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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
- -i
- 'QUAL>1 && (GT="AA" || GT="Aa")'
- -Oz
- --threads=$(inputs.threads)
- $(inputs.bcf)
inputs:
- id: threads
type: int
- id: bcf
type: File
secondaryFiles: [.csi]
outputs:
- id: vcf
type: stdout
stdout: out.changes.vcf.gz
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