Cumulus WDL workflows and Dockerfiles
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
2.6.3 August 2, 2024
Update Demultiplexing workflow to work with Stratocumulus v0.2.4.
2.6.2 June 19, 2024
Solve the issue of Cellranger workflow with cellranger-arc.
cellranger_arc_version
default is now “2.0.2.strato” which is compatible with workflow v2.6.1 or later.
2.6.1 May 8, 2024
In Cellranger workflow: Add new genome references for single-cell/nucleus RNA-Seq: GRCh38-2024-A for human, GRCm39-2024-A for mouse, and GRCh38_and_GRCm39-2024-A for human and mouse.
In Spaceranger workflow: Add a new probe set mouse_probe_v2 for mouse.
Some underlying workflow improvement.
2.6.0 April 22, 2024
Update:
In Cellranger workflow:
Upgrade cellranger_version default to
8.0.0
.Upgrade cumulus_feature_barcoding version default to
0.11.3
.
In Spaceranger workflow:
Upgrade spaceranger_version default to
3.0.0
.Support Visium HD data.