`oxo-flow config`#

Inspect and manage workflow configuration.

Usage#

oxo-flow config <COMMAND>

Actions#

Action	Description
`show`	Show workflow metadata and configuration variables
`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 v0.23.2 — Rust-native 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 that exactly matches another rule's output string creates an edge in the DAG. Beyond exact matches, the DAG builder also connects: concrete inputs against producer outputs containing wildcards (e.g., input mapped/A.bam matches producer output mapped/{sample}.bam), glob inputs (mapped/*.bam) against any producer output the glob matches, and directory inputs against outputs under that directory — all best-effort; unmatched inputs are simply treated as source files.

Notes#

config show displays workflow metadata (name, version, description, author) and configuration variables
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

oxo-flow config#