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 ^^^^^^^^^^^^^^^^^^^^^^^^ .. list-table:: :widths: 15 5 30 :header-rows: 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 ^^^^^^^^^^^^^^^^^^^^^^^^^^ .. list-table:: :widths: 15 5 30 :header-rows: 1 * - 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 ^^^^^^^^^^^^^^^^^^^^^^^^^^ .. list-table:: :widths: 15 5 30 :header-rows: 1 * - 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 ^^^^^^^^^^^^^^^^^^^^^^^^^^ .. list-table:: :widths: 15 5 30 :header-rows: 1 * - 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 ^^^^^^^^^^^^^^^^^^^^^^^^^^ .. list-table:: :widths: 15 5 30 :header-rows: 1 * - 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 ^^^^^^^^^^^^^^^^^^^^^^^^^^ .. list-table:: :widths: 15 5 30 :header-rows: 1 * - 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 ^^^^^^^^^^^^^^^^^^^^^^^^^^ .. list-table:: :widths: 15 5 30 :header-rows: 1 * - 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 ^^^^^^^^^^^^^^^^^^^^^^^^ .. list-table:: :widths: 15 5 30 :header-rows: 1 * - 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 ^^^^^^^^^^^^^^^^^^^^^^^^ .. list-table:: :widths: 15 5 30 :header-rows: 1 * - 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 ^^^^^^^^^^^^^^^^^^^^^^^^^^ .. list-table:: :widths: 15 5 30 :header-rows: 1 * - 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 ^^^^^^^^^^^^^^^^^^^^^^^^^^ .. list-table:: :widths: 15 5 30 :header-rows: 1 * - 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 ^^^^^^^^^^^^^^^^^^^^^^^^ .. list-table:: :widths: 15 5 30 :header-rows: 1 * - 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 ^^^^^^^^^^^^^^^^^^^^^^^^ .. list-table:: :widths: 15 5 30 :header-rows: 1 * - 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 ^^^^^^^^^^^^^^^^^^^^^^^^^ .. list-table:: :widths: 15 5 30 :header-rows: 1 * - 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 ^^^^^^^^^^^^^^^^^^^^^^^^^ .. list-table:: :widths: 15 5 30 :header-rows: 1 * - 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 .. _Dockstore: https://dockstore.org/ .. _Terra: https://app.terra.bio .. _Broad Method Registry: https://portal.firecloud.org/?return=terra#methods