Question: Output going to stdout?
8 weeks ago by
ForrestBear • 30
ForrestBear • 30 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
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