Workflow: vqsr-flow.cwl
Fetched 2023-01-10 16:57:40 GMT
Verified with cwltool version 3.1.20221201130942
run vqsr flow, including vqsr rcal, vqsr apply and plot
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
BSD 2-clause "Simplified" License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| srand | Long (Optional) | ||
| max_mq | Double (Optional) | ||
| threads | Integer (Optional) | ||
| max_iter | Integer (Optional) | ||
| var_type | String (Optional) | ||
| input_vcf | File | ||
| reference | File | ||
| resources | https://w3id.org/cwl/view/git/845f4699c5fce96a4c708a553b3701c9cf296653/stage/vqsr-flow.cwl#resources/resource[] | ||
| annotation | String[] | ||
| output_file | String | ||
| sensitivity | Double (Optional) | ||
| max_gaussians | Integer (Optional) | ||
| aggregate_data | File[] (Optional) | ||
| advanced_options | |||
| max_neg_gaussians | Integer (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| plot |
../algo/plot.cwl
(CommandLineTool)
|
||
| vqsr_apply |
../algo/vqsr-apply.cwl
(CommandLineTool)
|
||
| vqsr_recal |
../algo/vqsr-recal.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output | File | ||
| plot_output | File (Optional) | ||
| tranches_output | File |
Permalink:
https://w3id.org/cwl/view/git/845f4699c5fce96a4c708a553b3701c9cf296653/stage/vqsr-flow.cwl
