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broadinstitute / pooled-cell-painting-profiling-recipe

:woman_cook: Recipe repository for image-based profiling of Pooled Cell Painting experiments
BSD 3-Clause "New" or "Revised" License
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Process cells #13

Closed ErinWeisbart closed 4 years ago

ErinWeisbart commented 4 years ago

Here's the draft of 2.process-cells. I think it's good to go through line 132. After line 133 # Add metadata is where I need the major help.

(Also, I haven't run it through black yet.)

ErinWeisbart commented 4 years ago

I think it's now fully functional and ready for a real review! The only thing that I haven't addressed in comments is that the final metadata_site.tsv doesn't look exactly the same as the output for CP074B. It has columns that were dropped in CP074B. The list of columns kept was hardcoded in CP074B. It's not a lot of extra columns so it didn't seem worth it to me to introduce a list that would have to be edited in config, especially as one can instead drop it to the necessary columns at the start of future manipulation. But I certainly defer to you on this point.