Workflow: Report generation workflow
Fetched 2023-01-11 14:17:45 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
GNU Affero General Public License v3.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| gvcf | File [VCF] | Gathered GVCF | |
| sample | String | Sample Name | |
| headhtml | File [HTML] | Header for HTML report | |
| tailhtml | File [HTML] | Footer for HTML report | |
| clinvarvcf | File [VCF] | Reference VCF for ClinVar | |
| reportfunc | File | Function used to create HTML report |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| annotate |
annotate-vcf.cwl
(CommandLineTool)
|
Annotate and filter VCF | |
| gvcf-to-vcf |
gvcf-to-vcf.cwl
(CommandLineTool)
|
Convert GVCF to VCF | |
| generate-report |
generate-report.cwl
(CommandLineTool)
|
Generate ClinVar Report |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| report | File [HTML] | ClinVar variant report |
Permalink:
https://w3id.org/cwl/view/git/7521f8770b81d944aad3c1e0fd7ef5a886600190/WGS-processing/cwl/helper/report-wf.cwl
