MappingReport.scala 1.55 KB
Newer Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
package nl.lumc.sasc.biopet.pipelines.mapping

import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportSection, ReportPage, ReportBuilder }
import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport

class MappingReport(val root: Configurable) extends ReportBuilderExtension {
  val builder = MappingReport
}

/**
 * Created by pjvanthof on 24/06/15.
 */
object MappingReport extends ReportBuilder {
  /** Name of report */
  val reportName = "Mapping Report"

  /** 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(
      "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp")
    ) ::: bamMetricsPage.sections,
      Map()
    )
  }
}