Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx agentmods add skills/45ck/open-genome-agent/nextflow-runnernpx skills add 45ck/open-genome-agent --skill nextflow-runnergit clone --depth 1 https://github.com/45ck/open-genome-agentWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/45ck/open-genome-agent/nextflow-runner)<a href="https://agentmods.dev/skills/45ck/open-genome-agent/nextflow-runner"><img src="https://agentmods.dev/badge/skills/45ck/open-genome-agent/nextflow-runner.svg" alt="Measured on agentmods" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00031 | $0.00252 |
| Opus 5 | $0.00015 | $0.00126 |
| Sonnet 5 | $0.00006 | $0.00050 |
| Haiku 4.5 | $0.00003 | $0.00025 |
Grade A, and why
nextflow-runner scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 5d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
What it actually says
Nextflow runner
Run or prepare reproducible Nextflow workflows for heavy genomics jobs. Use only for explicit workflow execution, not routine question answering.
When to use
- raw-read or heavy pipeline execution is explicitly requested
- the environment is ready for Nextflow
Do not use when
- a VCF-first local analysis is sufficient
Expected outputs
workflow_run.jsonpipeline_logs/
Goal
Handle heavy pipeline execution in a reproducible way.
Procedure
- Confirm that pipeline execution is explicitly requested.
- Validate environment assumptions before running anything expensive.
- Prefer schema-driven configuration and captured manifests over handwritten one-off commands.
- Save pipeline commands, params, and logs into the run directory.
Guardrails
- Do not run large workflows implicitly.
- Do not treat a pipeline launch as success; monitor completion and surface failures.
- Keep this skill separate from lightweight local questioning.
References
See references/README.md for durable notes and scripts/ for deterministic helpers.
What ships with it
2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 5d ago First seen · 41 lines · 31 tokens per session scan A d51d80bb2a24
nextflow-runner is a skill published in the GitHub repository 45ck/open-genome-agent (4 stars, last pushed 2mo ago), licensed MIT. It adds 31 tokens to every session and 252 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
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