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/jonasscheid/claude-nfcore-plugin/modulesnpx skills add jonasscheid/claude-nfcore-plugin --skill modulesgit clone --depth 1 https://github.com/jonasscheid/claude-nfcore-pluginWhat 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 | $0.00065 | $0.02134 |
| Opus 5 | $0.00032 | $0.01067 |
| Sonnet 5 | $0.00013 | $0.00427 |
| Haiku 4.5 | $0.00006 | $0.00213 |
Grade A, and why
modules 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 2d 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 — 279 lines — stays where its author put it; the contents beside it link to each section on GitHub.
nf-core Modules & Subworkflows
Manage modules and subworkflows: create, install, update, patch, and lint.
Read ${CLAUDE_PLUGIN_ROOT}/shared/conventions.md for nf-core conventions and package manager setup.
Read ${CLAUDE_PLUGIN_ROOT}/shared/module-template.md for module structure and templates.
nf-core Migration Roadmap
Update this table as Nextflow and nf-core evolve. Last updated: Feb 2026.
| Feature | Enforce? | Allow in Linting | In Template | Required | Notes |
|---|---|---|---|---|---|
| Strict syntax | ENFORCE | — | Q2 2026 | Q2 2026 | CRITICAL deadline. Run nextflow lint . |
| Version topics in modules | ENFORCE | Q4 2025 | Mid-2026 | Mid-2026 | Already allowed by linting |
| Workflow output | Don't enforce | — | Mid-2026 | Q4 2026 | Coming soon |
| Static types & records | Don't enforce | Mid-2026 | Q4 2026 | Q2 2027 | Gradual rollout |
| New process syntax | Don't enforce | Mid-2026 | Q4 2026 | Q2 2027 | Gradual rollout |
Quick Commands — Modules
Replace <cmd> with the configured package manager prefix (see Setup in conventions.md).
| Action | Command |
|---|---|
| List remote modules | <cmd> nf-core modules list remote |
| List installed modules | <cmd> nf-core modules list local |
| Module info | <cmd> nf-core modules info <module> |
| Install module | <cmd> nf-core modules install <tool/subtool> |
| Install specific version | <cmd> nf-core modules install <module> --sha <commit> |
| Create module | <cmd> nf-core modules create tool/subtool |
| Update module | <cmd> nf-core modules update <module> |
| Update all | <cmd> nf-core modules update --all |
| Preview updates | <cmd> nf-core modules update --preview |
| Create patch | <cmd> nf-core modules patch <module> |
| Remove patch | <cmd> nf-core modules patch <module> --remove |
| Lint module | <cmd> nf-core modules lint <module> |
| Lint all | <cmd> nf-core modules lint --all |
| Test module | <cmd> nf-test test modules/nf-core/<tool>/<subtool>/ |
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.
- 2d ago First seen · 279 lines · 65 tokens per session scan A 7d3274e937c5
modules is a skill published in the GitHub repository jonasscheid/claude-nfcore-plugin (10 stars, last pushed 3mo ago), licensed MIT. It adds 65 tokens to every session and 2,134 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 2026-08-31.
Other skills, from other repositories
instrument-data-to-allotrope
Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS systems, data lakes, or downstream analysis. Supports auto-detection of instrument types. Outputs include full…
exploratory-data-analysis
Perform bounded, local exploratory analysis of explicitly supported scientific files. Use for redacted CSV/TSV/JSON profiles; optional NumPy, HDF5, FASTA/FASTQ, and basic image metadata inspection; missingness/leakage audits; outlier and transformation sensitivity; and rigorous EDA report scaffolds. Other domain…
mapping-to-snomed
Maps clinical concept spans extracted by OpenMed to SNOMED CT concepts through a USER-SUPPLIED terminology server (the user's own Ontoserver, Snowstorm, or UMLS/UTS), never a bundled vocabulary. Use when the user wants to code findings, disorders, procedures, body structures, or substances to SNOMED CT, run an ECL…
auditing-subgroup-fairness
Audit an OpenMed NER or de-identification model for performance disparities across demographic subgroups (sex, age band, race/ethnicity when available) using openmed.eval.fairnessreport. Use when the user wants per-subgroup recall and leakage, wants to check whether de-identification under-protects a group, wants to…
overleaf-sync
Two-way sync between a local paper directory and an Overleaf project, so ARIS audit/edit workflows stay on the local copy while collaborators edit in the Overleaf web UI. Use when user says "同步 overleaf", "overleaf sync", "推送到 overleaf", "connect overleaf", "Overleaf 桥接", "pull overleaf", "push overleaf", or wants to…
mixed-precision
Use FP16/BF16 mixed precision to accelerate training and reduce memory. Use when optimizing GPU performance.