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

2.1.1 July 18, 2022

  • Make cumulus workflow work with Cromwell v81+.

2.1.0 July 13, 2022

New Features:

  • Add CellBender workflow for ambient RNA removal.

  • CellRanger:

    • For ATAC-Seq data, add ARC-v1 chemistry keyword for analyzing only the ATAC part of 10x multiome data. See CellRanger scATAC-seq sample sheet section for details.
    • For antibody/hashing/citeseq/crispr data, add multiome chemistry keyword for the feature barcoding on 10x multiome data.
  • STARsolo:

    • In workflow output, besides mtx format gene-count matrices, the workflow also generates matrices in 10x-compatible hdf5 format.


  • CellRanger: For antibody/hashing/citeseq/crispr data,

    • cumulus_feature_barcoding v0.9.0+ now supports multi-threading and faster gzip file I/O.
  • Workflows check if output_directory is a valid Cloud URI based on the given backend value before execution. (Feature request #322 )


  • Genome Reference:

  • Default version upgrade:

    • Update cellranger default to v7.0.0.
    • Update cellranger-atac default to v2.1.0.
    • Update cellranger-arc default to v2.0.1.
    • Update cumulus_feature_barcoding default to v0.10.0.
    • STARsolo workflow uses STAR v2.7.10a by default.