Use a unique subsampling scheme name for the example profile
The original county-level subsampling scheme for the example profile used the
same name as the default "county" scheme we provide. This commit renames that
scheme to "custom-county" to avoid conflicts with the default schemes.
@@ -16,7 +16,7 @@ builds:
# 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: county # use a custom subsampling scheme defined below
+ subsampling_scheme: custom-county # use a custom subsampling scheme defined below
region: North America
country: USA
division: Washington
@@ -60,18 +60,11 @@ builds:
# Define custom subsampling logic for county-level builds.
subsampling:
- county:
+ custom-county:
# Focal samples for location
focal:
group_by: "year month"
- # augur filter's `seq_per_group` and `max_sequences` are mutually
- # exclusive, but one of these arguments is required for each subsampling
- # scheme. To override these defaults in your own subsampling schemes of
- # the same name, provide a value for the limit you want to use and an
- # empty entry for the limit you don't use. The entry below demonstrates
- # this approach.
seq_per_group: 300
- max_sequences:
# 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}')"
@@ -80,7 +73,6 @@ subsampling:
related:
group_by: "country year month"
seq_per_group: 20
- max_sequences:
exclude: "--exclude-where 'location={location}'"
priorities:
type: "proximity"
@@ -90,7 +82,6 @@ subsampling:
contextual:
group_by: "country year month"
seq_per_group: 10
- max_sequences:
exclude: "--exclude-where 'location={location}'"
# Here, you can specify what type of auspice_config you want to use
