Adding normalize step to recipe #16
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| --- | ||
| normalize: | ||
| perform: true | ||
| output_basedir: data/profiles |
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Everywhere else so far we've set config defaults to single folders instead of nested folders.
Do we need to maintain this in case someone is working in an OS that uses \ not / ? Though I guess we have / at the end of all of our paths, so never mind on that remark.
I guess I just want to point this out and it's not necessarily a problem.
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great catch - yes this is definitely something to be mindful of. Fortunately, pathlib is great and will take care of that issue under the hood.
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Also note that we are modeling the directory structure in this project from cytomining/profiling-handbook#54 (comment)
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Here, we add the normalization step to the pooled cell painting recipe. We use
pycytominer.normalize()to perform the normalization, and we include all options in an updated config file.I describe a very important TODO/caveat/improvement in #15 - The script works and will keep us marching forward, but we should stop and think about this single-cell problem soon.