From e07267db2d69860c2c24e4e3f2abfe8f071b3d89 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sat, 15 Aug 2015 21:46:46 +0200
Subject: [PATCH] Skipping parts of report when they are skipped in the
pipeline
---
.../pipelines/mapping/MappingReport.scala | 26 +++++++++++--------
1 file changed, 15 insertions(+), 11 deletions(-)
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
index c855736f7..980802aeb 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
@@ -35,18 +35,22 @@ object MappingReport extends ReportBuilder {
/** Root page for single BamMetrcis report */
def indexPage = {
- val bamMetricsPage = BammetricsReport.bamMetricsPage(summary, sampleId, libId)
- ReportPage(List("QC" -> FlexiprepReport.flexiprepPage) ::: bamMetricsPage.subPages ::: List(
- "Versions" -> ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
- )), Map()),
- "Files" -> ReportPage(List(), List(
- "Input fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp"),
- "After QC fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp"),
- "Bam files per lib" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp", Map("sampleLevel" -> false))
- ), Map())
- ), List(
+ val skipFlexiprep = summary.getValue(sampleId, libId, "mapping", "settings", "skip_flexiprep").getOrElse(false) == true
+ val bamMetricsPage = if (summary.getValue(sampleId, libId, "mapping", "settings", "skip_metrics").getOrElse(false) == true) {
+ Some(BammetricsReport.bamMetricsPage(summary, sampleId, libId))
+ } else None
+ ReportPage((if (skipFlexiprep) Nil else List("QC" -> FlexiprepReport.flexiprepPage)) :::
+ bamMetricsPage.map(_.subPages).getOrElse(Nil) ::: List(
+ "Versions" -> ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
+ )), Map()),
+ "Files" -> ReportPage(List(), (if (skipFlexiprep) Nil else List(
+ "Input fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp"),
+ "After QC fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp"))) :::
+ List("Bam files per lib" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp", Map("sampleLevel" -> false))
+ ), Map())
+ ), List(
"Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp")
- ) ::: bamMetricsPage.sections,
+ ) ::: bamMetricsPage.map(_.sections).getOrElse(Nil),
Map()
)
}
--
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