Skip travel history adjustment
For open builds, the `{trait}_exposure` metadata is identical to the
`{trait}` value. Thus we can skip the travel history adjustment
rule. This necessitates updates to which values we use for DTA.
@@ -79,61 +79,33 @@ builds:
filter:
exclude_where: "division='USA' purpose_of_sequencing='S dropout'"
-# if different exposure traits should be used for some builds, specify here
-# otherwise the default exposure in defaults/parameters.yaml will used
-exposure:
- global:
- trait: "region"
- exposure: "region_exposure"
-
- africa:
- trait: "country"
- exposure: "country_exposure"
-
- asia:
- trait: "country"
- exposure: "country_exposure"
-
- europe:
- trait: "country"
- exposure: "country_exposure"
-
- south-america:
- trait: "country"
- exposure: "country_exposure"
-
- north-america:
- trait: "division"
- exposure: "division_exposure"
-
- oceania:
- trait: "division"
- exposure: "division_exposure"
+# Open metadata does not have "exposure" data (i.e. travel history)
+skip_travel_history_adjustment: true
# if different traits should be reconstructed for some builds, specify here
# otherwise the default trait config in defaults/parameters.yaml will used
traits:
global:
sampling_bias_correction: 2.5
- columns: ["region_exposure"]
+ columns: ["region"]
europe:
sampling_bias_correction: 2.5
- columns: ["country_exposure"]
+ columns: ["country"]
africa:
sampling_bias_correction: 2.5
- columns: ["country_exposure"]
+ columns: ["country"]
asia:
sampling_bias_correction: 2.5
- columns: ["country_exposure"]
+ columns: ["country"]
south-america:
sampling_bias_correction: 2.5
- columns: ["country_exposure"]
+ columns: ["country"]
north-america:
sampling_bias_correction: 2.5
- columns: ["division_exposure"]
+ columns: ["division"]
oceania:
sampling_bias_correction: 2.5
- columns: ["division_exposure"]
+ columns: ["division"]
files:
description: "nextstrain_profiles/nextstrain/nextstrain_description.md"
