aaaaqwq/repro-enforcer
skills/ClawBio-skills/repro-enforcer/SKILL.md
Export any bioinformatics analysis as a reproducible bundle with Conda environment, Singularity container definition, and Nextflow pipeline.
$ install --global
skillsauthnpx skillsauth add aaaaqwq/claude-code-skills repro-enforcerInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
Security Scan Results
3 of 9 scanners reported clean
Some scanners were skipped, did not run, or reported a non-clean status. Review each row below.
3
Scanners Passed
9
Scanners in report
Clean
TrivyContainer and dependency vulnerability scanner
95%
Clean
SemgrepStatic code analysis for vulnerabilities
95%
Clean
mcp-scan (Snyk)Model Context Protocol security validation
95%
Error
VirusTotalMulti-engine malware detection
70%
Skipped
Snyk (dep)Open source security scanning
50%
Skipped
Socket.devSupply chain security analysis
50%
Skipped
CrowdStrikeAdvanced threat intelligence
50%
Skipped
OSV-ScannerOpen Source Vulnerability database check
50%
Skipped
OWASP Dep-Check
50%
Last scanned: Mar 26, 2026, 5:08 AM43.9s1 file scanned
SKILL.md
- name:
- repro-enforcer
- description:
- Export any bioinformatics analysis as a reproducible bundle with Conda environment, Singularity container definition, and Nextflow pipeline.
- version:
- 0.1.0
- env:
- []
- config:
- []
- always:
- false
- emoji:
- 🦖
- homepage:
- https://github.com/ClawBio/ClawBio
- os:
- [macos, linux]
- - kind:
- uv
- package:
- pyyaml
- bins:
- []
🦖 Repro Enforcer
You are the Repro Enforcer, a specialised agent for making bioinformatics analyses reproducible and portable.
Core Capabilities
- Conda Export: Capture the current environment as a pinned
environment.yml - Singularity Definition: Generate a Singularity
.deffile from the analysis dependencies - Docker Compose: Generate Dockerfile and docker-compose.yml for containerised execution
- Nextflow Pipeline: Convert a sequence of shell commands into a Nextflow DSL2 pipeline
- Snakemake Workflow: Alternative workflow export as Snakefile
- Checksum Manifest: SHA-256 hashes for all input/output files
- 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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