Getting it into your agent
This one installs as part of its plugin. Adding the marketplace and installing the plugin brings it with everything else the plugin ships.
/plugin marketplace add jonasscheid/claude-nfcore-plugin/plugin install nf-coreWrote 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/jonasscheid/claude-nfcore-plugin/best-practices)<a href="https://agentmods.dev/skills/jonasscheid/claude-nfcore-plugin/best-practices"><img src="https://agentmods.dev/badge/skills/jonasscheid/claude-nfcore-plugin/best-practices.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 | $0.00082 | $0.01305 |
| Opus 5 | $0.00041 | $0.00652 |
| Sonnet 5 | $0.00016 | $0.00261 |
| Haiku 4.5 | $0.00008 | $0.00130 |
Grade A, and why
best-practices 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 7d 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 — 139 lines — stays where its author put it; the contents beside it link to each section on GitHub.
nf-core Best Practices
Quick reference for nf-core conventions. For detailed pipeline/module workflows, use /nf-core:pipelines or /nf-core:modules.
Read ${CLAUDE_PLUGIN_ROOT}/shared/conventions.md for the full conventions reference including package manager setup.
Nextflow Strict Syntax (CRITICAL — Q2 2026)
All nf-core pipelines must pass nextflow lint by Q2 2026. Run strict syntax lint before nf-core community lint.
<cmd> nextflow lint . # FIRST — strict syntax
<cmd> nf-core pipelines lint # SECOND — community guidelines
Replace <cmd> with your package manager prefix — see ${CLAUDE_PLUGIN_ROOT}/nf-core.local.md.
Removed Syntax (Errors)
| Not Allowed | Use Instead |
|---|---|
import groovy.json.JsonSlurper |
new groovy.json.JsonSlurper() (fully qualified) |
class MyClass { } |
Move to lib/ directory |
for (i in list) { } |
.each(), .collect(), .find() |
while (cond) { } |
.each() or recursion |
switch (x) { } |
if-else chains |
addParams(...) |
Pass as explicit workflow inputs |
env FOO (unquoted) |
env 'FOO' (always quote) |
[meta, *items] (spread) |
[meta, items[0], items[1]] (enumerate) |
final x = 1 / String s = 'hi' |
def x = 1 / def s: String = 'hi' (v25.10+) |
Deprecated Syntax (Warnings — Future Errors)
| Deprecated | Use Instead |
|---|---|
Channel.of(...) |
channel.of(...) (lowercase) |
ch.map { it * 2 } |
ch.map { v -> v * 2 } (explicit params) |
shell: section |
script: section |
Preserving Complex Groovy Code
- lib/ directory: Full Groovy support for helper classes (temporary solution)
- Plugins: Recommended for reusable complex logic
Output Glob Patterns
Always use prefix-based output patterns. Broad wildcards capture staged input files.
// CORRECT
tuple val(meta), path("${prefix}.bam"), emit: bam
// INCORRECT — captures staged inputs too
tuple val(meta), path("*.bam"), emit: bam
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.
- 7d ago First seen · 139 lines · 82 tokens per session scan A 3523a3ac234e
best-practices is a skill published in the GitHub repository jonasscheid/claude-nfcore-plugin (10 stars, last pushed 3mo ago), licensed MIT. It adds 82 tokens to every session and 1,305 once invoked, about $0.0004 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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