Commit d030c0bf authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

adding carp report to the pipeline

parent d091609d
......@@ -40,7 +40,10 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
def this() = this(null)
override def defaults = ConfigUtils.mergeMaps(Map(
"mapping" -> Map("skip_markduplicates" -> true, "aligner" -> "bwa-mem")
"mapping" -> Map(
"skip_markduplicates" -> true,
"aligner" -> "bwa-mem"
)
), super.defaults)
def summaryFile = new File(outputDir, "Carp.summary.json")
......@@ -117,6 +120,13 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
}
}
override def reportClass = {
val carp = new CarpReport(this)
carp.outputDir = new File(outputDir, "report")
carp.summaryFile = summaryFile
Some(carp)
}
def init() = {
// ensure that no samples are called 'control' since that is our reserved keyword
require(!sampleIds.contains("control"),
......
package nl.lumc.sasc.biopet.pipelines.carp
import nl.lumc.sasc.biopet.core.report.{ ReportSection, ReportPage, MultisampleReportBuilder }
import nl.lumc.sasc.biopet.core.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
import scala.io.Source
/**
* Created by pjvanthof on 25/06/15.
*/
class CarpReport {
class CarpReport(val root: Configurable) extends ReportBuilderExtension {
val builder = CarpReport
}
object CarpReport extends MultisampleReportBuilder {
......
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