Cumulus workflows overviewΒΆ

Cumulus workflows are written in WDL language, and published on Dockstore. Below is an overview of them:

Workflow First Version Date Added Function
Cellranger 0.1.0 2018-07-27 Run Cell Ranger tools, which include extracting sequence reads using cellranger mkfastq or cellranger-atac mkfastq, generating count matrix using cellranger count or cellranger-atac count, running cellranger vdj or feature-barcode extraction.
Spaceranger 1.2.0 2021-01-19 Run Space Ranger tools to process spatial transcriptomics data, which includes extracting sequence reads using spaceranger mkfastq, and generating count matrix using spaceranger count.
STARsolo 1.2.0 2021-01-19 Run STARsolo to generate gene-count matrices fro FASTQ files.
Demultiplexing 0.3.0 2018-10-24 Run tools (demuxEM, souporcell, or popscle) for cell-hashing/nucleus-hashing/genetic-pooling analysis.
Cumulus 0.1.0 2018-07-27 Run cumulus analysis module for variable gene selection, batch correction, PCA, diffusion map, clustering, visualization, differential expression analysis, cell type annotation, etc.
Cellranger_create_reference 0.12.0 2019-12-14 Run Cell Ranger tools to build sc/snRNA-seq references.
Cellranger_atac_create_reference 0.12.0 2019-12-14 Run Cell Ranger tools to build scATAC-seq references.
cellranger_vdj_create_reference 0.12.0 2019-12-14 Run Cell Ranger tools to build single-cell immune profiling references.
STARsolo_create_reference 2.0.0 2022-03-14 Run STAR to build sc/snRNA-seq references for STARsolo count.
Cellranger_atac_aggr 0.13.0 2020-02-07 Run Cell Ranger tools to aggregate scATAC-seq samples.
Smart-Seq2 0.5.0 2018-11-18 Run HISAT2/STAR/Bowtie2-RSEM to generate gene-count matrices for SMART-Seq2 data from FASTQ files.
Smart-Seq2_create_reference 0.12.0 2019-12-14 Generate user-customized genome references for SMART-Seq2 data.