Remove args stub from module template to satisfy language server

[jfy133]

I don't know if there is a linting check for this though...

People can add it back in if needed within the stub

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

[mirpedrol]

Let's wait to merge this until v3.2.0, so we don't have bigger changes in a patch release. I am blocking the merge but changes LGTM 🙂

[jfy133]

Fine with me (although arguably a very small change)

[mirpedrol]

ok to merge now :)

[awgymer]

Would it be potentially better to do echo $args in the stub section?

This has a couple of benefits over dropping the $args:

• maintains consistency between script and stub section logic
• adds a simplistic level of testing that args are behaving as expected
• keeps the language server happy

[jfy133]

I had thought the same thing as one option @awgymer , but was outvoted

https://nfcore.slack.com/archives/C043UU89KKQ/p1737099337825629

[awgymer]

That is a shame. It seems like people have a different view of the purpose of stub to me.

I wish it would behave more strictly as a "ran the pipeline as if it were real except never actually executed the script" mode.

I have had this open issue for some time in nextflow because sometimes you have more complex logic for e.g. determining if you should add a --reference ${fasta} arg into your script, and that logic can run fine and quickly in stub mode but you currently can't test it in-place using stub (you have to duplicate the entire logic from script, which I still think is worth doing but I guess others do not 🥲)

[jfy133]

Bring it up on the slack channel! I don't mind changing the PR myself :)

[awgymer]

Are normies allowed to join and comment in #team-maintainers 🤔

[jfy133]

Are normies allowed to join and comment in #team-maintainers 🤔

Yes :)