defaults.yaml

data_provenances:
  - gisaid
  - open

variant_classifications:
  - nextstrain_clades
  - pango_lineages

geo_resolutions:
  - global
  - usa

gisaid:
  s3_metadata: s3://nextstrain-ncov-private/metadata.tsv.zst
  subset_columns:
    - strain
    - date
    - country
    - division
    - clade_nextstrain
    - Nextclade_pango
    - QC_overall_status

  nextstrain_clades:
    global:
      seq_count_options: >-
        --clade-column clade_nextstrain
        --filter-columns QC_overall_status
        --filter-query "QC_overall_status != 'bad'"

    usa:
      seq_count_options: >-
        --location-column division
        --clade-column clade_nextstrain
        --filter-columns QC_overall_status country
        --filter-query "QC_overall_status != 'bad' & country == 'USA'"

  pango_lineages:
    global:
      seq_count_options: >-
        --clade-column Nextclade_pango
        --filter-columns QC_overall_status
        --filter-query "QC_overall_status != 'bad'"

    usa:
      seq_count_options: >-
        --location-column division
        --clade-column Nextclade_pango
        --filter-columns QC_overall_status country
        --filter-query "QC_overall_status != 'bad' & country == 'USA'"

open:
  s3_metadata: s3://nextstrain-data/files/ncov/open/metadata.tsv.zst
  subset_columns:
    - strain
    - date
    - country
    - division
    - clade_nextstrain
    - Nextclade_pango
    - QC_overall_status

  nextstrain_clades:
    global:
      seq_count_options: >-
        --clade-column clade_nextstrain
        --filter-columns QC_overall_status
        --filter-query "QC_overall_status != 'bad'"
    usa:
      seq_count_options: >-
        --location-column division
        --clade-column clade_nextstrain
        --filter-columns QC_overall_status country
        --filter-query "QC_overall_status != 'bad' & country == 'USA'"

  pango_lineages:
    global:
      seq_count_options: >-
        --clade-column Nextclade_pango
        --filter-columns QC_overall_status
        --filter-query "QC_overall_status != 'bad'"
    usa:
      seq_count_options: >-
        --location-column division
        --clade-column Nextclade_pango
        --filter-columns QC_overall_status country
        --filter-query "QC_overall_status != 'bad' & country == 'USA'"

s3_dst: s3://nextstrain-data/files/workflows/forecasts-ncov
cloudfront_domain: 'data.nextstrain.org'