Cumulus WDL workflows and Dockerfiles

Release License Docs

All of our docker images are publicly available on Quay and Docker Hub. Our workflows use Quay as the default Docker registry. Users can use Docker Hub as the Docker registry by entering cumulusprod for the workflow input “docker_registry”, or enter a custom registry name of their own choice.

If you use Cumulus in your research, please consider citing:

Li, B., Gould, J., Yang, Y. et al. “Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq”. Nat Methods 17, 793–798 (2020).

Release Highlights in Current Stable

2.3.0 October 30, 2022

New Features:


  • In Cellranger workflow:

    • Upgrade cellranger_version default to 7.0.1.
    • Upgrade cellranger_arc_version default to 2.0.2.
  • In Cellranger_create_reference workflow: upgrade cellranger_version default to 7.0.1.

  • In Cellranger_vdj_create_reference workflow: upgrade cellranger_version default to 7.0.1.