Valeur seersholm 2024

[YuejiaoHuang]

Pull Request

This PR is for a

• New Publication(s)
• Correction

For the following list(s):

• ancientmetagenome-environmental (README)
• ancientmetagenome-hostassociated (README)
• ancientsinglegenome-hostassociated (README)

This is to close

PR Workflow

1. Open this PR with sample metadata on the samples metadata sheet (:tada: you're already here!)
2. Wait for checks for sample metdata to pass
3. (If checks fail) make corrections, and push changes to this branch (no need to open a new PR!)
4. (Once passed) comment on this PR @spaam-bot please autofill <table_name> <project_id> to get a half-filled template! (may take a minute or so to get the comment with the file)
5. Fill in the template, and verify autofilled data correct!
6. Once filled in, append(!) the new rows from the TEMPLATE file to the end of the corresponding library metadata file, and update this PR
7. Wait for checks for library metadata to pass
8. Request review!

Pre-review checklist (new publications)

• Publication is published
  • Preprints currently not accepted?
• Checked the publication is not already in the database?
• Checked samples in this publication are not previously published data?
  • Newly re-sequenced metagenomes are OK!
• Samples are shotgun metagenomes and not amplicon data
  • Note: hostassociated-singlegenome may also contain whole-genome enriched data
• Checked the list follows conventions as described in the corresponding sample type's README file (e.g. using ERS/SRS accession codes for ENA/SRA)?
• Once sample table validation completed Library metadata has been added
  • Use @spaam-bot please autofill <table_name> <project_id> to get a half-filled template! May take a minute or so to get the comment with the file
  • Fill in template, and verify autofill data correct!
  • Once filled in, append(!) the new rows to the end of the corresponding library metadata file
• Changelog is updated to include the publication under 'Added'?

[YuejiaoHuang]

@spaam-bot please autofill ancientsinglegenome-hostassociated Seersholm2024

[jfy133]

@spaam-bot please autofill ancientsinglegenome-hostassociated Seersholm2024

[github-actions]

Autofill success! 🎉

Autofill log:

�[32mAMDirT [INFO]: ancientsinglegenome-hostassociated_libraries.tsv is valid�[0m
�[32mAMDirT [INFO]: ENA API is up�[0m
�[32mAMDirT [INFO]: Found 353 libraries�[0m
�[32mAMDirT [INFO]: Writing libraries metadata to TEMPLATE_Seersholm2024_ancientsinglegenome-hostassociated_libraries.tsv�[0m

Download the attempted autofilled library file by pressing this link.

You can now fill in the remainder of the columns, and append to the end of the corresponding library file.
Please remember this service attempts to pull relevant metadata from the ENA, but metadata is not always correct!

Warning

Always check accuracy of pre-filled columns before adding to the library table!