Workflow: Cell Ranger Aggregate (RNA+ATAC)

Fetched 2025-02-17 19:11:05 GMT

Cell Ranger Aggregate (RNA+ATAC) Combines outputs from multiple runs of “Cell Ranger Count (RNA+ATAC)” pipeline. The results of this workflow are primarily used in “Single-Cell Multiome ATAC and RNA-Seq Filtering Analysis” pipeline.

children parents
Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

Inputs

ID Type Title Doc
alias String Analysis name
threads Cores/CPUs

Parallelization parameter to define the number of cores/CPUs that can be utilized simultaneously. Default: 4

memory_limit Integer (Optional)
indices_folder Directory Cell Ranger Reference Sample

Any \"Cell Ranger Reference Sample\" that builds a reference genome package of a selected species for quantifying gene expression and chromatin accessibility. This sample can be obtained from \"Cell Ranger Reference (RNA, ATAC, RNA+ATAC)\" pipeline.

gem_well_labels String[]
normalization_mode Library depth normalization

When \"depth\" normalization is selected, subsample reads from higher-depth GEM wells until we equalize the 1) median number of unique fragments per cell for each ATAC library, 2) mean number of reads that are confidently mapped to the transcriptome per cell for each gene expression library.

annotation_gtf_file File
rna_molecule_info_h5 File[] Cell Ranger RNA+ATAC Sample

Any \"Cell Ranger RNA+ATAC Sample\" that produces both gene expression and chromatin accessibility data from a single 10x Genomics library

barcode_metrics_report File[]
atac_fragments_file_from_count File[]

Steps

ID Runs Label Doc
aggregate_counts
../tools/cellranger-arc-aggr.cwl (CommandLineTool)
Cell Ranger Aggregate (RNA+ATAC)

Cell Ranger Aggregate (RNA+ATAC)

Combines outputs from multiple runs of “Cell Ranger Count (RNA+ATAC)” pipeline.

Parameters set by default: --disable-ui - no need in any UI when running in Docker container --id - hardcoded to `aggregated` as we want to return the content of the outputs folder as separate outputs

Skipped parameters: --nosecondary --dry --noexit --nopreflight --description --peaks --jobmode --mempercore --maxjobs --jobinterval --overrides --uiport

Tool calls \"cellranger-arc aggr\" command that takes as input a CSV file specifying a list of cellranger-arc count output files for each GEM well being aggregated and produces a single feature-barcode matrix containing all the data. When combining multiple GEM wells, the barcode sequences for each channel are distinguished by a GEM well suffix appended to the barcode sequence. By default, the reads from each GEM well are subsampled such that all GEM wells have the same effective sequencing depth for both ATAC and gene expression modalities; for the ATAC data it is measured in terms of median unique fragments per cell and for gene expression it is measured in terms of the average number of reads that are confidently mapped to the transcriptome per cell. However, it is possible to turn off this normalization altogether.

cellbrowser_build
../tools/cellbrowser-build-cellranger-arc.cwl (CommandLineTool)
Cell Ranger ARC Count/Aggregate to UCSC Cell Browser

Cell Ranger ARC Count/Aggregate to UCSC Cell Browser

Exports clustering results from Cell Ranger ARC Count Chromatin Accessibility and Gene Expression or Cell Ranger ARC Aggregate experiments into compatible with UCSC Cell Browser format

compress_raw_feature_bc_matrices_folder
../tools/tar-compress.cwl (CommandLineTool)
TAR compress

TAR compress =========================================

Creates compressed TAR file from a folder

compress_secondary_analysis_report_folder
../tools/tar-compress.cwl (CommandLineTool)
TAR compress

TAR compress =========================================

Creates compressed TAR file from a folder

compress_filtered_feature_bc_matrix_folder
../tools/tar-compress.cwl (CommandLineTool)
TAR compress

TAR compress =========================================

Creates compressed TAR file from a folder

Outputs

ID Type Label Doc
grouping_data File Example of datasets grouping

Example of TSV file to define datasets grouping

html_data_folder Directory UCSC Cell Browser data

Directory with UCSC Cell Browser data

cellbrowser_report File UCSC Cell Browser

UCSC Cell Browser HTML index file

web_summary_report File Cell Ranger Summary

Report generated by Cell Ranger

atac_fragments_file File ATAC fragments

Count and barcode information for every ATAC fragment observed in the experiment in TSV format.

atac_peaks_bed_file File ATAC peaks

Locations of open-chromatin regions identified in this sample. These regions are referred to as \"peaks\".

loupe_browser_track File Loupe Browser visualization

Loupe Browser visualization file with all the analysis outputs

aggregation_metadata File Aggregation metadata

Aggregation metadata file in CSV format

metrics_summary_report File Run summary metrics

Cell Ranger generated run summary metrics in CSV format

atac_peak_annotation_file File ATAC peaks annotations

Annotations of peaks based on genomic proximity alone. Note, that these are not functional annotations and they do not make use of linkage with RNA data.

raw_feature_bc_matrices_h5 File Raw feature barcode matrix, HDF5

Raw feature barcode matrix stored as a CSC sparse matrix in hdf5 format. The rows consist of all the gene and peak features concatenated together and the columns consist of all observed barcodes with non-zero signal for either ATAC or gene expression.

aggregate_counts_stderr_log File Error log, cellranger-arc aggr step

stderr log generated by cellranger-arc aggr

aggregate_counts_stdout_log File Output log, cellranger-arc aggr step

stdout log generated by cellranger-arc aggr

filtered_feature_bc_matrix_h5 File Filtered feature barcode matrix, HDF5

Filtered feature barcode matrix stored as a CSC sparse matrix in hdf5 format. The rows consist of all the gene and peak features concatenated together (identical to raw feature barcode matrix) and the columns are restricted to those barcodes that are identified as cells.

raw_feature_bc_matrices_folder File Raw feature barcode matrix, MEX

Raw feature barcode matrix stored as a CSC sparse matrix in MEX format. The rows consist of all the gene and peak features concatenated together and the columns consist of all observed barcodes with non-zero signal for either ATAC or gene expression.

secondary_analysis_report_folder File Secondary analysis

Various secondary analyses that utilize the ATAC, RNA data, and their linkage: dimensionality reduction and clustering results for the ATAC and RNA data, differential expression, and differential accessibility for all clustering results above and linkage between ATAC and RNA data.

filtered_feature_bc_matrix_folder File Filtered feature barcode matrix, MEX

Filtered feature barcode matrix stored as a CSC sparse matrix in MEX format. The rows consist of all the gene and peak features concatenated together (identical to raw feature barcode matrix) and the columns are restricted to those barcodes that are identified as cells.

Permalink: https://w3id.org/cwl/view/git/69643d8c15f5357a320aa7e2f6adb2e71302fd20/workflows/cellranger-arc-aggr.cwl