GearsSingleReport.scala 1.83 KB
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/**
 * Biopet is built on top of GATK Queue for building bioinformatic
 * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
 * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
 * should also be able to execute Biopet tools and pipelines.
 *
 * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
 *
 * Contact us at: sasc@lumc.nl
 *
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 * A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
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 * license; For commercial users or users who do not want to follow the AGPL
 * license, please contact us to obtain a separate license.
 */
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package nl.lumc.sasc.biopet.pipelines.gears

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import nl.lumc.sasc.biopet.core.report._
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import nl.lumc.sasc.biopet.utils.config.Configurable
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class GearsSingleReport(val root: Configurable) extends ReportBuilderExtension {
  def builder = GearsSingleReport
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}

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object GearsSingleReport extends ReportBuilder {
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  // TODO: Add dustbin analysis (aggregated)
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  // TODO: Add alignment stats per sample for the dustbin analysis

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  override def extFiles = super.extFiles ++ List("js/gears.js", "js/krona-2.0.js", "img/krona/loading.gif", "img/krona/hidden.png", "img/krona/favicon.ico")
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    .map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
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  def indexPage = {
    ReportPage(
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      List(
        "Versions" -> ReportPage(List(), List((
          "Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
          ))), Map())
      ),
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      List(
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        "Gears intro" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSingleFront.ssp"),
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        "Kraken analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp")
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      ),
      pageArgs
    )
  }

  def reportName = "Gears :: Metagenomics Report"

}