Commit 9968c43a authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Style fixes

parent 012fc811
...@@ -79,10 +79,12 @@ object BammetricsReport extends ReportBuilder { ...@@ -79,10 +79,12 @@ object BammetricsReport extends ReportBuilder {
List( List(
"Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"), "Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
"Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp", Map("showPlot" -> true)) "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", ) ++ (if (wgsExecuted) List("Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
Map("showPlot" -> true))) else Nil) ++ Map("showPlot" -> true)))
( if (rnaExecuted) List("Rna coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp", else Nil) ++
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) Map("metricsTag" -> metricsTag)
) )
} }
...@@ -329,13 +331,13 @@ object BammetricsReport extends ReportBuilder { ...@@ -329,13 +331,13 @@ object BammetricsReport extends ReportBuilder {
} }
/** /**
* Generate a line plot for rna coverage * Generate a line plot for rna coverage
* @param outputDir OutputDir for the tsv and png file * @param outputDir OutputDir for the tsv and png file
* @param prefix Prefix of the tsv and png file * @param prefix Prefix of the tsv and png file
* @param summary Summary class * @param summary Summary class
* @param libraryLevel Default false, when set true plot will be based on library stats instead of sample stats * @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 * @param sampleId Default it selects all sampples, when sample is giving it limits to selected sample
*/ */
def rnaHistogramPlot(outputDir: File, def rnaHistogramPlot(outputDir: File,
prefix: String, prefix: String,
summary: Summary, summary: Summary,
......
...@@ -46,14 +46,16 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder { ...@@ -46,14 +46,16 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
"Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp", "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))) ++
(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",
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", (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", List("QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",
Map("showPlot" -> true, "showTable" -> false)), Map("showPlot" -> true, "showTable" -> false)),
"QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp", "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
Map("showPlot" -> true, "showTable" -> false)) Map("showPlot" -> true, "showTable" -> false))
), ),
pageArgs pageArgs
) )
} }
......
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