Inspect

This module performs the extraction of useful metrics that can be either shown on the standard output or saved them to file, in CSV or Parquet format.

Usage

The minimal command is cl inspect --input-path <PATH> --output-path <PATH>, where input-path is the path to the AVITI data folder and output-path is the directory where the outputs will be placed.

Options

• --stats-json: Path to the cell2stats 'RunStats.json' file. Required only if different from <INPUT_PATH>/RunStats.json.
• --panel-json: Path to the cell2stats 'Panel.json' file. Required only if different from <INPUT_PATH>/Panel.json.
• --raw-parquet: Path to the cell2stats 'RawCellStats.parquet' file. Required only if different from <INPUT_PATH>/RawCellStats.parquet.
• --wells: Comma-separated list of wells to include in the analysis. By default, all wells will be used.
• --batches: Comma-separated list of batches to include in the analysis. By default, all batches will be used.
• --stats-list: Comma-separated list of metrics to produce. Accepted values include 'All', 'BatchWell', 'Well', 'Count', 'Correlation'. Default: All.
• --format: It can be one of 'csv', 'parquet' or 'stdout'. Default is 'csv'.