Commit e270ea9d authored by Peter van 't Hof's avatar Peter van 't Hof

Added multisample krona plot

parent 38e13cdd
......@@ -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(
......
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