Repo config file for lint / format

[ewels]

Putting down some ideas for a potential new config file to be used by the new Nextflow lint and format commands.

Starting position:

• Can't use nextflow.config as separation of concerns, also potentially a bit recursive
• Want to make as generic as possible so it can be future-proofed (eg. not .nextflowignore to ignore files only, adaptable for more functionality)
• Common file format for easy interoperability

To make it clear what this is for, I'd suggest calling this thing nextflowrc, following the *nix convention with rc files for startup config / actions. It could be a hidden .nextflowrc.* dotfile or not, I could go either way.

With this, my initial stab is either YAML or TOML. Here's a very rough first draft with some suggestions for things that we may want to configure

nextflowrc.yml

lint:
   exclude:
      - "testing/*"
      - "docs/**/*.nf"
   output-format: concise
format:
   exclude:
      - modules
   spaces: 4
   harshil-alignment: true

Or toml, as used by pyproject.toml and netlify.toml etc:

nextflowrc.toml

[lint]
exclude = ["myworkdir/*", "snippets/**/*.nf"]
output-format = "extended"

[format]
exclude = ["modules"]
tabs = true
harshil-alignment = false

Note that we could support multiple formats, though I'm not sure that this would add much.

To avoid the proliferation of root-level config files, it may be possible for @nf-core to consider adopting this new file to replace .nf-core.yml (probably optionally), in an nf-core section in the file.

Thoughts + feedback welcome!

[ewels]

Follow-on thoughts:

• We should load .editorconfig if present and use those values for config around indentation etc. These presets should have lower priority than any Nextflow config file. Example, website
• We should merge tower.yml into this file, for example under a seqera section.

[ewels]

Similar to .editorconfig, could also read .prettierrc.yml to pick up tabwidth and various other options, eg. here

[maxulysse]

Both format looks human readable, so I'm happy.
And having such a single file is a good idea, especially if we can have a nf-core section and a seqera one

[mahesh-panchal]

Agreed. Leaning towards toml, but would be happy with either.

[jfy133]

I'm pro toml

[JoseEspinosa]

I'd say that yaml is more widely adopted, but if it doesn't need to interact with other tools toml seems to be simpler and we will avoid indentation issues 👅

[fasterius]

I'm very much in favour of toml, and I've seem its adoption increase in recent times, even for tools that previously used yaml.

[pditommaso]

Could .editorconfig be enough?

[ewels]

Could .editorconfig be enough?

I wondered the same, I had a brief look into it but I don't think that it can be extended unfortunately. Not without it becoming invalid for editorconfig. If anyone else thinks otherwise I'd be happy to be shown that I'm wrong though! 😅 I really dislike dotfile / config files polluting repository root dirs 😓