Commit c639a8b7 authored by rhpvorderman's avatar rhpvorderman

Defutured MultiSampleMapping

parent f7c21823
......@@ -342,11 +342,12 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
FlexiprepReadSummary.values(summary, runId, samples, libraries, sampleId, libId)
val flexiprepBaseSummary =
FlexiprepBaseSummary.values(summary, runId, samples, libraries, sampleId, libId)
val bamMetricsReportValues = BammetricsReport.bamMetricsPageValues(summary, Some(sampleId), libId)
Future {
ReportPage(
List("Libraries" -> generateLibraryPage(args),
"Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), None)) ++
"Alignment" -> BammetricsReport.bamMetricsPage(bamMetricsReportValues)) ++
(if (centrifugeExecuted)
List(
"Centrifuge analysis" -> Future.successful(ReportPage(
......@@ -418,9 +419,16 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
mustHaveLibrary = true),
Duration.Inf) >= 1
val flexiprepPageSummaries = FlexiprepReport.flexiprepPageSummaries(summary, sampleId, libId)
val bamMetricsReportValues = BammetricsReport.bamMetricsPageValues(summary, Some(sampleId), Some(libId))
val centrifugeAllMappingsReportValues = GearsKronaPlot.values(summary, runId, "gearscentrifuge","centrifuge_report",samples,libraries,Some(sampleId),Some(libId), centrifugeTag = Some("centrifuge"))
val centrifugeUniqueMappingsReportValues = GearsKronaPlot.values(summary, runId, "gearscentrifuge","centrifuge_unique_report",samples,libraries,Some(sampleId),Some(libId), centrifugeTag = Some("centrifuge"))
val krakenDustbinAnalysisReportValues = GearsKronaPlot.values(summary, runId, "gearskraken","krakenreport",samples,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, runId, samples, libraries, Some(sampleId),Some(libId))
Future {
ReportPage(
("Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId))) ::
("Alignment" -> BammetricsReport.bamMetricsPage(bamMetricsReportValues)) ::
(if (flexiprepExecuted)
List("QC" -> FlexiprepReport.flexiprepPage(flexiprepPageSummaries))
else Nil) :::
......@@ -430,12 +438,12 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
ReportPage(List(),
List("All mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
Map("summaryStatsTag" -> "centrifuge_report"))),
centrifugeAllMappingsReportValues)),
Map()))),
List("Unique mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
Map("summaryStatsTag" -> "centrifuge_unique_report"))),
Map("summaryModuleTag" -> "gearscentrifuge", "centrifugeTag" -> Some("centrifuge"))
centrifugeUniqueMappingsReportValues)),
Map("summaryPipelineName" -> "gearscentrifuge", "centrifugeTag" -> Some("centrifuge"))
)))
else
Nil) ::: (if (krakenExecuted)
......@@ -443,17 +451,17 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
"Dustbin analysis" -> Future.successful(
ReportPage(List(),
List("Krona Plot" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp")),
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",krakenDustbinAnalysisReportValues)),
Map())))
else Nil),
"Alignment" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp") ::
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp", alignmentSummaryReportValues) ::
(if (flexiprepExecuted)
List(
"QC reads" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",flexiprepReadSummaryReportValues),
"QC bases" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp", flexiprepBaseSummaryReportValues)
)
else Nil),
args
......
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