Implement tests with nf-test

[grst]

Pytest workflow makes it easier to maintain larger test suites and also allows to check outputs.

cf. nf-core/tools#605, nf-core/rnaseq#546, https://github.com/nf-core/sarek/tree/dev/tests

Testing scenarios:

• Run pipeline with more than one file
• different parameter combinations
• different filenames and folder structures for cellranger
• run subworkflows with and without index
• different protocols, if we manage to get the test files

[grst]

I'm pretty sure the latest bugs in 2.5.0 would have been caught by that.

@fmalmeida, do you already have something in the internal pipeline that you could upstream here?

[fmalmeida]

Yes,
We have some internal nf-tests that we can start merging it here, adapting it to check only the public modules.

[fmalmeida]

Is there a nf-core pipeline already standardized with nf-test so that I can "copy" the same standards in terms of organization and setup?

[grst]

e.g. https://github.com/nf-core/ampliseq/tree/dev or https://github.com/nf-core/spatialtranscriptomics, but not sure if this qualifies as "standardized".

Modules can since very recently be tested with nf-test in nf-core/modules. There's even documentation for that https://nf-co.re/docs/contributing/modules#writing-nf-test-tests

[fmalmeida]

Hi @grst ,
Added the first one, for alevin aligner.
If you can take a look at that one already while I add the others, just to see if there is anything very clear that should be done different or it is fine as is.
😄

[grst]

Is there a PR I can look at 👀?

[fmalmeida]

Did not open, is still in the branch (shown in the right menu)

I can open a draft if you prefer.

[grst]

I see, thanks! I opened one now, makes it easier to discuss...

[fmalmeida]

Hello hello,
This was merged/solved by #291