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nf-core

Hej! I have recently opened an <https://github.com/nf-core/tools/issues/4122|issue> and corresponding <https://github.com/nf-core/tools/pull/4124|PR> to suggest a resolution. However, what I am actually here for, is that a pytest is failing: <https://github.com/nf-core/tools/blob/d6d6e1464b900839b7be21ed0cc4bcbe63d50ff0/tests/modules/lint/test_main_nf.py#L145-L147|test_topics_and_emits_version_check> expects that there are lint warnings for module `bioawk` based on the assumption that the module relies on versions YAML. However, the module has recently been updated to used topic channels instead, so the assumption is no longer valid. The test is then failing for `dev`  and all recent branches/PRs in the repo.

Perhaps you were already aware of this, but since I didn't find any open issue about it, I opened a bug report: <https://github.com/nf-core/tools/issues/4125>

I could open a PR for fixing it, but it is unclear if this check should be removed or if a different module, that still relies on versions YAML, should be used instead. So I wanted to discuss it with you here first!
What are your thoughts on this? :thinking_face:

yes, sorry for not commenting about this on your PR or making an issue. <https://nfcore.slack.com/archives/CE5LG7WMB/p1773664486417699?thread_ts=1773663543.742669&amp;cid=CE5LG7WMB>
am finishing up a PR to fix this. thanks so much for reaching out!

Ah alright! Great then! And no worries at all, of course! :slightly_smiling_face:
Then you get the satisfaction of also closing the Bug report hehehe! :grin:

<https://github.com/nf-core/tools/pull/4126> if you have time for a quick review :slightly_smiling_face:

I took a look but I'm quite new to this and I have some trouble understanding the changes... Could you add some information to the issue and/or PR description to explain the decision and why these changes solve the problem? :thinking_face:

Also, it looks like 2 other pytests are failing, but I haven't looked into why!

yes, I needed to update the upstream modules. will update the tests accordingly

Ah alright! Then just let me know when you need me to take another look at it! :grin:

test are sucessfull now and I added a bit more description to the PR.

Thanks for the thorough review! Let me know the next time you are around Alfa 3 at Scilifelab and you will get the last limited-edition shiny nf-core infrastructure stickers :wink:

Ehhhh wow! I'll be around next Monday so maybe I can catch you then? :star-struck:

And thank you for taking the time to add an explanation for the changes, it really helped to understand the code! And thanks for the review  of my PR too! :grin: