workflows/fastq2fasta/bcftools-view.cwl


1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19

#!/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
  - $(inputs.vcf)
inputs:
  - id: vcf
    type: File
outputs:
  - id: bcf
    type: stdout
stdout: $(inputs.vcf.nameroot).bcf