Commit bcbb2916 authored by Peter van 't Hof's avatar Peter van 't Hof

Style fixes

parent 10248b22
......@@ -17,10 +17,10 @@ package nl.lumc.sasc.biopet.core.report
import java.io._
import nl.lumc.sasc.biopet.core.ToolCommandFunction
import nl.lumc.sasc.biopet.utils.summary.db.Schema.{Library, Module, Pipeline, Sample}
import nl.lumc.sasc.biopet.utils.summary.db.Schema.{ Library, Module, Pipeline, Sample }
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.{LibraryId, SampleId}
import nl.lumc.sasc.biopet.utils.{IoUtils, Logging, ToolCommand}
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.{ LibraryId, SampleId }
import nl.lumc.sasc.biopet.utils.{ IoUtils, Logging, ToolCommand }
import org.broadinstitute.gatk.utils.commandline.Input
import org.fusesource.scalate.TemplateEngine
......@@ -204,7 +204,7 @@ trait ReportBuilder extends ToolCommand {
)
}
val rootPage = indexPage.map { x => x.copy(subPages = x.subPages ::: generalPages(sampleId, libId))}
val rootPage = indexPage.map { x => x.copy(subPages = x.subPages ::: generalPages(sampleId, libId)) }
// total = ReportBuilder.countPages(rootPage)
logger.info(total + " pages to be generated")
......@@ -276,7 +276,7 @@ trait ReportBuilder extends ToolCommand {
}
def pipelineName
def pipelineName: String
/** Files page, can be used general or at sample level */
def filesPage(sampleId: Option[Int] = None, libraryId: Option[Int] = None): Future[ReportPage] = {
......
......@@ -78,7 +78,7 @@ object GearsReport extends MultisampleReportBuilder {
ReportPage(
List(centrifugePage, krakenPage, qiimeClosedPage, qiimeOpenPage).flatten ::: List(
"Samples" -> generateSamplesPage(pageArgs)
),
),
List(
"Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp")) ++
List(
......
......@@ -56,10 +56,10 @@ object MappingReport extends ReportBuilder {
} else None
ReportPage((if (skipFlexiprep) Nil else List("QC" -> FlexiprepReport.flexiprepPage)) :::
bamMetricsPage.map(_.subPages).getOrElse(Nil) :::
(if (krakenExecuted) List("Gears - Metagenomics" -> Future(ReportPage(List(), List(
"Sunburst analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp"
)), Map())))
else Nil), List(
(if (krakenExecuted) List("Gears - Metagenomics" -> Future(ReportPage(List(), List(
"Sunburst analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp"
)), Map())))
else Nil), List(
"Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp")
) ::: bamMetricsPage.map(_.sections).getOrElse(Nil),
Map()
......
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