Update ingest to pathogen-repo-template #234
Conversation
Part of work to update this repo to match the pathogen-repo-template. We are removing the `source-data` directory and consolidating everything into the config directory since there's really no functional difference between them.
Part of work to update this repo to match the pathogen-repo-template. Simplify directory structure by putting the core Snakemake rules in a "rules" directory.
Part of work to update this repo to match the pathogen-repo-template. Always provide default config values that can then easily be overridden with --configfiles/--config options. This makes it simpler to change a subset of config values or extend the default configs. Renames the config/ to defaults/ to reflect this change. Match changes in pathogen-repo-template in nextstrain/pathogen-repo-guide#27
Part of work to update this repo to match the pathogen-repo-template. Simplify the core workflow by moving the Nextstrain automation specific rules to the new build config.
Match changes in pathogen-repo-template nextstrain/pathogen-repo-guide@5e1b1ef
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Not sure what's going on with the pre-commit.ci failure. All tests pass when I run
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Test run completed successfully and the metadata diff output to the test #scratch channel included the 10 new sequences that have become available since this morning's automated ingest run. No other data changes were reported. |
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pre-commit.ci failure should be unrelated to changes in this PR. It is likely to be the same failure that is on the master branch. I see the same failure locally after rebasing this branch onto master. I'm going to leave the pre-commit.ci failure in this PR alone since it will be fixed separately in #233 (or we can exclude .github/dependabot.yml in the .yamlfmt config) |
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Merging since test run was successful. Will monitor automated runs the next couple of days. |
Description of proposed changes
Update ingest directory to match pathogen-repo-template layout.
This PR does not change any output data formats to not break any downstream uses of the data, i.e. the fields for the NDJSON and metadata.tsv were not changed.
Checklist