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.
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
6
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
6
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