Agent skill

repro-enforcer

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

View SKILL.md on GitHub Repository
Stars 163
Forks 31

Install this agent skill to your Project

npx add-skill https://github.com/majiayu000/claude-skill-registry/tree/main/skills/other/other/repro-enforcer

Metadata

Additional technical details for this skill

openclaw 
{
    "os": [
        "macos",
        "linux"
    ],
    "emoji": "\ud83e\udd96",
    "always": false,
    "install": [
        {
            "bins": [],
            "kind": "uv",
            "package": "pyyaml"
        }
    ],
    "homepage": "https://github.com/ClawBio/ClawBio",
    "requires": {
        "env": [],
        "bins": [
            "python3"
        ],
        "config": []
    }
}

SKILL.md

🦖 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).

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