search

biocore / metagenomics_pooling_notebook

Jupyter notebooks to assist with sample processing
MIT License
8 stars 16 forks source link

Refactored Plate Replication functionality added to Metapool #128

Closed charles-cowart closed 1 year ago

charles-cowart commented 1 year ago

Initial migrating of Rodolfo's new notebook functions to metapool. Minimal changes made to support the new notebook in development.

antgonza commented 1 year ago

Can you add tests before I review?

charles-cowart commented 1 year ago

@antgonza Ready for review. The code that supports each test is a little repetitive, and the metadata files could be named better.

charles-cowart commented 1 year ago

@antgonza Eh, I cleaned up the notebook some - I removed the functionality that was no longer needed and replaced it with a call to the new PlateReplication() code. It's very complete and very well commented but references a specific project a lot. I didn't include the needed data files as one of them was very large. I think we could do with some smaller sample-files but I'll need to work with @RodolfoSalido or @mmbryant23 on that.

RodolfoSalido commented 1 year ago

Just tested this and looks good. However, we didn't add the functionality of adding the 'contains_replicates' flag to the sample_sheet for the SPP to parse it. We had agreed on this when we were discussing the scope of this effort. Screen Shot 2023-06-23 at 12 43 18 PM The functions that would need some changes are likely make_sample_sheet() and validate_and_scrub_sample_sheet. I have added another key to the Bioinformatics dictionary: 'contains_replicates' that gets a boolean True/False. Screen Shot 2023-06-23 at 12 44 39 PM

Should I raise this as a new issue ?

antgonza commented 1 year ago

Yes, please open a new issue. Thank you for confirming that it almost works as expected.