Buchwald2024

[Darcy220606]

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 #1140

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'?

[Darcy220606]

@spaam-bot please autofill ancientmetagenome-environmental Buchwald2024

[alexhbnr]

Hi @Darcy220606,

Thanks for contributing this publication. All looks good so far. I only updated the strand type of the libraries because the authors cite to single-stranded DNA papers for their library building.

Out of curiosity, how did you infer the sample and library names? I couldn't find a proper table of these in the manuscript and could only stitch them together from ENA.

[Darcy220606]

Thanks @alexhbnr for the review. Indeed, I also inferred the samples and libraries names from the names of the submitted ftps from the ENA table.

[jfy133]

As @alexhbnr is busy atm in Croatia, I will finish the review!

[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

[jfy133]

Made refines me to sampel metadata, library metadata looks good after Alex's change.

I find it weird the library IDs are shorter than the samples... but I guess they are unique enough here that it works.

Thank's @Darcy220606 !