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Commit a4292fbc authored by Peter van 't Hof's avatar Peter van 't Hof
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Fixed path

parent 90b5c62d
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Showing with 3 additions and 3 deletions
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @ a4292fbc
......@@ -46,7 +46,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
def indexPage = {
val krakenExecuted = summary.getSampleValues("gearskraken", "stats", "krakenreport").values.forall(_.isDefined)
val centrifugeExecuted = summary.getSampleValues("gearskraken", "stats", "centrifuge_report").values.forall(_.isDefined)
val centrifugeExecuted = summary.getSampleValues("gearscentrifuge", "stats", "centrifuge_report").values.forall(_.isDefined)
val wgsExecuted = summary.getSampleValues("bammetrics", "stats", "wgs").values.exists(_.isDefined)
val rnaExecuted = summary.getSampleValues("bammetrics", "stats", "rna").values.exists(_.isDefined)
val insertsizeExecuted = summary.getSampleValues("bammetrics", "stats", "CollectInsertSizeMetrics", "metrics").values.exists(_ != Some(None))
......@@ -116,7 +116,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
/** Single sample page */
def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {
val krakenExecuted = summary.getValue(Some(sampleId), None, "gearskraken", "stats", "krakenreport").isDefined
val centrifugeExecuted = summary.getValue(Some(sampleId), None, "gearskraken", "stats", "centrifuge_report").isDefined
val centrifugeExecuted = summary.getValue(Some(sampleId), None, "gearscentrifuge", "stats", "centrifuge_report").isDefined
val flexiprepExecuted = summary.getLibraryValues("flexiprep")
.exists { case ((sample, lib), value) => sample == sampleId && value.isDefined }
......@@ -147,7 +147,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
/** Library page */
def libraryPage(sampleId: String, libId: String, args: Map[String, Any]): ReportPage = {
val krakenExecuted = summary.getValue(Some(sampleId), Some(libId), "gearskraken", "stats", "krakenreport").isDefined
val centrifugeExecuted = summary.getValue(Some(sampleId), Some(libId), "gearskraken", "stats", "centrifuge_report").isDefined
val centrifugeExecuted = summary.getValue(Some(sampleId), Some(libId), "gearscentrifuge", "stats", "centrifuge_report").isDefined
val flexiprepExecuted = summary.getValue(Some(sampleId), Some(libId), "flexiprep").isDefined
ReportPage(
......
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