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 skills add ma-compbio-lab/SkillFoundry --skill nf-core-pipeline-listgit clone --depth 1 https://github.com/ma-compbio-lab/SkillFoundryWrote 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/ma-compbio-lab/skillfoundry/nf-core-pipeline-list)<a href="https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/nf-core-pipeline-list"><img src="https://agentmods.dev/badge/skills/ma-compbio-lab/skillfoundry/nf-core-pipeline-list/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/nf-core-pipeline-list"><img src="https://agentmods.dev/badge/skills/ma-compbio-lab/skillfoundry/nf-core-pipeline-list.svg" alt="Reviewed on agentmods" width="80" 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 | $0.00040 | $0.00462 |
| Opus 5 | $0.00020 | $0.00231 |
| Sonnet 5 | $0.00008 | $0.00092 |
| Haiku 4.5 | $0.00004 | $0.00046 |
Grade A, and why
nf-core-pipeline-list 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.
What it actually says
Purpose
Check that nf-core tools run correctly in the repo-local environment and return a deterministic pipeline summary.
When to use
- You need a quick nf-core installation check.
- You want a compact machine-readable view of available nf-core pipelines.
When not to use
- You need interactive parameter entry with
nf-core launch. - You need to download or execute a full nf-core pipeline.
Inputs
- Optional
--sortand--limit
Outputs
- Cleaned JSON summary with local and remote nf-core pipeline metadata
Requirements
- The repo-local toolchain at
slurm/envs/nextflow-tools - Network access for the remote pipeline catalog
Procedure
- Run
python3 skills/reproducible-workflows/nf-core-pipeline-list/scripts/list_nfcore_pipelines.py --limit 5. - Inspect
counts.remote_workflowsand the returnedremote_workflowsentries. - Use the names and release metadata as a starting point for later nf-core workflows.
Validation
- The wrapper runs
nf-core pipelines listsuccessfully through the repo-local environment. - The malformed multiline JSON emitted by the CLI is cleaned and parsed.
- At least one remote pipeline is returned.
Failure modes and fixes
- JSON parse issues: use the provided wrapper instead of calling
nf-core --jsondirectly. - Empty remote list: check outbound network access and retry.
Safety and limits
- This skill verifies catalog access only.
- It does not prove that any specific nf-core pipeline can be executed locally.
Examples
python3 .../list_nfcore_pipelines.py --sort pulled --limit 3
Provenance
- nf-core tools installation docs: https://nf-co.re/docs/nf-core-tools/installation
- nf-core pipelines list docs: https://nf-co.re/docs/nf-core-tools/pipelines/list
Related skills
nextflow-hello-workflowsnakemake-toy-workflow-starter
What ships with it
7 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
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 · 55 lines · 40 tokens per session scan A 455fd2cf7dd6
nf-core-pipeline-list is a skill published in the GitHub repository ma-compbio-lab/SkillFoundry (39 stars, last pushed 4mo ago), licensed Apache-2.0. It adds 40 tokens to every session and 462 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 2026-09-03.
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