EV-clade-algorithm/config.yaml at master · hodcroftlab/EV-clade-algorithm · GitHub

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# config.yaml - all virus parameters in one place
# Users edit ONE file; no per-virus JSON configs needed

# Global defaults
defaults:
  local_tree: false
  max_date: 2026-12-31
  min_date: 2020-01-01
  date_range_type: "tip_date"
  alias: "default" # default or manual
  proteins: []
  weights:
    VP1:
      default: 1
  clade_key: "clade_membership" # name of metadata field to store clade membership in auspice JSON (e.g. "clade_membership")

# Virus-specific parameters (overrides global defaults)
## Structure:
#      <virus>: (virus_name)
#          <parameters> (used for algorithm)

viruses:
  ev-d68:
    # Input source
    tree_url: "https://nextstrain.org/charon/getDataset?prefix=groups/hodcroftlab/enterovirus/d68/genome"

    # Algorithm parameters (virus-specific tuned values)
    cutoff: 1.3
    divergence_addition: 1
    divergence_scale: 5
    min_size: 30
    bushiness_branch_scale: 9
    branch_length_scale: 5

  ev-a71:
    tree_url: "https://nextstrain.org/charon/getDataset?prefix=groups/hodcroftlab/enterovirus/A71/whole-genome"
    cutoff: 1.1
    divergence_addition: 0.9
    divergence_scale: 32
    min_size: 20
    bushiness_branch_scale: 13
    branch_length_scale: 8

  cva16:
    tree_url: "https://nextstrain.org/charon/getDataset?prefix=groups/hodcroftlab/coxsackievirus/A16/whole-genome"
    cutoff: 1.1
    divergence_addition: 0.5
    divergence_scale: 5
    min_size: 20
    bushiness_branch_scale: 20
    branch_length_scale: 8

  cva10:
    tree_url: "https://nextstrain.org/charon/getDataset?prefix=groups/hodcroftlab/coxsackievirus/A10/whole-genome"
    cutoff: 1.1
    divergence_addition: 0.5
    min_size: 20
    bushiness_branch_scale: 25
    # branch_length_scale: 10
    # divergence_scale: 10

# Parameter sweep ranges (for sensitivity analysis)
sweep:
  cutoff: [0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5]
  divergence_addition: [0.5, 0.7, 0.9, 1.1]
  divergence_scale: [0.1, 1, 5, 10, 20]
  min_size: [5, 10, 15, 20, 25]
  bushiness_branch_scale: [5, 10, 100]
  branch_length_scale: [2, 10, 20]