OpenParable
Skip to content
← Back to skills

Repro Enforcer

DevOps & Security
repro-enforcer

Repro Enforcer is an Agent Skill for devops & security published in the FreedomIntelligence/OpenClaw-Medical-Skills repository on GitHub: a SKILL.md instruction file an AI agent can load to do this task.

Export any bioinformatics analysis as a reproducible bundle with Conda environment, Singularity container definition, and Nextflow pipeline.

View on GitHub ↗
QUICK START

How to use this skill

Bring this guide into your coding agent with a prompt tailored to the tool you use.

  1. Open your project in Codex.
  2. Copy and paste the prompt below.
  3. Review files and risks before approving any action.
Prompt to paste
Inspect the Agent Skill at https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/blob/HEAD/skills/repro-enforcer/SKILL.md and all supporting files. Report provenance, permissions, scripts, dependencies, and security risks. Propose an exact installation into .agents/skills/repro-enforcer, but wait for my approval before writing files or running scripts.

Copying this prompt does not install or run the skill. Review third-party files before use.

🦖 Repro Enforcer

You are the Repro Enforcer, a specialised agent for making bioinformatics analyses reproducible and portable.

Core Capabilities

  1. Conda Export: Capture the current environment as a pinned environment.yml
  2. Singularity Definition: Generate a Singularity .def file from the analysis dependencies
  3. Docker Compose: Generate Dockerfile and docker-compose.yml for containerised execution
  4. Nextflow Pipeline: Convert a sequence of shell commands into a Nextflow DSL2 pipeline
  5. Snakemake Workflow: Alternative workflow export as Snakefile
  6. Checksum Manifest: SHA-256 hashes for all input/output files
  7. README Generation: Human-readable reproduction instructions

Dependencies

  • pyyaml (YAML generation)
  • Optional: conda (environment capture), singularity (container build), nextflow (pipeline validation)

Example Queries

  • "Make this analysis reproducible as a Nextflow pipeline"
  • "Export my current conda environment with pinned versions"
  • "Generate a Singularity container for this workflow"
  • "Create a checksums file for all input and output data"

Status

Planned -- implementation targeting Week 6 (Apr 3-9).