repro-enforcer
Export any bioinformatics analysis as a reproducible bundle with Conda environment, Singularity container definition, and Nextflow pipeline.
npx skills add BioTender-max/awesome-bio-agent-skills --skill repro-enforcer --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 🦖 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).
- Core Capabilities
- Dependencies
- Example Queries
- Status
What does the repro-enforcer skill do?
Export any bioinformatics analysis as a reproducible bundle with Conda environment, Singularity container definition, and Nextflow pipeline.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill repro-enforcer --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 144 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.