Is there a way to have nf-core tools run pipeline linting without trying to check for

/pipelines.json

?

oops, didn't know that we do that (turns out it is used during the RO-crate creeation to get the topics). will think about a fix for it

It's sort of an edge case, but due to some crappy VPN certificate my company uses, it gets some funky SSL error (known issue with the vpn provider) when I try to run it. But it did make me wonder if it was necessary for a standard linting, particularly if we support non nf-core ones. I can make an issue :)

just as additional info in case it helps, we have excluded 'rocreate' from the template features, and tools should skip this if the rocrate feature is not part of the template. But somehow it doesn't work.

yep, because it is in the template creation step and we didn't add a check for the skip_features there. will add it

I am going to ask @Júlia Mir to review that one pretty pleeeaassseee

approved 🙂 I was not able to test the full lint command because my json file is currently failing, but I reach the files_exist check so I think this means the rocrate error is fixed