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nf-core
Add nf-core lint to super-linter
https://github.com/github/super-linter#supported-linters
Snakemake is in there also, so I don't think they're opposed to smaller communities linters.
Is this an open source I can contribute to? I am relatively new to coding with Python.
Definately! I might be a bit of an undertaking though, it's mostly just hacking stuff together.
You could take a look at how snakefmt does it in super-linter and try to go from there. There was also talk about using groovy-lint so we might be able to just tack on the .nf extension to the list of files to lint inat for now. Check it out here https://github.com/grst/rnaseq/pull/3/files
Iām relatively new. I would love to figure out how I can understand how I can use my talents and skills to be a valuable resource for this project, I just must learn ton understand how all the coding works. Currently I am going through python intro courses, what do you recommend for me to build my understanding asap so that I can hop on this project? Thanks for your time Edmund.
On Dec 18, 2020, at 8:46 AM, Edmund Miller [email protected] wrote:
Definately! I might be a bit of an undertaking though, it's mostly just hacking stuff together.
You could take a look at how snakefmt does it in super-linter and try to go from there. There was also talk about using groovy-lint so we might be able to just tack on the .nf extension to the list of files to lint inat for now. Check it out here https://github.com/grst/rnaseq/pull/3/files https://github.com/grst/rnaseq/pull/3/files ā You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/nf-core/tools/issues/797#issuecomment-748198382, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASFOLFK7Y6MFDHMYQH7TQKLSVOBOPANCNFSM4UCOY57Q.
Super-Linter docker image is getting big, so I'm not sure that smaller communities linters would be accepted
You may check its little brother Mega-Linter ... that probably wouldn't accept smaller communities linters, but manage such requirement with a Mega-Linter plugin capability :)
As the plugin capability is quite new, I'd love your feedback and will provide support if necessary :)
https://nvuillam.github.io/mega-linter/plugins/
@nvuillam Thanks! I don't think they'll have an issue with it however since the snakemake formatter was accepted.
@Emiller88 - what would the benefit of adding this be?
I'm a little aware that many of the nf-core lint tests check that the pipeline matches the expected template. The template includes the automation to run the linter. So it might be a bit of a chicken-and-egg situation š
@Nico81019 - all of @nf-core is open source, yes, and this particular tool / repository is written in Python. However, this specific issue is probably not suited to what you're looking for.
I'd recommend taking a look at the issues we have which are tagged with the label first-timers-only. You can find them here: https://github.com/nf-core/tools/issues?q=is%3Aopen+is%3Aissue+label%3Afirst-timers-only
ps. Just realised that this issue had that label, which is probably why you came here š I'll see if I can tidy up the labels a little.
@Emiller88 - what would the benefit of adding this be?
Basically simplifying CI, we would just need super-linter for all the linting jobs. But I don't think I thought this through, nf-core lint is more specific to nf-core pipelines and not all nextflow pipelines. I think adding nextflow files to be linted by the groovy linter might cover this.
I guess then I'd like to petition to move all the yaml, md, editorconfig, and groovy linting to super-linter, and then have nf-core lint on the pipelines.