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ingest: use new augur curate commands #70

Merged
merged 7 commits into from
Jul 18, 2024
Merged

ingest: use new augur curate commands #70

merged 7 commits into from
Jul 18, 2024

Commits on Jul 18, 2024

  1. Replace vendored scripts with augur curate 

    Vendored scripts for the curate rule have been ported to `augur curate`
and are available starting from Augur 25.0.0.¹

¹ <https://github.com/nextstrain/augur/releases/tag/25.0.0>
    @j23414
    j23414 committed Jul 18, 2024
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  2. Add subset_metadata 

    Separate out selecting metadata columns into a rule to match the pathogen repo guide
    @j23414
    j23414 committed Jul 18, 2024
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  3. Drop unused and blank metadata columns

    @j23414
    j23414 committed Jul 18, 2024
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  4. Rename transform to curate 

    To conform to the pathogen-repo-guide

https://github.com/nextstrain/pathogen-repo-guide/blob/89b3c5dbc9b8f6a009f4a19c3ac56113bc5511ee/ingest/rules/curate.smk#L57
    @j23414
    j23414 committed Jul 18, 2024
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  5. git subrepo pull (merge) ingest/vendored 

    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"
    @j23414
    j23414 committed Jul 18, 2024
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  6. Add functional institution column

    @j23414
    j23414 committed Jul 18, 2024
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  7. Fixup: Rename transform to curate

    @j23414
    j23414 committed Jul 18, 2024
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