Commit 618ebeda authored by rhpvorderman's avatar rhpvorderman

Fix flexiprep bug and remove import ugliness in gears report

parent f1dc8c0f
......@@ -14,7 +14,6 @@
<%@ var multisample: Boolean = true %>
<%@ var allSamples: Seq[Sample] %>
<%@ var allLibraries: Seq[Library] %>
<%-- variables to be added to remove dependency upon futures --%>
<%@ var settings: Map[(Int, Int), Map[String, Option[Any]]] %>
<%@ var paired: Boolean %>
<%@ var samples: Seq[Sample] %>
......
......@@ -295,8 +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"))
val seqstatStats: Map[(Int, Int), Map[String, Option[Any]]] =
......
......@@ -16,36 +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.FlexiprepReport
import nl.lumc.sasc.biopet.pipelines.gears
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}
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.{NoLibrary, NoModule, SampleId}
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.{ModuleName, NoLibrary, NoModule, SampleId}
import nl.lumc.sasc.biopet.utils.summary.db.Schema.Library
import nl.lumc.sasc.biopet.utils.summary.db.Schema.Sample
import scala.concurrent.{Await, Future}
import scala.concurrent.duration.Duration
import scala.concurrent.{Await, Future}
/**
* Report for Gears
......
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