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| # Note that this differs from the search paths used in | ||
| # resolve_config_path(). | ||
| # This is the preferred default moving forwards, and the plan is to | ||
| # eventually update resolve_config_path() to use AUGUR_SEARCH_PATHS. |
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Here's a draft of what that could look like: nextstrain/avian-flu@dadbde0...bbad70d.
I don't think it should block this PR, but that's what I have in mind. We could discuss at the next dev chat.
To be used by various Augur commands and pathogen workflows, starting with augur subsample in the measles repo.
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This removes files and non-existent directories.
This removes references such as "..", for clarity while debugging.
joverlee521
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Feb 4, 2026
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Latest change LGTM, only left a non-blocking comment.
Co-authored-by: Jover Lee <joverlee521@gmail.com>
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Description of proposed changes
To be used by various Augur commands and pathogen workflows, starting with augur subsample in the measles repo.
Review threads
AUGUR_SEARCH_PATHS?AUGUR_SEARCH_PATHSbe used inresolve_config_path()?Related issue(s)
Used in nextstrain/measles#90
Checklist
Checks passN/AIf adding a script, add an entry for it in the README.N/A