ShivaReport.scala 1010 Bytes
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package nl.lumc.sasc.biopet.pipelines.shiva

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import nl.lumc.sasc.biopet.core.report.{ReportSection, MultisampleReportBuilder, ReportPage}
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import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport

/**
 * Created by pjvan_thof on 3/30/15.
 */
object ShivaReport extends MultisampleReportBuilder {
  def samplePage(sampleId: String, args: Map[String, Any]) = {
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    ReportPage(Map("Libraries" -> generateLibraryPage(args)), List(
      "Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/core/report/ShivaVariantcalling.ssp")
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    ), args)
  }

  def libraryPage(libId: String, args: Map[String, Any]) = {
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    ReportPage(Map("Flexiprep" -> FlexiprepReport.indexPage), List(), args)
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  }

  def reportName = "Title Test"

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  def generalPage = ReportPage(Map(), List(
    "Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/core/report/ShivaVariantcalling.ssp"),
    "Flexiprep" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepSummary.ssp")
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  ), Map())

  // FIXME: Not yet finished
}