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

2.5.0 February 3, 2024


  • In Cellranger workflow:

    • Add multi_disk_space input for specifying disk size used by Fixed RNA Profiling or 10x multiome jobs, which usually take large amount.

  • In Cellbender workflow:

    • With 0.3.0 default Cell Bender version, users don’t need to always specify expected_cells or total_droplets_included input.


  • In Cellranger workflow:

    • Upgrade cellranger_version default to 7.2.0.

    • Upgrade cumulus_feature_barcoding version default to 0.11.2.

    • Add GRCh38 VDJ v7.1.0 reference: GRCh38_vdj_v7.1.0.

  • In Spaceranger workflow:

    • Upgrade spaceranger_version default to 2.1.1.

  • In Demultiplexing workflow:

    • Upgrade souporcell_version default to 2.5.

  • In Cellbender workflow:

    • Upgrade cellbender_version default to 0.3.0.