Commit e9c73310 authored by rhpvorderman's avatar rhpvorderman

Fix formatting

parent 9d27d507
...@@ -61,22 +61,23 @@ object MappingReport extends ReportBuilder { ...@@ -61,22 +61,23 @@ object MappingReport extends ReportBuilder {
Map("skip_flexiprep" -> List("skip_flexiprep"), "skip_metrics" -> List("skip_metrics")) Map("skip_flexiprep" -> List("skip_flexiprep"), "skip_metrics" -> List("skip_metrics"))
) )
val skipFlexiprep = mappingSettings.get("skip_flexiprep").flatten.getOrElse(false) == true val skipFlexiprep = mappingSettings.get("skip_flexiprep").flatten.getOrElse(false) == true
val bamMetricsPageValues = BammetricsReport.bamMetricsPageValues(summary,sampleId,libId) val bamMetricsPageValues = BammetricsReport.bamMetricsPageValues(summary, sampleId, libId)
val flexiprepReportPageValues = FlexiprepReport.flexiprepPageSummaries(summary, sampleId.get, libId.get) val flexiprepReportPageValues =
FlexiprepReport.flexiprepPageSummaries(summary, sampleId.get, libId.get)
val bamMetricsPage = val bamMetricsPage =
if (mappingSettings.get("skip_metrics").flatten.getOrElse(false) == false) { if (mappingSettings.get("skip_metrics").flatten.getOrElse(false) == false) {
Some(BammetricsReport.bamMetricsPage(bamMetricsPageValues)) Some(BammetricsReport.bamMetricsPage(bamMetricsPageValues))
} else None } else None
Future { Future {
ReportPage( ReportPage(
(if (skipFlexiprep) Nil (if (skipFlexiprep) Nil
else List("QC" -> FlexiprepReport.flexiprepPage(flexiprepReportPageValues))) ::: else List("QC" -> FlexiprepReport.flexiprepPage(flexiprepReportPageValues))) :::
bamMetricsPage.map(_.subPages).getOrElse(Nil), bamMetricsPage.map(_.subPages).getOrElse(Nil),
List( List(
"Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp") "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp")
) ::: bamMetricsPage.map(_.sections).getOrElse(Nil), ) ::: bamMetricsPage.map(_.sections).getOrElse(Nil),
Map() Map()
) )
}
} }
} }
}
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