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builds.yaml
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builds.yaml
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# This is where we define which builds we'd like to run.
# This example includes 4 separate builds, ranging from the regional (global) to location (county) level.
# You can comment-out, remove, or add as many builds as you'd like.
# Each build needs a name, a defined subsampling process, and geographic attributes used for subsampling.
# Geography is specified by build attributes (e.g., `region`, `country`, `division`, `location`) that are referenced from subsampling schemes.
# The default config file, `./defaults/parameters.yaml` has reasonable default subsampling methods for each geographic resolution.
# These subsample primarily from the area of interest ("focus"), and add in background ("contextual") sequences from the rest of the world.
# Contextual sequences that are genetically similar to (hamming distance) and geographically near the focal sequences are heavily prioritized.
# In this example, we use these default methods. See other templates for examples of how to customize this subsampling scheme.
builds:
# Focus on King County (location) in Washington State (division) in the USA (country)
# with a build name that will produce the following URL fragment on Nextstrain/auspice:
# /ncov/north-america/usa/washington/king-county
north-america_usa_washington_king-county: # name of the build; this can be anything
subsampling_scheme: custom-county # use a custom subsampling scheme defined below
region: North America
country: USA
division: Washington
location: King County
# Whatever your finest geographic scale is (here, 'location' since we are doing a county in the USA)
# list 'up' from here the geographic area that location is in.
# Here, King County is in Washington state, is in USA, is in North America.
# Zoom out one level: this build focuses on all of Washington State
# with a build name that will produce the following URL fragment on Nextstrain/auspice:
# /ncov/north-america/usa/washington
north-america_usa_washington:
subsampling_scheme: division # use a default subsampling scheme defined in defaults/parameters.yaml
region: North America
country: USA
division: Washington
# Here, Washington state is in USA, is in North America.
# This build focuses on the entire U.S.
# with a build name that will produce the following URL fragment on Nextstrain/auspice:
# /ncov/north-america/usa
north-america_usa:
subsampling_scheme: country
region: North America
country: USA
# Here, USA is in North America
# This build focuses on all of North America
# with a build name that will produce the following URL fragment on Nextstrain/auspice:
# /ncov/north-america
north-america:
subsampling_scheme: region
region: North America
# This build samples evenly from the globe
# with a build name that will produce the following URL fragment on Nextstrain/auspice:
# /ncov/global
global:
subsampling_scheme: region_global
region: global
# Define custom subsampling logic for county-level builds.
subsampling:
custom-county:
# Focal samples for location
focal:
group_by: "year month"
seq_per_group: 300
# Use augur filter's query argument to filter strains with pandas-style logic expressions.
# This can be easier to read than the corresponding filter by exclusion.
query: --query "(country == '{country}') & (division == '{division}') & (location == '{location}')"
# Samples that are genetically related to the focal samples
related:
group_by: "country year month"
seq_per_group: 20
exclude: "--exclude-where 'location={location}'"
priorities:
type: "proximity"
focus: "focal"
# Contextual samples from the rest of the world
contextual:
group_by: "country year month"
seq_per_group: 10
exclude: "--exclude-where 'location={location}'"
# Here, you can specify what type of auspice_config you want to use
# and what description you want. These will apply to all the above builds.
# If you want to specify specific files for each build - you can!
# See the 'example_advanced_customization' builds.yaml
files:
auspice_config: "my_profiles/example/my_auspice_config.json"
description: "my_profiles/example/my_description.md"