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Commit f069ee1e authored by Peter van 't Hof's avatar Peter van 't Hof
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Hide insertsize plot on single end runs

parent a5bf52fd
Hide whitespace changes
Inline Side-by-side
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @ f069ee1e
......@@ -61,6 +61,8 @@ object BammetricsReport extends ReportBuilder {
val wgsExecuted = summary.getValue(sampleId, libId, metricsTag, "stats", "wgs").isDefined
val rnaExecuted = summary.getValue(sampleId, libId, metricsTag, "stats", "rna").isDefined
val insertsizeMetrics = summary.getValue(sampleId, libId, metricsTag, "stats", "CollectInsertSizeMetrics", "metrics").isDefined
val targets = (
summary.getValue(sampleId, libId, metricsTag, "settings", "amplicon_name"),
summary.getValue(sampleId, libId, metricsTag, "settings", "roi_name")
......@@ -77,9 +79,9 @@ object BammetricsReport extends ReportBuilder {
targets.map(t => t -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp", Map("target" -> Some(t)))),
Map())),
List(
"Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
"Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp", Map("showPlot" -> true))
) ++ (if (wgsExecuted) List("Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
"Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp")) ++
(if (insertsizeMetrics) List("Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp", Map("showPlot" -> true))
) else Nil) ++ (if (wgsExecuted) List("Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
Map("showPlot" -> true)))
else Nil) ++
(if (rnaExecuted) List("Rna coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp",
......
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @ f069ee1e
......@@ -28,6 +28,7 @@ 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 insertsizeExecuted = summary.getSampleValues("bammetrics", "stats", "CollectInsertSizeMetrics", "metrics").values.exists(_.isDefined)
val flexiprepExecuted = summary.getLibraryValues("flexiprep")
.exists { case ((sample, lib), value) => value.isDefined }
......@@ -44,9 +45,9 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
"Report" -> frontSection,
"Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)
),
"Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false))) ++
)) ++
(if (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",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)))
else Nil) ++
......
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