Commit c34233e0 authored by Peter van 't Hof's avatar Peter van 't Hof

Add config

parent 16ad72ab
......@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.core.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.summary.WriteSummary
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.function.InProcessFunction
import org.broadinstitute.gatk.utils.commandline.{Argument, Input}
......@@ -25,7 +26,7 @@ import org.broadinstitute.gatk.utils.commandline.{Argument, Input}
*
* Created by pjvanthof on 16/08/15.
*/
class CheckChecksum extends InProcessFunction {
class CheckChecksum(val parent: Configurable) extends InProcessFunction with Configurable {
@Input(required = true)
var inputFile: File = _
......
......@@ -208,7 +208,7 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
inputFile.md5 match {
case Some(checksum) =>
if (!SummaryQScript.checkChecksumCache.contains(inputFile.file)) {
val checkMd5 = new CheckChecksum
val checkMd5 = new CheckChecksum(this)
checkMd5.inputFile = inputFile.file
if (!SummaryQScript.md5sumCache.contains(inputFile.file))
addChecksum(inputFile.file)
......
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