ingest: use new augur curate commands #263
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Vendored scripts for the curate rule have been ported to `augur curate` and are available starting from Augur 25.0.0.¹ Includes minor file path renaming to match the pathogen-repo-guide. ¹ <https://github.com/nextstrain/augur/releases/tag/25.0.0>
Previously this was filled in with empty strings by the custom `ndjson-to-tsv-and-fasta` script. We've replaced vendored scripts with `augur curate` commands, so we no longer need this script, but now the workflow errors on this unexpected column. As discussed in #209, this column is not used anyways so just remove it.
subrepo: subdir: "ingest/vendored" merged: "258ab8c" upstream: origin: "https://github.com/nextstrain/ingest" branch: "main" commit: "258ab8c" git-subrepo: version: "0.4.6" origin: "https://github.com/ingydotnet/git-subrepo" commit: "110b9eb"
genehack
approved these changes
Jul 16, 2024
j23414
approved these changes
Jul 16, 2024
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Description of proposed changes
Updates the curate rule to use the new augur curate commands.
Updates ingest/vendored to pull in latest changes including nextstrain/ingest#45.
Includes additional change to remove
reversecolumn. See #209 for more context.Related issue(s)
Mirroring changes in nextstrain/pathogen-repo-guide#53
Resolves #262
Resolves #209
Checklist
<first author> et al.and the removal of thereversecolumn.