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bokulich-lab / q2-fondue

Functions for reproducibly Obtaining and Normalizing Data re-Used from Elsewhere
BSD 3-Clause "New" or "Revised" License
20 stars 6 forks source link

Replace input list with file of IDs #28

Closed lina-kim closed 3 years ago

lina-kim commented 3 years ago

Closes #8.

This solution does mean inputting a list of SRR IDs for metadata/sequence retrieval is no longer an option.

Testing/documentation IP; any and all feedback is much welcomed!

lina-kim commented 3 years ago

Thank you @misialq! So sorry for the late feedback, but your comments should be all addressed with the recent commits.

please update your branch with changes from the main (there was another change recently)

I did pull before the opening the PR, let me know if there's anything missing? A quick diff tells me it's up-to-date.

please update the tests, some are currently failing

Good call! That was more painful than I expected, but these tests should now be properly updated to account for the new input parameters.

in all QIIME 2 projects we follow the PEP8 style guide - you can run flake8 to check that everything adheres to that

Done. I normally use Black, but this is a cool alternative - any recommended configurations?