Remove protected source file from public artifacts

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

-package nl.lumc.sasc.biopet.extensions.gatk
-
-import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
-
-class AnalyzeCovariates(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.AnalyzeCovariates with GatkGeneral {
-}
-
-object AnalyzeCovariates {
-  def apply(root: Configurable, before: File, after: File, plots: File): AnalyzeCovariates = {
-    val ac = new AnalyzeCovariates(root)
-    ac.before = before
-    ac.after = after
-    ac.plots = plots
-    return ac
-  }
-}
\ No newline at end of file

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

-package nl.lumc.sasc.biopet.extensions.gatk
-
-import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
-
-class ApplyRecalibration(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.ApplyRecalibration with GatkGeneral {
-  override def afterGraph {
-    super.afterGraph
-
-    if (config.contains("scattercount")) scatterCount = config("scattercount")
-
-    nt = Option(getThreads(3))
-    memoryLimit = Option(nt.getOrElse(1) * 2)
-    ts_filter_level = config("ts_filter_level")
-  }
-}
-
-object ApplyRecalibration {
-  def apply(root: Configurable, input: File, output: File, recal_file: File, tranches_file: File, indel: Boolean = false): ApplyRecalibration = {
-    val ar = if (indel) new ApplyRecalibration(root) {
-      mode = org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
-      defaults ++= Map("ts_filter_level" -> 99.0)
-    }
-    else new ApplyRecalibration(root) {
-      mode = org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP
-      defaults ++= Map("ts_filter_level" -> 99.5)
-    }
-    ar.input :+= input
-    ar.recal_file = recal_file
-    ar.tranches_file = tranches_file
-    ar.out = output
-    return ar
-  }
-}
\ No newline at end of file

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

-package nl.lumc.sasc.biopet.extensions.gatk
-
-import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
-
-class BaseRecalibrator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.BaseRecalibrator with GatkGeneral {
-  memoryLimit = Option(4)
-  override val defaultVmem = "8G"
-
-  if (config.contains("scattercount")) scatterCount = config("scattercount")
-  if (config.contains("dbsnp")) knownSites :+= new File(config("dbsnp").asString)
-  if (config.contains("known_sites")) knownSites :+= new File(config("known_sites").asString)
-}
-
-object BaseRecalibrator {
-  def apply(root: Configurable, input: File, output: File): BaseRecalibrator = {
-    val br = new BaseRecalibrator(root)
-    br.input_file :+= input
-    br.out = output
-    br.afterGraph
-    return br
-  }
-}
\ No newline at end of file

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

-package nl.lumc.sasc.biopet.extensions.gatk
-
-import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
-
-class CombineGVCFs(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.CombineGVCFs with GatkGeneral {
-  if (config.contains("scattercount")) scatterCount = config("scattercount")
-}
-
-object CombineGVCFs {
-  def apply(root: Configurable, input: List[File], output: File): CombineGVCFs = {
-    val cg = new CombineGVCFs(root)
-    cg.variant = input
-    cg.o = output
-    return cg
-  }
-}
\ No newline at end of file

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

-package nl.lumc.sasc.biopet.extensions.gatk
-
-import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
-
-class CombineVariants(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.CombineVariants with GatkGeneral {
-  if (config.contains("scattercount")) scatterCount = config("scattercount")
-}
-
-object CombineVariants {
-  def apply(root: Configurable, input: List[File], output: File): CombineVariants = {
-    val cv = new CombineVariants(root)
-    cv.variant = input
-    cv.out = output
-    return cv
-  }
-}
\ No newline at end of file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala

-package nl.lumc.sasc.biopet.extensions.gatk
-
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
-
-trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction {
-  memoryLimit = Option(3)
-
-  if (config.contains("gatk_jar")) jarFile = config("gatk_jar")
-
-  override val defaultVmem = "7G"
-
-  if (config.contains("intervals", submodule = "gatk")) intervals = config("intervals", submodule = "gatk").asFileList
-  if (config.contains("exclude_intervals", submodule = "gatk")) excludeIntervals = config("exclude_intervals", submodule = "gatk").asFileList
-  reference_sequence = config("reference", submodule = "gatk")
-  gatk_key = config("gatk_key", submodule = "gatk")
-  if (config.contains("pedigree", submodule = "gatk")) pedigree = config("pedigree", submodule = "gatk").asFileList
-}

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

-package nl.lumc.sasc.biopet.extensions.gatk
-
-import java.io.File
-import nl.lumc.sasc.biopet.core.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
-
-  if (config.contains("dbsnp")) dbsnp = config("dbsnp")
-  if (config.contains("scattercount", "genotypegvcfs")) scatterCount = config("scattercount")
-
-  if (config("inputtype", default = "dna").asString == "rna") {
-    stand_call_conf = config("stand_call_conf", default = 20)
-    stand_emit_conf = config("stand_emit_conf", default = 0)
-  } else {
-    stand_call_conf = config("stand_call_conf", default = 30)
-    stand_emit_conf = config("stand_emit_conf", default = 0)
-  }
-}
-
-object GenotypeGVCFs {
-  def apply(root: Configurable, gvcfFiles: List[File], output: File): GenotypeGVCFs = {
-    val gg = new GenotypeGVCFs(root)
-    gg.variant = gvcfFiles
-    gg.out = output
-    return gg
-  }
-}
\ No newline at end of file

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

-package nl.lumc.sasc.biopet.extensions.gatk
-
-import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType
-
-class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.HaplotypeCaller with GatkGeneral {
-  override def afterGraph {
-    super.afterGraph
-
-    min_mapping_quality_score = config("minMappingQualityScore", default = 20)
-    if (config.contains("scattercount")) scatterCount = config("scattercount")
-    if (config.contains("dbsnp")) this.dbsnp = config("dbsnp")
-    this.sample_ploidy = config("ploidy")
-    nct = config("threads", default = 1)
-    bamOutput = config("bamOutput")
-    memoryLimit = Option(nct.getOrElse(1) * 2)
-    if (config.contains("allSitePLs")) this.allSitePLs = config("allSitePLs")
-    if (config.contains("output_mode")) {
-      import org.broadinstitute.gatk.tools.walkers.genotyper.OutputMode._
-      config("output_mode").asString match {
-        case "EMIT_ALL_CONFIDENT_SITES" => output_mode = EMIT_ALL_CONFIDENT_SITES
-        case "EMIT_ALL_SITES"           => output_mode = EMIT_ALL_SITES
-        case "EMIT_VARIANTS_ONLY"       => output_mode = EMIT_VARIANTS_ONLY
-        case e                          => logger.warn("output mode '" + e + "' does not exist")
-      }
-    }
-
-    if (config("inputtype", default = "dna").asString == "rna") {
-      dontUseSoftClippedBases = config("dontusesoftclippedbases", default = true)
-      stand_call_conf = config("stand_call_conf", default = 5)
-      stand_emit_conf = config("stand_emit_conf", default = 0)
-    } else {
-      dontUseSoftClippedBases = config("dontusesoftclippedbases", default = false)
-      stand_call_conf = config("stand_call_conf", default = 5)
-      stand_emit_conf = config("stand_emit_conf", default = 0)
-    }
-    if (bamOutput != null && nct.getOrElse(1) > 1) {
-      nct = Option(1)
-      logger.warn("BamOutput is on, nct/threads is forced to set on 1, this option is only for debug")
-    }
-  }
-
-  def useGvcf() {
-    emitRefConfidence = org.broadinstitute.gatk.tools.walkers.haplotypecaller.ReferenceConfidenceMode.GVCF
-    variant_index_type = GATKVCFIndexType.LINEAR
-    variant_index_parameter = config("variant_index_parameter", default = 128000)
-  }
-}

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

-package nl.lumc.sasc.biopet.extensions.gatk
-
-import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
-
-class IndelRealigner(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.IndelRealigner with GatkGeneral {
-  if (config.contains("scattercount")) scatterCount = config("scattercount")
-}
-
-object IndelRealigner {
-  def apply(root: Configurable, input: File, targetIntervals: File, outputDir: String): IndelRealigner = {
-    val ir = new IndelRealigner(root)
-    ir.input_file :+= input
-    ir.targetIntervals = targetIntervals
-    ir.out = new File(outputDir, input.getName.stripSuffix(".bam") + ".realign.bam")
-    return ir
-  }
-}
\ No newline at end of file

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

-package nl.lumc.sasc.biopet.extensions.gatk
-
-import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
-
-class PrintReads(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.PrintReads with GatkGeneral {
-  memoryLimit = Option(4)
-
-  override val defaultVmem = "8G"
-
-  if (config.contains("scattercount")) scatterCount = config("scattercount")
-}
-
-object PrintReads {
-  def apply(root: Configurable, input: File, output: File): PrintReads = {
-    val br = new PrintReads(root)
-    br.input_file :+= input
-    br.out = output
-    return br
-  }
-}
\ No newline at end of file

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

-package nl.lumc.sasc.biopet.extensions.gatk
-
-import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
-
-class RealignerTargetCreator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.RealignerTargetCreator with GatkGeneral {
-  override val defaultVmem = "6G"
-  memoryLimit = Some(2.5)
-
-  if (config.contains("scattercount")) scatterCount = config("scattercount")
-
-  if (config.contains("known")) known ++= config("known").asFileList
-}
-
-object RealignerTargetCreator {
-  def apply(root: Configurable, input: File, outputDir: String): RealignerTargetCreator = {
-    val re = new RealignerTargetCreator(root)
-    re.input_file :+= input
-    re.out = new File(outputDir, input.getName.stripSuffix(".bam") + ".realign.intervals")
-    return re
-  }
-}
\ No newline at end of file

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

-package nl.lumc.sasc.biopet.extensions.gatk
-
-import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
-
-class SelectVariants(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.SelectVariants with GatkGeneral {
-  if (config.contains("scattercount")) scatterCount = config("scattercount")
-}
-
-object SelectVariants {
-  def apply(root: Configurable, input: File, output: File): SelectVariants = {
-    val sv = new SelectVariants(root)
-    sv.variant = input
-    sv.out = output
-    return sv
-  }
-}
\ No newline at end of file

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

-package nl.lumc.sasc.biopet.extensions.gatk
-
-import nl.lumc.sasc.biopet.core.config.Configurable
-
-class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.UnifiedGenotyper with GatkGeneral {
-  override def afterGraph {
-    super.afterGraph
-
-    genotype_likelihoods_model = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.BOTH
-    if (config.contains("scattercount")) scatterCount = config("scattercount")
-    if (config.contains("dbsnp")) this.dbsnp = config("dbsnp")
-    this.sample_ploidy = config("ploidy")
-    nct = config("threads", default = 1)
-    memoryLimit = Option(nct.getOrElse(1) * 2)
-    if (config.contains("allSitePLs")) this.allSitePLs = config("allSitePLs")
-    if (config.contains("output_mode")) {
-      import org.broadinstitute.gatk.tools.walkers.genotyper.OutputMode._
-      config("output_mode").asString match {
-        case "EMIT_ALL_CONFIDENT_SITES" => output_mode = EMIT_ALL_CONFIDENT_SITES
-        case "EMIT_ALL_SITES"           => output_mode = EMIT_ALL_SITES
-        case "EMIT_VARIANTS_ONLY"       => output_mode = EMIT_VARIANTS_ONLY
-        case e                          => logger.warn("output mode '" + e + "' does not exist")
-      }
-    }
-
-    if (config("inputtype", default = "dna").asString == "rna") {
-      stand_call_conf = config("stand_call_conf", default = 5)
-      stand_emit_conf = config("stand_emit_conf", default = 0)
-    } else {
-      stand_call_conf = config("stand_call_conf", default = 5)
-      stand_emit_conf = config("stand_emit_conf", default = 0)
-    }
-  }
-}

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

-package nl.lumc.sasc.biopet.extensions.gatk
-
-import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
-
-class VariantAnnotator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantAnnotator with GatkGeneral {
-  if (config.contains("scattercount")) scatterCount = config("scattercount")
-  dbsnp = config("dbsnp")
-}
-
-object VariantAnnotator {
-  def apply(root: Configurable, input: File, bamFiles: List[File], output: File): VariantAnnotator = {
-    val va = new VariantAnnotator(root)
-    va.variant = input
-    va.input_file = bamFiles
-    va.out = output
-    return va
-  }
-}
\ No newline at end of file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala

-package nl.lumc.sasc.biopet.extensions.gatk
-
-import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
-
-class VariantEval(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantEval with GatkGeneral {
-  override def afterGraph {
-    super.afterGraph
-  }
-}
-
-object VariantEval {
-  def apply(root: Configurable, sample: File, compareWith: File,
-            output: File): VariantEval = {
-    val vareval = new VariantEval(root)
-    vareval.eval = Seq(sample)
-    vareval.comp = Seq(compareWith)
-    vareval.out = output
-    vareval.afterGraph
-    return vareval
-  }
-
-  def apply(root: Configurable, sample: File, compareWith: File,
-            output: File, ST: Seq[String], EV: Seq[String]): VariantEval = {
-    val vareval = new VariantEval(root)
-    vareval.eval = Seq(sample)
-    vareval.comp = Seq(compareWith)
-    vareval.out = output
-    vareval.noST = true
-    vareval.ST = ST
-    vareval.noEV = true
-    vareval.EV = EV
-    vareval.afterGraph
-    return vareval
-  }
-
-}
\ No newline at end of file

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

-package nl.lumc.sasc.biopet.extensions.gatk
-
-import java.io.File
-import nl.lumc.sasc.biopet.core.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 {
-  nt = Option(getThreads(4))
-  memoryLimit = Option(nt.getOrElse(1) * 2)
-
-  if (config.contains("dbsnp")) resource :+= new TaggedFile(config("dbsnp").asString, "known=true,training=false,truth=false,prior=2.0")
-
-  an = config("annotation", default = List("QD", "DP", "FS", "ReadPosRankSum", "MQRankSum")).asStringList
-  minNumBadVariants = config("minnumbadvariants")
-  maxGaussians = config("maxgaussians")
-}
-
-object VariantRecalibrator {
-  def apply(root: Configurable, input: File, recal_file: File, tranches_file: File, indel: Boolean = false): VariantRecalibrator = {
-    val vr = new VariantRecalibrator(root) {
-      override lazy val configName = "variantrecalibrator"
-      override def configPath: List[String] = (if (indel) "indel" else "snp") :: super.configPath
-      if (indel) {
-        mode = org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
-        defaults ++= Map("ts_filter_level" -> 99.0)
-        if (config.contains("mills")) resource :+= new TaggedFile(config("mills").asString, "known=false,training=true,truth=true,prior=12.0")
-      } else {
-        mode = org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP
-        defaults ++= Map("ts_filter_level" -> 99.5)
-        if (config.contains("hapmap")) resource +:= new TaggedFile(config("hapmap").asString, "known=false,training=true,truth=true,prior=15.0")
-        if (config.contains("omni")) resource +:= new TaggedFile(config("omni").asString, "known=false,training=true,truth=true,prior=12.0")
-        if (config.contains("1000G")) resource +:= new TaggedFile(config("1000G").asString, "known=false,training=true,truth=false,prior=10.0")
-      }
-    }
-    vr.input :+= input
-    vr.recal_file = recal_file
-    vr.tranches_file = tranches_file
-    return vr
-  }
-}
\ No newline at end of file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala

-package nl.lumc.sasc.biopet.pipelines.basty
-
-import java.io.File
-import nl.lumc.sasc.biopet.core.MultiSampleQScript
-import nl.lumc.sasc.biopet.core.PipelineCommand
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.Cat
-import nl.lumc.sasc.biopet.extensions.Raxml
-import nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline
-import nl.lumc.sasc.biopet.tools.BastyGenerateFasta
-import org.broadinstitute.gatk.queue.QScript
-
-class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
-  def this() = this(null)
-
-  class LibraryOutput extends AbstractLibraryOutput {
-  }
-
-  case class FastaOutput(variants: File, consensus: File, consensusVariants: File)
-  class SampleOutput extends AbstractSampleOutput {
-    var output: FastaOutput = _
-    var outputSnps: FastaOutput = _
-  }
-
-  defaults ++= Map("ploidy" -> 1, "use_haplotypecaller" -> false, "use_unifiedgenotyper" -> true, "joint_variantcalling" -> true)
-
-  var gatkPipeline: GatkPipeline = new GatkPipeline(this)
-  gatkPipeline.jointVariantcalling = true
-
-  def init() {
-    gatkPipeline.outputDir = outputDir
-    gatkPipeline.init
-  }
-
-  def biopetScript() {
-    gatkPipeline.biopetScript
-    addAll(gatkPipeline.functions)
-
-    val refVariants = addGenerateFasta(null, outputDir + "reference/", outputName = "reference")
-    val refVariantSnps = addGenerateFasta(null, outputDir + "reference/", outputName = "reference", snpsOnly = true)
-
-    runSamplesJobs()
-
-    val catVariants = Cat(this, refVariants.variants :: samplesOutput.map(_._2.output.variants).toList, outputDir + "fastas/variant.fasta")
-    add(catVariants)
-    val catVariantsSnps = Cat(this, refVariantSnps.variants :: samplesOutput.map(_._2.outputSnps.variants).toList, outputDir + "fastas/variant.snps_only.fasta")
-    add(catVariantsSnps)
-
-    val catConsensus = Cat(this, refVariants.consensus :: samplesOutput.map(_._2.output.consensus).toList, outputDir + "fastas/consensus.fasta")
-    add(catConsensus)
-    val catConsensusSnps = Cat(this, refVariantSnps.consensus :: samplesOutput.map(_._2.outputSnps.consensus).toList, outputDir + "fastas/consensus.snps_only.fasta")
-    add(catConsensusSnps)
-
-    val catConsensusVariants = Cat(this, refVariants.consensusVariants :: samplesOutput.map(_._2.output.consensusVariants).toList, outputDir + "fastas/consensus.variant.fasta")
-    add(catConsensusVariants)
-    val catConsensusVariantsSnps = Cat(this, refVariantSnps.consensusVariants :: samplesOutput.map(_._2.outputSnps.consensusVariants).toList, outputDir + "fastas/consensus.variant.snps_only.fasta")
-    add(catConsensusVariantsSnps)
-
-    val seed: Int = config("seed", default = 12345)
-    def addRaxml(input: File, outputDir: String, outputName: String) {
-      val raxmlMl = new Raxml(this)
-      raxmlMl.input = input
-      raxmlMl.m = config("raxml_ml_model", default = "GTRGAMMAX")
-      raxmlMl.p = seed
-      raxmlMl.n = outputName + "_ml"
-      raxmlMl.w = outputDir
-      raxmlMl.N = config("ml_runs", default = 20, submodule = "raxml")
-      add(raxmlMl)
-
-      val r = new scala.util.Random(seed)
-      val numBoot = config("boot_runs", default = 100, submodule = "raxml").asInt
-      val bootList = for (t <- 0 until numBoot) yield {
-        val raxmlBoot = new Raxml(this)
-        raxmlBoot.threads = 1
-        raxmlBoot.input = input
-        raxmlBoot.m = config("raxml_ml_model", default = "GTRGAMMAX")
-        raxmlBoot.p = seed
-        raxmlBoot.b = math.abs(r.nextInt)
-        raxmlBoot.w = outputDir
-        raxmlBoot.N = 1
-        raxmlBoot.n = outputName + "_boot_" + t
-        add(raxmlBoot)
-        raxmlBoot.getBootstrapFile
-      }
-
-      val cat = Cat(this, bootList.toList, outputDir + "/boot_list")
-      add(cat)
-
-      val raxmlBi = new Raxml(this)
-      raxmlBi.input = input
-      raxmlBi.t = raxmlMl.getBestTreeFile
-      raxmlBi.z = cat.output
-      raxmlBi.m = config("raxml_ml_model", default = "GTRGAMMAX")
-      raxmlBi.p = seed
-      raxmlBi.f = "b"
-      raxmlBi.n = outputName + "_bi"
-      raxmlBi.w = outputDir
-      add(raxmlBi)
-    }
-
-    addRaxml(catVariantsSnps.output, outputDir + "raxml", "snps")
-  }
-
-  // Called for each sample
-  def runSingleSampleJobs(sampleConfig: Map[String, Any]): SampleOutput = {
-    val sampleOutput = new SampleOutput