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fix(ingest): Small ingest fixes for multi-segmented viruses #2316

Merged
merged 10 commits into from
Jul 23, 2024
Merged

fix(ingest): Small ingest fixes for multi-segmented viruses #2316

merged 10 commits into from
Jul 23, 2024

Commits on Jul 22, 2024

  1. Fix process alignments - do not require nextclade dataset to include … 

    …clade name.
    @anna-parker
    anna-parker committed Jul 22, 2024
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  2. Make ncbi_virus_tax_id perSegment to work around prepro issues.

    @anna-parker
    anna-parker committed Jul 22, 2024
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  3. Allow options to group segmented metadata values under the same header.

    @anna-parker
    anna-parker committed Jul 22, 2024
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  4. Small webpage clean up.

    @anna-parker
    anna-parker committed Jul 22, 2024
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  5. Formatting fix.

    @anna-parker
    anna-parker committed Jul 22, 2024
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  6. Add more logging.

    @anna-parker
    anna-parker committed Jul 22, 2024
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  7. Allow ncbi_update_date to be different per segment.

    @anna-parker
    anna-parker committed Jul 22, 2024
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Commits on Jul 23, 2024

  1. Do not make ncbi_virus_tax_id segment-specific by default.

    @anna-parker
    anna-parker committed Jul 23, 2024
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  2. feat(ingest): Use tsv-utils again (4 lines) instead of Python script … 

    …(70 lines + extra file) (#2329)

* This might work already

* fix
    @corneliusroemer
    corneliusroemer authored Jul 23, 2024
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  3. Merge branch 'main' into ingest_fixes

    @anna-parker
    anna-parker authored Jul 23, 2024
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