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/nextflow-io/agent-skills/migrate-nextflow-codenpx skills add nextflow-io/agent-skills --skill migrate-nextflow-codegit clone --depth 1 https://github.com/nextflow-io/agent-skillsWhat 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 | $0.00063 | $0.00723 |
| Opus 5 | $0.00032 | $0.00362 |
| Sonnet 5 | $0.00013 | $0.00145 |
| Haiku 4.5 | $0.00006 | $0.00072 |
Grade A, and why
migrate-nextflow-code 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 3d 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.
How it starts
The opening of the file, as written. The whole thing — 37 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Migrate Nextflow Code
Migrate Nextflow pipeline code to satisfy newer language requirements. Each migration is detection-driven: a tool reports what must change, you apply behavior-preserving fixes, then re-run the tool until it is clean.
Requires Nextflow 26.04 or later (for the nextflow lint command and the strict syntax parser, which is the default from 26.04 onward).
nf-core pipelines — check the template version before starting. If the pipeline has a .nf-core.yml, check which version of nf-core/tools last generated its template. If nf_core_version is unspecified or less than 3.0.0, stop. Tell the user to upgrade their template first (nf-core pipelines sync) before attempting any code migrations. This will resolve syntax errors in the template code and provide a cleaner baseline.
How to use this skill
This SKILL.md is an index. Identify which migration the user needs from the table below, then read the matching reference file for the full detect → fix → verify procedure before doing any work. Each reference file is self-contained.
| Migration | Use when the user… | Read this file |
|---|---|---|
| Strict syntax | …has strict syntax errors, or asks to run nextflow lint to find and fix errors |
references/strict-syntax.md |
| Topic channels | …wants to replace the ch_versions plumbing (or another channel threaded through every workflow) with a topic channel |
references/topic-channels.md |
| Static typing | …wants to add static types — typed process/workflow inputs and outputs, records (replacing tuples), or typed params | references/static-typing.md |
| Workflow outputs | …wants to replace publishDir directives with workflow outputs — a top-level output {} block and a publish: section in the entry workflow |
references/workflow-outputs.md |
What ships with it
7 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.
- 3d ago First seen · 37 lines · 63 tokens per session scan A 7cdba1fd11ec
migrate-nextflow-code is a skill published in the GitHub repository nextflow-io/agent-skills (21 stars, last pushed 28d ago), licensed Apache-2.0. It adds 63 tokens to every session and 723 once invoked, about $0.0003 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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