From 9968c43a3db56ce40ae8f52fa03e28271ed59931 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 12 Jan 2016 15:32:01 +0100
Subject: [PATCH] Style fixes
---
.../bammetrics/BammetricsReport.scala | 24 ++++++++++---------
.../mapping/MultisampleMappingReport.scala | 12 ++++++----
2 files changed, 20 insertions(+), 16 deletions(-)
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 35d363952..10cecfb2d 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 330b73fd6..30e4e3e34 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
)
}
--
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