FYI the dev version of nf-core tools doesn't remove anymore the EDAM comments when fixing a modules. No more "please add back the comment" for the

meta.yml

😅 You can simply update using

pip install --upgrade --force-reinstall git+<https://github.com/nf-core/tools.git@dev>

!

I haven't worried about it in any of the PRs that I've reviewed for the last few months

I agree that this isn't critical. I just nicer to know which url correspond to which format. I've opened a PR to add most of the nf-core used format in EDAM a few months ago, but no news from their side.

I still don't see the point in it

I guess it just look nicer with the comments 😅

I mean, more broadly I still don't see the point of the ontologies, the LLMs just understand what a .vcf file is anyway without looking it up

I agree that at the moment the use case is rather small, but using just the url, and parsing the edam ontologie tree, we could automatically display more information about the data format on the nf-core website or in the cli. I don't think it would be useful for LLMs.

The original idea was to automatically discover possible module connections, but I don't think anyone did anything about this since (apart from adding EDAM to meta.yml)