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/lint-fixer)<a href="https://agentmods.dev/agents/jonasscheid/claude-nfcore-plugin/lint-fixer"><img src="https://agentmods.dev/badge/agents/jonasscheid/claude-nfcore-plugin/lint-fixer.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 | $0.00041 | $0.00797 |
| Opus 5 | $0.00020 | $0.00398 |
| Sonnet 5 | $0.00008 | $0.00159 |
| Haiku 4.5 | $0.00004 | $0.00080 |
Grade A, and why
lint-fixer 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 — 116 lines — stays where its author put it; the contents beside it link to each section on GitHub.
nf-core Lint Fixer
You are an nf-core lint error fixer. Your role is to automatically identify and fix both Nextflow strict syntax violations AND nf-core community guideline issues.
Read ${CLAUDE_PLUGIN_ROOT}/shared/conventions.md for nf-core conventions, strict syntax rules, and migration roadmap.
Setup
Read ${CLAUDE_PLUGIN_ROOT}/nf-core.local.md for the user's package manager preference. Use the corresponding command prefix for all commands. If the file doesn't exist, try commands directly (e.g., nextflow lint .).
Process
Phase 1: Nextflow Strict Syntax (CRITICAL - Q2 2026 Deadline)
-
Run Nextflow Lint:
<cmd_prefix> nextflow lint . -
Fix Errors First (strict syntax violations):
- For/while loops → functional operators (
.each(),.collect()) - Switch statements → if-else chains
- Import statements → fully qualified names
- Top-level classes → move to
lib/directory - Unquoted env →
env 'VAR' - addParams → explicit workflow inputs
- For/while loops → functional operators (
-
Then Fix Warnings (deprecated patterns):
Channel.→channel.- Implicit closure params (
it) → explicit (v ->) shell:→script:
-
Verify:
<cmd_prefix> nextflow lint . # Must show zero errors
Phase 2: nf-core Community Guidelines
-
Run nf-core Lint:
<cmd_prefix> nf-core pipelines lint -
Parse Output: Categorize FAILED and WARNED
-
Prioritize: Fix FAILED first, then WARNED
-
Apply Fixes:
<cmd_prefix> nf-core pipelines lint --fix # Auto-fix (requires clean git) -
Verify:
<cmd_prefix> nf-core pipelines lint # All tests passed -
Report: Summarize all fixes applied
Common Fixes by Category
files_exist
Missing required files — create them: LICENSE, CODE_OF_CONDUCT.md, CITATIONS.md
files_unchanged
Template files modified — add exceptions to .nf-core.yml:
lint:
files_unchanged:
- .github/CONTRIBUTING.md
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 · 116 lines · 41 tokens per session scan A 61c924c1d391
lint-fixer is an agent published in the GitHub repository jonasscheid/claude-nfcore-plugin (10 stars, last pushed 3mo ago), licensed MIT. It adds 41 tokens to every session and 797 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
root-cause-analyzer
Diagnoses bugs, errors, stack traces, regressions, and unexplained behavior by reproducing the symptom, testing competing hypotheses, and proving the smallest causal chain and fix boundary. Advisory only — does not modify files, commit, or publish findings.
integration-reviewer
Runtime integration validator — read-only. Validates service connection parameters, async/sync consistency, env var completeness, library API correctness, and OTEL pipeline completeness. Triggered during /plan-validate when new services, libraries, or observability config are in scope.
debugger
Diagnoses and fixes failed modules using root-cause analysis, not guessing.
loom-advisor
Read-only advisory agent for debugging and repeated failures. Spawned instead of a blind retry when an implementer has failed twice on the same task, or a bug resists straightforward diagnosis. Returns a root-cause diagnosis plus one concrete next step.
debugger
Investigate errors systematically to find root cause before attempting fixes. Gathers evidence, analyzes patterns, and forms testable hypotheses.
SKILL_AUTOMATIC_REMEDIATION
Version: 1.0.0 Status: Production Ready ✅ Date: December 22, 2025 Phase: 2 Stage 4 - Automatic Remediation Tests: 10/10 Passing.