if we are going to pick a gnomad filter gnomADe_AF is more in line wi…

[malachig]

…th common practice than gnomAD_AF

Ideally we would honor the selection of gnomAD_AF, gnomADe_AF or gnomADg_AF specified by the user in the YAML file. For example in an immuno.yaml:

- method: exact
  force_report_coordinates: true
  annotation:
    file: "gs://griffith-lab-workflow-inputs/human_GRCh38_ens95/known_variants/gnomad_fixed_b38_exome.vc
f.gz"
    secondary_files:
    - "gs://griffith-lab-workflow-inputs/human_GRCh38_ens95/known_variants/gnomad_fixed_b38_exome.vcf.gz.tbi"
    data_format: vcf
    name: gnomADe
    vcf_fields:
    - AF
    - AF_AFR
    - AF_AMR
    - AF_ASJ
    - AF_EAS
    - AF_FIN
    - AF_NFE
    - AF_OTH
    - AF_SAS
    gnomad_filter: true
    check_existing: true

Currently it doesn't seem to matter what one puts under name

[johnmaruska]

Just checked and a solution to allow user input at the YAML level is already included -- it's just not through the annotations block. The input gnomad_field_name is propagated up to the pipeline level, so if that is added as an input it should have the behavior expected of modifying name in the annotations block