Config Glossary

The brieflow config holds all of the parameters used for a brieflow run. Each notebook is used to configure the parameter variables, which are then saved to the config.yml. Each analysis requires a specific config.yml and the associated files (pool dataframe, cell classification model, etc). An example config for the main branch is outlined in tests/small_test_analysis/config/config.yml. While all of the parameters are explicity outlined in each notebook, we provide additional comments on some here as well:

• preprocess:sbs_samples_fp/preprocess:phenotype_samples_fp: Path to dataframes with one entry for an SBS/phenotype file’s path and the associated metadata (plate, well, tile, etc).

• sbs:df_design_path: Path to dataframe with SBS pool design information regarding gene, sgRNA, oligo, etc.

• *_combo_fp: Path to dataframe with wildcards for file processing in a particular module. Each combination usually corresponds to a one process that needs to be done with Snakemake. For example, each plate, well, tile combination in phenotype_combo_fp corresponds to one ND2 -> tiff file conversion during preprocessing.