Commit 4295a7bd authored by Peter van 't Hof's avatar Peter van 't Hof

Added QC page to gears report

parent 3d39733e
......@@ -3,6 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.gears
import java.io.File
import nl.lumc.sasc.biopet.core.report.{ ReportSection, ReportPage, MultisampleReportBuilder, ReportBuilderExtension }
import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
import nl.lumc.sasc.biopet.utils.config.Configurable
/**
......@@ -72,12 +73,14 @@ object GearsReport extends MultisampleReportBuilder {
/** Library page */
def libraryPage(sampleId: String, libId: String, args: Map[String, Any]): ReportPage = {
val flexiprepExecuted = summary.getLibraryValue(sampleId, libId, "flexiprep").isDefined
val krakenExecuted = summary.getValue(Some(sampleId), Some(libId), "gearskraken", "stats", "krakenreport").isDefined
val qiimeClosesOtuTable = summary.getValue(Some(sampleId), Some(libId), "gearsqiimeclosed", "files", "pipeline", "otu_table", "path")
.map(x => new File(x.toString))
ReportPage(
(if (krakenExecuted) List("Kraken" -> ReportPage(List(), List(
(if (flexiprepExecuted) List("QC" -> FlexiprepReport.flexiprepPage) else Nil
) ::: (if (krakenExecuted) List("Kraken" -> ReportPage(List(), List(
"Kraken analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)), Map()))
else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> ReportPage(List(), List(
......
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