Add beautiful citation directions via CITATION.cff in template

[d4straub]

Description of feature

The CITATION.cff in a github repo adds a handy citation field and also enhances zenodo entries substantially.

For example, the title and author list of https://zenodo.org/records/14332397 was improved to https://zenodo.org/records/14409147 by the addition of the cff file. That seems a considerable improvement to me.

I do not want to suggest to include in the cff file actual papers, but info about how to cite the software repo. That would also give a good platform to add ORCIDs and all (? guideline incoming?) code contributors.

Possibly the file could be generated partially automatic?

[muffato]

Thanks for creating the issue, @d4straub .

I should add a counterpoint to that. We also want to cite all the software used within the pipeline, which are currently manually tracked in CITATIONS.md. Text is typically something like

We ran the pipeline (A et al), which does X (B et al) and Y (C et al)

While CITATION.cff is great for the integration with Zenodo, it may give the wrong impression that all that needs to be cited is the pipeline itself.

[d4straub]

Thats a good point @muffato , but I assume that could be avoided by adding in message: a note saying that all software components shall be cited individually. The message might only appear in Zenodo, not in the github repo, though.

[mirpedrol]

#2059
CITATIONS.cff had to be removed before because it was causing problems with Zenodo :(

[d4straub]

@mirpedrol Yes, but this was because the CITATIONS.cff contained the nf-core publication, that would certainly lead to an unwanted result. Quote from above:

I do not want to suggest to include in the cff file actual papers, but info about how to cite the software repo.

[muffato]

#2059 CITATIONS.cff had to be removed before because it was causing problems with Zenodo :(

lol, I can see I approved that one 🙈 ! Like @d4straub said, the issue was it that was the CITATIONS.cff of nf-core, meaning that all Zenodo uploads were getting authors, titles, etc, of the nf-core paper. What we'd like here is to get a CITATIONS.cff that truly reflects the pipeline

[muffato]

Thats a good point @muffato , but I assume that could be avoided by adding in message: a note saying that all software components shall be cited individually. The message might only appear in Zenodo, not in the github repo, though.

@d4straub . Nice suggestion but I can't see the message on Zenodo records either :/

[d4straub]

I thought that message: in the cff appears in Zenodo in the Notes: section, as below. But I might be mistaken (never tried, no experience, only conjecture).

[muffato]

My bad. Yes, it's there