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

3.0.0 March 7, 2025

  • Overall highlights:

    • For data localization/delocalization on GCP, now use gcloud storage commands instead of gsutil, as gsutil is deprecated, and gcloud storage achieves some speed improvement.

    • Users no longer need to specify backend input for AWS or local backend, and it is now automatically figured out from output_directory location.

    • Remove support on mkfastq in Cellranger and Spaceranger workflows, as it will soon be removed from Cell Ranger and Space Ranger. Users need to run BCL Convert themselves first to generate FASTQ data.

    • For Cellranger and Spaceranger workflows, provide better support for shared computing environments like AWS Batch, GCP Batch and sHPC.

    • For resources like prebuilt references, they are now held in a single-region bucket gs://cumulus-ref in US-CENTRAL1 to reduce potentially higher network cost at users’ side from the previous multi-region bucket.

  • Cellranger workflow:

    • Upgrade cellranger_version default to 9.0.1.

    • Remove mkfastq related workflow inputs.

    • Remove run_count input as it’s always true.

    • Support input data format as a TAR file containing FASTQ files.

    • Change FeatureBarcodeFile column header to AuxFile (for backward compatibility, FeatureBarcodeFile is still accepted but not recommended).

    • Support all the 3 Sample Multiplexing methods provided since Cell Ranger v9.0. See details

    • For single-cell and single-nucleus RNA-seq:

      • Add new genome reference mRatBN7.2-2024-A

      • Remove Target Gene Expression-related inputs, as it’s no longer supported since Cell Ranger v7.2.0.

    • For feature barcoding:

      • Upgrade cumulus_feature_barcoding_version to 1.0.0.

      • The workflow now can automatically detect the chemistry type of the data:

        • auto by default: The workflow checks all possible assay types to decide the correct one.

        • threeprime: The workflow checks all 3’ assay types to decide the correct one.

        • fiveprime: The workflow checks all 5’ assay types to decide the correct one.

      • Reorg the keywords in Chemistry column of sample sheet: 5’ now only has 2 types, SC5Pv2 and SC5Pv3 for 5’ v2 and v3 chemistries where only R2 is used for alignment.

      • Support the new format of 10x cell barcode inclusion lists provided in Cell Ranger v9.0+.

      • Fix issue in processing UTF-encoded feature barcode files

    • For immune profiling:

      • Add types vdj_t, vdj_b and vdj_t_gd for DataType column. See 10x 5’ Immune Profiling Kit for details.

      • Remove chain input, as it is now automatically decided by user-specified DataType types.

      • For vdj_t_gd type samples, support the feature of specifying primer sequences used to enrich cDNA for V(D)J sequences. To enable it, provide a .txt file in AuxFile column of the sample, and it will be passed to --inner-enrichment-primers option of cellranger vdj in execution.

    • For Flex Gene Expression:

      • Remove ProbeSet column. The probe set is not automatically decided based on user-specified Reference name.

      • Support Flex probe sets v1.1 which are associated with 2024-A genome references.

    • For CellPlex using CMO:

      • Remove cmo_set input. If using custom CMOs in your experiment, just provide the custom feature reference file in AuxFile column of the cmo type sample.

  • Spaceranger workflow:

    • Upgrade spaceranger_version default to 3.1.3.

    • Remove mkfastq related workflow inputs.

    • Remove run_count input as it’s always true.

    • Remove support on Targeted Gene Expression analysis, as it’s no longer supported since Space Ranger v2.1.1.