportPage(
(if (centrifugeExecuted) List("Centriguge analysis" -> ReportPage(List(), List( (if (centrifugeExecuted) List("Centriguge analysis" -> ReportPage(List(), List(
"Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp" "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( else Nil) ::: (if (krakenExecuted) List("Kraken analysis" -> ReportPage(List(), List(
"Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp" "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)), Map())) )), Map()))
......
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