Workflow: Single-cell RNA-Seq Aggregate

Fetched 2023-01-08 18:23:28 GMT

Single-cell RNA-Seq Aggregate Aggregates gene expression data from multiple Single-cell 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

gem_well_labels String[]

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

molecule_info_h5 File[]

Molecule-level information used by cellranger aggr to aggregate samples into larger datasets

normalization_mode

Library depth normalization mode

Steps

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

Cell Ranger Aggregate

Aggregates outputs from multiple runs of Cell Ranger Count 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 --jobmode --mempercore --maxjobs --jobinterval --overrides --uiport

Not supported features: - Batch correction caused by different versions of the Single Cell Gene Expression chemistry is not supported as the generated metadata file doesn't include \"batch\" field.
cellbrowser_build
../tools/cellbrowser-build-cellranger.cwl (CommandLineTool)
Cell Ranger Count/Aggregate to UCSC Cell Browser

Cell Ranger Count/Aggregate to UCSC Cell Browser

Exports clustering results from Cell Ranger Count Gene Expression and Cell Ranger 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

loupe_browser_track File

Loupe Browser visualization and analysis file for aggregated results

aggregation_metadata File

Aggregation metadata in CSV format

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 aggr

aggregate_counts_stdout_log File

stdout log generated by cellranger aggr

compressed_html_data_folder File

Compressed folder with Cellbrowser formatted results
metrics_summary_report_json File

Aggregated run summary metrics in JSON format

filtered_feature_bc_matrix_h5 File

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

raw_feature_bc_matrices_folder File

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/e70b7fab45e4bd2abfb7dab2b8b1f79ce904ac69/workflows/sc-rna-aggregate-wf.cwl