Commit e07267db authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Skipping parts of report when they are skipped in the pipeline

parent 0ae99234
...@@ -35,18 +35,22 @@ object MappingReport extends ReportBuilder { ...@@ -35,18 +35,22 @@ object MappingReport extends ReportBuilder {
/** Root page for single BamMetrcis report */ /** Root page for single BamMetrcis report */
def indexPage = { def indexPage = {
val bamMetricsPage = BammetricsReport.bamMetricsPage(summary, sampleId, libId) val skipFlexiprep = summary.getValue(sampleId, libId, "mapping", "settings", "skip_flexiprep").getOrElse(false) == true
ReportPage(List("QC" -> FlexiprepReport.flexiprepPage) ::: bamMetricsPage.subPages ::: List( val bamMetricsPage = if (summary.getValue(sampleId, libId, "mapping", "settings", "skip_metrics").getOrElse(false) == true) {
"Versions" -> ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp" Some(BammetricsReport.bamMetricsPage(summary, sampleId, libId))
)), Map()), } else None
"Files" -> ReportPage(List(), List( ReportPage((if (skipFlexiprep) Nil else List("QC" -> FlexiprepReport.flexiprepPage)) :::
"Input fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp"), bamMetricsPage.map(_.subPages).getOrElse(Nil) ::: List(
"After QC fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp"), "Versions" -> ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
"Bam files per lib" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp", Map("sampleLevel" -> false)) )), Map()),
), Map()) "Files" -> ReportPage(List(), (if (skipFlexiprep) Nil else 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"))) :::
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") "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp")
) ::: bamMetricsPage.sections, ) ::: bamMetricsPage.map(_.sections).getOrElse(Nil),
Map() Map()
) )
} }
......
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