add run_batch script formatted for CPG #179
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I don't see any reason not to clean up run_batch_general, but if the major distinction is just path structure, any major reason to not to just have one script that takes a parameter for CPG? (Ie have the path structures in a dictionary with keys for Tbh, I've been longing for ages to make this a CLI with flags rather than the commenting and uncommenting nonsense, if you agree that it's reasonable to do one file here, this would be a good excuse to do that work too. What do you think? Could do it together next week? |
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(or do it yourself, of course, just if it makes it more fun) |
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No reason not to combine them. I made this version for a project I was working on and then thought it would be nice to polish and add to the repo, but the extra work to combine (and make CLI) seems worth it! |
| parser.add_argument( | ||
| "--plate-format", | ||
| dest="plate_format", | ||
| default=384, |
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Make sure that here and elsewhere (ie rows and columns), the default here matches the function default. Otherwise, if the user DOESN'T pass --plate-format, it will default to 384, so even if they passed rows, it would overwrite them with the 384 plate format.
| help="Name of the pipeline to overwrite defaults of Zproj.cppipe, illum.cppipe, qc.cppipe, assaydev.cppipe, analysis.cppipe.", | ||
| ) | ||
| parser.add_argument( | ||
| "--outputstructure", |
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Minor preference for this to be output-structure, but I don't feel strongly about it if you'd rather not
Adds a run_batch script with formatting that matches data organization in the Cell Painting Gallery.
Uses run_batch_general.py as template with updating, cleanup, and changed file structure
@bethac07 is there any reason that I shouldn't perform similar cleanup on run_batch_general.py: