Commit 0da332ac authored by Peter van 't Hof's avatar Peter van 't Hof

Removed insertsize plot on single end from report

parent 61896d06
...@@ -126,6 +126,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S ...@@ -126,6 +126,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
"skip_metrics" -> skipMetrics, "skip_metrics" -> skipMetrics,
"skip_flexiprep" -> skipFlexiprep, "skip_flexiprep" -> skipFlexiprep,
"skip_markduplicates" -> skipMarkduplicates, "skip_markduplicates" -> skipMarkduplicates,
"paired" -> inputR2.isDefined,
"aligner" -> aligner, "aligner" -> aligner,
"chunking" -> chunking, "chunking" -> chunking,
"number_of_chunks" -> (if (chunking) numberChunks.getOrElse(1) else None) "number_of_chunks" -> (if (chunking) numberChunks.getOrElse(1) else None)
......
...@@ -49,6 +49,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder { ...@@ -49,6 +49,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
val wgsExecuted = summary.getSampleValues("bammetrics", "stats", "wgs").values.exists(_.isDefined) val wgsExecuted = summary.getSampleValues("bammetrics", "stats", "wgs").values.exists(_.isDefined)
val rnaExecuted = summary.getSampleValues("bammetrics", "stats", "rna").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 insertsizeExecuted = summary.getSampleValues("bammetrics", "stats", "CollectInsertSizeMetrics", "metrics").values.exists(_ != Some(None))
val pairedFound = summary.getLibraryValues("mapping", "settings", "paired").exists(_._2 == Some(true))
val flexiprepExecuted = summary.getLibraryValues("flexiprep") val flexiprepExecuted = summary.getLibraryValues("flexiprep")
.exists { case ((sample, lib), value) => value.isDefined } .exists { case ((sample, lib), value) => value.isDefined }
...@@ -71,7 +72,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder { ...@@ -71,7 +72,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
List("Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp", List("Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false) Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)
)) ++ )) ++
(if (insertsizeExecuted) List("Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp", (if (insertsizeExecuted && pairedFound) List("Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false))) Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)))
else Nil) ++ else Nil) ++
(if (wgsExecuted) List("Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp", (if (wgsExecuted) List("Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
......
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