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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…
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The file delimiter sniffer addition gets the following error when reading in a gzip file.
```python
---------------------------------------------------------------------------
UnicodeDecodeError …
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In #23 (specifically https://github.com/broadinstitute/pooled-cell-painting-profiling-recipe/pull/23#discussion_r456045044) I suggested a column name change within the `0.preprocess` recipe module. Th…
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The function was written to accomodate the pooled cell painting project (see broadinstitute/pooled-cell-painting-analysis#29) and in this project, only the platemap has info. Therefore #21 should even…
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Currently, the config assumes one plate per experiment. This was the case for early experiments, but this will not be the case for large scale experiments. We should add options to save QC and profile…
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I am going through 4.image-and-segmentation.py in much more detail in #39 - the following code block is giving me some trouble:
https://github.com/broadinstitute/pooled-cell-painting-profiling-reci…
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This code block is giving me some trouble:
https://github.com/broadinstitute/pooled-cell-painting-profiling-recipe/blob/068c7eae79f56a50732fdf173902dc596c95ce3f/0.preprocess-sites/8.image-and-segme…
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It would be nice (though not necessary) to add in an additional setting that toggles True/False for overwriting existing files.
Default behavior in the .yaml should be set to true. But if, for exampl…
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We will need to rethink several decisions before the recipe is production-ready. We will use this issue to document these items.
## Checklist
- [ ] Determine where documentation lives (i.e. does…
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The following code block is giving me problems to reproduce 👇 (copied in full below as well)
https://github.com/broadinstitute/pooled-cell-painting-profiling-recipe/blob/6ff26253d6d653f012878ee16a…