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Rename "profiles" to "build-configs" #43

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merged 2 commits into from
Mar 1, 2024

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@j23414 j23414 commented Feb 29, 2024

Description of proposed changes

Match changes in pathogen-repo-guide: nextstrain/pathogen-repo-guide#27

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This commit renames the `config` directory to `defaults` in both the ingest
phylogenetic workflow. The `defaults.yaml` for configuraiton values is also
renamed to `config.yaml` to be consistent with the pathogen-repo-guide.

https://github.com/nextstrain/pathogen-repo-guide/tree/main/ingest/defaults
…d of "profiles".

This is consistent with the pathogen-repo-guide.

https://github.com/nextstrain/pathogen-repo-guide/tree/5509de0e315eb6acae513d2df4dfab874ff289b5/phylogenetic/build-configs/ci

However, note that the `ingest/profiles` does not need to be renamed because
it's actually using the Snakemake Profiles feature.

https://github.com/snakemake-profiles/doc
@j23414 j23414 linked an issue Feb 29, 2024 that may be closed by this pull request
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@j23414 j23414 requested a review from a team February 29, 2024 00:20
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@joverlee521 joverlee521 left a comment

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Changes here look good to me, thanks for following up!

As a future improvement, I think we can move the ingest Nextstrain automation rules/configs to ingest/build-configs. The change would look very similar to the changes I made in the mpox ingest workflow.

@j23414 j23414 merged commit cd95122 into main Mar 1, 2024
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@j23414 j23414 deleted the 34-rename-profiles-to-build-configs branch March 1, 2024 18:57
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Rename "profiles" to "build-configs"
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