Commit 8078bfbd authored by rhpvorderman's avatar rhpvorderman

Fix flexiprep bug and remove import ugliness in gears report

parent 618ebeda
......@@ -295,7 +295,8 @@ object FlexiprepReadSummary {
FlexiprepReport.readSummaryPlotLines("R2", summary, sampleId = sampleId)
val seqstatPaths = Map("num_total" -> List("reads", "num_total"))
val clippingPaths = Map("num_reads_discarded_too_short" -> List("num_reads_discarded_too_short"),
val clippingPaths = Map(
"num_reads_discarded_too_short" -> List("num_reads_discarded_too_short"),
"num_reads_discarded_too_long" -> List("num_reads_discarded_too_long"))
val trimmingPaths = Map("num_reads_discarded" -> List("num_reads_discarded_total"))
......
......@@ -16,8 +16,17 @@ package nl.lumc.sasc.biopet.pipelines.gears
import java.io.File
import nl.lumc.sasc.biopet.core.report.{MultisampleReportBuilder, ReportBuilderExtension, ReportPage, ReportSection}
import nl.lumc.sasc.biopet.pipelines.flexiprep.{FlexiprepBaseSummary, FlexiprepReadSummary, FlexiprepReport}
import nl.lumc.sasc.biopet.core.report.{
MultisampleReportBuilder,
ReportBuilderExtension,
ReportPage,
ReportSection
}
import nl.lumc.sasc.biopet.pipelines.flexiprep.{
FlexiprepBaseSummary,
FlexiprepReadSummary,
FlexiprepReport
}
import nl.lumc.sasc.biopet.pipelines.gears
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.utils.summary.db.Schema.{Library, Sample}
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment