Legacy versions on Broad Method Registry¶
As Cumulus is now switched to Dockstore for release, we no longer maintain the Cumulus workflows published on Broad Method Registry.
But Terra users can still check out the legacy snapshots listed below for usage.
Stable version - v1.5.1¶
| WDL | Snapshot | Function |
|---|---|---|
| cumulus/cellranger_workflow | 28 | 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. |
| cumulus/spaceranger_workflow | 3 | Run Space Ranger tools to process spatial transcriptomics data, which includes extracting sequence reads using spaceranger mkfastq, and generating count matrix using spaceranger count. |
| cumulus/star_solo | 7 | Run STARsolo to generate gene-count matrices fro FASTQ files. |
| cumulus/count | 18 | Run alternative tools (STARsolo, Optimus, Salmon alevin, or Kallisto BUStools) to generate gene-count matrices from FASTQ files. |
| cumulus/demultiplexing | 32 | Run tools (demuxEM, souporcell, or popscle) for cell-hashing/nucleus-hashing/genetic-pooling analysis. |
| cumulus/cellranger_create_reference | 10 | Run Cell Ranger tools to build sc/snRNA-seq references. |
| cumulus/cellranger_atac_aggr | 5 | Run Cell Ranger tools to aggregate scATAC-seq samples. |
| cumulus/cellranger_atac_create_reference | 4 | Run Cell Ranger tools to build scATAC-seq references. |
| cumulus/cellranger_vdj_create_reference | 4 | Run Cell Ranger tools to build single-cell immune profiling references. |
| cumulus/smartseq2 | 10 | Run HISAT2/STAR/Bowtie2-RSEM to generate gene-count matrices for SMART-Seq2 data from FASTQ files. |
| cumulus/smartseq2_create_reference | 10 | Generate user-customized genome references for SMART-Seq2 data. |
| cumulus/cumulus | 43 | Run cumulus analysis module for variable gene selection, batch correction, PCA, diffusion map, clustering, visualization, differential expression analysis, cell type annotation, etc. |
Stable version - v1.5.0¶
| WDL | Snapshot | Function |
|---|---|---|
| cumulus/cellranger_workflow | 26 | 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. |
| cumulus/spaceranger_workflow | 3 | Run Space Ranger tools to process spatial transcriptomics data, which includes extracting sequence reads using spaceranger mkfastq, and generating count matrix using spaceranger count. |
| cumulus/star_solo | 7 | Run STARsolo to generate gene-count matrices fro FASTQ files. |
| cumulus/count | 18 | Run alternative tools (STARsolo, Optimus, Salmon alevin, or Kallisto BUStools) to generate gene-count matrices from FASTQ files. |
| cumulus/demultiplexing | 31 | Run tools (demuxEM, souporcell, or popscle) for cell-hashing/nucleus-hashing/genetic-pooling analysis. |
| cumulus/cellranger_create_reference | 10 | Run Cell Ranger tools to build sc/snRNA-seq references. |
| cumulus/cellranger_atac_aggr | 5 | Run Cell Ranger tools to aggregate scATAC-seq samples. |
| cumulus/cellranger_atac_create_reference | 4 | Run Cell Ranger tools to build scATAC-seq references. |
| cumulus/cellranger_vdj_create_reference | 4 | Run Cell Ranger tools to build single-cell immune profiling references. |
| cumulus/smartseq2 | 10 | Run HISAT2/STAR/Bowtie2-RSEM to generate gene-count matrices for SMART-Seq2 data from FASTQ files. |
| cumulus/smartseq2_create_reference | 10 | Generate user-customized genome references for SMART-Seq2 data. |
| cumulus/cumulus | 43 | Run cumulus analysis module for variable gene selection, batch correction, PCA, diffusion map, clustering, visualization, differential expression analysis, cell type annotation, etc. |
Stable version - v1.4.0¶
| WDL | Snapshot | Function |
|---|---|---|
| cumulus/cellranger_workflow | 26 | 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. |
| cumulus/spaceranger_workflow | 3 | Run Space Ranger tools to process spatial transcriptomics data, which includes extracting sequence reads using spaceranger mkfastq, and generating count matrix using spaceranger count. |
| cumulus/star_solo | 6 | Run STARsolo to generate gene-count matrices fro FASTQ files. |
| cumulus/count | 18 | Run alternative tools (STARsolo, Optimus, Salmon alevin, or Kallisto BUStools) to generate gene-count matrices from FASTQ files. |
| cumulus/demultiplexing | 30 | Run tools (demuxEM, souporcell, or popscle) for cell-hashing/nucleus-hashing/genetic-pooling analysis. |
| cumulus/cellranger_create_reference | 10 | Run Cell Ranger tools to build sc/snRNA-seq references. |
| cumulus/cellranger_atac_aggr | 5 | Run Cell Ranger tools to aggregate scATAC-seq samples. |
| cumulus/cellranger_atac_create_reference | 4 | Run Cell Ranger tools to build scATAC-seq references. |
| cumulus/cellranger_vdj_create_reference | 4 | Run Cell Ranger tools to build single-cell immune profiling references. |
| cumulus/smartseq2 | 10 | Run HISAT2/STAR/Bowtie2-RSEM to generate gene-count matrices for SMART-Seq2 data from FASTQ files. |
| cumulus/smartseq2_create_reference | 10 | Generate user-customized genome references for SMART-Seq2 data. |
| cumulus/cumulus | 41 | Run cumulus analysis module for variable gene selection, batch correction, PCA, diffusion map, clustering, visualization, differential expression analysis, cell type annotation, etc. |
Stable version - v1.3.0¶
| WDL | Snapshot | Function |
|---|---|---|
| cumulus/cellranger_workflow | 15 | 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. |
| cumulus/spaceranger_workflow | 1 | Run Space Ranger tools to process spatial transcriptomics data, which includes extracting sequence reads using spaceranger mkfastq, and generating count matrix using spaceranger count. |
| cumulus/star_solo | 3 | Run STARsolo to generate gene-count matrices fro FASTQ files. |
| cumulus/count | 18 | Run alternative tools (STARsolo, Optimus, Salmon alevin, or Kallisto BUStools) to generate gene-count matrices from FASTQ files. |
| cumulus/demultiplexing | 22 | Run tools (demuxEM, souporcell, or demuxlet) for cell-hashing/nucleus-hashing/genetic-pooling analysis. |
| cumulus/cellranger_create_reference | 9 | Run Cell Ranger tools to build sc/snRNA-seq references. |
| cumulus/cellranger_atac_aggr | 2 | Run Cell Ranger tools to aggregate scATAC-seq samples. |
| cumulus/cellranger_atac_create_reference | 2 | Run Cell Ranger tools to build scATAC-seq references. |
| cumulus/cellranger_vdj_create_reference | 3 | Run Cell Ranger tools to build single-cell immune profiling references. |
| cumulus/smartseq2 | 7 | Run HISAT2/STAR/Bowtie2-RSEM to generate gene-count matrices for SMART-Seq2 data from FASTQ files. |
| cumulus/smartseq2_create_reference | 8 | Generate user-customized genome references for SMART-Seq2 data. |
| cumulus/cumulus | 36 | Run cumulus analysis module for variable gene selection, batch correction, PCA, diffusion map, clustering, visualization, differential expression analysis, cell type annotation, etc. |
Stable version - v1.2.0¶
| WDL | Snapshot | Function |
|---|---|---|
| cumulus/cellranger_workflow | 15 | 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. |
| cumulus/spaceranger_workflow | 1 | Run Space Ranger tools to process spatial transcriptomics data, which includes extracting sequence reads using spaceranger mkfastq, and generating count matrix using spaceranger count. |
| cumulus/star_solo | 3 | Run STARsolo to generate gene-count matrices fro FASTQ files. |
| cumulus/count | 18 | Run alternative tools (STARsolo, Optimus, Salmon alevin, or Kallisto BUStools) to generate gene-count matrices from FASTQ files. |
| cumulus/demultiplexing | 22 | Run tools (demuxEM, souporcell, or demuxlet) for cell-hashing/nucleus-hashing/genetic-pooling analysis. |
| cumulus/cellranger_create_reference | 9 | Run Cell Ranger tools to build sc/snRNA-seq references. |
| cumulus/cellranger_atac_aggr | 2 | Run Cell Ranger tools to aggregate scATAC-seq samples. |
| cumulus/cellranger_atac_create_reference | 2 | Run Cell Ranger tools to build scATAC-seq references. |
| cumulus/cellranger_vdj_create_reference | 3 | Run Cell Ranger tools to build single-cell immune profiling references. |
| cumulus/smartseq2 | 7 | Run HISAT2/STAR/Bowtie2-RSEM to generate gene-count matrices for SMART-Seq2 data from FASTQ files. |
| cumulus/smartseq2_create_reference | 8 | Generate user-customized genome references for SMART-Seq2 data. |
| cumulus/cumulus | 35 | Run cumulus analysis module for variable gene selection, batch correction, PCA, diffusion map, clustering, visualization, differential expression analysis, cell type annotation, etc. |
Stable version - v1.1.0¶
| WDL | Snapshot | Function |
|---|---|---|
| cumulus/cellranger_workflow | 14 | 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/star_solo | 3 | Run STARsolo to generate gene-count matrices fro FASTQ files. |
| cumulus/count | 16 | Run alternative tools (STARsolo, Optimus, Salmon alevin, or Kallisto BUStools) to generate gene-count matrices from FASTQ files. |
| cumulus/demultiplexing | 21 | Run tools (demuxEM, souporcell, or demuxlet) for cell-hashing/nucleus-hashing/genetic-pooling analysis. |
| cumulus/cellranger_create_reference | 9 | Run Cell Ranger tools to build sc/snRNA-seq references. |
| cumulus/cellranger_atac_aggr | 2 | Run Cell Ranger tools to aggregate scATAC-seq samples. |
| cumulus/cellranger_atac_create_reference | 2 | Run Cell Ranger tools to build scATAC-seq references. |
| cumulus/cellranger_vdj_create_reference | 3 | Run Cell Ranger tools to build single-cell immune profiling references. |
| cumulus/smartseq2 | 7 | Run HISAT2/STAR/Bowtie2-RSEM to generate gene-count matrices for SMART-Seq2 data from FASTQ files |
| cumulus/smartseq2_create_reference | 8 | Generate user-customized genome references for SMART-Seq2 data. |
| cumulus/cumulus | 34 | Run cumulus analysis module for variable gene selection, batch correction, PCA, diffusion map, clustering, visualization, differential expression analysis, cell type annotation, etc. |
Stable version - v1.0.0¶
| WDL | Snapshot | Function |
|---|---|---|
| cumulus/cellranger_workflow | 12 | 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/count | 14 | Run alternative tools (STARsolo, Optimus, Salmon alevin, or Kallisto BUStools) to generate gene-count matrices from FASTQ files. |
| cumulus/demultiplexing | 20 | Run tools (demuxEM, souporcell, or demuxlet) for cell-hashing/nucleus-hashing/genetic-pooling analysis. |
| cumulus/cellranger_create_reference | 9 | Run Cell Ranger tools to build sc/snRNA-seq references. |
| cumulus/cellranger_atac_aggr | 2 | Run Cell Ranger tools to aggregate scATAC-seq samples. |
| cumulus/cellranger_atac_create_reference | 2 | Run Cell Ranger tools to build scATAC-seq references. |
| cumulus/cellranger_vdj_create_reference | 3 | Run Cell Ranger tools to build single-cell immune profiling references. |
| cumulus/smartseq2 | 7 | Run HISAT2/STAR/Bowtie2-RSEM to generate gene-count matrices for SMART-Seq2 data from FASTQ files |
| cumulus/smartseq2_create_reference | 8 | Generate user-customized genome references for SMART-Seq2 data. |
| cumulus/cumulus | 31 | Run cumulus analysis module for variable gene selection, batch correction, PCA, diffusion map, clustering, visualization, differential expression analysis, cell type annotation, etc. |
| cumulus/cumulus_hashing_cite_seq | 10 | Run cumulus for cell-hashing/nucleus-hashing/CITE-Seq analysis |
Stable version - v0.15.0¶
| WDL | Snapshot | Function |
|---|---|---|
| cumulus/cellranger_workflow | 10 | 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/count | 14 | Run alternative tools (STARsolo, Optimus, Salmon alevin, or Kallisto BUStools) to generate gene-count matrices from FASTQ files. |
| cumulus/cellranger_create_reference | 8 | Run Cell Ranger tools to build sc/snRNA-seq references. |
| cumulus/cellranger_atac_aggr | 2 | Run Cell Ranger tools to aggregate scATAC-seq samples. |
| cumulus/cellranger_atac_create_reference | 2 | Run Cell Ranger tools to build scATAC-seq references. |
| cumulus/cellranger_vdj_create_reference | 2 | Run Cell Ranger tools to build single-cell immune profiling references. |
| cumulus/smartseq2 | 7 | Run HISAT2/STAR/Bowtie2-RSEM to generate gene-count matrices for SMART-Seq2 data from FASTQ files |
| cumulus/smartseq2_create_reference | 8 | Generate user-customized genome references for SMART-Seq2 data. |
| cumulus/cumulus | 24 | 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 | 16 | Run subcluster analysis using cumulus |
| cumulus/cumulus_hashing_cite_seq | 10 | Run cumulus for cell-hashing/nucleus-hashing/CITE-Seq analysis |
Stable version - v0.14.0¶
| WDL | Snapshot | Function |
|---|---|---|
| cumulus/cellranger_workflow | 8 | 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/count | 11 | Run alternative tools (STARsolo, Optimus, Salmon alevin, or Kallisto BUStools) to generate gene-count matrices from FASTQ files. |
| cumulus/cellranger_create_reference | 6 | Run Cell Ranger tools to build sc/snRNA-seq references. |
| cumulus/cellranger_atac_aggr | 1 | Run Cell Ranger tools to aggregate scATAC-seq samples. |
| cumulus/cellranger_atac_create_reference | 1 | Run Cell Ranger tools to build scATAC-seq references. |
| cumulus/cellranger_vdj_create_reference | 1 | Run Cell Ranger tools to build single-cell immune profiling references. |
| cumulus/smartseq2 | 7 | Run HISAT2/STAR/Bowtie2-RSEM to generate gene-count matrices for SMART-Seq2 data from FASTQ files |
| cumulus/smartseq2_create_reference | 8 | Generate user-customized genome references for SMART-Seq2 data. |
| cumulus/cumulus | 16 | 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 | 10 | Run subcluster analysis using cumulus |
| cumulus/cumulus_hashing_cite_seq | 8 | Run cumulus for cell-hashing/nucleus-hashing/CITE-Seq analysis |
Stable version - v0.13.0¶
| WDL | Snapshot | Function |
|---|---|---|
| cumulus/cellranger_workflow | 7 | 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/cellranger_create_reference | 1 | Run Cell Ranger tools to build sc/snRNA-seq references. |
| cumulus/cellranger_atac_aggr | 1 | Run Cell Ranger tools to aggregate scATAC-seq samples. |
| cumulus/cellranger_atac_create_reference | 1 | Run Cell Ranger tools to build scATAC-seq references. |
| cumulus/cellranger_vdj_create_reference | 1 | Run Cell Ranger tools to build single-cell immune profiling references. |
| cumulus/smartseq2 | 5 | Run Bowtie2 and RSEM to generate gene-count matrices for SMART-Seq2 data from FASTQ files |
| cumulus/smartseq2_create_reference | 4 | Generate user-customized genome references for SMART-Seq2 data. |
| cumulus/cumulus | 14 | 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 | 9 | Run subcluster analysis using cumulus |
| cumulus/cumulus_hashing_cite_seq | 7 | Run cumulus for cell-hashing/nucleus-hashing/CITE-Seq analysis |
Stable version - v0.12.0¶
| WDL | Snapshot | Function |
|---|---|---|
| cumulus/cellranger_workflow | 6 | 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/cellranger_create_reference | 1 | Run Cell Ranger tools to build sc/snRNA-seq references. |
| cumulus/cellranger_atac_create_reference | 1 | Run Cell Ranger tools to build scATAC-seq references. |
| cumulus/cellranger_vdj_create_reference | 1 | Run Cell Ranger tools to build single-cell immune profiling references. |
| cumulus/smartseq2 | 5 | Run Bowtie2 and RSEM to generate gene-count matrices for SMART-Seq2 data from FASTQ files |
| cumulus/smartseq2_create_reference | 4 | Generate user-customized genome references for SMART-Seq2 workflow. |
| cumulus/cumulus | 11 | 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 | 8 | Run subcluster analysis using cumulus |
| cumulus/cumulus_hashing_cite_seq | 6 | 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 |