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.

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