Workflow: Single-cell Multiome ATAC and RNA-Seq Aggregate

Fetched 2023-01-09 03:44:24 GMT

Single-cell Multiome ATAC and RNA-Seq Aggregate =========================================================== Aggregates data from multiple Single-cell Multiome ATAC and RNA-Seq Alignment experiments

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Inputs

ID Type Title Doc
threads Integer (Optional)

Number of threads for those steps that support multithreading

memory_limit Integer (Optional)

Maximum memory used (GB). The same will be applied to virtual memory

indices_folder Directory

Compatible with Cell Ranger ARC reference folder that includes STAR and BWA indices. Should be generated by \"cellranger-arc mkref\" command

gem_well_labels String[]

Array of GEM well identifiers to be used for labeling purposes only

normalization_mode

Library depth normalization mode

gex_molecule_info_h5 File[]

Array of GEX molecule-level information files in HDF5 format. Outputs from \"cellranger-arc count\" command.

barcode_metrics_report File[]

Array of files with the ATAC and GEX read count summaries generated for every barcode observed in the experiment. Outputs from \"cellranger-arc count\" command.

atac_fragments_file_from_count File[]

Array of files containing count and barcode information for every ATAC fragment observed in the experiment in TSV format. Outputs from \"cellranger-arc count\" command.

Steps

ID Runs Label Doc
aggregate_counts
../tools/cellranger-arc-aggr.cwl (CommandLineTool)
Cellranger ARC Aggregate

Cellranger ARC Aggregate ========================================================================

Aggregates outputs from multiple runs of Cell Ranger ARC Count Chromatin Accessibility and Gene Expression.

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

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

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

Creates compressed TAR file from a folder
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
web_summary_report File

Aggregated run summary metrics and charts in HTML format

atac_fragments_file File

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

atac_peaks_bed_file File

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

loupe_browser_track File

Loupe Browser visualization and analysis file for aggregated results

aggregation_metadata File

Aggregation metadata in CSV format

metrics_summary_report File

Aggregated run summary metrics in CSV format

atac_peak_annotation_file File

Annotations of peaks based on genomic proximity alone (for aggregated experiment). Note that these are not functional annotations and they do not make use of linkage with GEX data.

raw_feature_bc_matrices_h5 File

Aggregated unfiltered feature-barcode matrices containing all barcodes in HDF5 format

aggregate_counts_stderr_log File

stderr log generated by cellranger-arc aggr

aggregate_counts_stdout_log File

stdout log generated by cellranger-arc aggr

compressed_html_data_folder File

Compressed folder with CellBrowser formatted results

filtered_feature_bc_matrix_h5 File

Aggregated filtered feature-barcode matrices containing only cellular barcodes in HDF5 format

raw_feature_bc_matrices_folder File

Compressed folder with aggregated unfiltered feature-barcode matrices containing all barcodes in MEX format

secondary_analysis_report_folder File

Compressed folder with secondary analysis results including dimensionality reduction, cell clustering, and differential expression for aggregated results

filtered_feature_bc_matrix_folder File

Compressed folder with aggregated filtered feature-barcode matrices containing only cellular barcodes in MEX format

html json turtle jsonld rdfxml svg png dot zip ro yaml raw
Permalink: https://w3id.org/cwl/view/git/280cad66c2a5b2e1b66e4f8a5469942e88df5b74/workflows/sc-multiome-aggregate-wf.cwl