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. |