Merge Jackson2024

[iseultj]

Before merging - should I also add to single genome host assoc.? Raw reads & aligned bams available for T. forsythia and S. mutans (and bams aligned to T. denticola, but this is basically unusable in downstream analysis as is).

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)

This is to close #1160

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)

• [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 and not amplicon data
  • Note: 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] 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
• [x] Changelog is updated to include the publication under 'Added'?

[iseultj]

@spaam-bot please autofill ancientsinglegenome-hostassociated_libraries.tsv Jackson2024

[iseultj]

@spaam-bot please autofill ancientsinglegenome-hostassociated_libraries.tsv Jackson2024

[jfy133]

@iseultj it needs to be the table name without _libraries.tsv suffix, I realise now the terminology is unclear now 😅

[iseultj]

@iseultj it needs to be the table name without _libraries.tsv suffix, I realise now the terminology is unclear now 😅

Oh cool! that makes sense 😄 could you merge the other PR I made (#1162) so Streptococcus mutans is an allowed species? Thanks!

[jfy133]

@iseultj it needs to be the table name without _libraries.tsv suffix, I realise now the terminology is unclear now 😅

Oh cool! that makes sense 😄 could you merge the other PR I made (#1162) so Streptococcus mutans is an allowed species? Thanks!

I approved it, do you not have merge permissions?

[iseultj]

@iseultj it needs to be the table name without _libraries.tsv suffix, I realise now the terminology is unclear now 😅

Oh cool! that makes sense 😄 could you merge the other PR I made (#1162) so Streptococcus mutans is an allowed species? Thanks!

I approved it, do you not have merge permissions?

No, sorry!

[jfy133]

Oh! Ok! Merged for you!@

[iseultj]

@spaam-bot please autofill ancientsinglegenome-hostassociated Jackson2024

[iseultj]

All done - I think it might be better to get the ftp link for the submitted file rather than the file generated by the ENA/SRA though (which is what it does currently)- I have put ftp links and md5sums for the submitted files, because with the aligned bam, you get a generated fastq and have to realign anyway (which I assume people would prefer to go to the raw data for anyway). If you prefer the generated file, let me know and I'll modify it again :)

[jfy133]

@spaam-bot please autofill ancientsinglegenome-hostassociated Jackson2024

[jfy133]

@spaam-bot please autofill ancientmetagenome-hostassociated Jackson2024

[iseultj]

@spaam-bot please autofill ancientmetagenome-hostassociated Jackson2024

[iseultj]

@jfy133 I've made most of those changes - I don't think it really makes sense to treat them as one sample, given that when analysed there are 2 different genomes from each tooth, and if people want to include them in metagenomic analysis, each subsample of the tooth is pretty different. If you're ok with that, I think this is ready to merge - I have updated the dates and ftp links, and the automatically generated table is working well :)

[github-actions[bot]]

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