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#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.1
hints:
DockerRequirement:
dockerPull: "quay.io/biocontainers/freebayes:1.3.2--py37hc088bd4_0"
baseCommand: freebayes
arguments: [
--bam, $(inputs.bam),
# --region=$(inputs.contig):1-$(inputs.contig_end)
--ploidy, "1",
-f, $(inputs.ref_fasta)]
inputs:
- id: bam
type: File
# - id: contig
# type: string
# - id: contig_end
# type: int
- id: ref_fasta
type: File
outputs:
- id: vcf
type: stdout
stdout: var.vcf
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