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mycobactopia-org / MTBseq-nf

MTBSeq made simple and easy using Nextflow and nf-core standard.
https://doi.org/10.5281/zenodo.5498063
MIT License
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[MAINTENANCE] Adding a test workflow and updating the `Makefile` #61

Closed Mxrcon closed 2 years ago

Mxrcon commented 2 years ago

hey :wave:, as a small maintenance I tried to update the TEST workflow and updated the Makefile so we can run make run_test and test the complete run with docker and conda.

This might be an initial solution, but after the v1.0.0 release we can discuss an implementation of pytests and md5 checking. What do you think about it? I tested it here and apparently, it's working well.

Feel free to add your thoughts on the comments, I'll available to make any requested changes, we can also discuss the makefile implementation as this still very initial.

abhi18av commented 2 years ago

This might be an initial solution, but after the v1.0.0 release we can discuss an implementation of pytests and md5 checking. What do you think about it? I tested it here and apparently, it's working well.

Davi, for the time being, I think this would be overengineering on this pipeline since basically 3 tools are used. But definitely, I think that good mastery of testing nextflow pipeline is on our general roadmap (but not on this specific pipeline perhaps 🤔 )

I'd like to try out this https://github.com/askimed/nf-test

Mxrcon commented 2 years ago

I'd like to try out this https://github.com/askimed/nf-test

Yes! I'm really interested into learn testing and etc, maybe we can add this to WGS1 ou create a small repo like mtb-bioinformatics/modules and them try it!

abhi18av commented 2 years ago

I think that we're gonna take that approach, best to collaborate with nf-core/modules for the pipeline.

But that's long term, let's track this in a discussion perhaps?

Mxrcon commented 2 years ago

sure! completely agreed.