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/pipelines)<a href="https://agentmods.dev/skills/jonasscheid/claude-nfcore-plugin/pipelines"><img src="https://agentmods.dev/badge/skills/jonasscheid/claude-nfcore-plugin/pipelines.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 | $0.00067 | $0.02759 |
| Opus 5 | $0.00034 | $0.01380 |
| Sonnet 5 | $0.00013 | $0.00552 |
| Haiku 4.5 | $0.00007 | $0.00276 |
Grade A, and why
pipelines 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.
How it starts
The opening of the file, as written. The whole thing — 338 lines — stays where its author put it; the contents beside it link to each section on GitHub.
nf-core Pipelines
Full pipeline lifecycle: create, lint, schema, sync, and release.
Read ${CLAUDE_PLUGIN_ROOT}/shared/conventions.md for nf-core conventions and package manager setup.
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
Replace <cmd> with the configured package manager prefix (see Setup in conventions.md).
| Action | Command |
|---|---|
| Create pipeline | <cmd> nf-core pipelines create |
| Strict syntax lint | <cmd> nextflow lint . |
| Community lint | <cmd> nf-core pipelines lint |
| Lint with auto-fix | <cmd> nf-core pipelines lint --fix |
| Build schema | <cmd> nf-core pipelines schema build |
| Lint schema | <cmd> nf-core pipelines schema lint |
| Validate params | <cmd> nf-core pipelines schema validate <pipeline> params.json |
| Check sync status | <cmd> nf-core pipelines sync --show |
| Run sync | <cmd> nf-core pipelines sync |
| Run tests | <cmd> nf-test test |
Create Pipeline
Naming Rules
- Lowercase only:
rnaseqnotRNAseq - No punctuation:
methylseqnotmethyl-seq - Descriptive: Name should indicate data type or analysis
- Unique: Check existing pipelines at https://nf-co.re/pipelines
Commands
# Interactive (recommended)
<cmd> nf-core pipelines create
# Non-interactive
<cmd> nf-core pipelines create --name mypipeline --description "Description" --author "Name"
# From template YAML
<cmd> nf-core pipelines create --template-yaml template.yml
# Custom organization
<cmd> nf-core pipelines create --org myorg
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 · 338 lines · 67 tokens per session scan A 8a45e40fcbde
pipelines is a skill published in the GitHub repository jonasscheid/claude-nfcore-plugin (10 stars, last pushed 3mo ago), licensed MIT. It adds 67 tokens to every session and 2,759 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…
matlab
Build, review, migrate, and safely plan MATLAB or GNU Octave numerical workflows, including arrays, tabular/time data, tests, projects, graphics, MAT files, and explicit Python interoperability.
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…
phylogenetics
Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies.
research-engineer
An uncompromising Academic Research Engineer. Operates with absolute scientific rigor, objective criticism, and zero flair. Focuses on theoretical correctness, formal verification, and optimal implementation across any required technology.
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…