nf-core contributing overview tutorial update

[christopher-hakkaart]

This tutorial is generally really good. It was last updated in March 2022. It's been a massive year with new some tooling absent from this material.

• [x] Remove reference to atom in linting
• [x] Add a section about prettier and black after linting
• [ ] Add a section about subworkflows
• [ ] Update how to join nf-core the GitHub org in exercise 5 to direct everyone to Slack

[FranBonath]

Hej @Furentsu and @GerardoAcquaviva, do you happen to have a PR number for the changes you made to solve this issue?

[Furentsu]

Hi, we actually made two different PRs.

[Furentsu]

I don't understand why prettier check works locally, but it fails here on github...my pull request is #1708

[FranBonath]

it seems prettier has passed for this PR? In the beginning we had issues with having enough resources, so prettier failed on github. Maybe that was the problem here, too.

[Furentsu]

Right, but it doesn't seem to be able to merge my pull request somehow..

https://github.com/nf-core/nf-co.re/actions/runs/4544320764

[FranBonath]

I see. Maybe @ewels can have a look at that?

[ewels]

The PR appears to be merged already?

I can see what look like quite a few markdown errors in the diff though (by eye). Also I think the content needs some tweaking - we should mention Prettier instead of markdownlint (we switched tools a while back) and I don't think that we should talk about configuring black. We want everyone to use the same config, not mess with it 😬