Changelog

All notable changes to oxo-flow are documented in this file.

The format follows Keep a Changelog and this project adheres to Semantic Versioning.

Changelog entries are automatically generated by git-cliff from conventional commit messages.

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0.1.0 — 2026-04-05

Features

• Initial release of oxo-flow bioinformatics pipeline engine
• DAG-based workflow execution with topological sorting and parallel groups
• Environment management: conda, pixi, docker, singularity, venv
• Wildcard expansion engine for dynamic file patterns
• Resource-aware job scheduling (CPU, memory, GPU, disk)
• TOML-based .oxoflow workflow format
• Clinical-grade HTML/JSON report generation with Tera templates
• Container packaging (Dockerfile/Singularity definition generation)
• Cluster backends: SLURM, PBS, SGE, LSF
• REST API web interface (axum-based)
• Venus clinical tumor variant detection pipeline
• Comprehensive CLI with 13 subcommands:
  • run — execute a workflow
  • dry-run — simulate execution
  • validate — check workflow syntax and DAG
  • graph — visualize DAG in DOT format
  • report — generate HTML/JSON reports
  • env — manage environments (list, check)
  • package — generate container definitions
  • serve — start web API server
  • init — scaffold new projects
  • status — show checkpoint status
  • clean — remove workflow outputs
  • completions — generate shell completions