Commit 4e394bc9 authored by Ruben Vorderman's avatar Ruben Vorderman
Browse files

Start on defuturing readsummaryplot

parent 83188c3f
...@@ -67,6 +67,10 @@ ...@@ -67,6 +67,10 @@
#end #end
#if (showPlot) #if (showPlot)
#{
FlexiprepReport.readSummaryPlot(outputDir, "QC_Reads_R1","R1", summary, sampleId = sampleId)
if (paired) FlexiprepReport.readSummaryPlot(outputDir, "QC_Reads_R2","R2", summary, sampleId = sampleId)
}#
<div class="panel-body"> <div class="panel-body">
<div class="row"> <div class="row">
<div class="col-sm-6 col-md-6"> <div class="col-sm-6 col-md-6">
......
...@@ -16,13 +16,8 @@ package nl.lumc.sasc.biopet.pipelines.gears ...@@ -16,13 +16,8 @@ package nl.lumc.sasc.biopet.pipelines.gears
import java.io.File import java.io.File
import nl.lumc.sasc.biopet.core.report.{ import nl.lumc.sasc.biopet.core.report.{MultisampleReportBuilder, ReportBuilderExtension, ReportPage, ReportSection}
MultisampleReportBuilder, import nl.lumc.sasc.biopet.pipelines.flexiprep.{FlexiprepReadSummary, FlexiprepReport}
ReportBuilderExtension,
ReportPage,
ReportSection
}
import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
import nl.lumc.sasc.biopet.pipelines.gears import nl.lumc.sasc.biopet.pipelines.gears
import nl.lumc.sasc.biopet.utils.config.Configurable import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
...@@ -145,6 +140,8 @@ object GearsReport extends MultisampleReportBuilder { ...@@ -145,6 +140,8 @@ object GearsReport extends MultisampleReportBuilder {
"biomFile" -> new File(run.outputDir + File.separator + qiimeOpenOtuTable.get.path)) "biomFile" -> new File(run.outputDir + File.separator + qiimeOpenOtuTable.get.path))
))) )))
else None else None
val flexiprepReadSummary = FlexiprepReadSummary.values(summary,,runId,samples,libraries,sampleId,libId, true, false)
Future { Future {
ReportPage( ReportPage(
List(centrifugePage, krakenPage, qiimeClosedPage, qiimeOpenPage).flatten ::: List( List(centrifugePage, krakenPage, qiimeClosedPage, qiimeOpenPage).flatten ::: List(
...@@ -154,7 +151,7 @@ object GearsReport extends MultisampleReportBuilder { ...@@ -154,7 +151,7 @@ object GearsReport extends MultisampleReportBuilder {
List( List(
"QC reads" -> ReportSection( "QC reads" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp", "/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",
Map("showPlot" -> true, "showTable" -> false)), flexiprepReadSummary),
"QC bases" -> ReportSection( "QC bases" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp", "/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
Map("showPlot" -> true, "showTable" -> false)) Map("showPlot" -> true, "showTable" -> false))
......
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