Freebayes somatic workflow (CRAM)¶

FreeBayesSomaticWorkflowCram · 1 contributor · 1 version

This workflow uses the capabilities of freebayes to output all variants independent of the: diploid model which then in turn allows us to create a likelihood based difference between the normal sample and an arbitrary amount of samples. This allows a joint somatic genotyping of multiple samples of the same individual.

Quickstart¶

from janis_bioinformatics.tools.dawson.workflows.variantcalling.multisample.freebayes.freebayessomaticworkflow_cram import FreeBayesSomaticWorkflowCram

wf = WorkflowBuilder("myworkflow")

wf.step(
    "freebayessomaticworkflowcram_step",
    FreeBayesSomaticWorkflowCram(
        bams=None,
        reference=None,
        normalSample=None,
    )
)
wf.output("somaticOutVcf", source=freebayessomaticworkflowcram_step.somaticOutVcf)

OR

Install Janis
Ensure Janis is configured to work with Docker or Singularity.
Ensure all reference files are available:

Note

More information about these inputs are available below.

Generate user input files for FreeBayesSomaticWorkflowCram:

# user inputs
janis inputs FreeBayesSomaticWorkflowCram > inputs.yaml

inputs.yaml

bams:
- bams_0.cram
- bams_1.cram
normalSample: <value>
reference: reference.fasta

Run FreeBayesSomaticWorkflowCram with:

janis run [...run options] \
    --inputs inputs.yaml \
    FreeBayesSomaticWorkflowCram

Information¶

URL: No URL to the documentation was provided

ID:	`FreeBayesSomaticWorkflowCram`
URL:	No URL to the documentation was provided
Versions:	0.1.1
Authors:	Sebastian Hollizeck
Citations:
Created:	2019-10-18
Updated:	2020-12-10

Outputs¶

name	type	documentation
somaticOutVcf	Gzipped<File>

Workflow¶

Embedded Tools¶

Create genomic call regions	`CreateCallRegions/v0.1.0`
freebayes	`freebayes_cram/1.3.1`
Call Somatic Variants from freebayes	`callSomaticFreeBayes/0.1.8`
VcfLib: VcfCombine	`vcfcombine/v1.0.1`
VcfLib: VcfStreamSort	`vcfstreamsort/v1.0.1`
BCFTools: Normalize	`bcftoolsNorm/v1.9`
VcfLib: VcfAllelicPrimitives	`vcfallelicprimitives/v1.0.1`
VcfLib: VcfFixUp	`vcffixup/v1.0.1`
VcfLib: VcfUniqAlleles	`vcfuniqalleles/v1.0.1`
VcfLib: VcfUniq	`vcfuniq/v1.0.1`
BGZip	`bgzip/1.2.1`
Tabix	`tabix/1.2.1`

Additional configuration (inputs)¶

name	type	documentation
bams	Array<CramPair>	All bams to be analysed. Samples can be split over multiple bams as well as multiple samples can be contained in one bam as long as the sample ids are set properly.
reference	FastaFai	The reference the bams were aligned to, with a fai index.
normalSample	String	The sample id of the normal sample, as it is specified in the bam header.
regionSize	Optional<Integer>	the size of the regions, to parallelise the analysis over. This needs to be adjusted if there are lots of samples or very high depth sequencing in the analysis.
skipCov	Optional<Integer>	The depth per sample, at which the variant calling process will skip a region. This is used to ignore regions with mapping issues, like the centromeres as well as heterochromatin. A good value is 3 times the maximum expected coverage.
minCov	Optional<Integer>	Minimum coverage over all samples, to still call variants.
createCallRegions_equalize	Optional<Boolean>
callVariants_pooledDiscreteFlag	Optional<Boolean>	Assume that samples result from pooled sequencing. Model pooled samples using discrete genotypes across pools. When using this flag, set –ploidy to the number of alleles in each sample or use the –cnv-map to define per-sample ploidy.
callVariants_gtQuals	Optional<Boolean>	-= –genotype-qualities Calculate the marginal probability of genotypes and report as GQ in each sample field in the VCF output.
callVariants_strictFlag	Optional<Boolean>	Generate strict VCF format (FORMAT/GQ will be an int)
callVariants_pooledContinousFlag	Optional<Boolean>	Output all alleles which pass input filters, regardles of genotyping outcome or model.
callVariants_reportMaxGLFlag	Optional<Boolean>	–report-genotype-likelihood-max Report genotypes using the maximum-likelihood estimate provided from genotype likelihoods.
callVariants_noABPriorsFlag	Optional<Boolean>	-a –allele-balance-priors-off Disable use of aggregate probability of observation balance between alleles as a component of the priors.
callVariants_maxNumOfAlleles	Optional<Integer>	Evaluate only the best N SNP alleles, ranked by sum of supporting quality scores. (Set to 0 to use all; default: all)
callVariants_noPartObsFlag	Optional<Boolean>	Exclude observations which do not fully span the dynamically-determined detection window. (default, use all observations, dividing partial support across matching haplotypes when generating haplotypes.)
callVariants_useDupFlag	Optional<Boolean>	Include duplicate-marked alignments in the analysis. default: exclude duplicates marked as such in alignments
callVariants_minBaseQual	Optional<Integer>	-q –min-base-quality Q Exclude alleles from analysis if their supporting base quality is less than Q. default: 0
callVariants_minSupMQsum	Optional<Integer>	-Y –min-supporting-mapping-qsum Q Consider any allele in which and the sum of mapping qualities of supporting reads is at least Q. default: 0
callVariants_minSupQsum	Optional<Integer>	-R –min-supporting-allele-qsum Q Consider any allele in which the sum of qualities of supporting observations is at least Q. default: 0
callVariants_minAltFrac	Optional<Float>	-F –min-alternate-fraction N Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position. default: 0.05
callVariants_minAltQSum	Optional<Integer>	-3 –min-alternate-qsum N Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position. default: 0
callVariants_minAltTotal	Optional<Integer>	-G –min-alternate-total N Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis. default: 1
sortSomatic1_inMemoryFlag	Optional<Boolean>	load all sites and then sort in memory
normalizeSomatic1_outputType	Optional<String>	–output-type b\|u\|z\|v: Output compressed BCF (b), uncompressed BCF (u), compressed VCF (z), uncompressed VCF (v). Use the -Ou option when piping between bcftools subcommands to speed up performance by removing unnecessary compression/decompression and VCF←→BCF conversion.
normalizeSomatic1_outputFilename	Optional<Filename>	–output: When output consists of a single stream, write it to FILE rather than to standard output, where it is written by default.
allelicPrimitves_tagParsed	Optional<String>	Tag records which are split apart of a complex allele with this flag
allelicPrimitves_keepGenoFlag	Optional<Boolean>	Maintain genotype-level annotations when decomposing. Similar caution should be used for this as for –keep-info.
sortSomatic2_inMemoryFlag	Optional<Boolean>	load all sites and then sort in memory
normalizeSomatic2_outputType	Optional<String>	–output-type b\|u\|z\|v: Output compressed BCF (b), uncompressed BCF (u), compressed VCF (z), uncompressed VCF (v). Use the -Ou option when piping between bcftools subcommands to speed up performance by removing unnecessary compression/decompression and VCF←→BCF conversion.
normalizeSomatic2_outputFilename	Optional<Filename>	–output: When output consists of a single stream, write it to FILE rather than to standard output, where it is written by default.
sortFinal_inMemoryFlag	Optional<Boolean>	load all sites and then sort in memory

Workflow Description Language¶

version development

import "tools/CreateCallRegions_v0_1_0.wdl" as C
import "tools/freebayes_cram_1_3_1.wdl" as F
import "tools/callSomaticFreeBayes_0_1_8.wdl" as C2
import "tools/vcfcombine_v1_0_1.wdl" as V
import "tools/vcfstreamsort_v1_0_1.wdl" as V2
import "tools/bcftoolsNorm_v1_9.wdl" as B
import "tools/vcfallelicprimitives_v1_0_1.wdl" as V3
import "tools/vcffixup_v1_0_1.wdl" as V4
import "tools/vcfuniqalleles_v1_0_1.wdl" as V5
import "tools/vcfuniq_v1_0_1.wdl" as V6
import "tools/bgzip_1_2_1.wdl" as B2
import "tools/tabix_1_2_1.wdl" as T

workflow FreeBayesSomaticWorkflowCram {
  input {
    Array[File] bams
    Array[File] bams_crai
    File reference
    File reference_fai
    Int? regionSize = 10000000
    String normalSample
    Int? skipCov = 500
    Int? minCov = 10
    Boolean? createCallRegions_equalize = true
    Boolean? callVariants_pooledDiscreteFlag = true
    Boolean? callVariants_gtQuals = true
    Boolean? callVariants_strictFlag = true
    Boolean? callVariants_pooledContinousFlag = true
    Boolean? callVariants_reportMaxGLFlag = true
    Boolean? callVariants_noABPriorsFlag = true
    Int? callVariants_maxNumOfAlleles = 4
    Boolean? callVariants_noPartObsFlag = true
    Boolean? callVariants_useDupFlag = false
    Int? callVariants_minBaseQual = 1
    Int? callVariants_minSupMQsum = 0
    Int? callVariants_minSupQsum = 0
    Float? callVariants_minAltFrac = 0.01
    Int? callVariants_minAltQSum = 70
    Int? callVariants_minAltTotal = 2
    Boolean? sortSomatic1_inMemoryFlag = true
    String? normalizeSomatic1_outputType = "v"
    String? normalizeSomatic1_outputFilename = "normalised.vcf"
    String? allelicPrimitves_tagParsed = "DECOMPOSED"
    Boolean? allelicPrimitves_keepGenoFlag = true
    Boolean? sortSomatic2_inMemoryFlag = true
    String? normalizeSomatic2_outputType = "v"
    String? normalizeSomatic2_outputFilename = "normalised.vcf"
    Boolean? sortFinal_inMemoryFlag = true
  }
  call C.CreateCallRegions as createCallRegions {
    input:
      reference=reference,
      reference_fai=reference_fai,
      regionSize=select_first([regionSize, 10000000]),
      equalize=select_first([createCallRegions_equalize, true])
  }
  scatter (c in createCallRegions.regions) {
     call F.freebayes_cram as callVariants {
      input:
        bams=bams,
        bams_crai=bams_crai,
        reference=reference,
        reference_fai=reference_fai,
        region=c,
        strictFlag=select_first([callVariants_strictFlag, true]),
        pooledDiscreteFlag=select_first([callVariants_pooledDiscreteFlag, true]),
        pooledContinousFlag=select_first([callVariants_pooledContinousFlag, true]),
        maxNumOfAlleles=select_first([callVariants_maxNumOfAlleles, 4]),
        noPartObsFlag=select_first([callVariants_noPartObsFlag, true]),
        useDupFlag=select_first([callVariants_useDupFlag, false]),
        minBaseQual=select_first([callVariants_minBaseQual, 1]),
        minSupQsum=select_first([callVariants_minSupQsum, 0]),
        minSupMQsum=select_first([callVariants_minSupMQsum, 0]),
        minAltFrac=select_first([callVariants_minAltFrac, 0.01]),
        minAltQSum=select_first([callVariants_minAltQSum, 70]),
        minAltTotal=select_first([callVariants_minAltTotal, 2]),
        minCov=select_first([minCov, 10]),
        noABPriorsFlag=select_first([callVariants_noABPriorsFlag, true]),
        reportMaxGLFlag=select_first([callVariants_reportMaxGLFlag, true]),
        gtQuals=select_first([callVariants_gtQuals, true]),
        skipCov=(select_first([skipCov, 500]) * length(bams))
    }
  }
  scatter (c in callVariants.out) {
     call C2.callSomaticFreeBayes as callSomatic {
      input:
        vcf=c,
        normalSampleName=normalSample
    }
  }
  call V.vcfcombine as combineRegions {
    input:
      vcf=callSomatic.out
  }
  call V2.vcfstreamsort as sortSomatic1 {
    input:
      vcf=combineRegions.out,
      inMemoryFlag=select_first([sortSomatic1_inMemoryFlag, true])
  }
  call B.bcftoolsNorm as normalizeSomatic1 {
    input:
      vcf=sortSomatic1.out,
      outputFilename=select_first([normalizeSomatic1_outputFilename, "normalised.vcf"]),
      reference=reference,
      reference_fai=reference_fai,
      outputType=select_first([normalizeSomatic1_outputType, "v"])
  }
  call V3.vcfallelicprimitives as allelicPrimitves {
    input:
      vcf=normalizeSomatic1.out,
      tagParsed=select_first([allelicPrimitves_tagParsed, "DECOMPOSED"]),
      keepGenoFlag=select_first([allelicPrimitves_keepGenoFlag, true])
  }
  call V4.vcffixup as fixSplitLines {
    input:
      vcf=allelicPrimitves.out
  }
  call V2.vcfstreamsort as sortSomatic2 {
    input:
      vcf=fixSplitLines.out,
      inMemoryFlag=select_first([sortSomatic2_inMemoryFlag, true])
  }
  call B.bcftoolsNorm as normalizeSomatic2 {
    input:
      vcf=sortSomatic2.out,
      outputFilename=select_first([normalizeSomatic2_outputFilename, "normalised.vcf"]),
      reference=reference,
      reference_fai=reference_fai,
      outputType=select_first([normalizeSomatic2_outputType, "v"])
  }
  call V5.vcfuniqalleles as uniqueAlleles {
    input:
      vcf=normalizeSomatic2.out
  }
  call V2.vcfstreamsort as sortFinal {
    input:
      vcf=uniqueAlleles.out,
      inMemoryFlag=select_first([sortFinal_inMemoryFlag, true])
  }
  call V6.vcfuniq as uniqVcf {
    input:
      vcf=sortFinal.out
  }
  call B2.bgzip as compressFinal {
    input:
      file=uniqVcf.out
  }
  call T.tabix as indexFinal {
    input:
      inp=compressFinal.out
  }
  output {
    File somaticOutVcf = indexFinal.out
    File somaticOutVcf_tbi = indexFinal.out_tbi
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.2
label: Freebayes somatic workflow (CRAM)
doc: |-
  This workflow uses the capabilities of freebayes to output all variants independent of the
          diploid model which then in turn allows us to create a likelihood based difference between
          the normal sample and an arbitrary amount of samples.
          This allows a joint somatic genotyping of multiple samples of the same individual.

requirements:
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement
- class: ScatterFeatureRequirement

inputs:
- id: bams
  doc: |-
    All bams to be analysed. Samples can be split over multiple bams as well as multiple samples can be contained in one bam as long as the sample ids are set properly.
  type:
    type: array
    items: File
  secondaryFiles:
  - pattern: .crai
- id: reference
  doc: The reference the bams were aligned to, with a fai index.
  type: File
  secondaryFiles:
  - pattern: .fai
- id: regionSize
  doc: |-
    the size of the regions, to parallelise the analysis over. This needs to be adjusted if there are lots of samples or very high depth sequencing in the analysis.
  type: int
  default: 10000000
- id: normalSample
  doc: The sample id of the normal sample, as it is specified in the bam header.
  type: string
- id: skipCov
  doc: |-
    The depth per sample, at which the variant calling process will skip a region. This is used to ignore regions with mapping issues, like the centromeres as well as heterochromatin. A good value is 3 times the maximum expected coverage.
  type: int
  default: 500
- id: minCov
  doc: Minimum coverage over all samples, to still call variants.
  type: int
  default: 10
- id: createCallRegions_equalize
  type: boolean
  default: true
- id: callVariants_pooledDiscreteFlag
  doc: |-
    Assume that samples result from pooled sequencing. Model pooled samples using discrete genotypes across pools. When using this flag, set --ploidy to the number of alleles in each sample or use the --cnv-map to define per-sample ploidy.
  type: boolean
  default: true
- id: callVariants_gtQuals
  doc: |2-
     -= --genotype-qualities Calculate the marginal probability of genotypes and report as GQ in each sample field in the VCF output.
  type: boolean
  default: true
- id: callVariants_strictFlag
  doc: Generate strict VCF format (FORMAT/GQ will be an int)
  type: boolean
  default: true
- id: callVariants_pooledContinousFlag
  doc: |-
    Output all alleles which pass input filters, regardles of genotyping outcome or model.
  type: boolean
  default: true
- id: callVariants_reportMaxGLFlag
  doc: |2-
     --report-genotype-likelihood-max Report genotypes using the maximum-likelihood estimate provided from genotype likelihoods.
  type: boolean
  default: true
- id: callVariants_noABPriorsFlag
  doc: |2-
     -a --allele-balance-priors-off Disable use of aggregate probability of observation balance between alleles as a component of the priors.
  type: boolean
  default: true
- id: callVariants_maxNumOfAlleles
  doc: |-
    Evaluate only the best N SNP alleles, ranked by sum of supporting quality scores. (Set to 0 to use all; default: all)
  type: int
  default: 4
- id: callVariants_noPartObsFlag
  doc: |-
    Exclude observations which do not fully span the dynamically-determined detection window. (default, use all observations, dividing partial support across matching haplotypes when generating haplotypes.)
  type: boolean
  default: true
- id: callVariants_useDupFlag
  doc: |-
    Include duplicate-marked alignments in the analysis. default: exclude duplicates marked as such in alignments
  type: boolean
  default: false
- id: callVariants_minBaseQual
  doc: |2-
     -q --min-base-quality Q Exclude alleles from analysis if their supporting base quality is less than Q. default: 0
  type: int
  default: 1
- id: callVariants_minSupMQsum
  doc: |2-
     -Y --min-supporting-mapping-qsum Q Consider any allele in which and the sum of mapping qualities of supporting reads is at least Q. default: 0
  type: int
  default: 0
- id: callVariants_minSupQsum
  doc: |2-
     -R --min-supporting-allele-qsum Q Consider any allele in which the sum of qualities of supporting observations is at least Q. default: 0
  type: int
  default: 0
- id: callVariants_minAltFrac
  doc: |2-
     -F --min-alternate-fraction N Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position. default: 0.05
  type: float
  default: 0.01
- id: callVariants_minAltQSum
  doc: |2-
     -3 --min-alternate-qsum N Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position. default: 0
  type: int
  default: 70
- id: callVariants_minAltTotal
  doc: |2-
     -G --min-alternate-total N Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis. default: 1
  type: int
  default: 2
- id: sortSomatic1_inMemoryFlag
  doc: load all sites and then sort in memory
  type: boolean
  default: true
- id: normalizeSomatic1_outputType
  doc: |-
    --output-type b|u|z|v: Output compressed BCF (b), uncompressed BCF (u), compressed VCF (z), uncompressed VCF (v). Use the -Ou option when piping between bcftools subcommands to speed up performance by removing unnecessary compression/decompression and VCF←→BCF conversion.
  type: string
  default: v
- id: normalizeSomatic1_outputFilename
  doc: |-
    --output: When output consists of a single stream, write it to FILE rather than to standard output, where it is written by default.
  type:
  - string
  - 'null'
  default: normalised.vcf
- id: allelicPrimitves_tagParsed
  doc: Tag records which are split apart of a complex allele with this flag
  type: string
  default: DECOMPOSED
- id: allelicPrimitves_keepGenoFlag
  doc: |-
    Maintain genotype-level annotations when decomposing.  Similar caution should be used for this as for --keep-info.
  type: boolean
  default: true
- id: sortSomatic2_inMemoryFlag
  doc: load all sites and then sort in memory
  type: boolean
  default: true
- id: normalizeSomatic2_outputType
  doc: |-
    --output-type b|u|z|v: Output compressed BCF (b), uncompressed BCF (u), compressed VCF (z), uncompressed VCF (v). Use the -Ou option when piping between bcftools subcommands to speed up performance by removing unnecessary compression/decompression and VCF←→BCF conversion.
  type: string
  default: v
- id: normalizeSomatic2_outputFilename
  doc: |-
    --output: When output consists of a single stream, write it to FILE rather than to standard output, where it is written by default.
  type:
  - string
  - 'null'
  default: normalised.vcf
- id: sortFinal_inMemoryFlag
  doc: load all sites and then sort in memory
  type: boolean
  default: true

outputs:
- id: somaticOutVcf
  type: File
  secondaryFiles:
  - pattern: .tbi
  outputSource: indexFinal/out

steps:
- id: createCallRegions
  label: Create genomic call regions
  in:
  - id: reference
    source: reference
  - id: regionSize
    source: regionSize
  - id: equalize
    source: createCallRegions_equalize
  run: tools/CreateCallRegions_v0_1_0.cwl
  out:
  - id: regions
- id: callVariants
  label: freebayes
  in:
  - id: bams
    source: bams
  - id: reference
    source: reference
  - id: region
    source: createCallRegions/regions
  - id: strictFlag
    source: callVariants_strictFlag
  - id: pooledDiscreteFlag
    source: callVariants_pooledDiscreteFlag
  - id: pooledContinousFlag
    source: callVariants_pooledContinousFlag
  - id: maxNumOfAlleles
    source: callVariants_maxNumOfAlleles
  - id: noPartObsFlag
    source: callVariants_noPartObsFlag
  - id: useDupFlag
    source: callVariants_useDupFlag
  - id: minBaseQual
    source: callVariants_minBaseQual
  - id: minSupQsum
    source: callVariants_minSupQsum
  - id: minSupMQsum
    source: callVariants_minSupMQsum
  - id: minAltFrac
    source: callVariants_minAltFrac
  - id: minAltQSum
    source: callVariants_minAltQSum
  - id: minAltTotal
    source: callVariants_minAltTotal
  - id: minCov
    source: minCov
  - id: noABPriorsFlag
    source: callVariants_noABPriorsFlag
  - id: reportMaxGLFlag
    source: callVariants_reportMaxGLFlag
  - id: gtQuals
    source: callVariants_gtQuals
  - id: _callVariants_skipCov_skipCov
    source: skipCov
  - id: _callVariants_skipCov_bams
    source: bams
  - id: skipCov
    valueFrom: |-
      $((inputs._callVariants_skipCov_skipCov * inputs._callVariants_skipCov_bams.length))
  scatter:
  - region
  run: tools/freebayes_cram_1_3_1.cwl
  out:
  - id: out
- id: callSomatic
  label: Call Somatic Variants from freebayes
  in:
  - id: vcf
    source: callVariants/out
  - id: normalSampleName
    source: normalSample
  scatter:
  - vcf
  run: tools/callSomaticFreeBayes_0_1_8.cwl
  out:
  - id: out
- id: combineRegions
  label: 'VcfLib: VcfCombine'
  in:
  - id: vcf
    source: callSomatic/out
  run: tools/vcfcombine_v1_0_1.cwl
  out:
  - id: out
- id: sortSomatic1
  label: 'VcfLib: VcfStreamSort'
  in:
  - id: vcf
    source: combineRegions/out
  - id: inMemoryFlag
    source: sortSomatic1_inMemoryFlag
  run: tools/vcfstreamsort_v1_0_1.cwl
  out:
  - id: out
- id: normalizeSomatic1
  label: 'BCFTools: Normalize'
  in:
  - id: vcf
    source: sortSomatic1/out
  - id: outputFilename
    source: normalizeSomatic1_outputFilename
  - id: reference
    source: reference
  - id: outputType
    source: normalizeSomatic1_outputType
  run: tools/bcftoolsNorm_v1_9.cwl
  out:
  - id: out
- id: allelicPrimitves
  label: 'VcfLib: VcfAllelicPrimitives'
  in:
  - id: vcf
    source: normalizeSomatic1/out
  - id: tagParsed
    source: allelicPrimitves_tagParsed
  - id: keepGenoFlag
    source: allelicPrimitves_keepGenoFlag
  run: tools/vcfallelicprimitives_v1_0_1.cwl
  out:
  - id: out
- id: fixSplitLines
  label: 'VcfLib: VcfFixUp'
  in:
  - id: vcf
    source: allelicPrimitves/out
  run: tools/vcffixup_v1_0_1.cwl
  out:
  - id: out
- id: sortSomatic2
  label: 'VcfLib: VcfStreamSort'
  in:
  - id: vcf
    source: fixSplitLines/out
  - id: inMemoryFlag
    source: sortSomatic2_inMemoryFlag
  run: tools/vcfstreamsort_v1_0_1.cwl
  out:
  - id: out
- id: normalizeSomatic2
  label: 'BCFTools: Normalize'
  in:
  - id: vcf
    source: sortSomatic2/out
  - id: outputFilename
    source: normalizeSomatic2_outputFilename
  - id: reference
    source: reference
  - id: outputType
    source: normalizeSomatic2_outputType
  run: tools/bcftoolsNorm_v1_9.cwl
  out:
  - id: out
- id: uniqueAlleles
  label: 'VcfLib: VcfUniqAlleles'
  in:
  - id: vcf
    source: normalizeSomatic2/out
  run: tools/vcfuniqalleles_v1_0_1.cwl
  out:
  - id: out
- id: sortFinal
  label: 'VcfLib: VcfStreamSort'
  in:
  - id: vcf
    source: uniqueAlleles/out
  - id: inMemoryFlag
    source: sortFinal_inMemoryFlag
  run: tools/vcfstreamsort_v1_0_1.cwl
  out:
  - id: out
- id: uniqVcf
  label: 'VcfLib: VcfUniq'
  in:
  - id: vcf
    source: sortFinal/out
  run: tools/vcfuniq_v1_0_1.cwl
  out:
  - id: out
- id: compressFinal
  label: BGZip
  in:
  - id: file
    source: uniqVcf/out
  run: tools/bgzip_1_2_1.cwl
  out:
  - id: out
- id: indexFinal
  label: Tabix
  in:
  - id: inp
    source: compressFinal/out
  run: tools/tabix_1_2_1.cwl
  out:
  - id: out
id: FreeBayesSomaticWorkflowCram