Add Fontani2023

[Darcy220606]

Pull Request

This PR is for a

• [x] New Publication(s)
• [ ] Correction

For the following list(s):

• [ ] ancientmetagenome-environmental (README)
• [x] ancientmetagenome-hostassociated (README)
• [ ] ancientsinglegenome-hostassociated (README)

New Publication

Publication Information

This pull request is to add samples from the following publication(s): 10.1038/s41598-023-39250-y

This is to close #1100

Checklist

• [x] Publication is published (preprints currently not accepted)?
• [x] Checked the publication is not already in the database?
• [x] Checked samples in this publication are not previously published data (newly re-sequenced metagenomes are OK!)?
• [x] Samples are shotgun metagenomes (hostassociated-singlegenome may also contain whole-genome enriched data)?
• [x] 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)?
• [x] Changelog is updated to include the publication under 'Added'?
• [ ] Pull request has passed validation checks (see automated comment from github-bot)?
• [ ] Review requested from @SPAAM-community/ancientmetagenomedir?
• [ ] (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:

[Darcy220606]

Hey @jfy133, It seems the checks are failing in the comment PR step with exit code 403 = that the bot doesnt have the right permission to write a comment in the PR somehow. Any thoughts about why thats the case ?

[maxibor]

Hey @Darcy220606, Are you sure the DOI you put in the PR is the correct one ?

[Darcy220606]

Hey @Darcy220606, Are you sure the DOI you put in the PR is the correct one ? Hey @maxibor Well they state their DOI as https://doi.org/10.1038/s41598-023-39250-y so i added it as 10.1038/s41598-023-39250-y.

[jfy133]

@Darcy220606 no idea why :( it is working for @DianaSpurite on the other PR...

But in the meantime, Checks Tabs > Artifacts > results.zip reports:

AMDirT, version 1.4.6
# 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]

@Darcy220606 the CI fails because you're coming from a fork not a branch.

Commenting permissions do not extend outside the repo unfortunately ;(

[Darcy220606]

@Darcy220606 the CI fails because you're coming from a fork not a branch.

Commenting permissions do not extend outside the repo unfortunately ;(

Good to know for future PRs :D

[Darcy220606]

Samples

• There are many Pietra sant'Angelo in Italy so you have to check the locality too ;)
• Dates should be rounded to the nearest century

Libraries

• I m assumng the polymerase is AmpliTaq gold, as the cited paper is the Santa-Cruz prptocol, and for all library preps they test they used AmpliTaq Gold for the library amp prior indexing

@Darcy220606 if you're happy with my corrections COMMIT and then merge, otherwise leave a comment if you disagree :)

Just commited your suggestions @jfy133 . Thanks! I dont have access to merge so please go ahead :)

[jfy133]

Thanbk you very much @Darcy220606 !