Workflow: workflow.cwl
Fetched 2024-05-18 09:28:35 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| index | File | ||
| db_path | Directory | ||
| threads | Integer (Optional) | ||
| fastq_directory | Directory |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| get-otu |
cwl/getOTU.cwl
(CommandLineTool)
|
Retrieve OTU from kraken2 report |
|
| kraken2 |
cwl/kraken2.cwl
(CommandLineTool)
|
Kraken2 mapping |
|
| check-input |
cwl/checkInput.cwl
(Workflow)
|
||
| humanmapper |
cwl/humanMapper.cwl
(CommandLineTool)
|
Filter human reads |
|
| kraken-biom |
cwl/kraken-biom.cwl
(CommandLineTool)
|
Get .biom from kraken results |
|
| compute-alpha |
cwl/computeAlpha.cwl
(CommandLineTool)
|
||
| count-total-otu |
cwl/countTotalOTU.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| unmapped_R1 | File[] | ||
| unmapped_R2 | File[] | ||
| get-otu_output | File[] | ||
| kraken2_output | File[] | ||
| kraken2_report | File[] | ||
| kraken-biom_output | File | ||
| compute-alpha_output | File | ||
| count-total-otu_output | File |
Permalink:
https://w3id.org/cwl/view/git/558ceeb623254a7872ec522f78eb8bf54dd4e3e7/workflow.cwl
