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oxo-flow

lint

Traitome/oxo-flow

`oxo-flow lint`#

Run best-practice linting checks on a .oxoflow file.

Usage#

oxo-flow lint [OPTIONS] <WORKFLOW>

Arguments#

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

Options#

Option	Short	Default	Description
`--strict`	—	—	Treat warnings as errors (non-zero exit)

Examples#

Run standard linting#

oxo-flow lint pipeline.oxoflow

Run strict linting#

oxo-flow lint pipeline.oxoflow --strict

Output#

oxo-flow 0.6.1 — Bioinformatics Pipeline Engine
  warning [W003]: rule has no description (rule: bwa_align)
  warning [W004]: rule has a shell command but no log file specified (rule: bwa_align)
  info [W007]: leaf rule (no dependents) could be marked as target = true (rule: fastqc)

Summary: 0 error(s), 2 warning(s), 1 info

Notes#

Linting checks for common mistakes, missing metadata, and potential performance issues
Rules are checked for valid input/output patterns and environment declarations
Use --strict to ensure high-quality workflow definitions in production environments