diff --git a/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala b/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala index b9dc7718a722b30d46d91bd1e376bcc438dc51fe..d1e8a51d380ef1369bff4a6aaeb2a0f44a2dcdec 100644 --- a/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala +++ b/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala @@ -75,15 +75,15 @@ object BammetricsReport extends ReportBuilder { libId: Option[Int], metricsTag: String = "bammetrics"): Map[String, Any] = { val wgsExecuted = summary.getStatsSize(runId, - metricsTag, - "wgs", - sample = sampleId.map(SampleId), - library = libId.map(LibraryId)) >= 1 + metricsTag, + "wgs", + sample = sampleId.map(SampleId), + library = libId.map(LibraryId)) >= 1 val rnaExecuted = summary.getStatsSize(runId, - metricsTag, - "rna", - sample = sampleId.map(SampleId), - library = libId.map(LibraryId)) >= 1 + metricsTag, + "rna", + sample = sampleId.map(SampleId), + library = libId.map(LibraryId)) >= 1 val insertsizeMetrics = summary .getStatKeys( @@ -113,9 +113,11 @@ object BammetricsReport extends ReportBuilder { case _ => Nil } - val covstatsPlotValuesArray = ArrayBuffer[(String, Map[String,Any])]() + val covstatsPlotValuesArray = ArrayBuffer[(String, Map[String, Any])]() 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 @@ -143,7 +145,7 @@ object BammetricsReport extends ReportBuilder { libraries, sampleId, libId, - showPlot= true + showPlot = true ) val insertSizeReportValues = BammetricsReportPage.insertSizeValues( summary, @@ -152,15 +154,28 @@ object BammetricsReport extends ReportBuilder { libraries, sampleId, libId, - showPlot= true + showPlot = true ) val wgsHistogramReportValues = BammetricsReportPage.wgsHistogramValues( - summary,runId, samples, libraries, sampleId, libId, showPlot = true + summary, + runId, + samples, + libraries, + sampleId, + libId, + showPlot = true ) val rnaHistogramReportValues = BammetricsReportPage.rnaHistogramValues( - summary,runId, samples, libraries, sampleId, libId, showPlot = true + summary, + runId, + samples, + libraries, + sampleId, + libId, + showPlot = true ) - Map("wgsExecuted" -> wgsExecuted, + Map( + "wgsExecuted" -> wgsExecuted, "rnaExecuted" -> rnaExecuted, "insertsizeMetrics" -> insertsizeMetrics, "targetSettings" -> targetSettings, @@ -181,15 +196,15 @@ object BammetricsReport extends ReportBuilder { metricsTag: String = "bammetrics"): Future[ReportPage] = { val wgsExecuted: Boolean = summary.getStatsSize(runId, - metricsTag, - "wgs", - sample = sampleId.map(SampleId), - library = libId.map(LibraryId)) >= 1 + metricsTag, + "wgs", + sample = sampleId.map(SampleId), + library = libId.map(LibraryId)) >= 1 val rnaExecuted: Boolean = summary.getStatsSize(runId, - metricsTag, - "rna", - sample = sampleId.map(SampleId), - library = libId.map(LibraryId)) >= 1 + metricsTag, + "rna", + sample = sampleId.map(SampleId), + library = libId.map(LibraryId)) >= 1 val insertsizeMetrics: Boolean = summary .getStatKeys( @@ -219,21 +234,33 @@ object BammetricsReport extends ReportBuilder { case _ => Nil } - val covstatsPlotValuesArray = ArrayBuffer[(String, Map[String,Any])]() - for (t <- targets) { - covstatsPlotValuesArray += Tuple2(t,BammetricsReportPage.covstatsPlotValues(summary, runId, sampleId, libId, Some(t))) - } + val covstatsPlotValuesArray = ArrayBuffer[(String, Map[String, Any])]() + for (t <- targets) { + covstatsPlotValuesArray += Tuple2( + t, + BammetricsReportPage.covstatsPlotValues(summary, runId, sampleId, libId, Some(t))) + } val covstatsPlotValuesList: List[(String, Map[String, Any])] = covstatsPlotValuesArray.toList - val alignmentSummaryReportValues: Map[String, Any] = BammetricsReportPage.alignmentSummaryValues( + val alignmentSummaryReportValues: Map[String, Any] = + BammetricsReportPage.alignmentSummaryValues( + summary, + runId, + samples, + libraries, + sampleId, + libId + ) + val mappingQualityReportValues: Map[String, Any] = BammetricsReportPage.mappingQualityValues( summary, runId, samples, libraries, sampleId, - libId + libId, + showPlot = true ) - val mappingQualityReportValues: Map[String, Any] = BammetricsReportPage.mappingQualityValues( + val clippingReportValues: Map[String, Any] = BammetricsReportPage.clippingValues( summary, runId, samples, @@ -242,50 +269,55 @@ object BammetricsReport extends ReportBuilder { libId, showPlot = true ) - val clippingReportValues: Map[String, Any] = BammetricsReportPage.clippingValues( + val insertSizeReportValues: Map[String, Any] = BammetricsReportPage.insertSizeValues( summary, runId, samples, libraries, sampleId, libId, - showPlot= true + showPlot = true ) - val insertSizeReportValues: Map[String, Any] = BammetricsReportPage.insertSizeValues( + val wgsHistogramReportValues: Map[String, Any] = BammetricsReportPage.wgsHistogramValues( summary, runId, samples, libraries, sampleId, libId, - showPlot= true - ) - val wgsHistogramReportValues: Map[String, Any] = BammetricsReportPage.wgsHistogramValues( - summary,runId, samples, libraries, sampleId, libId, showPlot = true + showPlot = true ) val rnaHistogramReportValues: Map[String, Any] = BammetricsReportPage.rnaHistogramValues( - summary,runId, samples, libraries, sampleId, libId, showPlot = true + summary, + runId, + samples, + libraries, + sampleId, + libId, + showPlot = true ) Future { ReportPage( if (targets.isEmpty) List() else List( - "Targets" -> Future.successful( - ReportPage( - List(), - covstatsPlotValuesList.map(covstats => - covstats._1 -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp", - covstats._2)), - Map()))), + "Targets" -> Future.successful(ReportPage( + List(), + covstatsPlotValuesList.map(covstats => + covstats._1 -> ReportSection( + "/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp", + covstats._2)), + Map() + ))), List( "Summary" -> ReportSection( - "/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",alignmentSummaryReportValues), + "/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp", + alignmentSummaryReportValues), "Mapping Quality" -> ReportSection( "/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp", mappingQualityReportValues), "Clipping" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp", - clippingReportValues) + clippingReportValues) ) ++ (if (insertsizeMetrics) List( diff --git a/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReportPage.scala b/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReportPage.scala index 1e2559314cf88e2b45d1678329d3fd1c5ff14a95..ac88ff483d9c9c122392075855b8d81a3a3b3c9d 100644 --- a/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReportPage.scala +++ b/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReportPage.scala @@ -271,8 +271,6 @@ object BammetricsReportPage { sampleId.map(SampleId).get, libId.map(LibraryId).getOrElse(NoLibrary), statsPaths) - Map("plotFile" -> plotFile, "values" -> values, - "target" -> target, - "metricsTag" -> metricsTag) + Map("plotFile" -> plotFile, "values" -> values, "target" -> target, "metricsTag" -> metricsTag) } }