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.

Latest version

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 data.
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 - v0.12.0

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