Commit e9c73310 authored by rhpvorderman's avatar rhpvorderman

Fix formatting

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