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feat(deposition): submit EMBL flatfile instead of fasta for better nucleotide metadata #2947

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merged 21 commits into from
Oct 4, 2024

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@anna-parker anna-parker commented Oct 4, 2024

resolves #

preview URL: https://test-adding-authors.loculus.org/

Summary

Adding AUTHORS as a field to the manifest file was not successful, from reading the docs it has become clear to us that instead of submitting the sequence as a fasta we should submit a flat file, flat files allow us to set metadata fields and the authors field.

Docs: https://ena-docs.readthedocs.io/en/latest/submit/fileprep/flat-file-example.html
Flat file: annotations: https://www.ebi.ac.uk/ena/WebFeat/.
As we are submitting as a broker it is important that we add the AUTHORS to the assembly: https://ena-docs.readthedocs.io/en/latest/faq/data_brokering.html#authorship.

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PR Checklist

  • All necessary documentation has been adapted.
  • The implemented feature is covered by an appropriate test.

@anna-parker anna-parker added the preview Triggers a deployment to argocd label Oct 4, 2024
@anna-parker anna-parker force-pushed the test_adding_authors branch 2 times, most recently from b9b0177 to d78cce0 Compare October 4, 2024 08:22
@anna-parker anna-parker marked this pull request as ready for review October 4, 2024 15:22
@corneliusroemer corneliusroemer changed the title Test adding authors feat(deposition): submit EMBL flatfile instead of fasta for better nucleotide metadata Oct 4, 2024
ena-submission/Snakefile Outdated Show resolved Hide resolved
@corneliusroemer corneliusroemer merged commit 60aa2e4 into main Oct 4, 2024
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2 participants