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). https://doi.org/10.1038/s41592-020-0905-x

Release Highlights in Current Stable

4.0.1 Dec 14, 2025

  • Cellranger workflow:

    • For Flex data, avoid using genome reference when no_bam = true and cellranger_version >= "8.0.0".

4.0.0 Nov 26, 2025

  • Cellranger workflow:

    • Support library-level chemistry for Flex data processing. This is needed when Flex and CITE-Seq libraries have probe barcodes at different read pairs, which causes the auto-detection to fail (e.g. MFRP-Ab-R1 for CITE-Seq library, MFRP-RNA for Flex library). (PR 446)

    • Upgrade cellranger_version default to 10.0.0.

    • Upgrade cellranger_arc_version* default to 2.1.0, with associated important feature changes:

      • The 20,000 total cell limit is removed.

      • Add secondary input for running secondary analysis or not, with default false.

    • Upgrade cellranger_atatc_version default to 2.2.0, with associated important feature changes:

      • The 20,000 total cell limit is removed.

      • The force_cells input can be any positive integer, which is no longer restricted to be smaller than 20,000.

      • Add secondary input for running secondary analysis or not, with default false.

    • Add 2024-A transcriptome references for Cell Ranger ARC and ATAC: GRCh38-2024-A_arc and GRCm39-2024-A_arc.

  • Spaceranger workflow:

    • Upgrade spaceranger_version default to 4.0.1, with associated important feature changes:

      • Support Visium HD 3’. To enable it, in the sample sheet, leave the ProbeSet column blank for such samples, or skip this column if all samples are Visium HD 3’.

      • Add Visium probesets v2.1 which are bundled with 2024-A transcriptome references: human_probe_v2.1 and mouse_probe_v2.1.