filter_krakenuniq, krakenuniq2krona, krakenuniq_abundance_matrix scripts overlap

NBISweden / aMeta

Ancient microbiome snakemake workflow

MIT License

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filter_krakenuniq, krakenuniq2krona, krakenuniq_abundance_matrix scripts overlap #88

Closed clami66 closed 2 years ago

clami66 commented 2 years ago

All these scripts perform a filtering step on krakenuniq.output where hits are filtered by breadth/depth of coverage, the parameters are the same. It would be good to isolate this part of the processing to a separate, common script for better maintainability

percyfal commented 2 years ago

Indeed. And here is where I would push for the CLI-based python package setup which would allow for

separate tests with e.g. pytest
making the scripts truly standalone and accessible with e.g. aMeta-krakenfilter

ZoePochon commented 2 years ago

Yes, we were thinking the same with Emrah. It would make the dag more unterstandable if there is an inbetween rule for filtering and this three rules come after.