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vdblab / vdblab-shotgun

Shotgun metagenomic sequencing processing pipeline
MIT License
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Change submodule validates #76

Closed miraep8 closed 8 months ago

miraep8 commented 9 months ago

I have been reusing parts from the vdblab-shotgun in my new snakemake pipeline using the module import capacity. Unfortunately one downside of having the validate calls in the individual .smk files is that it enforces all the requirements of the config.schema.yaml file from vdblab-shotgun onto whatever snakefile is trying to use it! By removing these valideas and setting skip_validate to True (thanks Nick!) I am able to get around these requirements.

Personally I really like that these are very modular components, I think that this requirement for validation within these sub components makes them less reusable. Open to another way to solve this problem as well, for now just putting this here as a means to start the conversation.

Cheers!

miraep8 commented 9 months ago

Whoops! The lint tests are keeping me honest.

nickp60 commented 9 months ago

Sorry about all the snakefmt issues -- those are all my fault!

nickp60 commented 9 months ago

Looks good to me! Thanks for doing this.

miraep8 commented 8 months ago

Alright, cheers - will merge for now then. Happy to return to this at a future point if it makes sense though regarding larger design choices about how to control modularity with this pipeline.