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nf-core / tools

Python package with helper tools for the nf-core community.
https://nf-co.re
MIT License
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Github Actions CI tests for -profile conda and -profile singularity #815

Open drpatelh opened 3 years ago

drpatelh commented 3 years ago

Currently, all of the Github Actions CI tests that we use to test that the pipeline functions (using a minimal dataset) are run as -profile test,docker. This just tests whether the pipeline will run with Docker, however, with the advent of DSL2 the processes we were using to create this Docker image are much more detached because the Conda, Singularity and Docker definitions are now all obtained from different sources. Developers tend to test with one of these methods so it would be great to have CI tests for all of them just to make sure they are working.

For example, I just noticed a Conda conflict issue because I explicitly tested -profile test,conda before releasing the rnaseq pipeline https://github.com/nf-core/rnaseq/pull/535/commits/c2a7fffcd46a61bc860a1dd929d37dc9391e06a8.

maxulysse commented 3 years ago

I'm starting to look into that for sarek. cf https://github.com/nf-core/sarek/pull/338/checks?check_run_id=1792906176

sateeshperi commented 1 year ago

@drpatelh given that conda tests on CI are unreliable and testing for singularity might be an overkill for the runners, your thoughts on closing this issue?