Commit 56766d98 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Change gentrap report to multisample mapping report

parent be731b74
......@@ -15,10 +15,9 @@
*/
package nl.lumc.sasc.biopet.pipelines.gentrap
import nl.lumc.sasc.biopet.core.report.{ReportBuilderExtension, ReportSection}
import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingReportTrait
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportSection, ReportPage, MultisampleReportBuilder }
import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
/**
* Class to generate report for [[Gentrap]]
......@@ -29,68 +28,9 @@ class GentrapReport(val root: Configurable) extends ReportBuilderExtension {
def builder = GentrapReport
}
object GentrapReport extends MultisampleReportBuilder {
object GentrapReport extends MultisampleMappingReportTrait {
/** Root page for the carp report */
def indexPage = {
//Source.fromInputStream(getClass.getResourceAsStream("/nl/lumc/sasc/biopet/pipelines/carp/carpFont.ssp")).foreach(print(_))
ReportPage(
List("Samples" -> generateSamplesPage(pageArgs)) ++
Map("Files" -> filesPage,
"Versions" -> ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
)), Map())
),
List(
"Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gentrap/gentrapFront.ssp"),
"Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)
),
"Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)),
"QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",
Map("showPlot" -> true, "showTable" -> false)),
"QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
Map("showPlot" -> true, "showTable" -> false))
),
pageArgs
)
}
/** Files page, can be used general or at sample level */
def filesPage: ReportPage = 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)) //,
//"Preprocessed bam files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp",
// Map("pipelineName" -> "shiva", "fileTag" -> "preProcessBam"))
), Map())
/** Single sample page */
def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {
ReportPage(List(
"Libraries" -> generateLibraryPage(args),
"Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), None),
"Files" -> filesPage
), List(
"Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
if (summary.libraries(sampleId).size > 1) Map("showPlot" -> true) else Map()),
"Preprocessing" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp", Map("sampleLevel" -> true)),
"QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
"QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
), args)
}
/** Library page */
def libraryPage(sampleId: String, libId: String, args: Map[String, Any]): ReportPage = {
ReportPage(List(
"Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId)),
"QC" -> FlexiprepReport.flexiprepPage
), List(
"Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
"QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
"QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
), args)
}
override def frontSection = ReportSection("/nl/lumc/sasc/biopet/pipelines/gentrap/gentrapFront.ssp")
/** Name of the report */
def reportName = "Gentrap Report"
......
......@@ -15,15 +15,13 @@
*/
package nl.lumc.sasc.biopet.pipelines.shiva
import java.io.{ File, PrintWriter }
import java.io.{File, PrintWriter}
import nl.lumc.sasc.biopet.core.report._
import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingReportTrait
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.report._
import nl.lumc.sasc.biopet.utils.summary.{ Summary, SummaryValue }
import nl.lumc.sasc.biopet.utils.rscript.StackedBarPlot
import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
import nl.lumc.sasc.biopet.utils.summary.{Summary, SummaryValue}
/**
* With this extension the report is executed within a pipeline
......
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