gisaid.yaml

#### Parameters which define which builds to produce via this config ###
builds:
  h5nx: 
    - all-time
    - 2y
  h5n1: 
    - all-time
    - 2y
  h7n9: 
    - all-time
  h9n2: 
    - all-time

segments:
  - pb2
  - pb1
  - pa
  - ha
  - np
  - na
  - mp
  - ns

#### Parameters which define the input source ####
s3_src:
  name: gisaid
  metadata: s3://nextstrain-data-private/files/workflows/avian-flu/metadata.tsv.zst
  sequences: s3://nextstrain-data-private/files/workflows/avian-flu/{segment}/sequences.fasta.zst
local_ingest: false
# P.S. To use local ingest files, comment out s3_src and change to local_ingest: fauna


#### Parameters which control large overarching aspects of the build
target_sequences_per_tree: 3000
same_strains_per_segment: false


#### Config files ####
reference: config/{subtype}/reference_{subtype}_{segment}.gb
auspice_config: config/{subtype}/auspice_config_{subtype}.json
colors: config/{subtype}/colors_{subtype}.tsv
lat_longs: config/{subtype}/lat_longs_{subtype}.tsv
include_strains: config/{subtype}/include_strains_{subtype}_{time}.txt
dropped_strains: config/{subtype}/dropped_strains_{subtype}.txt
clades_file: clade-labeling/{subtype}-clades.tsv
description: config/description_gisaid.md


#### Rule-specific parameters ####
filter:
  # rule parameters are typically defined for each build - e.g.
  # min_length.h5nx.2y = ... The "FALLBACK" key (e.g. min_length.FALLBACK)
  # is used as a fallback value if nothing is specifically defined
  # for the subtype/time combination.
  # Some parameters have an extra hierarchy of segment, some don't
  min_length:
    FALLBACK:
      pb2: 2100
      pb1: 2100
      pa: 2000
      ha: 1600
      np: 1400
      na: 1270
      mp: 900
      ns: 800

  min_date:
    h5nx:
      all-time: 1996
      2y: 2Y
    h5n1:
      all-time: 1996
      2y: 2Y
    h7n9:
      all-time: 2013
    h9n2:
      all-time: 1966

  group_by:
    h5nx:
      all-time: subtype country year
      2y: subtype region month host
    h5n1:
      all-time: region country year
      2y: subtype region month host
    h7n9:
      all-time: division year
    h9n2:
      all-time: country year

  exclude_where:
    FALLBACK: host=laboratoryderived host=ferret host=unknown host=other host=host country=? region=? gisaid_clade=3C.2

refine:
  coalescent: const
  date_inference: marginal

  clock_filter_iqd:
    FALLBACK: 4

  root:
    FALLBACK: false

  __clock_std_dev:  &clock_std_dev  0.00211 # YAML anchor so we can reference this value

  clock_rates:
    FALLBACK:            # anything not specified by a subtype/time combination
        pb2: ''          # falls back to FALLBACK, and the empty string means no
        pb1: ''          # supplied clock rate, i.e. infer the clock
        pa: ''
        ha: ''
        np: ''
        na: ''
        mp: ''
        ns: ''
    h5nx:
      2y:
        pb2: [0.00287, *clock_std_dev]
        pb1: [0.00267, *clock_std_dev]
        pa: [0.00238, *clock_std_dev]
        ha: [0.0048, *clock_std_dev]
        np: [0.0022, *clock_std_dev]
        na: [0.0028, *clock_std_dev]
        mp: [0.0017, *clock_std_dev]
        ns: [0.0017, *clock_std_dev]
    h5n1:
      2y:
        pb2: [0.00287, *clock_std_dev]
        pb1: [0.00264, *clock_std_dev]
        pa: [0.00248, *clock_std_dev]
        ha: [0.00455, *clock_std_dev]
        np: [0.00252, *clock_std_dev]
        na: [0.00349, *clock_std_dev]
        mp: [0.00191, *clock_std_dev]
        ns: [0.00249, *clock_std_dev]


ancestral:
  inference: joint
  root_seq:
    FALLBACK: false

traits:
  columns:
    h5nx:
      all-time: region
      2y: region
    h5n1:
      all-time: region country
      2y: region country
    h7n9:
      all-time: country division
    h9n2:
      all-time: region country

  sampling_bias_correction:
    FALLBACK: false

  confidence:
    FALLBACK: true

export:
  title:
    FALLBACK: false # use the title in the auspice JSON
    # TODO - if we parameterise this here we can use the subtype wildcard to customise the title