Question: Output going to stdout?
1
gravatar for ForrestBear
16 months ago by
ForrestBear30
Curii
ForrestBear30 wrote:

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
cwl • 505 views
ADD COMMENTlink modified 16 months ago by Michael R. Crusoe1.8k • written 16 months ago by ForrestBear30
5
gravatar for Michael R. Crusoe
16 months ago by
Common Workflow Language project
Michael R. Crusoe1.8k wrote:
outputs: 
  - id: output
    type: stdout

stdout: sorted-output.vcf

:-)

ADD COMMENTlink written 16 months ago by Michael R. Crusoe1.8k
1

Thanks so much, Mr C! :)

ADD REPLYlink written 16 months ago by ForrestBear30
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