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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"
ShellCommandRequirement: {}
baseCommand: bcftools
arguments:
- consensus
- -i
- 'QUAL > 10 && GT="a"'
- -Hla
- -f
- $(inputs.ref_fasta)
- $(inputs.vcf)
- {shellQuote: false, valueFrom: "|"}
- sed
- "s/^>.*/>$(inputs.sample_id)/g"
inputs:
- id: ref_fasta
type: File
- id: vcf
type: File
secondaryFiles: [.csi]
- id: sample_id
type: string
outputs:
- id: out_fasta
type: stdout
stdout: sequence.fasta
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