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oxo-flow report#

Generate reports from a workflow definition.

Usage#

oxo-flow report [OPTIONS] <WORKFLOW>

Arguments#

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

Options#

Option Short Default Description
--format -f html Output format: html or json
--output -o stdout Output file path
--checkpoint — .oxo-flow/checkpoint.json Path to checkpoint file for execution metrics
--verbose -v — Enable debug-level logging

Examples#

Generate HTML report to stdout#

oxo-flow report pipeline.oxoflow

Write HTML to file#

oxo-flow report pipeline.oxoflow -o report.html

Generate JSON report#

oxo-flow report pipeline.oxoflow -f json -o report.json

Output#

The HTML report is a self-contained single file with embedded CSS. The JSON report includes structured sections with workflow metadata, rule details, and configuration.

Clinical Reporting#

Clinical-Grade Quality#

Reports generated by oxo-flow report are designed for clinical-grade accuracy, traceability, and auditability. Every step logs its provenance, inputs, outputs, software versions, and execution environment.

ACMG/AMP Variant Classification#

ACMG (American College of Medical Genetics and Genomics) and AMP (Association for Molecular Pathology) jointly published guidelines for the interpretation of sequence variants. These guidelines define a five-tier classification system:

Tier Classification Clinical Meaning
Tier I / Pathogenic Strong clinical significance Disease-causing; actionable for patient care
Tier II / Likely Pathogenic Potential clinical significance High confidence of disease association
Tier III / VUS Uncertain significance Insufficient evidence; re-evaluate periodically
Tier IV / Likely Benign Probably not disease-causing Strong evidence against pathogenicity
Benign No clinical significance Confirmed benign polymorphism

oxo-flow's VariantClassification enum models both the somatic (Tier I–IV, per AMP/ASCO/CAP) and germline (Pathogenic–Benign, per ACMG) classification frameworks. The reporting system uses these classifications to generate clinical-grade HTML/PDF reports with variant tables, biomarker summaries, and compliance audit metadata.

Notes#

  • If --output is not specified, the report is written to stdout
  • HTML reports can be opened directly in any web browser
  • JSON reports are suitable for programmatic processing and integration with other tools
  • The [report] section in the .oxoflow file can customize report templates and sections