Commit 9d27d507 authored by rhpvorderman's avatar rhpvorderman

Fix typo's

parent 9a7a81d7
......@@ -85,8 +85,7 @@
#for (field <- fields)
<td>${results(field)}</td>
#end
#end
</tr>
</tr>
#end
#end
</tbody>
......
......@@ -50,7 +50,7 @@ object MappingReport extends ReportBuilder {
.map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
/** Root page for single BamMetrcis report */
def indexPage: Future[ReportPage] = Future {
def indexPage: Future[ReportPage] = {
val mappingSettings = summary.getSettingKeys(
runId,
"mapping",
......@@ -61,13 +61,16 @@ 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 bamMetricsPage =
if (mappingSettings.get("skip_metrics").flatten.getOrElse(false) == false) {
Some(BammetricsReport.bamMetricsPage(summary, sampleId, libId))
Some(BammetricsReport.bamMetricsPage(bamMetricsPageValues))
} else None
ReportPage(
Future {
ReportPage(
(if (skipFlexiprep) Nil
else List("QC" -> FlexiprepReport.flexiprepPage(summary, sampleId.get, libId.get))) :::
else List("QC" -> FlexiprepReport.flexiprepPage(flexiprepReportPageValues))) :::
bamMetricsPage.map(_.subPages).getOrElse(Nil),
List(
"Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp")
......@@ -76,3 +79,4 @@ object MappingReport extends ReportBuilder {
)
}
}
}
......@@ -283,61 +283,61 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
/** Single sample page */
def samplePage(sampleId: Int, args: Map[String, Any]): Future[ReportPage] = {
val krakenExecuted = Await.result(summary.getStatsSize(runId,
"gearskraken",
"krakenreport",
library = NoLibrary,
sample = sampleId),
Duration.Inf) >= 1
"gearskraken",
"krakenreport",
library = NoLibrary,
sample = sampleId),
Duration.Inf) >= 1
val centrifugeExecuted = Await.result(summary.getStatsSize(runId,
"gearscentrifuge",
"centrifuge_report",
library = NoLibrary,
sample = sampleId,
mustHaveSample = true),
Duration.Inf) >= 1
"gearscentrifuge",
"centrifuge_report",
library = NoLibrary,
sample = sampleId,
mustHaveSample = true),
Duration.Inf) >= 1
val flexiprepExecuted = Await.result(
summary.getStatsSize(runId, "flexiprep", sample = sampleId, mustHaveLibrary = true),
Duration.Inf) >= 1
val centrifugeAllMappingsReportValues = GearsKronaPlot.values(summary,
runId,
"gearscentrifuge",
"centrifuge_report",
samples,
libraries,
sampleId,
libId,
Some("centrifuge"))
runId,
"gearscentrifuge",
"centrifuge_report",
samples,
libraries,
sampleId,
libId,
Some("centrifuge"))
val centrifugeUniqueMappingsReportValues = GearsKronaPlot.values(summary,
runId,
"gearscentrifuge",
"centrifuge_unique_report",
samples,
libraries,
sampleId,
libId)
runId,
"gearscentrifuge",
"centrifuge_unique_report",
samples,
libraries,
sampleId,
libId)
val dustbinAnalysisReportValues = GearsKronaPlot.values(summary,
runId,
"gearskraken",
"krakenreport",
samples,
libraries,
sampleId,
libId)
runId,
"gearskraken",
"krakenreport",
samples,
libraries,
sampleId,
libId)
val alignmentSummaryReportValues = BammetricsReportPage.alignmentSummaryValues(summary,
runId,
samples,
libraries,
sampleId,
libId,
showPlot = true)
runId,
samples,
libraries,
sampleId,
libId,
showPlot = true)
val preprocessingReportValues = BammetricsReportPage.alignmentSummaryValues(summary,
runId,
samples,
libraries,
sampleId,
libId,
sampleLevel = true)
runId,
samples,
libraries,
sampleId,
libId,
sampleLevel = true)
val flexiprepReadSummary =
FlexiprepReadSummary.values(summary, runId, samples, libraries, sampleId, libId)
val flexiprepBaseSummary =
......@@ -348,34 +348,34 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
Future {
ReportPage(
List("Libraries" -> generateLibraryPage(args),
"Alignment" -> BammetricsReport.bamMetricsPage(bamMetricsReportValues)) ++
"Alignment" -> BammetricsReport.bamMetricsPage(bamMetricsReportValues)) ++
(if (centrifugeExecuted)
List(
"Centrifuge analysis" -> Future.successful(ReportPage(
List(
"Non-unique" -> Future.successful(
ReportPage(
List(),
List("All mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
centrifugeAllMappingsReportValues)),
Map()
))),
List("Unique mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
centrifugeUniqueMappingsReportValues)),
Map("summaryPipelineName" -> "gearscentrifuge")
)))
else
Nil) ::: (if (krakenExecuted)
List(
"Dustbin analysis" -> Future.successful(
ReportPage(List(),
List("Krona Plot" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
dustbinAnalysisReportValues)),
Map())))
else Nil),
List(
"Centrifuge analysis" -> Future.successful(ReportPage(
List(
"Non-unique" -> Future.successful(
ReportPage(
List(),
List("All mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
centrifugeAllMappingsReportValues)),
Map()
))),
List("Unique mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
centrifugeUniqueMappingsReportValues)),
Map("summaryPipelineName" -> "gearscentrifuge")
)))
else
Nil) ::: (if (krakenExecuted)
List(
"Dustbin analysis" -> Future.successful(
ReportPage(List(),
List("Krona Plot" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
dustbinAnalysisReportValues)),
Map())))
else Nil),
List(
"Alignment" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
......@@ -385,18 +385,19 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
preprocessingReportValues)
) ++
(if (flexiprepExecuted)
List(
"QC reads" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",
flexiprepReadSummary),
"QC bases" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
flexiprepBaseSummary)
)
else Nil),
List(
"QC reads" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",
flexiprepReadSummary),
"QC bases" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
flexiprepBaseSummary)
)
else Nil),
args
)
}
}
/** Library page */
def libraryPage(sampleId: Int, libId: Int, args: Map[String, Any]): Future[ReportPage] = {
......@@ -517,4 +518,4 @@ 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