blob: dffdbe35b7ff1e52070fd6c77499d10f9dd2fbe6 (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
|
#!/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 > 1 && 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
|
