Guides
Each guide covers one job you might need to do with the pipeline.
| Guide | Covers |
|---|---|
| CellBender 0.2 or 0.3 | What differs between the two versions and which options each accepts |
| Cell and droplet counts | --cells, --droplets, the mapper preset, --min_umi, excluding features |
| Data on iRODS | Downloading sample folders from iRODS and giving the pipeline access to them |
| GPU queues and costcodes | Running on gpu, cub22-inference or tiger22-inference |
| Reruns and failures | Retries, -resume and --ignore_failed |