Cumulus workflows overview¶

Cumulus workflows are written in WDL language, and published on Dockstore. Below is an overview of them:

Workflow First Version Date Added Function
Cellranger 0.1.0 2018-07-27 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.
Spaceranger 1.2.0 2021-01-19 Run Space Ranger tools to process spatial transcriptomics data, which includes extracting sequence reads using spaceranger mkfastq, and generating count matrix using spaceranger count.
STARsolo 1.2.0 2021-01-19 Run STARsolo to generate gene-count matrices fro FASTQ files.
GeoMx_fastq_to_dcc 2.2.0 2022-10-04 Run Nanostring GeoMx Digital Spatial NGS Pipeline, and convert FASTQ files into DCC files.
GeoMx_dcc_to_count_matrix 2.2.0 2022-10-04 Take the DCC zip file from GeoMxFastqToDCC workflow, as well as other output of GeoMx DSP machine as the input, and generate an Area Of Interest (AOI) by probe count matrix with pathologists’ annotation.
Demultiplexing 0.3.0 2018-10-24 Run tools (demuxEM, souporcell, or popscle) for cell-hashing/nucleus-hashing/genetic-pooling analysis.
Cumulus 0.1.0 2018-07-27 Run cumulus analysis module for variable gene selection, batch correction, PCA, diffusion map, clustering, visualization, differential expression analysis, cell type annotation, etc.
Cellbender 2.1.0 2022-07-13 Run CellBender tool to remove technical artifacts from high-throughput single-cell/single-nucleus RNA sequencing data.
Cellranger_create_reference 0.12.0 2019-12-14 Run Cell Ranger tools to build sc/snRNA-seq references.
Cellranger_atac_create_reference 0.12.0 2019-12-14 Run Cell Ranger tools to build scATAC-seq references.
cellranger_vdj_create_reference 0.12.0 2019-12-14 Run Cell Ranger tools to build single-cell immune profiling references.
STARsolo_create_reference 2.0.0 2022-03-14 Run STAR to build sc/snRNA-seq references for STARsolo count.
Cellranger_atac_aggr 0.13.0 2020-02-07 Run Cell Ranger tools to aggregate scATAC-seq samples.
Smart-Seq2 0.5.0 2018-11-18 Run HISAT2/STAR/Bowtie2-RSEM to generate gene-count matrices for SMART-Seq2 data from FASTQ files.
Smart-Seq2_create_reference 0.12.0 2019-12-14 Generate user-customized genome references for SMART-Seq2 data.