builds.yaml

# Define locations for which builds should be created.
# For each build we specify a subsampling scheme via an explicit key.
# If the name of the focal geography differs from the build name this needs to
# be specified explicity as geographic_name. In addition, we require the
# geographic scale the build focuses on. Together name and scale serve a look-up
# in the geo_hierarchy to define region, country, division, etc
# Define custom rules for pre- or post-standard workflow processing of data.
custom_rules:
  - nextstrain_profiles/nextstrain/subsampling_ranges.smk
  - ecdc_profile/localrules.smk

inputs:
  - name: gisaid
    metadata: "s3://nextstrain-ncov-private/metadata.tsv.gz"
    sequences: "s3://nextstrain-ncov-private/sequences.fasta.gz"

S3_BUCKET: "nextstrain-ncov-private"
nextalign_bin: "nextalign"
genes: ["ORF1a", "ORF1b", "S", "ORF3a", "M", "N"]
use_nextalign: true

local_builds:
  austria:
    country_name: "Austria"
    divisions:
      - "Tyrol"
      - "Vorarlberg"
      - "Vienna"
      - "Styria"
      - "Carinthia"
      - "Upper Austria"
      - "Lower Austria"
      - "Salzburg"
      - "Burgenland"
  germany:
    country_name: "Germany"
    divisions:
      - "Schleswig-Holstein"
      - "Hamburg"
      - "Bremen"
      - "Brandenburg"
      - "Berlin"
      - "Thuringia"
      - "Niedersachsen"
      - "North Rhine Westphalia"
      - "Saxony"
      - "Saxony-Anhalt"
      - "Saarland"
      - "Hesse"
      - "Rheinland-Pfalz"
      - "Mecklenburg-Vorpommern"
      - "Baden-Wuerttemberg"
      - "Bavaria"

builds:
  europe:
    subsampling_scheme: custom_region
    geographic_scale: region
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
    region: Europe

  russia:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
    country: Russia
  serbia:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
    country: Serbia
  bosnia-and-herzegovina:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
    country: "Bosnia and Herzegovina"
  bulgaria:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
    country: Bulgaria
  latvia:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
    country: Latvia
  slovakia:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
    country: Slovakia
  slovenia:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
    country: Slovenia
  poland:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
    country: Poland
  belarus:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
    country: Belarus
  estonia:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
    country: Estonia
  lithuania:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
    country: Lithuania
  hungary:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
    country: Hungary
  croatia:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
    country: Croatia
  france:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
    country: France
  iceland:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
    country: Iceland
  norway:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
    country: Norway
  denmark:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    subclades: "ecdc_profile/subclades_denmark.tsv"
    country: Denmark
  netherlands:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
    country: Netherlands
  belgium:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
    country: Belgium
  luxembourg:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
    country: Luxembourg
  germany:
    subsampling_scheme: custom_country
    geographic_scale: country
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
    region: Europe
    country: Germany
  austria:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
    country: Austria
  switzerland:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
    country: Switzerland
  italy:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
    country: Italy
  spain:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
    country: Spain
  czech-republic:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
    country: Czech Republic
  united-kingdom:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
    country: United Kingdom
  ireland:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    country: Ireland
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
  finland:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    country: Finland
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
  sweden:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    country: Sweden
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
  portugal:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    country: Portugal
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
  greece:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    country: Greece
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
  israel:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    country: Israel
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
  romania:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    country: Romania
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
  turkey:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Europe
    country: Turkey
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"
  india:
    subsampling_scheme: custom_country
    geographic_scale: country
    region: Asia
    country: India
    subclades: "nextstrain_profiles/nextstrain/subclades_EU.tsv"

title: "Phylogenetic analysis of SARS-CoV-2 diversity in Europe"

traits:
  default:
    sampling_bias_correction: 2.5
    columns: ["region_exposure"]

exposure:
  default:
    trait: "region"
    exposure: "region_exposure"

files:
  colors: "ecdc_profile/colors.tsv"
  auspice_config: "ecdc_profile/auspice_config_ecdc.json"
  description: "ecdc_profile/description.md"

subsampling:
  # Custom subsampling logic for regions like Europe where grouping by country
  # is the smallest resolution required.
  custom_region:
    # Focal samples for region
    region_early:
      group_by: "country year month"
      max_sequences: 500
      exclude: "--exclude-where 'region!={region}'"
    # Contextual samples for region from the rest of the world
    global_early:
      group_by: "country year month"
      max_sequences: 500
      exclude: "--exclude-where 'region={region}'"
      priorities:
        type: "proximity"
        focus: "region_late"

    # Focal samples for region
    region_recent:
      group_by: "country year month"
      max_sequences: 500
      exclude: "--exclude-where 'region!={region}'"
    # Contextual samples for region from the rest of the world
    region_late:
      group_by: "country year month"
      max_sequences: 500
      exclude: "--exclude-where 'region!={region}'"
    # Contextual samples for region from the rest of the world
    global_late:
      group_by: "country year month"
      max_sequences: 700
      exclude: "--exclude-where 'region={region}'"
      priorities:
        type: "proximity"
        focus: "region_late"

  # Default subsampling logic for countries
  custom_country:
    # Focal samples for country
    country_early:
      group_by: "division year month"
      max_sequences: 500
      exclude: "--exclude-where 'country!={country}'"
    country_late:
      group_by: "division year month"
      max_sequences: 800
      exclude: "--exclude-where 'country!={country}'"
    country_recent:
      group_by: "division year month"
      max_sequences: 700
      exclude: "--exclude-where 'country!={country}'"
    # Contextual samples from country's region
    region_early:
      group_by: "country year month"
      max_sequences: 250
      exclude: "--exclude-where 'country={country}' 'region!={region}'"
      priorities:
        type: "proximity"
        focus: "country_early"
    # Contextual samples from the rest of the world,
    # excluding the current region to avoid resampling.
    global_early:
      group_by: "country year month"
      max_sequences: 300
      exclude: "--exclude-where 'region={region}'"
      priorities:
        type: "proximity"
        focus: "country_early"
    region_late:
      group_by: "country year month"
      max_sequences: 750
      exclude: "--exclude-where 'country={country}' 'region!={region}'"
      priorities:
        type: "proximity"
        focus: "country_late"
    # Contextual samples from the rest of the world,
    # excluding the current region to avoid resampling.
    global_late:
      group_by: "country year month"
      max_sequences: 500
      exclude: "--exclude-where 'region={region}'"
      priorities:
        type: "proximity"
        focus: "country_late"

  custom_division:
    # Focal samples for division
    division_recent:
      group_by: "year month"
      max_sequences: 1000
      sampling_scheme: "--probabilistic-sampling"
      exclude: "--exclude-where 'region!={region}' 'country!={country}' 'division!={division}'"
    country_recent:
      group_by: "division year month"
      max_sequences: 1000
      sampling_scheme: "--probabilistic-sampling"
      exclude: "--exclude-where 'country!={country}'"
    # Focal samples for division
    division_late:
      group_by: "year month"
      max_sequences: 500
      sampling_scheme: "--probabilistic-sampling"
      exclude: "--exclude-where 'region!={region}' 'country!={country}' 'division!={division}'"
    country_late:
      group_by: "division year month"
      max_sequences: 500
      sampling_scheme: "--probabilistic-sampling"
      exclude: "--exclude-where 'country!={country}'"
    country_early:
      group_by: "division year month"
      max_sequences: 300
      sampling_scheme: "--probabilistic-sampling"
      exclude: "--exclude-where 'country!={country}'"
    # Contextual samples from country's region
    region_late:
      group_by: "country year month"
      max_sequences: 200
      sampling_scheme: "--probabilistic-sampling"
      exclude: "--exclude-where 'country={country}' 'region!={region}'"
      priorities:
        type: "proximity"
        focus: "country_late"
    region_early:
      group_by: "country year month"
      max_sequences: 200
      sampling_scheme: "--probabilistic-sampling"
      exclude: "--exclude-where 'country={country}' 'region!={region}'"
      priorities:
        type: "proximity"
        focus: "country_late"
    # Contextual samples from the rest of the world,
    # excluding the current region to avoid resampling.
    global_early:
      group_by: "country year month"
      max_sequences: 100
      sampling_scheme: "--probabilistic-sampling"
      exclude: "--exclude-where 'region={region}'"
      priorities:
        type: "proximity"
        focus: "country_late"
    global_late:
      group_by: "country year month"
      max_sequences: 200
      sampling_scheme: "--probabilistic-sampling"
      exclude: "--exclude-where 'region={region}'"
      priorities:
        type: "proximity"
        focus: "country_late"