Commit b230161f authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Merge remote-tracking branch 'origin/develop' into feature-pipeable

Conflicts:
	public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
	public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
	public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
	public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
parents 1b160347 d1b4060c
......@@ -25,7 +25,7 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetFramework</artifactId>
<artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
......
......@@ -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 {
......
......@@ -25,7 +25,7 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetFramework</artifactId>
<artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
......
......@@ -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
......
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