move nextstrain subsamp to profile, turn down size
@@ -4,6 +4,8 @@ custom_rules:
# Define locations for which builds should be created.
# For each build we specify a subsampling scheme via an explicit key.
+# These subsampling schemes are defined at the bottom of this file.
+# (They override the defaults)
builds:
global:
subsampling_scheme: region_global
@@ -100,3 +102,43 @@ files:
s3_staging_url: s3://nextstrain-staging
slack_token: ~
slack_channel: "#ncov-gisaid-updates"
+
+subsampling:
+ # Custom subsampling logic for regions
+ region:
+ # Focal samples for region
+ region:
+ group_by: "division year month"
+ seq_per_group: 40
+ exclude: "--exclude-where 'region!={region}'"
+ # Contextual samples for region from the rest of the world
+ global:
+ group_by: "country year month"
+ seq_per_group: 4
+ exclude: "--exclude-where 'region={region}'"
+ priorities:
+ type: "proximity"
+ focus: "region"
+
+ # Custom subsampling logic for global region.
+ region_global:
+ global:
+ group_by: "country year month"
+ seq_per_group: 18
+
+ # Custom subsampling for regions like Europe where grouping by country
+ # is the smallest resolution requied
+ region_grouped_by_country:
+ # Focal samples for region
+ region:
+ group_by: "country year month"
+ seq_per_group: 54
+ exclude: "--exclude-where 'region!={region}'"
+ # Contextual samples for region from the rest of the world
+ global:
+ group_by: "country year month"
+ seq_per_group: 5
+ exclude: "--exclude-where 'region={region}'"
+ priorities:
+ type: "proximity"
+ focus: "region"
\ No newline at end of file
