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Commit 51c319f2 authored by Peter van 't Hof's avatar Peter van 't Hof
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Added clipping and mapping quality to multisamplemappingreport

parent 48d6de67
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mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @ 51c319f2
......@@ -72,8 +72,12 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
additionalSections ++
List("Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)
),"Mapping Quality" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)
),"Clipping" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)
)) ++
(if (pairedFound) List("Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
(if (pairedFound && insertsizeExecuted) 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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