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Commit a81bce67 authored by Peter van 't Hof's avatar Peter van 't Hof
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Moved config to utils

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