Commit 58c2b606 authored by rhpvorderman's avatar rhpvorderman

Defutured Bammetricsreport

parent e5b7192d
...@@ -126,10 +126,49 @@ object BammetricsReport extends ReportBuilder { ...@@ -126,10 +126,49 @@ object BammetricsReport extends ReportBuilder {
for (t <- targets) { for (t <- targets) {
covstatsPlotValuesArray += Tuple2(t,BammetricsReportPage.covstatsPlotValues(summary, runId, sampleId, libId, Some(t))) covstatsPlotValuesArray += Tuple2(t,BammetricsReportPage.covstatsPlotValues(summary, runId, sampleId, libId, Some(t)))
} }
val covstatsPlotValuesList = covstatsPlotValuesArray.toList val covstatsPlotValuesList = covstatsPlotValuesArray.toList
val alignmentSummaryReportValues = BammetricsReportPage.alignmentSummaryValues(
summary,
runId,
samples,
libraries,
sampleId,
libId
)
val mappingQualityReportValues = BammetricsReportPage.mappingQualityValues(
summary,
runId,
samples,
libraries,
sampleId,
libId,
showPlot = true
)
val clippingReportValues = BammetricsReportPage.clippingValues(
summary,
runId,
samples,
libraries,
sampleId,
libId,
showPlot= true
)
val insertSizeReportValues = BammetricsReportPage.insertSizeValues(
summary,
runId,
samples,
libraries,
sampleId,
libId,
showPlot= true
)
val wgsHistogramReportValues = BammetricsReportPage.wgsHistogramValues(
summary,runId, samples, libraries, sampleId, libId, showPlot = true
)
val rnaHistogramReportValues = BammetricsReportPage.rnaHistogramValues(
summary,runId, samples, libraries, sampleId, libId, showPlot = true
)
Future { Future {
ReportPage( ReportPage(
if (targets.isEmpty) List() if (targets.isEmpty) List()
...@@ -144,29 +183,29 @@ object BammetricsReport extends ReportBuilder { ...@@ -144,29 +183,29 @@ object BammetricsReport extends ReportBuilder {
Map()))), Map()))),
List( List(
"Summary" -> ReportSection( "Summary" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"), "/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",alignmentSummaryReportValues),
"Mapping Quality" -> ReportSection( "Mapping Quality" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp", "/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp",
Map("showPlot" -> true)), mappingQualityReportValues),
"Clipping" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp", "Clipping" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp",
Map("showPlot" -> true)) clippingReportValues)
) ++ ) ++
(if (insertsizeMetrics) (if (insertsizeMetrics)
List( List(
"Insert Size" -> ReportSection( "Insert Size" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp", "/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
Map("showPlot" -> true))) insertSizeReportValues))
else Nil) ++ (if (wgsExecuted) else Nil) ++ (if (wgsExecuted)
List( List(
"Whole genome coverage" -> ReportSection( "Whole genome coverage" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp", "/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
Map("showPlot" -> true))) wgsHistogramReportValues))
else Nil) ++ else Nil) ++
(if (rnaExecuted) (if (rnaExecuted)
List( List(
"Rna coverage" -> ReportSection( "Rna coverage" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp", "/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp",
Map("showPlot" -> true))) rnaHistogramReportValues))
else Nil), else Nil),
Map("metricsTag" -> metricsTag) Map("metricsTag" -> metricsTag)
) )
......
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