Lint warning when using a template

[Midnighter]

Description of the bug

When using a template instead of a script block inside of a process, I get the following lint warning:

Process name not used for versions.yml

which seems like a parsing bug of the linter.

Command used and terminal output

nf-core modules lint sratools/prefetch  # On currently open PR.

System information

nf-core, version 2.4.dev0

[Midnighter]

See nf-core/modules#1631 and the failing lint action.

[ewels]

(exact!) duplicate of #1557 😉

[Midnighter]

Actually no, different lint warning.

[ewels]

Apologies, rushing and misread 🙏🏻

# On currently open PR.

Can you avoid this in future issues please? I rarely get to them in time and usually have to spend ages figuring out what date the issue was posted and digging through git history to guess at which file was the one that caused the error 😅

Links to actions runs / file permalinks is best as it's quick to replicate then 👌🏻

[ewels]

ok I should stop working and go and eat. Just realised that your comment immediately after opening the issue was exactly that 👍🏻

[ewels]

...except the PR and failing lint action has the error from the other issue which I thought that you'd duplicated:

╭──────────────────────────────────────────────────────────────────────────────╮
│ [!] 1 Test Failed                                                            │
╰──────────────────────────────────────────────────────────────────────────────╯
╭──────────────────────────────────────────┬─────────────────┬─────────────────╮
│ Module name                              │ File path       │ Test message    │
├──────────────────────────────────────────┼─────────────────┼─────────────────┤
│ sratools/prefetch                        │ modules/sratoo… │ when: condition │
│                                          │                 │ has too many    │
│                                          │                 │ lines           │
╰──────────────────────────────────────────┴─────────────────┴─────────────────╯

I guess the force-push in that PR dropped reference to the original CI tests where this was happening.

Could you link to a reproducible example please? 🙏🏻

[Midnighter]

I'll provide more stable links in future, sorry. The warning is right there, though https://github.com/nf-core/modules/runs/6368191141?check_suite_focus=true#step%3A9%3A29=

[Midnighter]

To reproduce:

pip install -U https://github.com/nf-core/tools/archive/dev.zip

and in the modules repo:

nf-core modules lint custom/sratoolsncbisettings

[ewels]

Ahhh warning not error, that's why I didn't see it. Sorry 🤦🏻

[mirpedrol]

It seems that when using a template the linting checks for the script section (which is empty in that case) are also performed, thus the error.
Should we only perform the checks when there is a script section?
We could also include a template section to perform the linting, but I guess it will be varying a lot between different templates, won't it?

[ewels]

We could also include a template section to perform the linting, but I guess it will be varying a lot between different templates, won't it?

Yeah I wondered the same but I'm not sure that we can do much with this. I did wonder about checking for the version etc. but it would be fairly complex code and probably quite liable to break. There aren't loads of modules taking this approach so I'm not in a rush to do this for now.