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The code is already used in WNV¹ and measles². I placed the function at the very bottom because it should be the final configuration-related function to be used by any workflow, at least among functions run at Snakemake startup time. Docstring/README updated to reflect the new scope of config.smk. ¹ https://github.com/nextstrain/WNV/blob/b143897367fcf0f9ddb4151b891a7da192c124eb/phylogenetic/rules/config.smk#L62-L67 ² https://github.com/nextstrain/measles/blob/1a10742c5c04932f87e16e5c83e1e8ca840716cd/phylogenetic/rules/config.smk#L99-L104
This is not necessary since the variable is not assigned a new value within the function, but the same could be said for 'workflow' in resolve_config_path(). Adding for consistency.
This code is already used in measles¹ and is expected to be used by other repos. I placed the functions above resolve_config_path() because, while resolve_config_path() is used directly in Snakemake code, eventually it may be replaced by calls to resolve_filepaths() which uses it as a helper function. ¹ https://github.com/nextstrain/measles/blob/db993ffa3a0ab80bd46d68f5e30ee47023525bb8/phylogenetic/rules/config.smk#L29-L94
This was referenced Sep 30, 2025
joverlee521
approved these changes
Oct 1, 2025
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Description of proposed changes
Adds config-related functions that are planned for reuse across across pathogen repos.
Related issue(s)
write_config()is for nextstrain/pathogen-repo-guide#18resolve_filepaths()is for nextstrain/public#23Checklist
If adding a script, add an entry for it in the README.