Commit 607e9a1f authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix BIOPET-410

parent 204c72d0
...@@ -23,23 +23,22 @@ class GearsSingleReport(val root: Configurable) extends ReportBuilderExtension { ...@@ -23,23 +23,22 @@ class GearsSingleReport(val root: Configurable) extends ReportBuilderExtension {
object GearsSingleReport extends ReportBuilder { object GearsSingleReport extends ReportBuilder {
// TODO: Add dustbin analysis (aggregated)
// TODO: Add alignment stats per sample for the dustbin analysis
override def extFiles = super.extFiles ++ List("js/gears.js", "js/krona-2.0.js", "img/krona/loading.gif", "img/krona/hidden.png", "img/krona/favicon.ico") override def extFiles = super.extFiles ++ List("js/gears.js", "js/krona-2.0.js", "img/krona/loading.gif", "img/krona/hidden.png", "img/krona/favicon.ico")
.map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x)) .map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
def indexPage = { def indexPage = {
val krakenExecuted = summary.getValue(sampleId, libId, "gearskraken", "stats", "krakenreport").isDefined
val centrifugeExecuted = summary.getValue(sampleId, libId, "gearscentrifuge", "stats", "centrifuge_report").isDefined
ReportPage( ReportPage(
List( List(
"Versions" -> ReportPage(List(), List(( "Versions" -> ReportPage(List(),
"Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp" List(("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"))), Map())
))), Map())
),
List(
"Gears intro" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSingleFront.ssp"),
"Kraken analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp")
), ),
List("Gears intro" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSingleFront.ssp")) ++
(if (krakenExecuted) List("Kraken analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp")) else Nil) ++
(if (centrifugeExecuted) List("Centrifuge analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp", Map("summaryStatsTag" -> "centrifuge_report"))) else Nil),
pageArgs pageArgs
) )
} }
......
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