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

2.2.0 October 4, 2022

New Features:

  • Add Nanostring GeoMx DSP workflows. It consists of two steps:

    • GeoMxFastqToDCC workflow to convert FASTQ files into DCC files by wrapping Nanostring GeoMx Digital Spatial NGS Pipeline.
    • GeoMxDCCToCountMatrix workflow to generate probe count matrix from DCC files with pathologists’ annotation.


  • Spaceranger workflow:

    • Add support on 10x Space Ranger v2.0.0.
    • Add human_probe_v2 Probe Set for FFPE samples, which is compatible with CytAssist FFPE samples.
  • Upgrade cumulus_feature_barcoding_version default to v0.11.0 for Feature Barcoding in Cellranger workflow.

API Changes:

  • Across all workflows, for AWS backend:

    • All workflows now have awsQueueArn input, which is used for explicitly specifying the Arn string of an AWS Compute Environment.
    • Remove awsMaxRetries input for all workflows. Namely, use Cromwell’s default value 0.

Bug Fix:

  • Fix the issue on localizing GCP folders in Cellranger workflow for ATAC-Seq and 10x Multiome data.