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#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.1
hints:
DockerRequirement:
dockerPull: "quay.io/biocontainers/bcftools:1.10.2--hd2cd319_0"
baseCommand: bcftools
arguments:
- view
- --no-version
- -Ou
- -e'type=ref'
- --threads=$(inputs.threads)
- $(inputs.vcf)
inputs:
- id: vcf
type: File
- id: threads
type: int
outputs:
- id: bcf
type: stdout
stdout: $(inputs.vcf.nameroot).without-ref.bcf
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