Quick Start

1. Activate the environment

conda activate snakemake8

2. Verify Cell Ranger installation (optional)

sc-preprocess check-versions

3. Create a config file

Choose your modality (gex, atac, or arc) and generate a config with all parameters:

sc-preprocess init-config --modality gex --output pipeline_config.yaml

4. Dry run (recommended)

Preview what the pipeline will do without executing anything:

sc-preprocess run --config-file pipeline_config.yaml --cores 1 --dry-run

Optionally, visualize the workflow as a DAG:

sc-preprocess run --config-file pipeline_config.yaml --cores 1 --dag | dot -Tpng > dag.png

5. Run the pipeline

# Local execution
sc-preprocess run --config-file pipeline_config.yaml --cores 8

# HPC execution (with SLURM profile)
sc-preprocess run --config-file pipeline_config.yaml \
                             --cores all \
                             --snakemake-args --profile HPC_profiles