Commit 2fe05703 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Add summary to toucan

parent 3584a778
......@@ -16,6 +16,7 @@
package nl.lumc.sasc.biopet.pipelines.toucan
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand, Reference }
import nl.lumc.sasc.biopet.extensions.VariantEffectPredictor
import nl.lumc.sasc.biopet.tools.VepNormalizer
......@@ -27,7 +28,7 @@ import org.broadinstitute.gatk.queue.QScript
*
* Created by ahbbollen on 15-1-15.
*/
class Toucan(val root: Configurable) extends QScript with BiopetQScript with Reference {
class Toucan(val root: Configurable) extends QScript with BiopetQScript with SummaryQScript with Reference {
def this() = this(null)
@Input(doc = "Input VCF file", shortName = "Input", required = true)
......@@ -56,6 +57,11 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Ref
add(normalizer)
}
def summaryFile = new File(outputDir, "Toucan.summary.json")
def summaryFiles = Map()
def summarySettings = Map()
}
object Toucan extends PipelineCommand
\ No newline at end of file
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