Workflow: workflow.cwl
Fetched 2025-07-01 08:43:29 GMT
Verified with cwltool version 3.1.20221201130942
Implementing bamqc over and over again to get an idea of how easy or hard it is for a beginner to implement a basic workflow in different workflow systems.
- 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 |
|---|---|---|---|
| bamfile | File | ||
| bedfile | File | ||
| bamqc_pl | File | ||
| flagstat2json | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| bamqc |
bamqc.cwl
(CommandLineTool)
|
Run bamqc |
|
| flagstat |
flagstat.cwl
(CommandLineTool)
|
||
| flagstat_json |
flagstat2json.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bamqc_json | File | ||
| flagstatjson | File |
Permalink:
https://w3id.org/cwl/view/git/ceec932ee375423f7ee6ac28248c829909ad6927/cwl/workflow.cwl
