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repro-enforcer

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

Published by ClawBio ↗ClawBio/ClawBio

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repro-enforcer

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Use repro-enforcer to create a reproducible bundle for [bioinformatics analysis], including its environment definition, container definition, workflow, checksum manifest, and reproduction README.

Required inputs

  • [bioinformatics analysis]

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SKILL.md

name: repro-enforcerdescription: Export any bioinformatics analysis as a reproducible bundle with Conda environment, Singularity container definition,  and Nextflow pipeline.license: MITmetadata:   version: 0.1.0  openclaw:     requires:       bins:       - python3    always: false    emoji: 🦖    homepage: https://github.com/ClawBio/ClawBio    os:     - darwin    - linux    install:     - kind: uv      package: pyyaml

🦖 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).