Change repo to nf-core/actions

[edmundmiller]

Personally, I would love to see all nf-core testing workflows updated to use one install per repo per version, and then all tests are run off of that. I'm really inspired by Julia's testing workflow template. Unfortunately, Nextflow doesn't have as nice of a testing framework as Julia, so that may be a pipe dream.

That's nice. Do you not think that would work with nf-test?

That also makes me think we could move to a repo and pull in the GitHub actions like this repo https://github.com/magit/actions so it would just be:

steps:
    steps:
      - name: Install Nextflow
        uses: nf-core/actions/setup-nextflow@main
      - name: Install nf-core
        uses: nf-core/actions/setup-nf-core@main
      - name: Run nf-test
        uses: nf-core/actions/nf-test@main

Originally posted by @emiller88 in #19 (comment)

[MatthiasZepper]

What is the rationale to reinstall e.g. Nextflow frequently (caching aside) over running those actions requiring it in a Docker container that already has the required dependencies installed?

[MillironX]

Basically, because (until recently anyway) Nextflow behaves differently when inside of a Docker container than when it's outside of the container. (See docs, code).

[MatthiasZepper]

Basically, because (until recently anyway) Nextflow behaves differently when inside of a Docker container than when it's outside of the container. (See docs, code).

Okay, yes, that's reasonable - I wasn't aware that we are actually testing containerized tasks somewhere. Thanks for letting me know and the effort to provide me with precise links to docs and code! Fascinating to see how Nextflow handles the Docker execution in that case!

[edmundmiller]

I was debating setting this up for the new nf-test CI workflow that was being worked on. But I think these will sadly need to be separate actions. https://github.com/tj-actions Otherwise we'll have a new version every time any other actions have a release.

I think we back off this and just keep things simple with separate repos.