Workflow: scRNA-seq pipeline using Salmon and Alevin
Fetched 2024-11-27 16:33:05 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
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- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| threads | Integer | Number of threads for Salmon | |
| fastq_dir | Directory | FASTQ directory |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| salmon |
steps/salmon.cwl
(CommandLineTool)
|
Run Salmon Alevin tool on FASTQ input | |
| correct_barcodes |
steps/correct-barcodes.cwl
(CommandLineTool)
|
Correct SNARE-seq barcodes |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_dir | Directory | Full output of `salmon alevin` |
Permalink:
https://w3id.org/cwl/view/git/536d6ed4bc639b93a8d8bc1c1a694b848d4d6f32/salmon_quant.cwl
