Hint: This rule uses the preprocess.py step
This rule should do the following:
- Take the output of the download_data rule as input
- Specify parameters to filter the data such that the minimum number of cells is 3, the minimum number of genes is 200, the maximum percent of mitochondrial reads is 5%, and the number of highly variable genes to retain is 2000
- Output a processed '.h5ad' file. You should put this in some type of data directory. (Hint: can you specify different directories for raw and processed data?)
Hint: This rule uses the preprocess.py step
This rule should do the following: