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¶
2.2.0 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.
Updates:
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 value0
.
- All workflows now have
Bug Fix:
- Fix the issue on localizing GCP folders in Cellranger workflow for ATAC-Seq and 10x Multiome data.