Commit 2c840f96 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Merge remote-tracking branch 'remotes/origin/develop' into fix-BIOPET-746

parents 04434f88 08851b43
...@@ -17,8 +17,9 @@ package nl.lumc.sasc.biopet.extensions.gatk ...@@ -17,8 +17,9 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{GATKScatterFunction, LocusScatterFunction}
import nl.lumc.sasc.biopet.utils.config.Configurable import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ } import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Output, _}
class AnalyzeCovariates(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction { class AnalyzeCovariates(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "AnalyzeCovariates" def analysis_type = "AnalyzeCovariates"
......
...@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk ...@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.extensions.gatk.gather.GatherVcfs
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{GATKScatterFunction, LocusScatterFunction}
import nl.lumc.sasc.biopet.utils.VcfUtils import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.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
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Input, Output } import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Input, Output}
class ApplyRecalibration(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction { class ApplyRecalibration(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "ApplyRecalibration" def analysis_type = "ApplyRecalibration"
...@@ -41,7 +43,7 @@ class ApplyRecalibration(val parent: Configurable) extends CommandLineGATK with ...@@ -41,7 +43,7 @@ class ApplyRecalibration(val parent: Configurable) extends CommandLineGATK with
/** The output filtered and recalibrated VCF file in which each variant is annotated with its VQSLOD value */ /** The output filtered and recalibrated VCF file in which each variant is annotated with its VQSLOD value */
@Output(fullName = "out", shortName = "o", doc = "The output filtered and recalibrated VCF file in which each variant is annotated with its VQSLOD value", required = false, exclusiveOf = "", validation = "") @Output(fullName = "out", shortName = "o", doc = "The output filtered and recalibrated VCF file in which each variant is annotated with its VQSLOD value", required = false, exclusiveOf = "", validation = "")
@Gather(classOf[CatVariantsGatherer]) @Gather(classOf[GatherVcfs])
var out: File = _ var out: File = _
/** The truth sensitivity level at which to start filtering */ /** The truth sensitivity level at which to start filtering */
......
...@@ -17,10 +17,11 @@ package nl.lumc.sasc.biopet.extensions.gatk ...@@ -17,10 +17,11 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{ContigScatterFunction, GATKScatterFunction}
import nl.lumc.sasc.biopet.utils.VcfUtils import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.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
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, Input } import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Input, Output}
class BaseRecalibrator(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction { class BaseRecalibrator(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "BaseRecalibrator" def analysis_type = "BaseRecalibrator"
......
...@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk ...@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.extensions.gatk.gather.GatherVcfs
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{GATKScatterFunction, LocusScatterFunction}
import nl.lumc.sasc.biopet.utils.VcfUtils import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.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
import org.broadinstitute.gatk.utils.commandline.{ Gather, Input, Output, _ } import org.broadinstitute.gatk.utils.commandline.{Gather, Input, Output, _}
class CombineGVCFs(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction { class CombineGVCFs(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "CombineGVCFs" def analysis_type = "CombineGVCFs"
...@@ -45,7 +47,7 @@ class CombineGVCFs(val parent: Configurable) extends CommandLineGATK with Scatte ...@@ -45,7 +47,7 @@ class CombineGVCFs(val parent: Configurable) extends CommandLineGATK with Scatte
/** File to which the combined gVCF should be written */ /** File to which the combined gVCF should be written */
@Output(fullName = "out", shortName = "o", doc = "File to which the combined gVCF should be written", required = false, exclusiveOf = "", validation = "") @Output(fullName = "out", shortName = "o", doc = "File to which the combined gVCF should be written", required = false, exclusiveOf = "", validation = "")
@Gather(classOf[CatVariantsGatherer]) @Gather(classOf[GatherVcfs])
var out: File = _ var out: File = _
/** If specified, convert banded gVCFs to all-sites gVCFs */ /** If specified, convert banded gVCFs to all-sites gVCFs */
......
...@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk ...@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.extensions.gatk.gather.GatherVcfs
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{GATKScatterFunction, LocusScatterFunction}
import nl.lumc.sasc.biopet.utils.VcfUtils import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.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
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ } import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Output, _}
class CombineVariants(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction { class CombineVariants(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "CombineVariants" def analysis_type = "CombineVariants"
...@@ -33,7 +35,7 @@ class CombineVariants(val parent: Configurable) extends CommandLineGATK with Sca ...@@ -33,7 +35,7 @@ class CombineVariants(val parent: Configurable) extends CommandLineGATK with Sca
/** File to which variants should be written */ /** File to which variants should be written */
@Output(fullName = "out", shortName = "o", doc = "File to which variants should be written", required = false, exclusiveOf = "", validation = "") @Output(fullName = "out", shortName = "o", doc = "File to which variants should be written", required = false, exclusiveOf = "", validation = "")
@Gather(classOf[CatVariantsGatherer]) @Gather(classOf[GatherVcfs])
var out: File = _ var out: File = _
/** Determines how we should merge genotype records for samples shared across the ROD files */ /** Determines how we should merge genotype records for samples shared across the ROD files */
......
...@@ -18,11 +18,12 @@ import java.io.File ...@@ -18,11 +18,12 @@ import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.core.summary.Summarizable import nl.lumc.sasc.biopet.core.summary.Summarizable
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{GATKScatterFunction, LocusScatterFunction}
import nl.lumc.sasc.biopet.utils.VcfUtils import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.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
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ } import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Output, _}
import org.broadinstitute.gatk.utils.report.{ GATKReport, GATKReportTable } import org.broadinstitute.gatk.utils.report.{GATKReport, GATKReportTable}
class GenotypeConcordance(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction with Summarizable { class GenotypeConcordance(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction with Summarizable {
analysisName = "GenotypeConcordance" analysisName = "GenotypeConcordance"
......
...@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk ...@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.extensions.gatk.gather.GatherVcfs
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{GATKScatterFunction, LocusScatterFunction}
import nl.lumc.sasc.biopet.utils.VcfUtils import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.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
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ } import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Output, _}
class GenotypeGVCFs(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction { class GenotypeGVCFs(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "GenotypeGVCFs" def analysis_type = "GenotypeGVCFs"
...@@ -33,7 +35,7 @@ class GenotypeGVCFs(val parent: Configurable) extends CommandLineGATK with Scatt ...@@ -33,7 +35,7 @@ class GenotypeGVCFs(val parent: Configurable) extends CommandLineGATK with Scatt
/** File to which variants should be written */ /** File to which variants should be written */
@Output(fullName = "out", shortName = "o", doc = "File to which variants should be written", required = false, exclusiveOf = "", validation = "") @Output(fullName = "out", shortName = "o", doc = "File to which variants should be written", required = false, exclusiveOf = "", validation = "")
@Gather(classOf[CatVariantsGatherer]) @Gather(classOf[GatherVcfs])
var out: File = _ var out: File = _
/** Include loci found to be non-variant after genotyping */ /** Include loci found to be non-variant after genotyping */
......
...@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk ...@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.extensions.gatk.gather.{GatherVcfs, GatherBamFiles}
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{GATKScatterFunction, LocusScatterFunction}
import nl.lumc.sasc.biopet.utils.VcfUtils import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.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
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Input, Output } import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Input, Output}
class HaplotypeCaller(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction { class HaplotypeCaller(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "HaplotypeCaller" def analysis_type = "HaplotypeCaller"
...@@ -29,7 +31,7 @@ class HaplotypeCaller(val parent: Configurable) extends CommandLineGATK with Sca ...@@ -29,7 +31,7 @@ class HaplotypeCaller(val parent: Configurable) extends CommandLineGATK with Sca
/** File to which variants should be written */ /** File to which variants should be written */
@Output(fullName = "out", shortName = "o", doc = "File to which variants should be written", required = false, exclusiveOf = "", validation = "") @Output(fullName = "out", shortName = "o", doc = "File to which variants should be written", required = false, exclusiveOf = "", validation = "")
@Gather(classOf[CatVariantsGatherer]) @Gather(classOf[GatherVcfs])
var out: File = _ var out: File = _
/** What likelihood calculation engine to use to calculate the relative likelihood of reads vs haplotypes */ /** What likelihood calculation engine to use to calculate the relative likelihood of reads vs haplotypes */
...@@ -96,7 +98,7 @@ class HaplotypeCaller(val parent: Configurable) extends CommandLineGATK with Sca ...@@ -96,7 +98,7 @@ class HaplotypeCaller(val parent: Configurable) extends CommandLineGATK with Sca
/** File to which assembled haplotypes should be written */ /** File to which assembled haplotypes should be written */
@Output(fullName = "bamOutput", shortName = "bamout", doc = "File to which assembled haplotypes should be written", required = false, exclusiveOf = "", validation = "") @Output(fullName = "bamOutput", shortName = "bamout", doc = "File to which assembled haplotypes should be written", required = false, exclusiveOf = "", validation = "")
@Gather(classOf[MergeSamFiles]) @Gather(classOf[GatherBamFiles])
var bamOutput: File = _ var bamOutput: File = _
/** Automatically generated md5 for bamOutput */ /** Automatically generated md5 for bamOutput */
......
...@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk ...@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.extensions.gatk.gather.GatherBamFiles
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{ContigScatterFunction, GATKScatterFunction}
import nl.lumc.sasc.biopet.utils.VcfUtils import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.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
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ } import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Output, _}
class IndelRealigner(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction { class IndelRealigner(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "IndelRealigner" def analysis_type = "IndelRealigner"
...@@ -45,7 +47,7 @@ class IndelRealigner(val parent: Configurable) extends CommandLineGATK with Scat ...@@ -45,7 +47,7 @@ class IndelRealigner(val parent: Configurable) extends CommandLineGATK with Scat
/** Output bam */ /** Output bam */
@Output(fullName = "out", shortName = "o", doc = "Output bam", required = false, exclusiveOf = "", validation = "") @Output(fullName = "out", shortName = "o", doc = "Output bam", required = false, exclusiveOf = "", validation = "")
@Gather(classOf[MergeSamFiles]) @Gather(classOf[GatherBamFiles])
var out: File = _ var out: File = _
/** Automatically generated md5 for out */ /** Automatically generated md5 for out */
......
...@@ -3,6 +3,8 @@ package nl.lumc.sasc.biopet.extensions.gatk ...@@ -3,6 +3,8 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.extensions.gatk.gather.GatherVcfs
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{GATKScatterFunction, LocusScatterFunction}
import nl.lumc.sasc.biopet.utils.config.Configurable import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Input, Output} import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Input, Output}
...@@ -31,7 +33,7 @@ class MuTect2(val parent: Configurable) extends CommandLineGATK with ScatterGath ...@@ -31,7 +33,7 @@ class MuTect2(val parent: Configurable) extends CommandLineGATK with ScatterGath
/** Output file of the program. */ /** Output file of the program. */
@Output(fullName = "out", shortName = "o", required = false) @Output(fullName = "out", shortName = "o", required = false)
@Gather(classOf[CatVariantsGatherer]) @Gather(classOf[GatherVcfs])
var outputVcf: File = _ var outputVcf: File = _
/** /**
......
...@@ -17,6 +17,8 @@ package nl.lumc.sasc.biopet.extensions.gatk ...@@ -17,6 +17,8 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.extensions.gatk.gather.GatherBamFiles
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{ContigScatterFunction, GATKScatterFunction}
import nl.lumc.sasc.biopet.utils.config.Configurable import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline._ import org.broadinstitute.gatk.utils.commandline._
...@@ -27,7 +29,7 @@ class PrintReads(val parent: Configurable) extends CommandLineGATK with ScatterG ...@@ -27,7 +29,7 @@ class PrintReads(val parent: Configurable) extends CommandLineGATK with ScatterG
/** Write output to this BAM filename instead of STDOUT */ /** Write output to this BAM filename instead of STDOUT */
@Output(fullName = "out", shortName = "o", doc = "Write output to this BAM filename instead of STDOUT", required = false, exclusiveOf = "", validation = "") @Output(fullName = "out", shortName = "o", doc = "Write output to this BAM filename instead of STDOUT", required = false, exclusiveOf = "", validation = "")
@Gather(classOf[MergeSamFiles]) @Gather(classOf[GatherBamFiles])
var out: File = _ var out: File = _
/** Exclude all reads with this read group from the output */ /** Exclude all reads with this read group from the output */
......
...@@ -17,10 +17,11 @@ package nl.lumc.sasc.biopet.extensions.gatk ...@@ -17,10 +17,11 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{GATKScatterFunction, LocusScatterFunction}
import nl.lumc.sasc.biopet.utils.VcfUtils import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.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
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Input, _ } import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Input, _}
class RealignerTargetCreator(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction { class RealignerTargetCreator(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "RealignerTargetCreator" def analysis_type = "RealignerTargetCreator"
......
...@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk ...@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.extensions.gatk.gather.GatherVcfs
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{GATKScatterFunction, LocusScatterFunction}
import nl.lumc.sasc.biopet.utils.VcfUtils import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.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
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ } import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Output, _}
class SelectVariants(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction { class SelectVariants(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "SelectVariants" def analysis_type = "SelectVariants"
...@@ -41,7 +43,7 @@ class SelectVariants(val parent: Configurable) extends CommandLineGATK with Scat ...@@ -41,7 +43,7 @@ class SelectVariants(val parent: Configurable) extends CommandLineGATK with Scat
/** File to which variants should be written */ /** File to which variants should be written */
@Output(fullName = "out", shortName = "o", doc = "File to which variants should be written", required = false, exclusiveOf = "", validation = "") @Output(fullName = "out", shortName = "o", doc = "File to which variants should be written", required = false, exclusiveOf = "", validation = "")
@Gather(classOf[CatVariantsGatherer]) @Gather(classOf[GatherVcfs])
var out: File = _ var out: File = _
/** Include genotypes from this sample */ /** Include genotypes from this sample */
......
...@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk ...@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.extensions.gatk.gather.GatherVcfs
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{GATKScatterFunction, LocusScatterFunction}
import nl.lumc.sasc.biopet.utils.VcfUtils import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.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
import org.broadinstitute.gatk.utils.commandline.{ Gather, Input, Output, _ } import org.broadinstitute.gatk.utils.commandline.{Gather, Input, Output, _}
class UnifiedGenotyper(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction { class UnifiedGenotyper(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "UnifiedGenotyper" def analysis_type = "UnifiedGenotyper"
...@@ -221,7 +223,7 @@ class UnifiedGenotyper(val parent: Configurable) extends CommandLineGATK with Sc ...@@ -221,7 +223,7 @@ class UnifiedGenotyper(val parent: Configurable) extends CommandLineGATK with Sc
/** File to which variants should be written */ /** File to which variants should be written */
@Output(fullName = "out", shortName = "o", doc = "File to which variants should be written", required = false, exclusiveOf = "", validation = "") @Output(fullName = "out", shortName = "o", doc = "File to which variants should be written", required = false, exclusiveOf = "", validation = "")
@Gather(classOf[CatVariantsGatherer]) @Gather(classOf[GatherVcfs])
var out: File = _ var out: File = _
/** If provided, only these samples will be emitted into the VCF, regardless of which samples are present in the BAM file */ /** If provided, only these samples will be emitted into the VCF, regardless of which samples are present in the BAM file */
......
...@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk ...@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.extensions.gatk.gather.GatherVcfs
import nl.lumc.sasc.biopet.extensions.gatk.scatter.{GATKScatterFunction, LocusScatterFunction}
import nl.lumc.sasc.biopet.utils.VcfUtils import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.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
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ } import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Output, _}
class VariantAnnotator(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction { class VariantAnnotator(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "VariantAnnotator" def analysis_type = "VariantAnnotator"
...@@ -49,7 +51,7 @@ class VariantAnnotator(val parent: Configurable) extends CommandLineGATK with Sc ...@@ -49,7 +51,7 @@ class VariantAnnotator(val parent: Configurable) extends CommandLineGATK with Sc
/** File to which variants should be written */ /** File to which variants should be written */
@Output(fullName = "out", shortName = "o", doc = "File to which variants should be written", required = false, exclusiveOf = "", validation = "") @Output(fullName = "out", shortName = "o", doc = "File to which variants should be written", required = false, exclusiveOf = "", validation = "")
@Gather(classOf[CatVariantsGatherer]) @Gather(classOf[GatherVcfs])
var out: File = _ var out: File = _
/** One or more specific annotations to apply to variant calls */ /** One or more specific annotations to apply to variant calls */
......
...@@ -16,10 +16,11 @@ package nl.lumc.sasc.biopet.extensions.gatk ...@@ -16,10 +16,11 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File import java.io.File
import nl.lumc.sasc.biopet.extensions.gatk.gather.GatherVcfs
import nl.lumc.sasc.biopet.utils.VcfUtils import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.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
import org.broadinstitute.gatk.utils.commandline.{ Gather, Input, Output, _ } import org.broadinstitute.gatk.utils.commandline.{Gather, Input, Output, _}
class VariantRecalibrator(val parent: Configurable) extends CommandLineGATK { class VariantRecalibrator(val parent: Configurable) extends CommandLineGATK {
def analysis_type = "VariantRecalibrator" def analysis_type = "VariantRecalibrator"
...@@ -122,7 +123,7 @@ class VariantRecalibrator(val parent: Configurable) extends CommandLineGATK { ...@@ -122,7 +123,7 @@ class VariantRecalibrator(val parent: Configurable) extends CommandLineGATK {
/** The output recal file used by ApplyRecalibration */ /** The output recal file used by ApplyRecalibration */
@Output(fullName = "recal_file", shortName = "recalFile", doc = "The output recal file used by ApplyRecalibration", required = true, exclusiveOf = "", validation = "") @Output(fullName = "recal_file", shortName = "recalFile", doc = "The output recal file used by ApplyRecalibration", required = true, exclusiveOf = "", validation = "")
@Gather(classOf[CatVariantsGatherer]) @Gather(classOf[GatherVcfs])
var recal_file: File = _ var recal_file: File = _
/** The output tranches file used by ApplyRecalibration */ /** The output tranches file used by ApplyRecalibration */
......
...@@ -12,14 +12,14 @@ ...@@ -12,14 +12,14 @@
* license; For commercial users or users who do not want to follow the AGPL * license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license. * license, please contact us to obtain a separate license.
*/ */
package nl.lumc.sasc.biopet.extensions.gatk package nl.lumc.sasc.biopet.extensions.gatk.gather
import java.io.File import java.io.File
import java.util import java.util
import org.broadinstitute.gatk.engine.recalibration.BQSRGatherer import org.broadinstitute.gatk.engine.recalibration.BQSRGatherer
import org.broadinstitute.gatk.queue.function.InProcessFunction import org.broadinstitute.gatk.queue.function.InProcessFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output } import org.broadinstitute.gatk.utils.commandline.{Input, Output}
/** /**
* Created by pjvanthof on 05/04/2017. * Created by pjvanthof on 05/04/2017.
......
...@@ -12,9 +12,10 @@ ...@@ -12,9 +12,10 @@
* license; For commercial users or users who do not want to follow the AGPL * license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license. * license, please contact us to obtain a separate license.
*/ */
package nl.lumc.sasc.biopet.extensions.gatk package nl.lumc.sasc.biopet.extensions.gatk.gather
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.extensions.gatk.{CatVariants, CommandLineGATK}
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.queue.function.scattergather.{GatherFunction, ScatterGatherableFunction} import org.broadinstitute.gatk.queue.function.scattergather.{GatherFunction, ScatterGatherableFunction}
...@@ -26,6 +27,8 @@ import org.broadinstitute.gatk.queue.function.scattergather.{GatherFunction, Sca ...@@ -26,6 +27,8 @@ import org.broadinstitute.gatk.queue.function.scattergather.{GatherFunction, Sca
* \@Gather(className = "org.broadinstitute.gatk.queue.extensions.gatk.CatVariantsGatherer") * \@Gather(className = "org.broadinstitute.gatk.queue.extensions.gatk.CatVariantsGatherer")