Workflow: Report generation workflow

Fetched 2023-01-10 06:51:25 GMT
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Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

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