`oxo-flow debug`#

Debug a workflow by showing each rule with its fully resolved shell command, outputs, and dependencies. Useful for verifying that template variables are substituted correctly.

Usage#

oxo-flow debug <WORKFLOW> [OPTIONS]

Arguments#

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

Options#

Option	Short	Description
`--rule <NAME>`	`-r`	Show only a specific rule (by name)
`--ai`	—	Enable AI-powered command explanation
`--verbose`	`-v`	Enable debug-level logging

Examples#

Debug all rules in a workflow#

oxo-flow debug pipeline.oxoflow

Debug a specific rule#

oxo-flow debug pipeline.oxoflow -r bwa_align

Output#

For each rule, the debug command shows:

Rule name and description (when the rule declares one)
Outputs (with wildcard patterns expanded)
Shell (expanded) — the fully resolved shell command
Dependencies — other rules that must run first

oxo-flow v0.15.0 — Rust-native bioinformatics pipeline engine
Debug: Debugging 3 rules
── Rule: transform ──
  Outputs: ["data/filtered.csv"]
  Shell (expanded): head -1 data/raw.csv > data/filtered.csv
awk -F',' 'NR>1 && $3 > 500' data/raw.csv >> data/filtered.csv

  Dependencies: ["generate_data"]

Notes#

The debug command does not execute any shell commands
Template variables like {input}, {output}, and {threads} are substituted in the expanded view
Wildcard rules are expanded per sample before display: rule names get a _<sample> suffix (e.g. bwa_mem2_align_cohort_NA12878) and wildcard placeholders are replaced with concrete values
With --rule, use the full expanded rule name as shown in the output (for wildcard workflows, the template name like bwa_mem2_align will not match)
Use this command to verify variable substitution before running a workflow

oxo-flow debug#