Commit a81bce67 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Moved config to utils

parent 10e09e28
......@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.utils.config.Configurable
class AnalyzeCovariates(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.AnalyzeCovariates with GatkGeneral {
}
......
......@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.utils.config.Configurable
class ApplyRecalibration(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.ApplyRecalibration with GatkGeneral {
scatterCount = config("scattercount", default = 0)
......
......@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.utils.config.Configurable
class BaseRecalibrator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.BaseRecalibrator with GatkGeneral {
if (config.contains("scattercount")) scatterCount = config("scattercount", default = 1)
......
......@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.utils.config.Configurable
class CombineGVCFs(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.CombineGVCFs with GatkGeneral {
if (config.contains("scattercount")) scatterCount = config("scattercount")
......
......@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.utils.config.Configurable
class CombineVariants(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.CombineVariants with GatkGeneral {
if (config.contains("scattercount")) scatterCount = config("scattercount")
......
......@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.utils.config.Configurable
class GenotypeGVCFs(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.GenotypeGVCFs with GatkGeneral {
annotation ++= config("annotation", default = Seq("FisherStrand", "QualByDepth", "ChromosomeCounts")).asStringList
......
......@@ -5,7 +5,7 @@
*/
package nl.lumc.sasc.biopet.extensions.gatk.broad
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType
class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.HaplotypeCaller with GatkGeneral {
......
......@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.utils.config.Configurable
class IndelRealigner(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.IndelRealigner with GatkGeneral {
if (config.contains("scattercount")) scatterCount = config("scattercount")
......
......@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.utils.config.Configurable
class PrintReads(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.PrintReads with GatkGeneral {
if (config.contains("scattercount")) scatterCount = config("scattercount")
......
......@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.utils.config.Configurable
class RealignerTargetCreator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.RealignerTargetCreator with GatkGeneral {
if (config.contains("scattercount")) scatterCount = config("scattercount")
......
......@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.utils.config.Configurable
class SelectVariants(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.SelectVariants with GatkGeneral {
if (config.contains("scattercount")) scatterCount = config("scattercount")
......
......@@ -5,7 +5,7 @@
*/
package nl.lumc.sasc.biopet.extensions.gatk.broad
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.utils.config.Configurable
class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.UnifiedGenotyper with GatkGeneral {
if (config.contains("scattercount")) scatterCount = config("scattercount")
......
......@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.utils.config.Configurable
class VariantAnnotator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantAnnotator with GatkGeneral {
if (config.contains("scattercount")) scatterCount = config("scattercount")
......
......@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.utils.config.Configurable
class VariantEval(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantEval with GatkGeneral {
override def beforeGraph() {
......
......@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
class VariantRecalibrator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantRecalibrator with GatkGeneral {
......
......@@ -6,7 +6,7 @@
package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.core.PipelineCommand
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.pipelines.basty.BastyTrait
import org.broadinstitute.gatk.queue.QScript
......
......@@ -5,7 +5,7 @@
*/
package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import org.broadinstitute.gatk.queue.QScript
......
......@@ -5,7 +5,7 @@
*/
package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.extensions.gatk.broad.{ GenotypeGVCFs, SelectVariants }
import org.broadinstitute.gatk.queue.QScript
......
......@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import htsjdk.samtools.SamReaderFactory
import nl.lumc.sasc.biopet.core.{ MultiSampleQScript, PipelineCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.gatk.broad.{ CombineGVCFs, CombineVariants }
import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, SamToFastq }
......
......@@ -6,7 +6,7 @@
package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.extensions.gatk.broad.{ ApplyRecalibration, VariantAnnotator, VariantRecalibrator }
import org.broadinstitute.gatk.queue.QScript
......
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