Latest and stable versions on Terra¶
Cumulus is a fast growing project. As a result, we frequently update WDL snapshot versions on Terra. See below for latest and stable WDL versions you can use.
Latest version¶
| WDL | Snapshot | Function |
|---|---|---|
| cumulus/cellranger_workflow | 4 | Run Cell Ranger tools, which include extracting sequence reads using cellranger mkfastq or cellranger-atac mkfastq, generate count matrix using cellranger count or cellranger-atac count, run cellranger vdj or feature-barcode extraction |
| cumulus/smartseq2 | 3 | Run Bowtie2 and RSEM to generate gene-count matrices for SMART-Seq2 data from FASTQ files |
| cumulus/cumulus | 8 | Run cumulus analysis module for variable gene selection, batch correction, PCA, diffusion map, clustering, visualization, differential expression analysis, cell type annotation, etc. |
| cumulus/cumulus_subcluster | 5 | Run subcluster analysis using cumulus |
| cumulus/cumulus_hashing_cite_seq | 5 | Run cumulus for cell-hashing/nucleus-hashing/CITE-Seq analysis |
Stable version - v0.11.0¶
| WDL | Snapshot | Function |
|---|---|---|
| cumulus/cellranger_workflow | 4 | Run Cell Ranger tools, which include extracting sequence reads using cellranger mkfastq or cellranger-atac mkfastq, generate count matrix using cellranger count or cellranger-atac count, run cellranger vdj or feature-barcode extraction |
| cumulus/smartseq2 | 3 | Run Bowtie2 and RSEM to generate gene-count matrices for SMART-Seq2 data from FASTQ files |
| cumulus/cumulus | 8 | Run cumulus analysis module for variable gene selection, batch correction, PCA, diffusion map, clustering, visualization, differential expression analysis, cell type annotation, etc. |
| cumulus/cumulus_subcluster | 5 | Run subcluster analysis using cumulus |
| cumulus/cumulus_hashing_cite_seq | 5 | Run cumulus for cell-hashing/nucleus-hashing/CITE-Seq analysis |
Stable version - v0.10.0¶
| WDL | Snapshot | Function |
|---|---|---|
| cumulus/cellranger_workflow | 3 | Run Cell Ranger tools, which include extracting sequence reads using cellranger mkfastq or cellranger-atac mkfastq, generate count matrix using cellranger count or cellranger-atac count, run cellranger vdj or feature-barcode extraction |
| cumulus/smartseq2 | 3 | Run Bowtie2 and RSEM to generate gene-count matrices for SMART-Seq2 data from FASTQ files |
| cumulus/cumulus | 7 | Run cumulus analysis module for variable gene selection, batch correction, PCA, diffusion map, clustering, visualization, differential expression analysis, cell type annotation, etc. |
| cumulus/cumulus_subcluster | 4 | Run subcluster analysis using cumulus |
| cumulus/cumulus_hashing_cite_seq | 4 | Run cumulus for cell-hashing/nucleus-hashing/CITE-Seq analysis |
Stable version - HTAPP v2¶
| WDL | Snapshot | Function |
|---|---|---|
| regev/cellranger_mkfastq_count | 45 | Run Cell Ranger to extract FASTQ files and generate gene-count matrices for 10x genomics data |
| scCloud/smartseq2 | 5 | Run Bowtie2 and RSEM to generate gene-count matrices for SMART-Seq2 data from FASTQ files |
| scCloud/scCloud | 14 | Run scCloud analysis module for variable gene selection, batch correction, PCA, diffusion map, clustering and more |
| scCloud/scCloud_subcluster | 9 | Run subcluster analysis using scCloud |
| scCloud/scCloud_hashing_cite_seq | 9 | Run scCloud for cell-hashing/nucleus-hashing/CITE-Seq analysis |
Stable version - HTAPP v1¶
| WDL | Snapshot | Function |
|---|---|---|
| regev/cellranger_mkfastq_count | 39 | Run Cell Ranger to extract FASTQ files and generate gene-count matrices for 10x genomics data |
| scCloud/scCloud | 3 | Run scCloud analysis module for variable gene selection, batch correction, PCA, diffusion map, clustering and more |