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[wip]: Add the functionality of join metadata and clades #23

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wants to merge 7 commits into from
Closed

[wip]: Add the functionality of join metadata and clades #23

wants to merge 7 commits into from

Commits on Sep 18, 2023

  1. Copy join-metadata-and-clades.py from monkeypox 

    Copied from: https://github.com/nextstrain/monkeypox/blob/5969604dfe426745b789746427b580c69d484790/ingest/bin/join-metadata-and-clades.py
    @j23414
    j23414 committed Sep 18, 2023
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  2. fixup: drop comments

    @j23414
    j23414 committed Sep 18, 2023
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  3. fixup: add a minor check 

    Add a minor check to join-metadata-and-clades to ensure that all of the
sequences in the metadata file are included in the output.
    @j23414
    j23414 committed Sep 18, 2023
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  4. Make the nextclade column map customizable 

    Each pathogen can have unique columns in the Nextclade output
(e.g. ncov-ingest includes SC2 specific columns). This change makes the
nextclade column map customizable to support these.
    @j23414
    j23414 committed Sep 18, 2023
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  5. Parameterize nextclade id field

    @j23414
    j23414 committed Sep 18, 2023
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  6. drop VALUE_MISSING_DATA because variable is not used anywhere

    @j23414
    j23414 committed Sep 18, 2023
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Commits on Sep 19, 2023

  1. fixup: add pandas to ci

    @j23414
    j23414 committed Sep 19, 2023
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