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
quay.io/cumulus/ for the workflow
input “docker_registry”, or enter a custom registry URL of their own choice.
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!