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

2.4.1 May 30, 2023


  • In Cellranger workflow:

    • Fixed RNA Profiling now accepts custom probe set references.
  • In STARsolo workflow:

    • Add limitBAMsortRAM and outBAMsortingBinsN inputs to handle out-of-memory error in BAM sorting phase.
  • In GeoMx_fastq_to_dcc workflow:

    • Support multiple FASTQ folders as input.


  • In Demultiplexing workflow:

    • Upgrade souporcell_version to 2022.12, which is based on commit 9fb527 on 2022/12/13.
  • In STARsolo workflow:

    • Upgrade star_version to 2.7.10b.

Bug Fixes:

  • In Spaceranger workflow:

    • Fix the image localization issue for CytAssist samples.

2.4.0 January 28, 2023


  • In Cellranger workflow:

    • Upgrade cellranger_version default to 7.1.0.
    • Add Mouse probe set v1.0 for Fixed RNA Profiling analysis.
    • Add probe set v1.0.1 of both Human and Mouse for Fixed RNA Profiling analysis.
    • Upgrade cumulus_feature_barcoding version default to 0.11.1.
  • In Cellranger_create_reference workflow: upgrade cellranger_version default to 7.1.0.

  • In Cellranger_vdj_create_reference workflow: upgrade cellranger_version default to 7.1.0.

  • In Spaceranger workflow: upgrade spaceranger_version default to 2.0.1.