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repro-enforcer

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

Skill by ClawBio

IndexedMIT★ 1,166
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Works with Claude Code, Claude apps, Codex, Cursor, Gemini CLI, GitHub Copilot, VS Code, OpenCode, Goose, Windsurf. Read the repository before you give any tool access to your data.

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Asks which of your tools to add it to (Claude Code, Codex, Cursor, VS Code, Windsurf, Gemini CLI, Claude Desktop) and shows the change first. See https://agentmart.dev/cli.

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About

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

Use cases: data

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What this skill can do and what it asks for, from its SKILL.md. Checked Oct 25, 2026.

Tools
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Network hosts it talks to 1

  • codeload.github.com · found in install command

Files it touches

  • ~/.claude/skills/repro-enforcer

What's inside

Skill name
repro-enforcer
Description
Export any bioinformatics analysis as a reproducible bundle with Conda environment, Singularity container definition, and Nextflow pipeline.
License
MIT
Metadata
version: 0.1.0
Instructions
31 lines in SKILL.md · view on GitHub

Files (1)

  • SKILL.md

SKILL.md (first lines)

# 🦖 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).

From ClawBio/ClawBio, MIT.

More from ClawBio/ClawBio

Signals

Stars
1,166
Forks
288
Open issues
27
Last commit (this folder)
Apr 24, 2026 (6 months ago)
Last release
Sep 11, 2026 (1 month ago)

From GitHub (fetched Oct 24, 2026).

Details

Version
0.1.0
License
MIT
Repository
github.com/ClawBio/ClawBio
Website
clawbio.github.io/ClawBio/
First seen
Oct 24, 2026
Last checked
Oct 24, 2026
Source
GitHubgithub-graphql

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repro-enforcer skill. Agent Mart. https://agentmart.dev/skills/clawbio-repro-enforcer (last updated 2026-10-24)