Allowing non nf-core hosted packages to not fail linting

[chasemc]

Is your feature request related to a problem? Please describe

No

Describe the solution you'd like

I'm working on several projects where we aren't targeting submitting to nf-core but I would really like to take advantage of the tooling that nf-core provides in order to create a standardized project.

So far everything works great and I can remove nf-core specific things, however it would be really nice to be able to use the nf-core linter, ideally in CI. However, at least 2 lint checks will always fail if the project isn't a nf-core hosted project:

nextflow_config: Config manifest.name did not begin with nf-core/: autometa                                                                                                
nextflow_config: Config variable manifest.homePage did not begin with https://github.com/nf-core/: https://github.com/KwanLab/Autometa      

Describe alternatives you've considered

nf-core standard would be able to be adopted by a larger community if there was maybe a flag on the linter to ignore tests that only apply to nf-core hosted projects

[chasemc]

A bit of a blunt hammer but a .nf-core-lint.yml file containing nextflow_config: false works Documentation: https://nf-co.re/tools/#linting-config

[alexmanuele]

@chasemc Any possibility of revisiting this, or is it unaligned with nf-core goals?

Seems to me you could add a quick conditional around the code block on line 206 of lint/nextflow_config.py :

if "manifest.name" not in ignored:
    #check that the pipeline name starts with nf-core
    try:
    ...

This would allow users to pop manifest.name in their .nf-core.yml file and pass the lint.

[ewels]

Agreed, there should be a more fine-grained way to do this without disabling the entire config check.

Reopening this issue so that it doesn't get lost again.

[ewels]

Additional context - you can ignore specific config parameter names for the present / not-present checks:

https://github.com/nf-core/tools/blob/e0d00d3e09a996f59eb5ce6ebc4795452a5b1d39/nf_core/lint/nextflow_config.py#L157-L161

However, the failures in this issue do not have if clauses to allow them to be ignored:

https://github.com/nf-core/tools/blob/e0d00d3e09a996f59eb5ce6ebc4795452a5b1d39/nf_core/lint/nextflow_config.py#L206-L216

It's just a case of going through this code and checking ignore_configs so should be fairly easy.

[chasemc]

Not sure about the linting, but a hard problem lately is syncing to TEMPLATE which tries to re-add a bunch of nf-core branding.

[ewels]

@chasemc could you open a new issue about this please? That'll be a separate task.