Repro enforcer
Skill BioTender-max/awesome-bio-agent-skills/skills/clawbio/repro-enforcer
Export any bioinformatics analysis as a reproducible bundle with Conda environment, Singularity container definition, and Nextflow pipeline.From its SKILL.md
npx -y skills add BioTender-max/awesome-bio-agent-skills --skill repro-enforcerAssembled from the repository path, not quoted from the project. Check it against their README if it does not work.
One thing to look at
- no licenseNo license file was found in the repository. Code published without one is not open source by default, so using it at work is a question for whoever answers licensing questions where you are.
What its file declares
Copied from the file, not written here
The file declares its own license as MIT. That is the author’s claim about this one file, and it is not the same thing as the license GitHub reports for the repository, which is listed with the other numbers below.
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
- 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).
What ships with it
Read from the repository
Just SKILL.md. No reference files, no scripts.