`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)
`--ai`	—	—	Enable AI-powered semantic linting
`--verbose`	`-v`	—	Enable verbose (debug-level) logging
`--quiet`	—	—	Suppress non-essential output (errors only)
`--no-color`	—	—	Disable colored output
`--json`	—	—	Output machine-readable JSON to stdout

Examples#

Run standard linting#

oxo-flow lint pipeline.oxoflow

Run strict linting#

oxo-flow lint pipeline.oxoflow --strict

Output#

oxo-flow v0.15.0 — Rust-native bioinformatics pipeline engine
  warning [W003]: rule has no description (rule: bwa_align)
    hint: add a `description` field to the rule
  warning [W004]: rule has a shell command but no log file specified (rule: bwa_align)
    hint: add `log = "logs/bwa_align.log"` to the rule
  info [W007]: leaf rule (no dependents) could be marked as target = true (rule: fastqc)
  info [W025]: rule uses deprecated rule-level threads/memory (rule: bwa_align)
    hint: move `threads`/`memory` under `[rules.resources]`

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

Each diagnostic prints a hint: line (when a suggestion exists) showing the fix, matching the style of validate and run output. W007 suggests target = true: a rule marked as a target is built by default when oxo-flow run is invoked without an explicit -t, so marking the final leaf rules (like fastqc above) makes them part of the default run — see Workflow Format: Priority and Targeting. W025 flags the deprecated rule-level threads = N / memory = "8G" fields (removed in v0.15.0 in favor of [rules.resources]) so old workflows surface the migration instead of silently keeping their old settings — see Workflow Format: Rule resources.

Notes#

lint is a strict superset of validate: it runs every validate check (parsing, DAG, input existence) plus style linting and secret scanning — running validate separately after lint adds nothing
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

oxo-flow lint#