Entering edit mode
5.6 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! :)