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nextstrain-public.yaml
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nextstrain-public.yaml
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custom_rules:
- workflow/snakemake_rules/download_from_s3.smk
- profiles/nextstrain-public/rename.smk
- profiles/nextstrain-public/deploy.smk
# URL for auto-deploying builds
deploy_url: s3://nextstrain-data
fasta_fields:
- strain
- virus
- segment
- accession
- date
- date_submitted
- region
- country
- division
- location
- passage_category
- originating_lab
- submitting_lab
- age
- gender
prettify_fields:
- region
- country
- division
- location
- originating_lab
- submitting_lab
lat-longs: "config/lat_longs.tsv"
segments:
- ha
- na
tree:
tree-builder-args: "'-ninit 10 -n 4 -czb'"
submission_date_field: date_submitted
recency:
date_bins: [7, 30, 90]
date_bin_labels: ["last week", "last month", "last quarter"]
upper_bin_label: older
array-builds:
6M-hi-builds:
patterns:
lineage:
- h1n1pdm
- vic
min_date:
- 6M
reference_min_date:
- 6Y6M
resolution:
- 6m
build_name: "seasonal-flu_{lineage}_6m"
build_params: &shared-hi-build-params
auspice_name: "seasonal-flu_{lineage}_{{segment}}_{resolution}"
reference: "config/{lineage}/{{segment}}/reference.fasta"
annotation: "config/{lineage}/{{segment}}/genemap.gff"
tree_exclude_sites: "config/{lineage}/{{segment}}/exclude-sites.txt"
clades: "config/{lineage}/ha/clades.tsv"
subclades: "config/{lineage}/{{segment}}/subclades.tsv"
auspice_config: "config/{lineage}/auspice_config.json"
vaccines: "config/{lineage}/vaccine.json"
enable_glycosylation: true
enable_lbi: true
enable_titer_models: true
enable_embeddings: true
include: "'config/{lineage}/reference_strains.txt'"
exclude: "'config/{lineage}/outliers.txt'"
titer_collections:
- name: cdc_cell_hi
data: "data/{lineage}/cdc_ferret_cell_hi_titers.tsv"
subsamples: &subsampling-scheme
regions_except_europe:
filters: --query "(passage_category != 'egg') & (region != 'Europe') & (ha == True) & (na == True)" --group-by region year month --subsample-max-sequences 2700 --min-date {min_date} --exclude {exclude} --exclude-where passage=egg
priorities: "titers"
europe:
filters: --query "(passage_category != 'egg') & (region == 'Europe') & (ha == True) & (na == True)" --group-by country year month --subsample-max-sequences 300 --min-date {min_date} --exclude {exclude} --exclude-where passage=egg
priorities: "titers"
references:
filters: --query "(is_reference == True)" --min-date {reference_min_date} --exclude-where passage=egg
2Y-hi-builds:
patterns:
lineage:
- h1n1pdm
- vic
min_date:
- 2Y
reference_min_date:
- 8Y
resolution:
- 2y
build_name: "seasonal-flu_{lineage}_2y"
build_params:
auspice_name: "seasonal-flu_{lineage}_{{segment}}_{resolution}"
reference: "config/{lineage}/{{segment}}/reference.fasta"
annotation: "config/{lineage}/{{segment}}/genemap.gff"
tree_exclude_sites: "config/{lineage}/{{segment}}/exclude-sites.txt"
clades: "config/{lineage}/ha/clades.tsv"
subclades: "config/{lineage}/{{segment}}/subclades.tsv"
auspice_config: "config/{lineage}/{{segment}}/auspice_config.json"
vaccines: "config/{lineage}/vaccine.json"
enable_glycosylation: true
enable_lbi: true
enable_titer_models: true
enable_embeddings: true
include: "'config/{lineage}/reference_strains.txt'"
exclude: "'config/{lineage}/outliers.txt'"
titer_collections:
- name: cdc_cell_hi
data: "data/{lineage}/cdc_ferret_cell_hi_titers.tsv"
subsamples: *subsampling-scheme
3Y-hi-builds:
patterns:
lineage:
- h1n1pdm
- vic
min_date:
- 3Y
reference_min_date:
- 9Y
resolution:
- 3y
build_name: "seasonal-flu_{lineage}_3y"
build_params: *shared-hi-build-params
subsamples: *subsampling-scheme
6Y-hi-builds:
patterns:
lineage:
- h1n1pdm
- vic
min_date:
- 6Y
reference_min_date:
- 12Y
resolution:
- 6y
build_name: "seasonal-flu_{lineage}_6y"
build_params: *shared-hi-build-params
subsamples: *subsampling-scheme
12Y-hi-builds:
patterns:
lineage:
- h1n1pdm
- vic
min_date:
- 12Y
reference_min_date:
- 18Y
resolution:
- 12y
build_name: "seasonal-flu_{lineage}_12y"
build_params: *shared-hi-build-params
subsamples: *subsampling-scheme
6M-fra-builds:
patterns:
min_date:
- 6M
reference_min_date:
- 6Y6M
resolution:
- 6m
build_name: "seasonal-flu_h3n2_6m"
build_params: &shared-fra-build-params
lineage: h3n2
auspice_name: "seasonal-flu_{lineage}_{{segment}}_{resolution}"
reference: "config/{lineage}/{{segment}}/reference.fasta"
annotation: "config/{lineage}/{{segment}}/genemap.gff"
tree_exclude_sites: "config/{lineage}/{{segment}}/exclude-sites.txt"
clades: "config/{lineage}/ha/clades.tsv"
subclades: "config/{lineage}/{{segment}}/subclades.tsv"
auspice_config: "config/{lineage}/auspice_config.json"
vaccines: "config/{lineage}/vaccine.json"
enable_glycosylation: true
enable_lbi: true
enable_titer_models: true
enable_embeddings: true
include: "'config/{lineage}/reference_strains.txt'"
exclude: "'config/{lineage}/outliers.txt'"
titer_collections:
- name: cdc_cell_fra
data: "data/h3n2/cdc_ferret_cell_fra_titers.tsv"
subsamples: *subsampling-scheme
# 2Y H3N2 builds are a special case where we enable forecasts.
2Y-fra-builds:
patterns:
min_date:
- 2Y
reference_min_date:
- 8Y
resolution:
- 2y
build_name: "seasonal-flu_h3n2_2y"
build_params:
lineage: h3n2
auspice_name: "seasonal-flu_{lineage}_{{segment}}_{resolution}"
reference: "config/{lineage}/{{segment}}/reference.fasta"
annotation: "config/{lineage}/{{segment}}/genemap.gff"
tree_exclude_sites: "config/{lineage}/{{segment}}/exclude-sites.txt"
clades: "config/{lineage}/ha/clades.tsv"
subclades: "config/{lineage}/{{segment}}/subclades.tsv"
emerging_subclades: "config/h3n2/{{segment}}/emerging_subclades.tsv"
auspice_config: "config/{lineage}/{{segment}}/auspice_config.json"
vaccines: "config/{lineage}/vaccine.json"
enable_glycosylation: true
enable_lbi: true
enable_titer_models: true
enable_forecasts: false
enable_embeddings: true
include: "'config/{lineage}/reference_strains.txt'"
exclude: "'config/{lineage}/outliers.txt'"
titer_collections:
- name: cdc_cell_fra
data: "data/h3n2/cdc_ferret_cell_fra_titers.tsv"
subsamples: *subsampling-scheme
3Y-fra-builds:
patterns:
min_date:
- 3Y
reference_min_date:
- 9Y
resolution:
- 3y
build_name: "seasonal-flu_h3n2_3y"
build_params: *shared-fra-build-params
subsamples: *subsampling-scheme
6Y-fra-builds:
patterns:
min_date:
- 6Y
reference_min_date:
- 12Y
resolution:
- 6y
build_name: "seasonal-flu_h3n2_6y"
build_params: *shared-fra-build-params
subsamples: *subsampling-scheme
12Y-fra-builds:
patterns:
min_date:
- 12Y
reference_min_date:
- 18Y
resolution:
- 12y
build_name: "seasonal-flu_h3n2_12y"
build_params: *shared-fra-build-params
subsamples: *subsampling-scheme
# H3N2-specific fitness model
fitness_model:
models:
- cTiter_x-ne_star
- ne_star-lbi
best_model: cTiter_x-ne_star
delta_months: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12]
pivot_interval: 6
delta_pivots: 1
months_back_for_current_samples: 6
max_years_for_distances: 5
number_of_forecast_samples: 1
excluded_node_data_fields:
- aa_muts
- aa_sequences
- muts
- num_date_confidence
- sequence