Workflow: Running cellranger count and lineage inference
Fetched 2025-09-13 13:40:17 GMT
Verified with cwltool version 3.1.20230201224320
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| chemistry | String (Optional) | ||
| reference | Directory | ||
| sample_name | String | ||
| fastq_directory | Directory[] | ||
| lineage_min_cells | Integer (Optional) | ||
| lineage_min_features | Integer (Optional) | ||
| lineage_reference_data | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| count |
../tools/cellranger_count.cwl
(CommandLineTool)
|
Run Cell Ranger Count | |
| lineage |
../tools/cellmatch_lineage.cwl
(CommandLineTool)
|
Running a script to identify lineage of cells |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| counts_out_dir | Directory | ||
| lineage_cellmatch_lineage_out_dir | Directory |
Permalink:
https://w3id.org/cwl/view/git/bfcb5ffbea3d00a38cc03595d41e53ea976d599d/definitions/subworkflows/single_cell_rnaseq.cwl
