Add testing using nf-test

nf-core / molkart

A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)

https://nf-co.re/molkart

MIT License

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Add testing using nf-test #12

Closed FloWuenne closed 9 months ago

FloWuenne commented 1 year ago

Description of feature

Implement pipeline tests using the new nf-test plugin.

kbestak commented 1 year ago

I'll start a branch for this, 1st goal is implementing a test on the pipeline-level, then we can go and add nf-test to nf-core modules, maybe also local modules.

kbestak commented 11 months ago

Important features to test:

Full pipeline run with Cellpose and Mesmer (clahe included) - single channel
Full pipeline run with all Cellpose and Mesmer (clahe included) - two images
ilastik with single-channel image - already an nf-core module so this should be working
create training crops (just 1 ROI)
Test custom model for Cellpose option?

FloWuenne commented 11 months ago

Everything expect for full-test will be implemented with #25 !

kbestak commented 10 months ago

Full test added with https://github.com/nf-core/molkart/pull/39 Let's check the config files (saw a couple of TODOs) and then we can close this issue.