Workflow: Cell Ranger Aggregate
Cell Ranger Aggregate =====================
- Selected
- |
- Default Values
- Nested Workflows
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- Inputs/Outputs
Inputs
ID | Type | Title | Doc |
---|---|---|---|
alias | String | Experiment short name/Alias | |
threads | Integer (Optional) | Number of threads |
Number of threads for those steps that support multithreading |
memory_limit | Integer (Optional) | Maximum memory used (GB) |
Maximum memory used (GB). The same will be applied to virtual memory |
gem_well_labels | String[] | scRNA-Seq Cell Ranger Experiment |
Array of GEM well identifiers to be used for labeling purposes only |
molecule_info_h5 | File[] | scRNA-Seq Cell Ranger Experiment |
Molecule-level information from individual runs of cellranger count |
normalization_mode | Library depth normalization mode |
Library depth normalization mode |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
aggregate_counts |
../tools/cellranger-aggr.cwl
(CommandLineTool)
|
Cellranger aggr - aggregates data from multiple Cellranger runs |
Tool calls \"cellranger aggr\" command to combine output files from \"cellranger count\"
(the molecule_info.h5 file from each run) into 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. Each GEM well is
a physically distinct set of GEM partitions, but draws barcode sequences randomly from the
pool of valid barcodes, known as the barcode whitelist. To keep the barcodes unique when
aggregating multiple libraries, we append a small integer identifying the GEM well to the
barcode nucleotide sequence, and use that nucleotide sequence plus ID as the unique identifier
in the feature-barcode matrix. For example, AGACCATTGAGACTTA-1 and AGACCATTGAGACTTA-2 are
distinct cell barcodes from different GEM wells, despite having the same barcode nucleotide
sequence. This number, which tells us which GEM well this barcode sequence came from, is
called the GEM well suffix. The numbering of the GEM wells will reflect the order that the
GEM wells were provided in the \"molecule_info_h5\" and \"gem_well_labels\" inputs. |
cellbrowser_build |
../tools/cellbrowser-build-cellranger.cwl
(CommandLineTool)
|
Converts Cellranger outputs into the data structure supported by UCSC CellBrowser |
|
compress_html_data_folder |
../tools/tar-compress.cwl
(CommandLineTool)
|
Compresses input directory to tar.gz |
|
compress_raw_feature_bc_matrices_folder |
../tools/tar-compress.cwl
(CommandLineTool)
|
Compresses input directory to tar.gz |
|
compress_secondary_analysis_report_folder |
../tools/tar-compress.cwl
(CommandLineTool)
|
Compresses input directory to tar.gz |
|
compress_filtered_feature_bc_matrix_folder |
../tools/tar-compress.cwl
(CommandLineTool)
|
Compresses input directory to tar.gz |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
html_data_folder | Directory | Folder with not compressed CellBrowser formatted results |
Folder with not compressed CellBrowser formatted results |
cellbrowser_report | File | CellBrowser formatted Cellranger report |
CellBrowser formatted Cellranger report |
web_summary_report | File | Aggregated run summary metrics and charts in HTML format |
Aggregated run summary metrics and charts in HTML format |
loupe_browser_track | File | Loupe Browser visualization and analysis file for aggregated results |
Loupe Browser visualization and analysis file for aggregated results |
aggregation_metadata | File | Aggregation metadata in CSV format |
Aggregation metadata in CSV format |
raw_feature_bc_matrices_h5 | File | Aggregated unfiltered feature-barcode matrices in HDF5 format |
Aggregated unfiltered feature-barcode matrices containing all barcodes in HDF5 format |
aggregate_counts_stderr_log | File | stderr log generated by cellranger aggr |
stderr log generated by cellranger aggr |
aggregate_counts_stdout_log | File | stdout log generated by cellranger aggr |
stdout log generated by cellranger aggr |
compressed_html_data_folder | File | Compressed folder with CellBrowser formatted results |
Compressed folder with CellBrowser formatted results |
metrics_summary_report_json | File | Aggregated run summary metrics in JSON format |
Aggregated run summary metrics in JSON format |
filtered_feature_bc_matrix_h5 | File | Aggregated filtered feature-barcode matrices in HDF5 format |
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 |
Compressed folder with aggregated unfiltered feature-barcode matrices containing all barcodes in MEX format |
secondary_analysis_report_folder | File | Compressed folder with aggregated secondary analysis results |
Compressed folder with secondary analysis results including dimensionality reduction, cell clustering, and differential expression of aggregated results |
filtered_feature_bc_matrix_folder | File | Compressed folder with aggregated filtered feature-barcode matrices |
Compressed folder with aggregated filtered feature-barcode matrices containing only cellular barcodes in MEX format |
https://w3id.org/cwl/view/git/581156366f91861bd4dbb5bcb59f67d468b32af3/workflows/cellranger-aggr.cwl