Commit 16ad72ab authored by Peter van 't Hof's avatar Peter van 't Hof

Adding config to CheckValidateFastq

parent 63249826
......@@ -16,9 +16,9 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
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}
import org.broadinstitute.gatk.utils.commandline.Input
import scala.io.Source
......@@ -27,7 +27,7 @@ import scala.io.Source
*
* Created by pjvanthof on 16/08/15.
*/
class CheckValidateFastq extends InProcessFunction {
class CheckValidateFastq(val parent: Configurable) extends InProcessFunction with Configurable {
@Input(required = true)
var inputLogFile: File = _
......
......@@ -132,7 +132,7 @@ class Flexiprep(val parent: Configurable)
add(validateFastq)
if (config("abort_on_corrupt_fastq", default = true)) {
val checkValidateFastq = new CheckValidateFastq
val checkValidateFastq = new CheckValidateFastq(this)
checkValidateFastq.inputLogFile = validateFastq.jobOutputFile
checkValidateFastq.jobOutputFile = new File(outputDir, ".check.validate_fastq.log.out")
add(checkValidateFastq)
......@@ -309,7 +309,7 @@ class Flexiprep(val parent: Configurable)
add(validateFastq)
if (config("abort_on_corrupt_fastq", default = true)) {
val checkValidateFastq = new CheckValidateFastq
val checkValidateFastq = new CheckValidateFastq(this)
checkValidateFastq.inputLogFile = validateFastq.jobOutputFile
checkValidateFastq.jobOutputFile = new File(outputDir, ".check.validate_fastq.qc.log.out")
add(checkValidateFastq)
......
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