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Commit 3a302742 authored by Peter van 't Hof's avatar Peter van 't Hof
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fixing report

parent 2d3a083a
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mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @ 3a302742
......@@ -49,7 +49,8 @@ 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 insertsizeExecuted = summary.getSampleValues("bammetrics", "stats", "CollectInsertSizeMetrics", "metrics").values.exists(_ != Some(None))
val pairedFound = summary.getLibraryValues("mapping", "settings", "paired").exists(_._2 == Some(true))
val mappingExecuted = summary.getLibraryValues("mapping").nonEmpty
val pairedFound = !mappingExecuted || summary.getLibraryValues("mapping", "settings", "paired").exists(_._2 == Some(true))
val flexiprepExecuted = summary.getLibraryValues("flexiprep")
.exists { case ((sample, lib), value) => value.isDefined }
......@@ -72,7 +73,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
List("Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)
)) ++
(if (insertsizeExecuted && pairedFound) List("Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
(if (pairedFound) List("Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)))
else Nil) ++
(if (wgsExecuted) List("Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
......
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