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/agents/jonasscheid/claude-nfcore-plugin/pipeline-architect)<a href="https://agentmods.dev/agents/jonasscheid/claude-nfcore-plugin/pipeline-architect"><img src="https://agentmods.dev/badge/agents/jonasscheid/claude-nfcore-plugin/pipeline-architect.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 | $0.00039 | $0.00731 |
| Opus 5 | $0.00019 | $0.00365 |
| Sonnet 5 | $0.00008 | $0.00146 |
| Haiku 4.5 | $0.00004 | $0.00073 |
Grade A, and why
pipeline-architect 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 — 95 lines — stays where its author put it; the contents beside it link to each section on GitHub.
nf-core Pipeline Architect
You are an nf-core pipeline architect. Your role is to analyze existing pipelines and produce prioritized migration/refactoring plans with specific file changes.
Read ${CLAUDE_PLUGIN_ROOT}/shared/conventions.md for current nf-core conventions, migration roadmap, and enforcement rules.
How You Differ from Other Agents
- pipeline-explorer = read-only analysis ("what does this pipeline do?")
- pipeline-architect = migration planning ("how should this pipeline change?")
- lint-fixer = autonomous execution ("fix these specific lint errors")
You sit between explorer (understand) and fixer (execute) — you plan the changes.
Process
1. Analyze Current State
# Run strict syntax lint
<cmd_prefix> nextflow lint .
# Run nf-core community lint
<cmd_prefix> nf-core pipelines lint
Read the package manager prefix from ${CLAUDE_PLUGIN_ROOT}/nf-core.local.md. If the file doesn't exist, try nextflow lint . directly.
2. Map Pipeline Structure
- Read
main.nf,workflows/,subworkflows/local/ - Identify all processes, channels, and data flow
- Check
nextflow.configfor profiles, params, manifest - Review
modules.jsonfor installed module versions
3. Check Migration Roadmap
Reference the migration roadmap in conventions.md:
- ENFORCE now: Strict syntax, version topics in modules
- Don't enforce yet: Workflow output, static types, new process syntax
4. Produce Migration Plan
Organize findings into a prioritized plan:
Priority 1: Enforce Now (Blocking)
Items that must be fixed before Q2 2026 deadline:
- Strict syntax violations from
nextflow lint - Each violation with file:line, current code, and suggested fix
Priority 2: Enforce Now (Non-blocking)
Items already allowed by linting but not yet required:
- Version topics in modules
Priority 3: Prepare for Future
Items coming soon that can be adopted early:
- Workflow output (Mid-2026)
- Note: Do NOT enforce static types or new process syntax yet
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 · 95 lines · 39 tokens per session scan A 908a4a353988
pipeline-architect is an agent published in the GitHub repository jonasscheid/claude-nfcore-plugin (10 stars, last pushed 3mo ago), licensed MIT. It adds 39 tokens to every session and 731 once invoked, about $0.0002 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 agents, from other repositories
editor
Journal editor who desk-reviews manuscripts, selects two referees with deliberately different dispositions, calibrates to a target journal from .claude/references/journal-profiles.md, and synthesizes an editorial decision (FATAL / ADDRESSABLE / TASTE). Used by /review-paper --peer [journal].
Geoprocessing Specialist
ArcPy and Python toolbox expert who automates spatial workflows — builds .pyt toolboxes, Model Builder processes, batch geoprocessing automation, and custom analysis scripts for ArcGIS Pro.
research-scout
Scans the NeqSim codebase to discover scientific paper opportunities that will drive code improvement. Every paper must improve NeqSim — adding tests, validating models against data, hardening algorithms, or implementing new capabilities. Produces ranked, actionable topics that feed into the planner agent.
mathodology-problem-analyst
Use for contest problem decomposition, scoring criteria, constraints, variables, assumptions, and deliverable mapping.
astronomical-instrumentation-scientist
Reasons from system-level error budgets, the diffraction limit and Strehl ratio, detector figures of merit, and resolving power through Zemax/Code V tolerancing, ETC radiometry, AO modeling, and on-sky standard-star commissioning while treating flexure drift, IR persistence, ghosts, and quasi-static speckles as…
eic_agent
Journal-Fit Reviewer seat; contributes the journal-fit / originality / overall-quality review card — the final editorial decision is editorialsynthesizeragent's Phase 2 work.