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Commit 3427e4e1 authored by Peter van 't Hof's avatar Peter van 't Hof
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Code improvement

parent 800ad479
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Showing with 4 additions and 7 deletions
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @ 3427e4e1
......@@ -29,8 +29,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
val wgsExecuted = summary.getSampleValues("bammetrics", "stats", "wgs").values.exists(_.isDefined)
val rnaExecuted = summary.getSampleValues("bammetrics", "stats", "rna").values.exists(_.isDefined)
val flexiprepExecuted = summary.getLibraryValues("flexiprep")
.filter(_._2.isDefined)
.nonEmpty
.exists { case ((sample, lib), value) => value.isDefined }
ReportPage(
List("Samples" -> generateSamplesPage(pageArgs)) ++
......@@ -67,8 +66,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
/** Files page, can be used general or at sample level */
def filesPage: ReportPage = {
val flexiprepExecuted = summary.getLibraryValues("flexiprep")
.filter(_._2.isDefined)
.nonEmpty
.exists { case ((sample, lib), value) => value.isDefined }
ReportPage(List(), (if (flexiprepExecuted) List(
"Input fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp"),
......@@ -82,9 +80,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
/** Single sample page */
def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {
val flexiprepExecuted = summary.getLibraryValues("flexiprep")
.filter(_._1._1 == sampleId)
.filter(_._2.isDefined)
.nonEmpty
.exists { case ((sample, lib), value) => sample == sampleId && value.isDefined }
ReportPage(List(
"Libraries" -> generateLibraryPage(args),
......@@ -103,6 +99,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
/** Library page */
def libraryPage(sampleId: String, libId: String, args: Map[String, Any]): ReportPage = {
val flexiprepExecuted = summary.getValue(Some(sampleId), Some(libId), "flexiprep").isDefined
ReportPage(
("Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId))) ::
(if (flexiprepExecuted) List("QC" -> FlexiprepReport.flexiprepPage) else Nil),
......
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