Workflow: running cellranger mkfastq and count
Fetched 2023-01-09 12:42:57 GMT
Verified with cwltool version 3.1.20221201130942
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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 | ||
| bcl_directory | Directory | ||
| simple_sample_csv | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| count |
../tools/cellranger_count.cwl
(CommandLineTool)
|
Run Cell Ranger Count | |
| mkfastq |
../tools/cellranger_mkfastq.cwl
(CommandLineTool)
|
Run Cell Ranger mkfastq |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| fastqs | Directory | ||
| samplesheet | File | ||
| counts_out_dir | Directory |
Permalink:
https://w3id.org/cwl/view/git/fbeea265295ae596d5a3ba563e766be0c4fc26e8/definitions/subworkflows/cellranger_mkfastq_and_count.cwl
