Commit 189a25d4 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added html report to pipeline

parent 759b7f36
......@@ -19,6 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.FullVersion
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import nl.lumc.sasc.biopet.extensions.picard.{ MergeSamFiles, SortSam }
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
import nl.lumc.sasc.biopet.extensions.tools.{ MergeTables, WipeReads }
......@@ -53,6 +54,13 @@ class Gentrap(val root: Configurable) extends QScript
// alternative constructor for initialization with empty configuration
def this() = this(null)
override def reportClass: Option[ReportBuilderExtension] = {
val report = new GentrapReport(this)
report.outputDir = new File(outputDir, "report")
report.summaryFile = summaryFile
Some(report)
}
/** Split aligner to use */
var aligner: String = config("aligner", default = "gsnap")
......
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