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oxo-flow format#

Reformat a .oxoflow file into canonical TOML form.

Usage#

oxo-flow format [OPTIONS] <WORKFLOW>

Arguments#

Argument Description
<WORKFLOW> Path to the .oxoflow workflow file

Options#

Option Short Default Description
--output -o stdout Write formatted output to a file
--check — — Check if the file is already formatted (exit non-zero if not)

Examples#

Format and print to stdout#

oxo-flow format pipeline.oxoflow

Save formatted output to a new file#

oxo-flow format pipeline.oxoflow -o formatted.oxoflow

Check formatting in CI#

oxo-flow format pipeline.oxoflow --check

Output#

oxo-flow 0.6.1 — Bioinformatics Pipeline Engine
[workflow]
name = "my-pipeline"
version = "0.1.0"

[[rules]]
name = "step1"
input = ["input.txt"]
output = ["output.txt"]
shell = "cat input.txt > output.txt"

Notes#

  • The formatter ensures consistent indentation and key ordering
  • Using --check is recommended for CI/CD pipelines to enforce style consistency
  • Comments are preserved during reformatting