`oxo-flow debug`#

Debug a workflow by showing each rule with its fully resolved shell command, resource requirements, environment, dependencies, and metadata. 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)
`--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
Inputs and outputs (with wildcard patterns)
Shell command — both the raw template and the expanded version
Resources — threads, memory, GPU specifications
Environment — conda, docker, singularity, modules, etc.
Dependencies — both file-based and explicit depends_on
Tags — categorization labels
Format hints — declared file formats
Metadata — arbitrary domain-specific key-value pairs
Wildcards — wildcard names extracted from patterns

── Rule: bwa_align ──
  Description: Align reads to reference genome
  Inputs: ["trimmed/{sample}_R1.fastq.gz", "trimmed/{sample}_R2.fastq.gz"]
  Outputs: ["aligned/{sample}.sorted.bam"]
  Shell (template): bwa mem -t {threads} {config.reference} {input} | samtools sort -o {output}
  Shell (expanded): bwa mem -t 16 {config.reference} trimmed/{sample}_R1.fastq.gz trimmed/{sample}_R2.fastq.gz | samtools sort -o aligned/{sample}.sorted.bam
  Resources: threads=16, memory=32G
  Environment: docker
  Dependencies: ["trim_reads"]
  Tags: ["alignment"]
  Wildcards: ["sample"]

Notes#

The debug command does not execute any shell commands
Template variables like {input}, {output}, and {threads} are substituted in the expanded view
Wildcard placeholders like {sample} remain unresolved since actual values depend on input file discovery at runtime
Use this command to verify variable substitution before running a workflow

oxo-flow debug#