Commit 4b067c66 authored by akaljuvee's avatar akaljuvee

-

parent e60b100f
......@@ -48,6 +48,12 @@ trait ShivaReportTrait extends MultisampleMappingReportTrait {
case _ => false
}
def svCallingExecuted = summary.getSettingKeys(runId, "shiva", NoModule, keyValues = Map("sv_calling" -> List("sv_calling"))).get("sv_calling")
.flatten match {
case Some(true) => true
case _ => false
}
override def frontSection = ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp")
override def pipelineName = "shiva"
......@@ -107,9 +113,10 @@ trait ShivaReportTrait extends MultisampleMappingReportTrait {
/** Single sample page */
override def samplePage(sampleId: Int, args: Map[String, Any]): ReportPage = {
val variantcallingSection = if (variantcallingExecuted) List("Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp")) else Nil
val variantcallingSection = if (variantcallingExecuted) List("SNV Calling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp")) else Nil
val svSection = if (svCallingExecuted) List("SV Calling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariantsSv.ssp")) else Nil
val oldPage = super.samplePage(sampleId, args)
oldPage.copy(sections = variantcallingSection ++ oldPage.sections)
oldPage.copy(sections = variantcallingSection ++ svSection ++ oldPage.sections)
}
/** Name of the report */
......@@ -163,4 +170,10 @@ trait ShivaReportTrait extends MultisampleMappingReportTrait {
plot.width = Some(200 + (samples.count(s => sampleId.getOrElse(s) == s) * 10))
plot.runLocal()
}
def formatVcfFilePath(vcfFilePath: Option[Any]): Any = {
//val prefix = summary.getValue("meta", "output_dir").getOrElse("").toString
//vcfFilePath.collect { case a => "./" + a.toString.stripPrefix(prefix + File.separator) }
""
}
}
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