Commit e9c73310 authored by rhpvorderman's avatar rhpvorderman

Fix formatting

parent 9d27d507
......@@ -61,8 +61,9 @@ object MappingReport extends ReportBuilder {
Map("skip_flexiprep" -> List("skip_flexiprep"), "skip_metrics" -> List("skip_metrics"))
)
val skipFlexiprep = mappingSettings.get("skip_flexiprep").flatten.getOrElse(false) == true
val bamMetricsPageValues = BammetricsReport.bamMetricsPageValues(summary,sampleId,libId)
val flexiprepReportPageValues = FlexiprepReport.flexiprepPageSummaries(summary, sampleId.get, libId.get)
val bamMetricsPageValues = BammetricsReport.bamMetricsPageValues(summary, sampleId, libId)
val flexiprepReportPageValues =
FlexiprepReport.flexiprepPageSummaries(summary, sampleId.get, libId.get)
val bamMetricsPage =
if (mappingSettings.get("skip_metrics").flatten.getOrElse(false) == false) {
Some(BammetricsReport.bamMetricsPage(bamMetricsPageValues))
......@@ -78,5 +79,5 @@ object MappingReport extends ReportBuilder {
Map()
)
}
}
}
}
......@@ -451,25 +451,16 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
libraries,
Some(sampleId),
Some(libId))
val alignmentSummaryReportValues = BammetricsReportPage.alignmentSummaryValues(
summary,
runId,
samples,
libraries,
Some(sampleId),
Some(libId))
val flexiprepReadSummaryReportValues = FlexiprepReadSummary.values(summary,
runId,
samples,
libraries,
Some(sampleId),
Some(libId))
val flexiprepBaseSummaryReportValues = FlexiprepBaseSummary.values(summary,
val alignmentSummaryReportValues = BammetricsReportPage.alignmentSummaryValues(summary,
runId,
samples,
libraries,
Some(sampleId),
Some(libId))
val flexiprepReadSummaryReportValues =
FlexiprepReadSummary.values(summary, runId, samples, libraries, Some(sampleId), Some(libId))
val flexiprepBaseSummaryReportValues =
FlexiprepBaseSummary.values(summary, runId, samples, libraries, Some(sampleId), Some(libId))
Future {
ReportPage(
("Alignment" -> BammetricsReport.bamMetricsPage(bamMetricsReportValues)) ::
......@@ -487,8 +478,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
List("Unique mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
centrifugeUniqueMappingsReportValues)),
Map("summaryPipelineName" -> "gearscentrifuge",
"centrifugeTag" -> Some("centrifuge"))
Map("summaryPipelineName" -> "gearscentrifuge", "centrifugeTag" -> Some("centrifuge"))
)))
else
Nil) ::: (if (krakenExecuted)
......@@ -517,5 +507,4 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
)
}
}
}
}
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