Entering edit mode
6.6 years ago
ForrestBear
▴
30
I'm struggling to represent this syntax with CWL:
vcf-sort -c in_file.vcf > out_file.vcf
Specifically with routing the outfile, as right now, it looks like this will push to stdout.txt.
I'm sure this is simple, but, guidance is appreciated.
cwlVersion: v1.0
class: CommandLineTool
requirements:
- class: DockerRequirement
dockerPull: preprocess
inputs:
vcf:
type: File
inputBinding:
position: 1
prefix: -c
outputs:
- id: output
type: File
outputBinding:
glob: "sorted-output.vcf"
baseCommand: vcf-sort
Thanks so much, Mr C! :)