run nextflow workflow with github CI

[tischi]

@BioinfoTongLI @krokicki

Did you ever try to run NF workflows using GitHub actions?

I think that could be useful to:

1. demonstrate that it should also work on some arbitrary Linux computer
2. automatically test that the current workflow runs through

[krokicki]

Hi @tischi, I haven't tried this yet but I would really like to get it working. I hope to have time to work on it in February. The way I would first try approaching it would be similar to what the Sarek pipeline is doing here: https://github.com/nf-core/sarek/blob/dev/.github/workflows/ci.yml

They use the new nf-test testing framework, which looks very nice: https://www.nf-test.com

There's a talk about how to use it here: https://www.youtube.com/watch?v=K9B7JRkMpQ4

[BioinfoTongLI]

Me either. No expeirence with that.
And 👍 on what @krokicki wrote. I was about to mention the same stuffs 😄
nf-test seem to be THE testing framework. But pytest should also work.

[tischi]

Awesome! I will keep you up to data in case we are getting something working along those lines also here at our EMBL GitLab instance.