- 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/d147d1d1fafeeea06bd09d9479337b0f5aab43b0/WGS-processing/cwl/helper/report-wf.cwl