cwlVersion: v1.2
class: Workflow
id: kfdrc-jointgenotyping-refinement-workflow
label: Kids First DRC Joint Genotyping Workflow
doc: |
  # Kids First DRC Joint Genotyping Workflow
  Kids First Data Resource Center Joint Genotyping Workflow (cram-to-deNovoGVCF). Cohort sample variant calling and genotype refinement.
  Note: The DNA annotation has been significantly upgraded since v2.2.3, if you'd like to use the old version, revert to that release.

  Using existing gVCFs, likely from GATK Haplotype Caller, we follow this workflow: [Germline short variant discovery (SNPs + Indels)](https://software.broadinstitute.org/gatk/best-practices/workflow?id=11145), to create family joint calling and joint trios (typically mother-father-child) variant calls. Peddy is run to raise any potential issues in family relation definitions and sex assignment.

  If you would like to run this workflow using the cavatica public app, a basic primer on running public apps can be found [here](https://www.notion.so/d3b/Starting-From-Scratch-Running-Cavatica-af5ebb78c38a4f3190e32e67b4ce12bb).
  Alternatively, if you'd like to run it locally using `cwltool`, a basic primer on that can be found [here](https://www.notion.so/d3b/Starting-From-Scratch-Running-CWLtool-b8dbbde2dc7742e4aff290b0a878344d) and combined with app-specific info from the readme below.
  This workflow is the current production workflow, equivalent to this [Cavatica public app](https://cavatica.sbgenomics.com/public/apps#cavatica/apps-publisher/kfdrc-jointgenotyping-refinement-workflow).

  ![data service logo](https://github.com/d3b-center/d3b-research-workflows/raw/master/doc/kfdrc-logo-sm.png)

  ### Runtime Estimates
  - Trio of 6 GB gVCFs Input: 540 Minutes & ~$6.95

  ### Tips To Run:
  1. inputs vcf files are the gVCF files from GATK Haplotype Caller, need to have the index **.tbi** files copy to the same project too.
  1. If you are experiencing issues with Variant Recalibration either in VariantRecalibrator or ApplyVQSR, consider adjusting the max_gaussians. If a dataset gives fewer variants than the expected scale, the number of Gaussians for training should be turned down. Lowering the max-Gaussians forces the program to group variants into a smaller number of clusters, which results in more variants per cluster.
  1. ped file in the input shows the family relationship between samples, the format should be the same as in GATK website [link](https://gatkforums.broadinstitute.org/gatk/discussion/7696/pedigree-ped-files), the Individual ID, Paternal ID and Maternal ID must be the same as in the inputs vcf files header.
  1. Here we recommend to use GRCh38 as reference genome to do the analysis, positions in gVCF should be GRCh38 too.
  1. Reference locations:
      - https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0/
      - kfdrc bucket: s3://kids-first-seq-data/broad-references/, s3://kids-first-seq-data/pipeline-references/
      - cavatica: https://cavatica.sbgenomics.com/u/kfdrc-harmonization/kf-references/
  1. Suggested inputs:
      -  Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz
      -  Homo_sapiens_assembly38.dbsnp138.vcf
      -  hapmap_3.3.hg38.vcf.gz
      -  Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
      -  1000G_omni2.5.hg38.vcf.gz
      -  1000G_phase1.snps.high_confidence.hg38.vcf.gz
      -  Homo_sapiens_assembly38.dict
      -  Homo_sapiens_assembly38.fasta.fai
      -  Homo_sapiens_assembly38.fasta
      -  1000G_phase3_v4_20130502.sites.hg38.vcf
      -  hg38.even.handcurated.20k.intervals
      -  homo_sapiens_merged_vep_105_GRCh38.tar.gz, from ftp://ftp.ensembl.org/pub/release-105/variation/indexed_vep_cache/ - variant effect predictor cache.
      - gnomad_v3.1.1.custom.echtvar.zip
      -  wgs_evaluation_regions.hg38.interval_list
  1. Optional inputs:
      - dbNSFP4.3a_grch38.gz
        - dbNSFP4.3a_grch38.gz.tbi
        - dbNSFP4.3a_grch38.readme.txt
      - CADDv1.6-38-gnomad.genomes.r3.0.indel.tsv.gz
      - CADDv1.6-38-whole_genome_SNVs.tsv.gz
      - clinvar_20220507_chr.vcf.gz


  ## Import info on cloning the git repo
  This repo takes advantage of the git submodule feature.
  The germline annotation workflow is maintained in a different repo.
  Therefore, in order to get the rest of the code after cloning, you need to run: `git submodule init` and `git submodule update`.
  Currently this workflow uses tools from `v1.1.0` of the annotation workflow.
  If that is updated, submodule should be as well.
  More info on how this works [here](https://git-scm.com/book/en/v2/Git-Tools-Submodules)

  ### Annotation sub workflow
  Information of default annotation performed can be found in the [Kids First DRC Germline SNV Annotation Workflow docs](kf-annotation-tools/docs/GERMLINE_SNV_ANNOT_README.md)

  ## Other Resources
  - dockerfiles: https://github.com/d3b-center/bixtools

requirements:
- class: ScatterFeatureRequirement
- class: SubworkflowFeatureRequirement

inputs:
  input_vcfs: {type: 'File[]', doc: 'Input array of individual sample gVCF files'}
  axiomPoly_resource_vcf: {type: File, doc: 'Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz', "sbg:suggestedValue": {
      class: File, path: 60639016357c3a53540ca7c7, name: Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz}}
  axiomPoly_resource_tbi: {type: 'File?', doc: 'Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz.tbi', "sbg:suggestedValue": {
      class: File, path: 6063901d357c3a53540ca81b, name: Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz.tbi}}
  dbsnp_vcf: {type: File, doc: 'Homo_sapiens_assembly38.dbsnp138.vcf', "sbg:suggestedValue": {class: File, path: 6063901f357c3a53540ca84b,
      name: Homo_sapiens_assembly38.dbsnp138.vcf}}
  dbsnp_idx: {type: 'File?', doc: 'Homo_sapiens_assembly38.dbsnp138.vcf.idx', "sbg:suggestedValue": {class: File, path: 6063901e357c3a53540ca834,
      name: Homo_sapiens_assembly38.dbsnp138.vcf.idx}}
  hapmap_resource_vcf: {type: File, doc: 'Hapmap genotype SNP input vcf', "sbg:suggestedValue": {class: File, path: 60639016357c3a53540ca7be,
      name: hapmap_3.3.hg38.vcf.gz}}
  hapmap_resource_tbi: {type: 'File?', doc: 'Hapmap genotype SNP input tbi', "sbg:suggestedValue": {class: File, path: 60639016357c3a53540ca7c5,
      name: hapmap_3.3.hg38.vcf.gz.tbi}}
  mills_resource_vcf: {type: File, doc: 'Mills_and_1000G_gold_standard.indels.hg38.vcf.gz', "sbg:suggestedValue": {class: File, path: 6063901a357c3a53540ca7f3,
      name: Mills_and_1000G_gold_standard.indels.hg38.vcf.gz}}
  mills_resource_tbi: {type: 'File?', doc: 'Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi', "sbg:suggestedValue": {class: File,
      path: 6063901c357c3a53540ca806, name: Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi}}
  omni_resource_vcf: {type: File, doc: '1000G_omni2.5.hg38.vcf.gz', "sbg:suggestedValue": {class: File, path: 6063901e357c3a53540ca835,
      name: 1000G_omni2.5.hg38.vcf.gz}}
  omni_resource_tbi: {type: 'File?', doc: '1000G_omni2.5.hg38.vcf.gz.tbi', "sbg:suggestedValue": {class: File, path: 60639016357c3a53540ca7b1,
      name: 1000G_omni2.5.hg38.vcf.gz.tbi}}
  one_thousand_genomes_resource_vcf: {type: File, doc: '1000G_phase1.snps.high_confidence.hg38.vcf.gz, high confidence snps', "sbg:suggestedValue": {
      class: File, path: 6063901c357c3a53540ca80f, name: 1000G_phase1.snps.high_confidence.hg38.vcf.gz}}
  one_thousand_genomes_resource_tbi: {type: 'File?', doc: '1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi, high confidence snps',
    "sbg:suggestedValue": {class: File, path: 6063901e357c3a53540ca845, name: 1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi}}
  ped: {type: File, doc: 'Ped file for the family relationship'}
  reference_dict: {type: 'File?', doc: 'Homo_sapiens_assembly38.dict', "sbg:suggestedValue": {class: File, path: 60639019357c3a53540ca7e7,
      name: Homo_sapiens_assembly38.dict}}
  reference_fai: {type: 'File?', doc: 'Homo_sapiens_assembly38.fasta.fai', "sbg:suggestedValue": {class: File, path: 60639016357c3a53540ca7af,
      name: Homo_sapiens_assembly38.fasta.fai}}
  reference_fasta: {type: File, doc: 'Homo_sapiens_assembly38.fasta', "sbg:suggestedValue": {class: File, path: 60639014357c3a53540ca7a3,
      name: Homo_sapiens_assembly38.fasta}}
  snp_sites_vcf: {type: File, doc: '1000G_phase3_v4_20130502.sites.hg38.vcf', "sbg:suggestedValue": {class: File, path: 60639016357c3a53540ca7b5,
      name: 1000G_phase3_v4_20130502.sites.hg38.vcf}}
  snp_sites_idx: {type: 'File?', doc: '1000G_phase3_v4_20130502.sites.hg38.vcf.idx', "sbg:suggestedValue": {class: File, path: 6063901d357c3a53540ca819,
      name: 1000G_phase3_v4_20130502.sites.hg38.vcf.idx}}
  unpadded_intervals_file: {type: File, doc: 'hg38.even.handcurated.20k.intervals', "sbg:suggestedValue": {class: File, path: 5f500135e4b0370371c051b1,
      name: hg38.even.handcurated.20k.intervals}}
  wgs_evaluation_interval_list: {type: File, doc: 'wgs_evaluation_regions.hg38.interval_list', "sbg:suggestedValue": {class: File,
      path: 60639017357c3a53540ca7d3, name: wgs_evaluation_regions.hg38.interval_list}}
  snp_max_gaussians: {type: 'int?', doc: "Interger value for max gaussians in SNP VariantRecalibration. If a dataset gives fewer variants
      than the expected scale, the number of Gaussians for training should be turned down. Lowering the max-Gaussians forces the program
      to group variants into a smaller number of clusters, which results in more variants per cluster."}
  indel_max_gaussians: {type: 'int?', doc: "Interger value for max gaussians in INDEL VariantRecalibration. If a dataset gives fewer
      variants than the expected scale, the number of Gaussians for training should be turned down. Lowering the max-Gaussians forces
      the program to group variants into a smaller number of clusters, which results in more variants per cluster."}
  output_basename: string
  tool_name: {type: 'string?', default: "multi.vqsr.filtered.denovo.vep_105", doc: "File name string suffix to use for output files"}
  # Annotation
  bcftools_annot_clinvar_columns: {type: 'string?', doc: "csv string of columns from annotation to port into the input vcf", default: "INFO/ALLELEID,INFO/CLNDN,INFO/CLNDNINCL,INFO/CLNDISDB,INFO/CLNDISDBINCL,INFO/CLNHGVS,INFO/CLNREVSTAT,INFO/CLNSIG,INFO/CLNSIGCONF,INFO/CLNSIGINCL,INFO/CLNVC,INFO/CLNVCSO,INFO/CLNVI"}
  echtvar_anno_zips: {type: 'File[]?', doc: "Annotation ZIP files for echtvar anno", "sbg:suggestedValue": [{class: File, path: 65c64d847dab7758206248c6,
        name: gnomad.v3.1.1.custom.echtvar.zip}]}
  clinvar_annotation_vcf: {type: 'File?', secondaryFiles: ['.tbi'], doc: "additional bgzipped annotation vcf file"}
  # VEP-specific
  vep_ram: {type: 'int?', default: 32, doc: "In GB, may need to increase this value depending on the size/complexity of input"}
  vep_cores: {type: 'int?', default: 36, doc: "Number of cores to use. May need to increase for really large inputs"}
  vep_buffer_size: {type: 'int?', default: 100000, doc: "Increase or decrease to balance speed and memory usage"}
  vep_cache: {type: 'File', doc: "tar gzipped cache from ensembl/local converted cache", "sbg:suggestedValue": {class: File, path: 6332f8e47535110eb79c794f,
      name: homo_sapiens_merged_vep_105_indexed_GRCh38.tar.gz}}
  dbnsfp: {type: 'File?', secondaryFiles: [.tbi, ^.readme.txt], doc: "VEP-formatted plugin file, index, and readme file containing
      dbNSFP annotations"}
  dbnsfp_fields: {type: 'string?', doc: "csv string with desired fields to annotate. Use ALL to grab all", default: 'SIFT4G_pred,Polyphen2_HDIV_pred,Polyphen2_HVAR_pred,LRT_pred,MutationTaster_pred,MutationAssessor_pred,FATHMM_pred,PROVEAN_pred,VEST4_score,VEST4_rankscore,MetaSVM_pred,MetaLR_pred,MetaRNN_pred,M-CAP_pred,REVEL_score,REVEL_rankscore,PrimateAI_pred,DEOGEN2_pred,BayesDel_noAF_pred,ClinPred_pred,LIST-S2_pred,Aloft_pred,fathmm-MKL_coding_pred,fathmm-XF_coding_pred,Eigen-phred_coding,Eigen-PC-phred_coding,phyloP100way_vertebrate,phyloP100way_vertebrate_rankscore,phastCons100way_vertebrate,phastCons100way_vertebrate_rankscore,TWINSUK_AC,TWINSUK_AF,ALSPAC_AC,ALSPAC_AF,UK10K_AC,UK10K_AF,gnomAD_exomes_controls_AC,gnomAD_exomes_controls_AN,gnomAD_exomes_controls_AF,gnomAD_exomes_controls_nhomalt,gnomAD_exomes_controls_POPMAX_AC,gnomAD_exomes_controls_POPMAX_AN,gnomAD_exomes_controls_POPMAX_AF,gnomAD_exomes_controls_POPMAX_nhomalt,Interpro_domain,GTEx_V8_gene,GTEx_V8_tissue'}
  merged: {type: 'boolean?', doc: "Set to true if merged cache used", default: true}
  cadd_indels: {type: 'File?', secondaryFiles: [.tbi], doc: "VEP-formatted plugin file and index containing CADD indel annotations"}
  cadd_snvs: {type: 'File?', secondaryFiles: [.tbi], doc: "VEP-formatted plugin file and index containing CADD SNV annotations"}
  intervar: {type: 'File?', doc: "Intervar vcf-formatted file. Exonic SNVs only - for more comprehensive run InterVar. See docs for
      custom build instructions", secondaryFiles: [.tbi]}

outputs:
  collectvariantcallingmetrics: {type: 'File[]', doc: 'Variant calling summary and detailed metrics files', outputSource: picard_collectvariantcallingmetrics/output}
  peddy_html: {type: 'File[]', doc: 'html summary of peddy results', outputSource: peddy/output_html}
  peddy_csv: {type: 'File[]', doc: 'csv details of peddy results', outputSource: peddy/output_csv}
  peddy_ped: {type: 'File[]', doc: 'ped format summary of peddy results', outputSource: peddy/output_peddy}
  cgp_vep_annotated_vcf: {type: 'File[]', outputSource: annotate_vcf/annotated_vcf}

steps:
  prepare_reference:
    run: ../subworkflows/prepare_reference.cwl
    in:
      input_fasta: reference_fasta
      input_fai: reference_fai
      input_dict: reference_dict
    out: [indexed_fasta, reference_dict]
  index_axiomPoly:
    run: ../tools/tabix_index.cwl
    in:
      input_file: axiomPoly_resource_vcf
      input_index: axiomPoly_resource_tbi
    out: [output]
  index_dbsnp:
    run: ../tools/gatk_indexfeaturefile.cwl
    in:
      input_file: dbsnp_vcf
      input_index: dbsnp_idx
    out: [output]
  index_hapmap:
    run: ../tools/tabix_index.cwl
    in:
      input_file: hapmap_resource_vcf
      input_index: hapmap_resource_tbi
    out: [output]
  index_mills:
    run: ../tools/tabix_index.cwl
    in:
      input_file: mills_resource_vcf
      input_index: mills_resource_tbi
    out: [output]
  index_omni:
    run: ../tools/tabix_index.cwl
    in:
      input_file: omni_resource_vcf
      input_index: omni_resource_tbi
    out: [output]
  index_1k:
    run: ../tools/tabix_index.cwl
    in:
      input_file: one_thousand_genomes_resource_vcf
      input_index: one_thousand_genomes_resource_tbi
    out: [output]
  index_snp:
    run: ../tools/gatk_indexfeaturefile.cwl
    in:
      input_file: snp_sites_vcf
      input_index: snp_sites_idx
    out: [output]
  dynamicallycombineintervals:
    run: ../tools/script_dynamicallycombineintervals.cwl
    label: 'Combine intervals'
    doc: 'Merge interval lists based on number of gVCF inputs'
    in:
      input_vcfs: input_vcfs
      interval: unpadded_intervals_file
    out: [out_intervals]
  gatk_import_genotype_filtergvcf_merge:
    run: ../tools/gatk_import_genotype_filtergvcf_merge.cwl
    label: 'Genotype, filter, & merge'
    doc: 'Use GATK GenomicsDBImport, VariantFiltration GenotypeGVCFs, and picard MakeSitesOnlyVcf to genotype, filter and merge gVCF
      based on known sites'
    hints:
    - class: sbg:AWSInstanceType
      value: r5.4xlarge
    in:
      input_vcfs: input_vcfs
      interval: dynamicallycombineintervals/out_intervals
      dbsnp_vcf: index_dbsnp/output
      reference_fasta: prepare_reference/indexed_fasta
    scatter: [interval]
    out: [variant_filtered_vcf, sites_only_vcf]
  gatk_gathervcfs:
    run: ../tools/gatk_gathervcfs.cwl
    label: 'Gather VCFs'
    doc: 'Merge VCFs scattered from previous step'
    in:
      input_vcfs: gatk_import_genotype_filtergvcf_merge/sites_only_vcf
    out: [output]
  gatk_snpsvariantrecalibratorcreatemodel:
    run: ../tools/gatk_snpsvariantrecalibratorcreatemodel.cwl
    label: 'GATK VariantRecalibrator SNPs'
    doc: 'Create recalibration model for snps using GATK VariantRecalibrator, tranch values, and known site VCFs'
    in:
      dbsnp_resource_vcf: index_dbsnp/output
      hapmap_resource_vcf: index_hapmap/output
      omni_resource_vcf: index_omni/output
      one_thousand_genomes_resource_vcf: index_1k/output
      sites_only_variant_filtered_vcf: gatk_gathervcfs/output
      max_gaussians: snp_max_gaussians
    out: [model_report]
  gatk_indelsvariantrecalibrator:
    run: ../tools/gatk_indelsvariantrecalibrator.cwl
    label: 'GATK VariantRecalibrator Indels'
    doc: 'Create recalibration model for indels using GATK VariantRecalibrator, tranch values, and known site VCFs'
    in:
      axiomPoly_resource_vcf: index_axiomPoly/output
      dbsnp_resource_vcf: index_dbsnp/output
      mills_resource_vcf: index_mills/output
      sites_only_variant_filtered_vcf: gatk_gathervcfs/output
      max_gaussians: indel_max_gaussians
    out: [recalibration, tranches]
  gatk_snpsvariantrecalibratorscattered:
    run: ../tools/gatk_snpsvariantrecalibratorscattered.cwl
    label: 'GATK VariantRecalibrator Scatter'
    doc: 'Create recalibration model for known sites from input data using GATK VariantRecalibrator, tranch values, and known site
      VCFs'
    hints:
    - class: sbg:AWSInstanceType
      value: r5.4xlarge
    in:
      sites_only_variant_filtered_vcf: gatk_import_genotype_filtergvcf_merge/sites_only_vcf
      model_report: gatk_snpsvariantrecalibratorcreatemodel/model_report
      hapmap_resource_vcf: index_hapmap/output
      omni_resource_vcf: index_omni/output
      one_thousand_genomes_resource_vcf: index_1k/output
      dbsnp_resource_vcf: index_dbsnp/output
      max_gaussians: snp_max_gaussians
    scatter: [sites_only_variant_filtered_vcf]
    out: [recalibration, tranches]
  gatk_gathertranches:
    run: ../tools/gatk_gathertranches.cwl
    label: 'GATK GatherTranches'
    doc: 'Gather tranches from SNP variant recalibrate scatter'
    in:
      tranches: gatk_snpsvariantrecalibratorscattered/tranches
    out: [output]
  gatk_applyrecalibration:
    run: ../tools/gatk_applyrecalibration.cwl
    label: 'GATK ApplyVQSR'
    doc: 'Apply recalibration to snps and indels'
    hints:
    - class: sbg:AWSInstanceType
      value: r5.4xlarge
    in:
      indels_recalibration: gatk_indelsvariantrecalibrator/recalibration
      indels_tranches: gatk_indelsvariantrecalibrator/tranches
      input_vcf: gatk_import_genotype_filtergvcf_merge/variant_filtered_vcf
      snps_recalibration: gatk_snpsvariantrecalibratorscattered/recalibration
      snps_tranches: gatk_gathertranches/output
    scatter: [input_vcf, snps_recalibration]
    scatterMethod: dotproduct
    out: [recalibrated_vcf]
  gatk_gatherfinalvcf:
    run: ../tools/gatk_gatherfinalvcf.cwl
    label: 'GATK GatherVcfsCloud'
    doc: 'Combine resultant VQSR VCFs'
    in:
      input_vcfs: gatk_applyrecalibration/recalibrated_vcf
      output_basename: output_basename
    out: [output]
  peddy:
    run: ../tools/kfdrc_peddy_tool.cwl
    label: 'Peddy'
    doc: 'QC family relationships and sex assignment'
    in:
      ped: ped
      vqsr_vcf: gatk_gatherfinalvcf/output
      output_basename: output_basename
    out: [output_html, output_csv, output_peddy]
  picard_collectvariantcallingmetrics:
    run: ../tools/picard_collectvariantcallingmetrics.cwl
    label: 'CollectVariantCallingMetrics'
    doc: 'picard calculate variant calling metrics'
    in:
      input_vcf: gatk_gatherfinalvcf/output
      reference_dict: prepare_reference/reference_dict
      output_basename: output_basename
      dbsnp_vcf: index_dbsnp/output
      wgs_evaluation_interval_list: wgs_evaluation_interval_list
    out: [output]
  gatk_calculategenotypeposteriors:
    in:
      ped: ped
      reference_fasta: prepare_reference/indexed_fasta
      snp_sites: index_snp/output
      vqsr_vcf: gatk_gatherfinalvcf/output
      output_basename: output_basename
    out: [output]
    run: ../tools/gatk_calculategenotypeposteriors.cwl
  gatk_variantfiltration:
    in:
      cgp_vcf: gatk_calculategenotypeposteriors/output
      reference_fasta: prepare_reference/indexed_fasta
      output_basename: output_basename
    out: [output]
    run: ../tools/gatk_variantfiltration.cwl
  gatk_variantannotator:
    in:
      cgp_filtered_vcf: gatk_variantfiltration/output
      ped: ped
      reference_fasta: prepare_reference/indexed_fasta
      output_basename: output_basename
    out: [output]
    run: ../tools/gatk_variantannotator.cwl
  annotate_vcf:
    run: ../kf-annotation-tools/workflows/kfdrc-germline-snv-annot-workflow.cwl
    in:
      indexed_reference_fasta: prepare_reference/indexed_fasta
      input_vcf: gatk_variantannotator/output
      output_basename: output_basename
      tool_name: tool_name
      bcftools_annot_clinvar_columns: bcftools_annot_clinvar_columns
      echtvar_anno_zips: echtvar_anno_zips
      clinvar_annotation_vcf: clinvar_annotation_vcf
      vep_ram: vep_ram
      vep_cores: vep_cores
      vep_buffer_size: vep_buffer_size
      vep_cache: vep_cache
      dbnsfp: dbnsfp
      dbnsfp_fields: dbnsfp_fields
      cadd_indels: cadd_indels
      cadd_snvs: cadd_snvs
      merged: merged
      intervar: intervar
    out: [annotated_vcf]


$namespaces:
  sbg: https://sevenbridges.com
hints:
- class: sbg:maxNumberOfParallelInstances
  value: 2
"sbg:license": Apache License 2.0
"sbg:publisher": KFDRC
"sbg:categories":
- GATK
- GENOTYPING
- JOINT
- PEDDY
- VCF
- VEP
"sbg:links":
- id: 'https://github.com/kids-first/kf-jointgenotyping-workflow/releases/tag/v2.4.0'
  label: github-release