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Add stub runs in CI/CD #43

Open AlexVCaron opened 1 day ago

AlexVCaron commented 1 day ago

Stubs are not executed in CI/CD and could be wrongly implemented. We need to add to each component tested a stub run as well.

AlexVCaron commented 22 hours ago

Implementing the stub run in the github workflows is quite easy. However, nf-test is not really equipped to do it the way we'd need it to.

The way @gagnonanthony proposed in the meeting - creating new test cases for stub runs - is the only way to go right now. I really don't want to go that way, as it would weighten the code a lot and take a lot of time.

Also, there was a lot of activity on the nf-core side about that a little while ago (askimed/nf-test#227). I'll stir the pot a bit on that end to check where the idea is going. I propose we put this on hold for now and wait for more info before going further. @arnaudbore @gagnonanthony