# Stand-alone build config demonstrating `augur subsample` proximity sampling.
#
# This produces a single 'genome/north-america-outbreak-example' build that
# focuses on Montana measles cases alongside their nearest genetic context

builds:
  - genome/north-america-outbreak-example

# We use PPX restricted data for this example
additional_inputs:
  - name: ppx_restricted
    metadata: "s3://nextstrain-data/files/workflows/measles/metadata_restricted.tsv.zst"
    sequences: "s3://nextstrain-data/files/workflows/measles/sequences_restricted.fasta.zst"

files:
    auspice_config: "auspice_config.json"

subsample:
    genome/north-america-outbreak-example:
        samples:
            genotype-d8:
                exclude_where:
                    - "genotype_ppx!=D8"
                exclude: dropped_strains.txt
                drop_sample: true
            background:
                context_sample: genotype-d8
                max_sequences: 500
                group_by:
                    - region
                    - year
            montana-outbreak:
                context_sample: genotype-d8
                min_date: "2025-01-01"
                exclude_where:
                    - "division!=Montana"
            nearest-strains:
                method: hamming
                focal_sample: montana-outbreak
                context_sample: genotype-d8
                k: 20
                ignore_missing_data: all

refine:
    genome/north-america-outbreak-example:
        --timetree
        --coalescent opt
        --date-inference marginal
        --date-confidence
        --clock-filter-iqd 8
        --stochastic-resolve
        --divergence-units mutations-per-site

traits:
    genome/north-america-outbreak-example:
        columns:
            - division
        sampling_bias_correction: 3

export:
    genome/north-america-outbreak-example:
      metadata_columns: "strain division location dataUseTerms restrictedUntil PPX_accession INSDC_accession"
      warning: >-
        This dataset represents an example usage of augur subsample with proximity sampling
        to focus on Montana measles cases