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