Commit 9d27d507 authored by rhpvorderman's avatar rhpvorderman

Fix typo's

parent 9a7a81d7
......@@ -85,7 +85,6 @@
#for (field <- fields)
<td>${results(field)}</td>
#end
#end
</tr>
#end
#end
......
......@@ -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
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 {
)
}
}
}
......@@ -397,6 +397,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
args
)
}
}
/** Library page */
def libraryPage(sampleId: Int, libId: Int, args: Map[String, Any]): Future[ReportPage] = {
......@@ -517,4 +518,4 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
}
}
}
}
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