Workflow: msi.cwl
Fetched 2024-04-28 14:14:55 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- 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 |
|---|---|---|---|
| model | File | ||
| threads | Integer | ||
| tumor_bam | File[] | ||
| normal_bam | File[] | ||
| sample_name | String[] | ||
| coverage_data | Directory (Optional) | ||
| microsatellites | File | ||
| project_name_msi | String (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| admie |
../../cwl_tools/msi/admie.cwl
(CommandLineTool)
|
||
| msisensor |
../../cwl_tools/msi/msisensor.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| plots | File[] (Optional) | ||
| admie_stderr | File | ||
| admie_stdout | File | ||
| admie_results | File | ||
| msisensor_main | File[] | ||
| distance_vectors | File | ||
| msisensor_stderr | File[] | ||
| msisensor_stdout | File[] | ||
| msisensor_somatic | File[] | ||
| msisensor_germline | File[] | ||
| msisensor_distribution | File[] |
Permalink:
https://w3id.org/cwl/view/git/3441040dfaecba58150c13a95a6a93657b00778a/workflows/subworkflows/msi.cwl
