Merge pull request #160 from biopet/fix-BIOPET-747

Upgrade gather methods

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/AnalyzeCovariates.scala

@@ -17,8 +17,9 @@ package nl.lumc.sasc.biopet.extensions.gatk
 import java.io.File
 
 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 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 {
   def analysis_type = "AnalyzeCovariates"

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala

@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk
 import java.io.File
 
 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.config.Configurable
 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 {
   def analysis_type = "ApplyRecalibration"
@@ -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 */
   @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 = _
 
   /** The truth sensitivity level at which to start filtering */

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala

@@ -17,10 +17,11 @@ package nl.lumc.sasc.biopet.extensions.gatk
 import java.io.File
 
 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.config.Configurable
 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 {
   def analysis_type = "BaseRecalibrator"

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala

@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk
 import java.io.File
 
 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.config.Configurable
 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 {
   def analysis_type = "CombineGVCFs"
@@ -45,7 +47,7 @@ class CombineGVCFs(val parent: Configurable) extends CommandLineGATK with Scatte
 
   /** 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 = "")
-  @Gather(classOf[CatVariantsGatherer])
+  @Gather(classOf[GatherVcfs])
   var out: File = _
 
   /** If specified, convert banded gVCFs to all-sites gVCFs */

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala

@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk
 import java.io.File
 
 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.config.Configurable
 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 {
   def analysis_type = "CombineVariants"
@@ -33,7 +35,7 @@ class CombineVariants(val parent: Configurable) extends CommandLineGATK with Sca
 
   /** File to which variants should be written */
   @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 = _
 
   /** Determines how we should merge genotype records for samples shared across the ROD files */

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeConcordance.scala

@@ -18,11 +18,12 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
 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.config.Configurable
 import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
-import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
-import org.broadinstitute.gatk.utils.report.{ GATKReport, GATKReportTable }
+import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Output, _}
+import org.broadinstitute.gatk.utils.report.{GATKReport, GATKReportTable}
 
 class GenotypeConcordance(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction with Summarizable {
   analysisName = "GenotypeConcordance"

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala

@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk
 import java.io.File
 
 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.config.Configurable
 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 {
   def analysis_type = "GenotypeGVCFs"
@@ -33,7 +35,7 @@ class GenotypeGVCFs(val parent: Configurable) extends CommandLineGATK with Scatt
 
   /** File to which variants should be written */
   @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 = _
 
   /** Include loci found to be non-variant after genotyping */

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala

@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk
 import java.io.File
 
 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.config.Configurable
 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 {
   def analysis_type = "HaplotypeCaller"
@@ -29,7 +31,7 @@ class HaplotypeCaller(val parent: Configurable) extends CommandLineGATK with Sca
 
   /** File to which variants should be written */
   @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 = _
 
   /** 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
 
   /** 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 = "")
-  @Gather(classOf[MergeSamFiles])
+  @Gather(classOf[GatherBamFiles])
   var bamOutput: File = _
 
   /** Automatically generated md5 for bamOutput */

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/IndelRealigner.scala

@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk
 import java.io.File
 
 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.config.Configurable
 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 {
   def analysis_type = "IndelRealigner"
@@ -45,7 +47,7 @@ class IndelRealigner(val parent: Configurable) extends CommandLineGATK with Scat
 
   /** Output bam */
   @Output(fullName = "out", shortName = "o", doc = "Output bam", required = false, exclusiveOf = "", validation = "")
-  @Gather(classOf[MergeSamFiles])
+  @Gather(classOf[GatherBamFiles])
   var out: File = _
 
   /** Automatically generated md5 for out */

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/MuTect2.scala

@@ -3,6 +3,8 @@ package nl.lumc.sasc.biopet.extensions.gatk
 import java.io.File
 
 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 org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Input, Output}
 
@@ -31,7 +33,7 @@ class MuTect2(val parent: Configurable) extends CommandLineGATK with ScatterGath
 
   /** Output file of the program. */
   @Output(fullName = "out", shortName = "o", required = false)
-  @Gather(classOf[CatVariantsGatherer])
+  @Gather(classOf[GatherVcfs])
   var outputVcf: File = _
 
   /**

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/PrintReads.scala

@@ -17,6 +17,8 @@ package nl.lumc.sasc.biopet.extensions.gatk
 import java.io.File
 
 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 org.broadinstitute.gatk.utils.commandline._
 
@@ -27,7 +29,7 @@ class PrintReads(val parent: Configurable) extends CommandLineGATK with ScatterG
 
   /** 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 = "")
-  @Gather(classOf[MergeSamFiles])
+  @Gather(classOf[GatherBamFiles])
   var out: File = _
 
   /** Exclude all reads with this read group from the output */

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/RealignerTargetCreator.scala

@@ -17,10 +17,11 @@ package nl.lumc.sasc.biopet.extensions.gatk
 import java.io.File
 
 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.config.Configurable
 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 {
   def analysis_type = "RealignerTargetCreator"

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala

@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk
 import java.io.File
 
 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.config.Configurable
 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 {
   def analysis_type = "SelectVariants"
@@ -41,7 +43,7 @@ class SelectVariants(val parent: Configurable) extends CommandLineGATK with Scat
 
   /** File to which variants should be written */
   @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 = _
 
   /** Include genotypes from this sample */

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala

@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk
 import java.io.File
 
 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.config.Configurable
 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 {
   def analysis_type = "UnifiedGenotyper"
@@ -221,7 +223,7 @@ class UnifiedGenotyper(val parent: Configurable) extends CommandLineGATK with Sc
 
   /** File to which variants should be written */
   @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 = _
 
   /** If provided, only these samples will be emitted into the VCF, regardless of which samples are present in the BAM file */

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantAnnotator.scala

@@ -17,10 +17,12 @@ package nl.lumc.sasc.biopet.extensions.gatk
 import java.io.File
 
 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.config.Configurable
 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 {
   def analysis_type = "VariantAnnotator"
@@ -49,7 +51,7 @@ class VariantAnnotator(val parent: Configurable) extends CommandLineGATK with Sc
 
   /** File to which variants should be written */
   @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 = _
 
   /** One or more specific annotations to apply to variant calls */

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantRecalibrator.scala

@@ -16,10 +16,11 @@ package nl.lumc.sasc.biopet.extensions.gatk
 
 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.config.Configurable
 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 {
   def analysis_type = "VariantRecalibrator"
@@ -122,7 +123,7 @@ class VariantRecalibrator(val parent: Configurable) extends CommandLineGATK {
 
   /** 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 = "")
-  @Gather(classOf[CatVariantsGatherer])
+  @Gather(classOf[GatherVcfs])
   var recal_file: File = _
 
   /** The output tranches file used by ApplyRecalibration */

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BqsrGather.scala → biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/gather/BqsrGather.scala

@@ -12,14 +12,14 @@
  * license; For commercial users or users who do not want to follow the AGPL
  * 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.util
 
 import org.broadinstitute.gatk.engine.recalibration.BQSRGatherer
 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.

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CatVariantsGather.scala → biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/gather/CatVariantsGatherer.scala

@@ -12,9 +12,10 @@
  * license; For commercial users or users who do not want to follow the AGPL
  * 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.extensions.gatk.{CatVariants, CommandLineGATK}
 import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
 import org.broadinstitute.gatk.queue.function.scattergather.GatherFunction
 
@@ -26,6 +27,8 @@ import org.broadinstitute.gatk.queue.function.scattergather.GatherFunction
  *           \@Gather(className = "org.broadinstitute.gatk.queue.extensions.gatk.CatVariantsGatherer")
  *           \@Output(doc="File to which variants should be written",required=true)
  *           protected VariantContextWriter writer = null;
+ *
+ *           @deprecated
  */
 class CatVariantsGatherer extends CatVariants(null) with GatherFunction {
   this.assumeSorted = true

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/gather/GatherBamFiles.scala

+package nl.lumc.sasc.biopet.extensions.gatk.gather
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.extensions.gatk.CommandLineGATK
+import nl.lumc.sasc.biopet.extensions.picard
+import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
+import org.broadinstitute.gatk.queue.function.scattergather.GatherFunction
+
+/**
+  * Created by pjvan_thof on 13-7-17.
+  */
+class GatherBamFiles extends picard.GatherBamFiles(null) with GatherFunction {
+  analysisName = "Gather_Bam_Files"
+
+  override val parent = originalFunction match {
+    case b: BiopetCommandLineFunction => b
+    case _                            => null
+  }
+
+  override def freezeFieldValues() {
+    val originalGATK = this.originalFunction.asInstanceOf[CommandLineGATK]
+
+    this.input = this.gatherParts.zipWithIndex map { case (input, index) => new TaggedFile(input, "input" + index) }
+    this.output = this.originalOutput
+
+    super.freezeFieldValues()
+  }
+
+}

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/gather/GatherVcfs.scala

+package nl.lumc.sasc.biopet.extensions.gatk.gather
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.extensions.gatk.CommandLineGATK
+import nl.lumc.sasc.biopet.extensions.picard
+import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
+import org.broadinstitute.gatk.queue.function.scattergather.GatherFunction
+
+/**
+  * Created by pjvan_thof on 12-7-17.
+  */
+class GatherVcfs extends picard.GatherVcfs(null) with GatherFunction {
+  analysisName = "Gather_Vcfs"
+
+  override val parent = originalFunction match {
+    case b: BiopetCommandLineFunction => b
+    case _                            => null
+  }
+
+  override def freezeFieldValues() {
+    val originalGATK = this.originalFunction.asInstanceOf[CommandLineGATK]
+
+    this.input = this.gatherParts.zipWithIndex map { case (input, index) => new TaggedFile(input, "input" + index) }
+    this.output = this.originalOutput
+
+    super.freezeFieldValues()
+  }
+
+}