Workflow: wgs-processing-wf.cwl
Fetched 2023-01-04 01:30:07 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| sample | String | ||
| fastqdir | Directory | ||
| headhtml | File | ||
| tailhtml | File | ||
| reference | File | ||
| clinvarvcf | File | ||
| knownsites | File | ||
| reportfunc | File | ||
| scattercount | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| getfastq |
helper/getfastq.cwl
(ExpressionTool)
|
Create array of gvcfs to process | |
| bwamem-gatk-report |
helper/bwamem-gatk-report-wf.cwl
(Workflow)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| gvcf | File[] | ||
| report | File[] |
Permalink:
https://w3id.org/cwl/view/git/36de0d12e1cc88d0fd7d6b401df6c6e403f8c809/WGS-processing/cwl/wgs-processing-wf.cwl
