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|
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: CommandLineTool
doc: |
This tool will extract SNVs from INDEL VCFs
$namespaces:
s: https://schema.org/
$schemas:
- https://schema.org/version/latest/schemaorg-current-https.rdf
s:author:
s:name: "Solomon Shorser"
s:email: "solomon.shorser@oicr.on.ca"
requirements:
- class: DockerRequirement
dockerPull: quay.io/pancancer/pcawg-oxog-tools
inputs:
- id: "#vcf"
type: File
inputBinding:
position: 1
outputs:
extracted_snvs:
type: File?
outputBinding:
glob: "*.extracted-SNVs.vcf.gz"
baseCommand: /opt/oxog_scripts/extract_snvs_from_indels.sh
|
