Commit 16f4925a authored by Peter van 't Hof's avatar Peter van 't Hof

Added bammetrics report to pipeline

parent 95de5080
......@@ -56,6 +56,17 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
def summarySettings = Map("amplicon_name" -> ampliconBedFile.collect { case x => x.getName.stripSuffix(".bed") },
"roi_name" -> roiBedFiles.map(_.getName.stripSuffix(".bed")))
override def reportClass = {
val bammetricsReport = new BammetricsReport(this)
bammetricsReport.outputDir = new File(outputDir, "report")
bammetricsReport.summaryFile = summaryFile
bammetricsReport.args = if (libId.isDefined) Map(
"sampleId" -> sampleId.getOrElse("."),
"libId" -> libId.getOrElse("."))
else Map("sampleId" -> sampleId.getOrElse("."))
Some(bammetricsReport)
}
/** executed before script */
def init() {
}
......
......@@ -2,11 +2,14 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics
import java.io.{ PrintWriter, File }
import nl.lumc.sasc.biopet.core.report.{ ReportBuilder, ReportPage, ReportSection }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.report.{ReportBuilderExtension, ReportBuilder, ReportPage, ReportSection}
import nl.lumc.sasc.biopet.core.summary.{ SummaryValue, Summary }
import nl.lumc.sasc.biopet.extensions.rscript.{ XYPlot, StackedBarPlot }
//TODO: Add basic report to BamMetrics as single pipeline
class BammetricsReport(val root: Configurable) extends ReportBuilderExtension {
val builder = BammetricsReport
}
/**
* Created by pjvan_thof on 3/30/15.
......@@ -54,7 +57,8 @@ object BammetricsReport extends ReportBuilder {
Map()))),
List(
"Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
"Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp", Map("showPlot" -> true))
"Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp", Map("showPlot" -> true)),
"Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp", Map("showPlot" -> true))
),
Map("metricsTag" -> metricsTag)
)
......
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