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broadinstitute / pooled-cell-painting-profiling-template

:hammer_and_wrench: Use me to version control Pooled Cell Painting data and processing pipelines
BSD 3-Clause "New" or "Revised" License
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Move plate_id to batch_id and enable customized analysis splits #26

Closed gwaybio closed 3 years ago

gwaybio commented 3 years ago

We should have been treating the input directory as a batch directory and not a plate directory. Moving forward, we will save the profiles and metadata information for multiple plates inside any given batch directory. The folders in this directory will be of the format: "plate-well-site".

We also need to enable a user to customize how the data are aggregated together in both QC and profiling. For instance, if a user wants to make well-level profiles, they should be able to control this in the experiment config file. Or, if a single plate contains multiple experimental conditions, each experimental condition should be handled independently.

This is a major upgrade to the template, that will require corresponding adjustments to the recipe and config files.

gwaybio commented 3 years ago

I believe I can simultaneously address #15 in this PR, but I am currently unsure exactly how.

gwaybio commented 3 years ago

I will add the corresponding recipe changes in broadinstitute/pooled-cell-painting-profiling-recipe#71

gwaybio commented 3 years ago

fixed