Commit f25519d7 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix format

parent 607e9a1f
......@@ -16,8 +16,8 @@ package nl.lumc.sasc.biopet.pipelines.gears
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.BiopetQScript.InputFile
import nl.lumc.sasc.biopet.core.{PipelineCommand, SampleLibraryTag}
import nl.lumc.sasc.biopet.extensions.{Gzip, Zcat}
import nl.lumc.sasc.biopet.core.{ PipelineCommand, SampleLibraryTag }
import nl.lumc.sasc.biopet.extensions.{ Gzip, Zcat }
import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import nl.lumc.sasc.biopet.utils.Logging
import nl.lumc.sasc.biopet.utils.config.Configurable
......
......@@ -30,15 +30,19 @@ object GearsSingleReport extends ReportBuilder {
val krakenExecuted = summary.getValue(sampleId, libId, "gearskraken", "stats", "krakenreport").isDefined
val centrifugeExecuted = summary.getValue(sampleId, libId, "gearscentrifuge", "stats", "centrifuge_report").isDefined
ReportPage(
List(
"Versions" -> ReportPage(List(),
List(("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"))), Map())
),
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),
(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
)
}
......
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