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joverlee521
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Oct 6, 2025
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General config improvements make sense to me 👍
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| build_name=r"genome|G|F", | ||
| resolution=r"all-time|6y|3y", |
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I was going to suggest these should be dynamic
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| build_name=r"genome|G|F", | |
| resolution=r"all-time|6y|3y", | |
| build_name="|".join(config["builds_to_run"]), | |
| resolution="|".join(config["resolutions_to_run"]), |
However I then realized that these already hardcoded due to the values in the config/distance_maps.tsv. Probably good to add a note here and add to config validation in the future.
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subrepo: subdir: "shared/vendored" merged: "37cf39c" upstream: origin: "https://github.com/nextstrain/shared" branch: "main" commit: "37cf39c" git-subrepo: version: "0.4.9" origin: "https://github.com/ingydotnet/git-subrepo" commit: "4f60dd7"
Useful for debugging.
augur filter has never taken a reference file as input, so my guess is this was originally copied by mistake.
Preparing to make changes to the config that would have broken this. It seems fine to hardcode along with the already hardcoded sample size.
This will make it easier to compare changes in the switch to augur subsample which will define all parameters in config.
This shouldn't rely on config from another rule.
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Description of proposed changes
Small adjustments to config, particularly around filtering and subsampling.
Related issue(s)
Preparing for #103
Checklist
Update changelog