config.yaml

strain_id_field: "accession"
# Use 'Egypt 1951' as the reference and root, following Mencattelli et al, 2023
# https://www.nature.com/articles/s41467-023-42185-7
reference: "defaults/reference_global.gb"
root: "mid_point"

# Sequences must be FASTA and metadata must be TSV
# Both files must be zstd compressed
sequences_url: "https://data.nextstrain.org/files/workflows/WNV/sequences.fasta.zst"
metadata_url: "https://data.nextstrain.org/files/workflows/WNV/metadata.tsv.zst"

# Pull in metadata and sequences from the ingest workflow
input_metadata: "data/metadata.tsv"
input_sequences: "data/sequences.fasta"

#subsampling:
  #all: --min-length '9800' --query "country == 'USA' & accession != 'NC_009942'"

# Define named subsampling groups below (e.g., "state", "country", "region",
# etc.). The workflow will run an `augur filter` command with the arguments
# defined by each named group. Each `augur filter` command operates on all
# available metadata and sequences and produces a text file containing the list
# of strain names that passed the filters. The workflow will collect the union
# of all strain names from the subsampling files and output the corresponding
# subset of metadata and sequences that will be used to build the phylogeny.
#
# As an example, we could define two named subsampling groups like the
# following:
#
# ```
# subsampling:
#   state: --query "division == 'WA'" --subsample-max-sequences 5000
#   neighboring_state: --query "division in ['CA', 'ID', 'OR', 'NV']" --subsample-max-sequences 5000
# ```
#
# These named subsampling groups will translate to the following two `augur filter` commands:
#
# ```
# augur filter \
#   --sequences data/sequences_all.fasta \
#   --metadata data/metadata_all.tsv \
#   --query "division == 'WA'" --subsample-max-sequences 5000 \
#   --output-strains results/subsampled_strains_state.txt
#
# augur filter \
#   --sequences data/sequences_all.fasta \
#   --metadata data/metadata_all.tsv \
#   --query "division in ['CA', 'ID', 'OR', 'NV']" --subsample-max-sequences 5000 \
#   --output-strains results/subsampled_strains_neighboring_state.txt
# ```
#
# Then, the workflow will collect the strains from each command to extract the
# corresponding metadata and sequences with the following command:
#
# ```
# augur filter \
#   --sequences data/sequences_all.fasta \
#   --metadata data/metadata_all.tsv \
#   --exclude-all \
#   --include results/subsampled_strains_state.txt results/subsampled_strains_neighboring_state.txt \
#   --output-sequences results/sequences_filtered.fasta \
#   --output-metadata results/metadata_filtered.tsv
# ```
#
# This command excludes all strains by default and then forces the inclusion of
# the strains selected by the subsampling logic defined above.
subsampling:
  region: --query "is_lab_host != 'true'" --query-columns is_lab_host:str --min-length '9800' --group-by region year --subsample-max-sequences 3000 --exclude defaults/exclude.txt
  force_include: --exclude-all --include defaults/include.txt

refine:
  treetime_params: --coalescent opt --date-inference marginal --date-confidence --keep-polytomies --clock-rate 0.000755

traits:
  metadata_columns: [
    'region',
    'country',
    'lineage',
  ]

export:
  description: "defaults/description.md"
  auspice_config: "defaults/auspice_config_global.json"