`oxo-flow graph`#

Output the workflow DAG for visualization.

Usage#

oxo-flow graph [OPTIONS] <WORKFLOW>

Arguments#

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

Options#

Option	Short	Description
`--format <FORMAT>`	`-f`	Output format: `ascii` (terminal), `dot` (Graphviz), `dot-clustered` (level-grouped), `tree` (indented tree). Default: `ascii`
`--output <FILE>`	`-o`	Save output to a file (useful for dot/svg generation)
`--verbose`	`-v`	Enable debug-level logging
`--quiet`		Suppress non-essential output (errors only)
`--no-color`		Disable colored output

Examples#

Print ASCII graph to terminal (default)#

oxo-flow graph pipeline.oxoflow

Print DOT format#

oxo-flow graph pipeline.oxoflow -f dot

Render to PNG with Graphviz#

oxo-flow graph pipeline.oxoflow -f dot | dot -Tpng -o dag.png

Save DOT to file#

oxo-flow graph pipeline.oxoflow -f dot -o graph.dot

Render clustered view#

oxo-flow graph pipeline.oxoflow -f dot-clustered -o clustered.dot

Output Formats#

ASCII (default)#

┌─────────────────────────────────────────────────────────────────────┐
│ Workflow: wgs-germline-calling                                       │
│ Rules: 10, Dependencies: 11                                          │
└─────────────────────────────────────────────────────────────────────┘

  fastp_qc ──► bwa_mem2_align ──► mark_duplicates ──► bqsr_apply
       │                              │                    │
       ▼                              ▼                    ▼
  (parallel)                    (parallel)            (parallel)

  bqsr_apply ──► gatk_haplotypecaller ──► gatk_vqsr ──► annotate_variants

DOT#

digraph workflow {
    rankdir = TB;
    node [shape=box, style="rounded,filled", fillcolor="#e8f4f8"];
    "trim_reads" -> "align";
    "align" -> "sort_bam";
    "sort_bam" -> "mark_duplicates";
    "mark_duplicates" -> "call_variants";
}

Notes#

Default output is ASCII for terminal viewing
DOT format requires Graphviz (dot command) to render images. Install with:
- macOS: brew install graphviz
- Linux: apt install graphviz or yum install graphviz
- Conda: conda install graphviz
Nodes represent rules, edges represent dependencies
The graph direction is top-to-bottom (rankdir = TB)

Understanding Metrics#

The header shows key workflow metrics:

Metric	Meaning
Rules	Total workflow rules (DAG nodes)
Dependencies	Total edges connecting rules
Depth	Critical path length (longest chain)
Width	Maximum parallelism (rules at same level)

Dependencies count: The total number of edges in the DAG. When a rule has multiple input files from different upstream rules, each creates a separate edge. For example, a merge rule combining outputs from 3 parallel branches contributes 3 dependencies.

oxo-flow graph#