diff --git a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala index 35d363952be53d1a2159a7e16500f749be07fc08..10cecfb2d8c54ff18c78fc74385993bcf17312d7 100644 --- a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala +++ b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala @@ -79,10 +79,12 @@ object BammetricsReport extends ReportBuilder { 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", - Map("showPlot" -> true))) else Nil) ++ - ( if (rnaExecuted) List("Rna coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.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", + Map("showPlot" -> true))) + else Nil), Map("metricsTag" -> metricsTag) ) } @@ -329,13 +331,13 @@ object BammetricsReport extends ReportBuilder { } /** - * Generate a line plot for rna coverage - * @param outputDir OutputDir for the tsv and png file - * @param prefix Prefix of the tsv and png file - * @param summary Summary class - * @param libraryLevel Default false, when set true plot will be based on library stats instead of sample stats - * @param sampleId Default it selects all sampples, when sample is giving it limits to selected sample - */ + * Generate a line plot for rna coverage + * @param outputDir OutputDir for the tsv and png file + * @param prefix Prefix of the tsv and png file + * @param summary Summary class + * @param libraryLevel Default false, when set true plot will be based on library stats instead of sample stats + * @param sampleId Default it selects all sampples, when sample is giving it limits to selected sample + */ def rnaHistogramPlot(outputDir: File, prefix: String, summary: Summary, diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala index 330b73fd61a9b1e004e7c67bce5687b81e296815..30e4e3e3433838cc0e07af1e54c91dca0e796b8f 100644 --- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala +++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala @@ -46,14 +46,16 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder { "Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp", Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false))) ++ (if (wgsExecuted) List("Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp", - Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false))) else Nil) ++ + Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false))) + else Nil) ++ (if (rnaExecuted) List("Rna coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp", - Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false))) else Nil) ++ + Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false))) + else Nil) ++ List("QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp", Map("showPlot" -> true, "showTable" -> false)), - "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp", - Map("showPlot" -> true, "showTable" -> false)) - ), + "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp", + Map("showPlot" -> true, "showTable" -> false)) + ), pageArgs ) }