Rename "profiles" to "build-configs" #43
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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
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joverlee521
approved these changes
Feb 29, 2024
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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.
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Description of proposed changes
Match changes in pathogen-repo-guide: nextstrain/pathogen-repo-guide#27
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