Thanks so much, Mr C! :)
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ForrestBear •
Output going to stdout?
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
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Michael R. Crusoe
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written
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ForrestBear •
•
written
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ForrestBear •
1 answer
outputs:
- id: output
type: stdout
stdout: sorted-output.vcf
:-)
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Michael R. Crusoe
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