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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 [OPTIONS] <WORKFLOW>

Arguments#

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

Options#

Option Short Description
--rule <RULE_NAME> -r Show the expanded command for this rule only
--ai — Enable AI-powered command explanation
--verbose -v Enable debug-level logging (global)
--quiet — Suppress informational output, including the version banner (global)
--no-color — Disable colored output, also respects the NO_COLOR environment variable (global)

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 v0.23.2 — 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"]

All output (including the version banner) goes to stderr; the banner appears only on an interactive terminal and is suppressed by --quiet.

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 _<group>_<sample> suffix (or _<pair_id> for pair/scatter rules; 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