process_cells config mismatch

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 config mismatch #26

Closed ErinWeisbart closed 4 years ago

ErinWeisbart commented 4 years ago

In the config for process_cells we have prefilter-features as a Bool but in 2.process-cells.py is requires running 0.preprocess-sites.py first so that you have a prefilter file as input.

@gwaygenomics What is the goal of this config Bool? Do we want to update 2.process-cells.py to allow for not using a prefilter file? Or do we want to remove the input from the config?

gwaybio commented 4 years ago

yeah, i agree this is weird... lets remove prefilter-features from the config