Rozwalak2024

[rozwalak]

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)

Publication Information

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)?
• Library metadata has been added
• Changelog is updated to include the publication under 'Added'?
• Pull request has passed validation checks (see automated comment from github-bot)?
• (If applicable) Made a separate PR to add new categories to controlled lists (stored under /assets/enums, e.g. material or archive)? If so the corresponding PR is here:

[rozwalak]

@jfy133 Can you help me with these problems?

[jfy133]

@rozwalak if you look closely at the first error, you'll see you have a space at teh end of your project_id string ;)

The second, you need to make a second PR to update the corresponding enum file: https://github.com/SPAAM-community/AncientMetagenomeDir/tree/master/assets/enums, as described in the error :)

Once the second PR is merged in, you can fix the samplesheet(s), and then restart the test

[jfy133]

One main comment, otehrwise almost there, main issue is with the library table referring to raw reads not your new genbank assembly :)

[jfy133]

Thanks @rozwalak !

[github-actions]

AMDirT, version 1.5.0

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid