Cumulus WDL workflows and Dockerfiles

All of our docker images are publicly available on Docker Hub and Quay. Our workflows use Docker Hub as the default Docker registry. Users can use Quay as the Docker registry by entering for the workflow input docker_registry, or can enter a custom registry URL of their choice.

Version 0.10.0 October 2, 2019

scCloud 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.

cumulus 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 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!