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Repro enforcer

Skill aAAaqwq/AGI-Super-Team/skills/repro-enforcer

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

Install
npx -y skills add aAAaqwq/AGI-Super-Team --skill repro-enforcer

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

SKILL.md

1.6 KB, 272 tokens by cl100k_base, as published. Nobody here has run it

🦖 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).

What ships with it

Read from the repository

Just SKILL.md. No reference files, no scripts.

Keep looking

Skills are one crate of 325,949. Ordering is by how many stacks a row turns up in, so the top of any crate is what has actually been picked rather than what has the most stars.