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biopet.biopet
Commit c639a8b7 authored by rhpvorderman's avatar rhpvorderman
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Defutured MultiSampleMapping

parent f7c21823
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Showing with 17 additions and 9 deletions
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @ c639a8b7
...@@ -342,11 +342,12 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder { ...@@ -342,11 +342,12 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
FlexiprepReadSummary.values(summary, runId, samples, libraries, sampleId, libId) FlexiprepReadSummary.values(summary, runId, samples, libraries, sampleId, libId)
val flexiprepBaseSummary = val flexiprepBaseSummary =
FlexiprepBaseSummary.values(summary, runId, samples, libraries, sampleId, libId) FlexiprepBaseSummary.values(summary, runId, samples, libraries, sampleId, libId)
val bamMetricsReportValues = BammetricsReport.bamMetricsPageValues(summary, Some(sampleId), libId)
Future { Future {
ReportPage( ReportPage(
List("Libraries" -> generateLibraryPage(args), List("Libraries" -> generateLibraryPage(args),
"Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), None)) ++ "Alignment" -> BammetricsReport.bamMetricsPage(bamMetricsReportValues)) ++
(if (centrifugeExecuted) (if (centrifugeExecuted)
List( List(
"Centrifuge analysis" -> Future.successful(ReportPage( "Centrifuge analysis" -> Future.successful(ReportPage(
...@@ -418,9 +419,16 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder { ...@@ -418,9 +419,16 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
mustHaveLibrary = true), mustHaveLibrary = true),
Duration.Inf) >= 1 Duration.Inf) >= 1
val flexiprepPageSummaries = FlexiprepReport.flexiprepPageSummaries(summary, sampleId, libId) 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 { Future {
ReportPage( ReportPage(
("Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId))) :: ("Alignment" -> BammetricsReport.bamMetricsPage(bamMetricsReportValues)) ::
(if (flexiprepExecuted) (if (flexiprepExecuted)
List("QC" -> FlexiprepReport.flexiprepPage(flexiprepPageSummaries)) List("QC" -> FlexiprepReport.flexiprepPage(flexiprepPageSummaries))
else Nil) ::: else Nil) :::
...@@ -430,12 +438,12 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder { ...@@ -430,12 +438,12 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
ReportPage(List(), ReportPage(List(),
List("All mappings" -> ReportSection( List("All mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp", "/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
Map("summaryStatsTag" -> "centrifuge_report"))), centrifugeAllMappingsReportValues)),
Map()))), Map()))),
List("Unique mappings" -> ReportSection( List("Unique mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp", "/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
Map("summaryStatsTag" -> "centrifuge_unique_report"))), centrifugeUniqueMappingsReportValues)),
Map("summaryModuleTag" -> "gearscentrifuge", "centrifugeTag" -> Some("centrifuge")) Map("summaryPipelineName" -> "gearscentrifuge", "centrifugeTag" -> Some("centrifuge"))
))) )))
else else
Nil) ::: (if (krakenExecuted) Nil) ::: (if (krakenExecuted)
...@@ -443,17 +451,17 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder { ...@@ -443,17 +451,17 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
"Dustbin analysis" -> Future.successful( "Dustbin analysis" -> Future.successful(
ReportPage(List(), ReportPage(List(),
List("Krona Plot" -> ReportSection( List("Krona Plot" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp")), "/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",krakenDustbinAnalysisReportValues)),
Map()))) Map())))
else Nil), else Nil),
"Alignment" -> ReportSection( "Alignment" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp") :: "/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp", alignmentSummaryReportValues) ::
(if (flexiprepExecuted) (if (flexiprepExecuted)
List( List(
"QC reads" -> ReportSection( "QC reads" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"), "/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",flexiprepReadSummaryReportValues),
"QC bases" -> ReportSection( "QC bases" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp") "/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp", flexiprepBaseSummaryReportValues)
) )
else Nil), else Nil),
args args
......
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