Commit 268a45a7 authored by rhpvorderman's avatar rhpvorderman

Add appropriate some types for plot generator

parent 66d4e1a8
......@@ -16,7 +16,12 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import java.io.{File, PrintWriter}
import nl.lumc.sasc.biopet.core.report.{ReportBuilder, ReportBuilderExtension, ReportPage, ReportSection}
import nl.lumc.sasc.biopet.core.report.{
ReportBuilder,
ReportBuilderExtension,
ReportPage,
ReportSection
}
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.utils.rscript.StackedBarPlot
import nl.lumc.sasc.biopet.utils.summary.db.Schema.{Library, Sample}
......@@ -288,10 +293,10 @@ object FlexiprepReadSummary {
if (showPlot)
Some(FlexiprepReport.readSummaryPlotLines("R1", summary, sampleId = sampleId))
else None
val summaryPlotlinesR2: Some[Seq[String]] =
val summaryPlotlinesR2: Some[Seq[String]] =
if (showPlot && paired)
Some(FlexiprepReport.readSummaryPlotLines("R2", summary, sampleId = sampleId))
else None
else None
val seqstatPaths = Map("num_total" -> List("reads", "num_total"))
val clippingPaths = Map(
......@@ -371,7 +376,7 @@ object FlexiprepBaseSummary {
if (showPlot)
Some(FlexiprepReport.readSummaryPlotLines("R1", summary, sampleId = sampleId))
else None
val summaryPlotlinesR2: Some[Seq[String]] =
val summaryPlotlinesR2: Some[Seq[String]] =
if (showPlot && paired)
Some(FlexiprepReport.readSummaryPlotLines("R2", summary, sampleId = sampleId))
else None
......
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