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 {
/** 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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