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.
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.
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.
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.
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.
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.
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.
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
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
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
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
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
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
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