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¶
2.1.0 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.
- For ATAC-Seq data, add
STARsolo:
- In workflow output, besides
mtx
format gene-count matrices, the workflow also generates matrices in 10x-compatiblehdf5
format.
- In workflow output, besides
Improvements:
CellRanger: For antibody/hashing/citeseq/crispr data,
- cumulus_feature_barcoding v0.9.0+ now supports multi-threading and faster gzip file I/O.
Updates:
Genome Reference:
- Add Cellranger VDJ v7.0.0 genome references:
GRCh38_vdj_v7.0.0
andGRCm38_vdj_v7.0.0
in CellRanger scIR-seq sample sheet section.
- Add Cellranger VDJ v7.0.0 genome references:
Default version upgrade: