Organize outputs by lineage and geo resolution#7
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To support multiple geographic resolutions in this workflow with different data prep settings per resolution, this commit updates the workflow to more closely match the forecasts-ncov workflow. The config in `config/defaults.yaml` now has a `prepare_data` section that sets the thresholds per geographic resolution and a lineages list that includes all three major lineages. The workflow produces model results in files like `results/h3n2/country/mlr/MLR_results.json` or `results/h3n2/region/mlr/MLR_results.json`. This commit does not include the additional nested structure of the forecasts-ncov workflow of data provenance and variant classification, but we could add these if we think we'll want to build models with different combinations of those fields.
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genehack
approved these changes
Mar 7, 2025
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I'm going to merge this now. We can refine these changes in later commits, if there are issues. |
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Description of proposed changes
To support multiple geographic resolutions in this workflow with different data prep settings per resolution, this commit updates the workflow to more closely match the forecasts-ncov workflow. The config in
config/defaults.yamlnow has aprepare_datasection that sets the thresholds per geographic resolution and a lineages list that includes all three major lineages. The workflow produces model results in files likeresults/h3n2/country/mlr/MLR_results.jsonorresults/h3n2/region/mlr/MLR_results.json.This commit does not include the additional nested structure of the forecasts-ncov workflow of data provenance and variant classification, but we could add these if we think we'll want to build models with different combinations of those fields.
Related issue(s)
Related to #2
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