Modernize phylogenetic build [#2] #9
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joverlee521
reviewed
Jul 18, 2024
joverlee521
approved these changes
Jul 19, 2024
* Update template files to remove instructions and placeholders * Add Genbank and GFF references * Bring in phylo workflow from pathogen-repo-guide and modify to work
* Drop to Python 3.11 in GitHub pre-commit CI, to match actual development practice * Clean up formatting of several files * Convert all Markdown links to use reference dictionary at end of file * Add `log` and `benchmark` to all Snakemake rules that didn't have them * Remove `dump_ncbi_dataset_report` rule
Also adds logging redirects everywhere
subrepo: subdir: "ingest/vendored" merged: "980c010" upstream: origin: "https://github.com/nextstrain/ingest" branch: "main" commit: "258ab8c" git-subrepo: version: "0.4.7" origin: "https://github.com/ingydotnet/git-subrepo/" commit: "c9ec2a6"
* Switch Auspice to default color-by=region * Remove extra `metadata_columns` (and associated config) when calling `augur export v2` * Move `--columns` arg of `augur traits` into config * Add `--metadata-id-columns` arg to `augur traits` invocation -- fixes issue where traits were being improperly inferred * Use a mid-point tree rooting
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Description of proposed changes
Updates yellow-fever phylo build to match pathogen-repo-guide standard.
Also updates various ingest curation steps to use
augur curateinstead of vendored ingest scripts.Related issue(s)
#2 #8
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