repro-enforcer

What problem does it solve?

Many bioinformatics analyses are difficult to reproduce because runtime environments, container definitions, and workflow implementations are not captured or versioned consistently. Repro Enforcer automates exporting an analysis into a self-contained reproducibility bundle so collaborators and reviewers can rebuild the exact runtime, pipeline, and artifacts.

Core Features & Use Cases

• Conda Export: Capture and pin the current Conda environment into an environment.yml for deterministic package versions.
• Container Definitions: Generate Singularity .def files and Dockerfiles/docker-compose manifests to build portable containers.
• Workflow Conversion: Translate sequences of shell commands into Nextflow DSL2 pipelines or Snakemake workflows for scalable execution.
• Integrity & Documentation: Produce SHA-256 checksum manifests and a human-readable README with reproduction instructions.
• Use Case: Package an ad-hoc analysis into a reproducible artifact for publication, peer review, or long-term archiving.

Quick Start

Use the repro-enforcer skill to export my analysis folder as a reproducible bundle with a pinned Conda environment, a Singularity definition, and a Nextflow pipeline.