Add GitHubActions

[maxulysse]

• Add GitHub Actions

PR checklist

• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
• If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repo
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Make sure your code lints (nf-core lint .).
• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated

Learn more about contributing: https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md

[szilvajuhos]

Looks OK, but would be better to be reviewed by somebody who is more experienced in github stuff.

[maxulysse]

I think at the moment, that would be me ;-)

[drpatelh]

Good work @maxulysse ! So the only difference I can see between the Travis CI tests and GitHub Actions are the two additional files .github/workflows/ci.yml and .github/workflows/linting.yml ? These look much simpler and I think its probably nicer to have these two tests running separately. Are these file auto-detected and triggered on GitHub Actions if they are placed in .github/workflows/?

[drpatelh]

Much quicker than Travis too!

[maxulysse]

Files are indeed auto-detected and triggered when place in .github/workflows/.

I could have put all tests into one file, but I figured that it would be better to run both tests separately as we don't need to download the docker image as well for the linting.

It's also much easier to make a matrix with ENV variables so you can more easily test multiple versions of different tools, or in sarek case, make multiple tests.

And I just scratched the surface with linting and CI, we could automate responses on PR and issues and so on...

[drpatelh]

Yeah, I saw the matrix testing from the number of checks that were carried out. Definitely a great start. Thanks for doing this! It looks good enough to me but maybe @ewels @sven1103 want to give it a once over too?

[maxulysse]

And then we can all look at nf-core/tools#369 ;-)

[apeltzer]

Amazing job! Looks really good to me and I also like that you can split the lint and the actual tests in separate files...