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 skills add ammawla/encode-toolkit --skill pipeline-wgbsgit clone --depth 1 https://github.com/ammawla/encode-toolkitWrote 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/ammawla/encode-toolkit/pipeline-wgbs)<a href="https://agentmods.dev/skills/ammawla/encode-toolkit/pipeline-wgbs"><img src="https://agentmods.dev/badge/skills/ammawla/encode-toolkit/pipeline-wgbs.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 | $0.00103 | $0.04028 |
| Opus 5 | $0.00051 | $0.02014 |
| Sonnet 5 | $0.00021 | $0.00806 |
| Haiku 4.5 | $0.00010 | $0.00403 |
Grade A, and why
pipeline-wgbs 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 6d 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.
The source is not reproduced here
Licensed AGPL-3.0
The repository is licensed AGPL-3.0, which this catalogue does not treat as permission to reproduce the file. Read it at the source.
What ships with it
9 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.
- references/01-qc-trimming.md 2.3 KB
- references/02-bismark-alignment.md 3.2 KB
- references/03-dedup-filtering.md 2.6 KB
- references/04-methylation-calling.md 3.3 KB
- references/05-qc-metrics.md 3.4 KB
- references/literature.md 13 KB
- scripts/Dockerfile 2.4 KB
- scripts/main.nf 6.6 KB
- scripts/nextflow.config 3.2 KB
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.
- 6d ago First seen · 394 lines · 103 tokens per session scan A 244fce2495b4
pipeline-wgbs is a skill published in the GitHub repository ammawla/encode-toolkit (24 stars, last pushed 1mo ago), licensed AGPL-3.0. It adds 103 tokens to every session and 4,028 once invoked, about $0.0005 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 2026-08-30.
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