Quick Start

1. Activate the environment

conda activate snakemake8

2. Verify Cell Ranger installation (optional but recommended)

snakemake-run-cellranger check-versions

3. Create a config file:

snakemake-run-cellranger init-config --output pipeline_config.yaml

4. Run a workflow:

snakemake-run-cellranger run --config-file pipeline_config.yaml --cores 8