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Reduce from 2y context to 1y context
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@trvrb
trvrb committed Jul 25, 2024
1 parent 4dd3f2a commit 9e59c58
Showing 1 changed file with 51 additions and 51 deletions.
102 changes: 51 additions & 51 deletions nextstrain_profiles/nextstrain-gisaid/builds.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -174,14 +174,14 @@ subsampling:
focal_early:
group_by: "division year month"
max_sequences: 256
min_date: "--min-date 25M"
min_date: "--min-date 13M"
max_date: "--max-date 1M"
exclude: "--exclude-where 'region!={region}'"
# Early contextual samples from the rest of the world
context_early:
group_by: "country year month"
max_sequences: 64
min_date: "--min-date 25M"
min_date: "--min-date 13M"
max_date: "--max-date 1M"
exclude: "--exclude-where 'region={region}'"
# Recent focal samples for region
Expand All @@ -207,14 +207,14 @@ subsampling:
focal_early:
group_by: "division year month"
max_sequences: 256
min_date: "--min-date 26M"
min_date: "--min-date 14M"
max_date: "--max-date 2M"
exclude: "--exclude-where 'region!={region}'"
# Early contextual samples from the rest of the world
context_early:
group_by: "country year month"
max_sequences: 64
min_date: "--min-date 26M"
min_date: "--min-date 14M"
max_date: "--max-date 2M"
exclude: "--exclude-where 'region={region}'"
# Recent focal samples for region
Expand All @@ -240,14 +240,14 @@ subsampling:
focal_early:
group_by: "division year month"
max_sequences: 256
min_date: "--min-date 30M"
min_date: "--min-date 18M"
max_date: "--max-date 6M"
exclude: "--exclude-where 'region!={region}'"
# Early contextual samples from the rest of the world
context_early:
group_by: "country year month"
max_sequences: 64
min_date: "--min-date 30M"
min_date: "--min-date 18M"
max_date: "--max-date 6M"
exclude: "--exclude-where 'region={region}'"
# Recent focal samples for region
Expand Down Expand Up @@ -291,28 +291,28 @@ subsampling:
asia_early:
group_by: "division year month"
max_sequences: 120
min_date: "--min-date 25M"
min_date: "--min-date 13M"
max_date: "--max-date 1M"
exclude: "--exclude-where 'region!=Asia' 'country=China' 'country=India'"
# Early focal samples for China
china_early:
group_by: "division year month"
max_sequences: 80
min_date: "--min-date 25M"
min_date: "--min-date 13M"
max_date: "--max-date 1M"
exclude: "--exclude-where 'country!=China'"
# Early focal samples for India
india_early:
group_by: "division year month"
max_sequences: 80
min_date: "--min-date 25M"
min_date: "--min-date 13M"
max_date: "--max-date 1M"
exclude: "--exclude-where 'country!=India'"
# Early contextual samples from the rest of the world
context_early:
group_by: "country year month"
max_sequences: 70
min_date: "--min-date 25M"
min_date: "--min-date 13M"
max_date: "--max-date 1M"
exclude: "--exclude-where 'region=Asia'"
# Recent focal samples for Asia
Expand Down Expand Up @@ -352,28 +352,28 @@ subsampling:
asia_early:
group_by: "division year month"
max_sequences: 120
min_date: "--min-date 26M"
min_date: "--min-date 14M"
max_date: "--max-date 2M"
exclude: "--exclude-where 'region!=Asia' 'country=China' 'country=India'"
# Early focal samples for China
china_early:
group_by: "division year month"
max_sequences: 80
min_date: "--min-date 26M"
min_date: "--min-date 14M"
max_date: "--max-date 2M"
exclude: "--exclude-where 'country!=China'"
# Early focal samples for India
india_early:
group_by: "division year month"
max_sequences: 80
min_date: "--min-date 26M"
min_date: "--min-date 14M"
max_date: "--max-date 2M"
exclude: "--exclude-where 'country!=India'"
# Early contextual samples from the rest of the world
context_early:
group_by: "country year month"
max_sequences: 70
min_date: "--min-date 26M"
min_date: "--min-date 14M"
max_date: "--max-date 2M"
exclude: "--exclude-where 'region=Asia'"
# Recent focal samples for Asia
Expand Down Expand Up @@ -413,28 +413,28 @@ subsampling:
asia_early:
group_by: "division year month"
max_sequences: 120
min_date: "--min-date 30M"
min_date: "--min-date 18M"
max_date: "--max-date 6M"
exclude: "--exclude-where 'region!=Asia' 'country=China' 'country=India'"
# Early focal samples for China
china_early:
group_by: "division year month"
max_sequences: 80
min_date: "--min-date 30M"
min_date: "--min-date 18M"
max_date: "--max-date 6M"
exclude: "--exclude-where 'country!=China'"
# Early focal samples for India
india_early:
group_by: "division year month"
max_sequences: 80
min_date: "--min-date 30M"
min_date: "--min-date 18M"
max_date: "--max-date 6M"
exclude: "--exclude-where 'country!=India'"
# Early contextual samples from the rest of the world
context_early:
group_by: "country year month"
max_sequences: 70
min_date: "--min-date 30M"
min_date: "--min-date 18M"
max_date: "--max-date 6M"
exclude: "--exclude-where 'region=Asia'"
# Recent focal samples for Asia
Expand Down Expand Up @@ -500,14 +500,14 @@ subsampling:
focal_early:
group_by: "country year month"
max_sequences: 256
min_date: "--min-date 25M"
min_date: "--min-date 13M"
max_date: "--max-date 1M"
exclude: "--exclude-where 'region!={region}'"
# Early contextual samples from the rest of the world
context_early:
group_by: "country year month"
max_sequences: 64
min_date: "--min-date 25M"
min_date: "--min-date 13M"
max_date: "--max-date 1M"
exclude: "--exclude-where 'region={region}'"
# Recent focal samples for region
Expand All @@ -533,14 +533,14 @@ subsampling:
focal_early:
group_by: "country year month"
max_sequences: 256
min_date: "--min-date 26M"
min_date: "--min-date 14M"
max_date: "--max-date 2M"
exclude: "--exclude-where 'region!={region}'"
# Early contextual samples from the rest of the world
context_early:
group_by: "country year month"
max_sequences: 64
min_date: "--min-date 26M"
min_date: "--min-date 14M"
max_date: "--max-date 2M"
exclude: "--exclude-where 'region={region}'"
# Recent focal samples for region
Expand All @@ -566,14 +566,14 @@ subsampling:
focal_early:
group_by: "country year month"
max_sequences: 256
min_date: "--min-date 30M"
min_date: "--min-date 18M"
max_date: "--max-date 6M"
exclude: "--exclude-where 'region!={region}'"
# Early contextual samples from the rest of the world
context_early:
group_by: "country year month"
max_sequences: 64
min_date: "--min-date 30M"
min_date: "--min-date 18M"
max_date: "--max-date 6M"
exclude: "--exclude-where 'region={region}'"
# Recent focal samples for region
Expand Down Expand Up @@ -609,55 +609,55 @@ subsampling:
# ~4500 total (expect ~3400)
# 10:1 ratio of recent to early
# recent is present to 1m, n = 4120
# early is 1m to 25m, n = 412
# early is 1m to 13M, n = 412
# regions are proportional to population size
nextstrain_global_1m:
africa_early:
group_by: "country year month"
max_sequences: 60
min_date: "--min-date 25M"
min_date: "--min-date 13M"
max_date: "--max-date 1M"
exclude: "--exclude-where 'region!=Africa'"
asia_early:
group_by: "country year month"
max_sequences: 80
min_date: "--min-date 25M"
min_date: "--min-date 13M"
max_date: "--max-date 1M"
exclude: "--exclude-where 'region!=Asia' 'country=China' 'country=India'"
china_early:
group_by: "division year month"
max_sequences: 70
min_date: "--min-date 25M"
min_date: "--min-date 13M"
max_date: "--max-date 1M"
exclude: "--exclude-where 'country!=China'"
europe_early:
group_by: "country year month"
max_sequences: 50
min_date: "--min-date 25M"
min_date: "--min-date 13M"
max_date: "--max-date 1M"
exclude: "--exclude-where 'region!=Europe'"
india_early:
group_by: "division year month"
max_sequences: 70
min_date: "--min-date 25M"
min_date: "--min-date 13M"
max_date: "--max-date 1M"
exclude: "--exclude-where 'country!=India'"
north_america_early:
group_by: "division year month"
max_sequences: 40
min_date: "--min-date 25M"
min_date: "--min-date 13M"
max_date: "--max-date 1M"
exclude: "--exclude-where 'region!=North America'"
south_america_early:
group_by: "country year month"
max_sequences: 36
min_date: "--min-date 25M"
min_date: "--min-date 13M"
max_date: "--max-date 1M"
exclude: "--exclude-where 'region!=South America'"
oceania_early:
group_by: "division year month"
max_sequences: 6
min_date: "--min-date 25M"
min_date: "--min-date 13M"
max_date: "--max-date 1M"
exclude: "--exclude-where 'region!=Oceania'"
africa_recent:
Expand Down Expand Up @@ -705,55 +705,55 @@ subsampling:
# ~4500 total (expect ~3400)
# 10:1 ratio of recent to early
# recent is present to 2m, n = 4120
# early is 2m to 26m, n = 412
# early is 2m to 14M, n = 412
# regions are proportional to population size
nextstrain_global_2m:
africa_early:
group_by: "country year month"
max_sequences: 60
min_date: "--min-date 26M"
min_date: "--min-date 14M"
max_date: "--max-date 2M"
exclude: "--exclude-where 'region!=Africa'"
asia_early:
group_by: "country year month"
max_sequences: 80
min_date: "--min-date 26M"
min_date: "--min-date 14M"
max_date: "--max-date 2M"
exclude: "--exclude-where 'region!=Asia' 'country=China' 'country=India'"
china_early:
group_by: "division year month"
max_sequences: 70
min_date: "--min-date 26M"
min_date: "--min-date 14M"
max_date: "--max-date 2M"
exclude: "--exclude-where 'country!=China'"
europe_early:
group_by: "country year month"
max_sequences: 50
min_date: "--min-date 26M"
min_date: "--min-date 14M"
max_date: "--max-date 2M"
exclude: "--exclude-where 'region!=Europe'"
india_early:
group_by: "division year month"
max_sequences: 70
min_date: "--min-date 26M"
min_date: "--min-date 14M"
max_date: "--max-date 2M"
exclude: "--exclude-where 'country!=India'"
north_america_early:
group_by: "division year month"
max_sequences: 40
min_date: "--min-date 26M"
min_date: "--min-date 14M"
max_date: "--max-date 2M"
exclude: "--exclude-where 'region!=North America'"
south_america_early:
group_by: "country year month"
max_sequences: 36
min_date: "--min-date 26M"
min_date: "--min-date 14M"
max_date: "--max-date 2M"
exclude: "--exclude-where 'region!=South America'"
oceania_early:
group_by: "division year month"
max_sequences: 6
min_date: "--min-date 26M"
min_date: "--min-date 14M"
max_date: "--max-date 2M"
exclude: "--exclude-where 'region!=Oceania'"
africa_recent:
Expand Down Expand Up @@ -801,55 +801,55 @@ subsampling:
# ~4500 total (expect ~3400)
# 10:1 ratio of recent to early
# recent is present to 6m, n = 4120
# early is 6m to 30m, n = 412
# early is 6m to 18M, n = 412
# regions are proportional to population size
nextstrain_global_6m:
africa_early:
group_by: "country year month"
max_sequences: 60
min_date: "--min-date 30M"
min_date: "--min-date 18M"
max_date: "--max-date 6M"
exclude: "--exclude-where 'region!=Africa'"
asia_early:
group_by: "country year month"
max_sequences: 80
min_date: "--min-date 30M"
min_date: "--min-date 18M"
max_date: "--max-date 6M"
exclude: "--exclude-where 'region!=Asia' 'country=China' 'country=India'"
china_early:
group_by: "division year month"
max_sequences: 70
min_date: "--min-date 30M"
min_date: "--min-date 18M"
max_date: "--max-date 6M"
exclude: "--exclude-where 'country!=China'"
europe_early:
group_by: "country year month"
max_sequences: 50
min_date: "--min-date 30M"
min_date: "--min-date 18M"
max_date: "--max-date 6M"
exclude: "--exclude-where 'region!=Europe'"
india_early:
group_by: "division year month"
max_sequences: 70
min_date: "--min-date 30M"
min_date: "--min-date 18M"
max_date: "--max-date 6M"
exclude: "--exclude-where 'country!=India'"
north_america_early:
group_by: "division year month"
max_sequences: 40
min_date: "--min-date 30M"
min_date: "--min-date 18M"
max_date: "--max-date 6M"
exclude: "--exclude-where 'region!=North America'"
south_america_early:
group_by: "country year month"
max_sequences: 36
min_date: "--min-date 30M"
min_date: "--min-date 18M"
max_date: "--max-date 6M"
exclude: "--exclude-where 'region!=South America'"
oceania_early:
group_by: "division year month"
max_sequences: 6
min_date: "--min-date 30M"
min_date: "--min-date 18M"
max_date: "--max-date 6M"
exclude: "--exclude-where 'region!=Oceania'"
africa_recent:
Expand Down

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