phylo: Add standardized multiple inputs#339
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joverlee521 merged 6 commits intomasterfrom Oct 8, 2025
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subrepo: subdir: "shared/vendored" merged: "43e5a6f" upstream: origin: "https://github.com/nextstrain/shared" branch: "main" commit: "43e5a6f" git-subrepo: version: "0.4.6" origin: "https://github.com/ingydotnet/git-subrepo" commit: "110b9eb"
Note this does _not_ remove the support for `private_metadata` and `private_sequences` config params because they are used by the private INRB build to bypass the QC filtering for the contextual sequences. In the future we could explore using the inputs `name` to change filtering params, but I'll punt on that for now.
victorlin
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Add `min_version` in the shared `remote_files.smk` so that individual workflows that import it don't have to remember to add the version check. Based on feedback from @victorlin in mpox <nextstrain/mpox#339 (comment)>
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Will merge this by EOD tomorrow if there are no other comments. |
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Description of proposed changes
Use latest guidance for handling inputs based on nextstrain/pathogen-repo-guide#91.
Note this does not remove the support for
private_metadataandprivate_sequencesconfig params because they are used by the private INRB build to bypass the QC filtering for the contextual sequences.Related issue(s)
Resolves #324
nextstrain/public#25
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