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
Version 1.2.0 January 19, 2021¶
- Add spaceranger workflow:
- Wrap up spaceranger version 1.2.1
- On cellranger workflow:
- Fix workflow WDL to support both single index and dual index
- Add support for cellranger version 5.0.0 and 5.0.1
- Add support for targeted gene expression analysis
- Add support for
--no-bamoptions for cellranger count
--force-cellsoption for cellranger vdj as noted in cellranger 5.0.0 release note
- Add GRCh38_vdj_v5.0.0 and GRCm38_vdj_v5.0.0 references
- Bug fix on cumulus workflow.
- Reorganize the sidebar of Cumulus documentation website.
Version 1.1.0 December 28, 2020¶
- On cumulus workflow:
- Add CITE-Seq data analysis back. (See section Run CITE-Seq analysis for details)
- Add doublet detection. (See
- For tSNE visualization, only support FIt-SNE algorithm. (see
- Improve efficiency on log-normalization and DE tests.
- Support multiple marker JSON files used in cell type annotation. (see
- More preset gene sets provided in gene score calculation. (see
- Update the example of analyzing hashing and CITE-Seq data (see Example section) with the new workflows.
- Bug fix.
Version 1.0.0 September 23, 2020¶
- Add demultiplexing workflow for cell-hashing/nucleus-hashing/genetic-pooling analysis.
- Add support on CellRanger version
- Update cumulus workflow with Pegasus version
zarrfile format to handle data, which has a better I/O performance in general.
- Support focus analysis on Unimodal data, and appending other Unimodal data to it. (
appendinputs in cluster step).
- Quality-Control: Change
20.0; by default remove bounds on UMIs (
max_umisinputs in cluster step).
- Quality-Control: Automatically figure out name prefix of mitochondrial genes for
mm10genome reference data.
- Support signature / gene module score calculation. (
calc_signature_scoresinput in cluster step)
- Add Scanorama method to batch correction. (
correction_methodinput in cluster step).
- Calculate UMAP embedding by default, instead of FIt-SNE.
- Differential Expression (DE) analysis: remove inputs
aucas they are calculated by default. And cell-type annotation uses MWU test result by default.
- Update cumulus workflow with Pegasus version
- Remove cumulus_subcluster workflow.
Version 0.15.0 May 6, 2020¶
- Update all workflows to OpenWDL version 1.0.
- Cumulus now supports multi-job execution from Terra data table input.
- Cumulus generates Cirrocumulus input in
.cirrofolder, instead of a huge
Version 0.14.0 February 28, 2020¶
- Added support for gene-count matrices generation using alternative tools (STARsolo, Optimus, Salmon alevin, Kallisto BUStools).
- Cumulus can process demultiplexed data with remapped singlets names and subset of singlets.
- Update VDJ related inputs in Cellranger workflow.
- SMART-Seq2 and Count workflows are in OpenWDL version 1.0.
Version 0.13.0 February 7, 2020¶
- Added support for aggregating scATAC-seq samples.
- Cumulus now accepts mtx format input.
Version 0.12.0 December 14, 2019¶
- Added support for building references for sc/snRNA-seq, scATAC-seq, single-cell immune profiling, and SMART-Seq2 data.
Version 0.11.0 December 4, 2019¶
- Reorganized Cumulus documentation.
Version 0.10.0 October 2, 2019¶
- scCloud is renamed to Cumulus.
- Cumulus can accept either a sample sheet or a single file.
Version 0.7.0 Feburary 14, 2019¶
- Added support for 10x genomics scATAC assays.
- scCloud runs FIt-SNE as default.
Version 0.6.0 January 31, 2019¶
- Added support for 10x genomics V3 chemistry.
- Added support for extracting feature matrix for Perturb-Seq data.
- Added R script to convert output_name.seurat.h5ad to Seurat object. Now the raw.data slot stores filtered raw counts.
- Added min_umis and max_umis to filter cells based on UMI counts.
- Added QC plots and improved filtration spreadsheet.
- Added support for plotting UMAP and FLE.
- Now users can upload their JSON file to annotate cell types.
- Improved documentation.
- Added lightGBM based marker detection.
Version 0.5.0 November 18, 2018¶
- Added support for plated-based SMART-Seq2 scRNA-Seq data.
Version 0.4.0 October 26, 2018¶
- Added CITE-Seq module for analyzing CITE-Seq data.
Version 0.3.0 October 24, 2018¶
- Added the demuxEM module for demultiplexing cell-hashing/nuclei-hashing data.
Version 0.2.0 October 19, 2018¶
- Added support for V(D)J and CITE-Seq/cell-hashing/nuclei-hashing.
Version 0.1.0 July 27, 2018¶
- KCO tools released!