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oxo-flow config#

Inspect and manage workflow configuration.

Usage#

oxo-flow config <ACTION> [WORKFLOW] [KEY] [VALUE]

Actions#

Action Description
show Show all configuration variables from a workflow
stats Show workflow statistics (rules, dependencies, etc.)
check Alias for stats
get <KEY> Get a specific configuration variable value

Arguments#

Argument Description
<WORKFLOW> Path to the .oxoflow workflow file
<KEY> Configuration variable key (for get)

Examples#

Show configuration#

oxo-flow config show pipeline.oxoflow

Show workflow statistics#

oxo-flow config stats pipeline.oxoflow

Get a specific config value#

oxo-flow config get pipeline.oxoflow reference
# Output: /data/references/GRCh38/genome.fa

Output#

oxo-flow 0.6.1 — Bioinformatics Pipeline Engine
Workflow Configuration:
  Name:    germline-wgs
  Version: 1.0.0
  Desc:    Germline WGS variant calling pipeline

  Config Variables:
    genome = "hg38"
    threads = 16
    adapter = "AGATCGGAAGAG"

Understanding Dependencies#

The config stats command reports a dependencies count. Here's how to interpret it:

Metric Meaning
Rules Total number of workflow rules (nodes in DAG)
Dependencies Total number of edges between rules (connections in DAG)
Max depth Longest path from start to end (critical path length)

Dependency Calculation Example#

A workflow with 10 rules and 11 dependencies:

Rule A ──► Rule B ──► Rule C
     │              │
     └──► Rule D ───► Rule E
  • Rule B has 1 incoming edge (from A)
  • Rule C has 1 incoming edge (from B)
  • Rule D has 1 incoming edge (from A)
  • Rule E has 2 incoming edges (from C and D)
  • Total edges = 1 + 1 + 1 + 2 = 5 dependencies

Why can dependencies exceed rules?

Some rules depend on multiple upstream outputs (e.g., a merge rule that combines results from parallel branches). Each input file creates an edge in the DAG.

Notes#

  • config show displays metadata, configuration variables, includes, and execution groups
  • config stats provides a high-level overview of the workflow's complexity
  • config get exits with code 1 if the key is not found
  • config get returns values in their native TOML type representation