Scientific Agent Skills is a collection of reusable procedures that give AI agents capabilities for scientific research across areas such as biology, chemistry, medicine, and drug discovery. It is used by researchers and by people building AI scientist workflows with compatible coding agents. The catalogue contains many of the project's skills and supporting instructions.
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 K-Dense-AI/scientific-agent-skills --skill nextflowgit clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skillsWrote 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/k-dense-ai/scientific-agent-skills/nextflow)<a href="https://agentmods.dev/skills/k-dense-ai/scientific-agent-skills/nextflow"><img src="https://agentmods.dev/badge/skills/k-dense-ai/scientific-agent-skills/nextflow/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/k-dense-ai/scientific-agent-skills/nextflow"><img src="https://agentmods.dev/badge/skills/k-dense-ai/scientific-agent-skills/nextflow.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- Socket pass
- Snyk pass
- NVIDIA SkillSpector warn
SkillSpector: 2 findings, up to high
These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →
- high Supply Chain · line 40 Remote code is downloaded and executed. This bypasses code review and could introduce malicious code.Fix: Avoid downloading and executing remote scripts. Use trusted packages from PyPI/npm. If remote fetch is required, verify checksums and use HTTPS.
- medium Privilege Escalation · line 41 Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.Fix: Avoid sudo/root unless strictly required. Prefer least-privilege patterns. If elevation is needed, document the justification and scope.
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 | $0.00074 | $0.03678 |
| Opus 5.5 | $0.00030 | $0.01471 |
| Sonnet 5.5 | $0.00015 | $0.00736 |
| Haiku 4.5 | $0.00007 | $0.00368 |
Grade A, and why
nextflow scanned grade A with 1 finding 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 24d 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.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
curl -fsSL https://get.nextflow.io -o install-nextflow.sh How it starts
The opening of the file, as written. The whole thing — 223 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Nextflow
Overview
Nextflow is a workflow language and runtime for building reproducible, portable, scalable data pipelines. It is dominant in bioinformatics but works for any data-heavy computation. nf-core is a community curating production-grade Nextflow pipelines, reusable modules, and the nf-core tooling on top of Nextflow.
Key ideas:
- Dataflow programming: pipelines are
processtasks connected by channels. Nextflow infers execution order and parallelism from data dependencies — there is no explicit scheduler to write. - Write once, run anywhere: the same pipeline runs locally, on HPC (SLURM, SGE, LSF, PBS), and on cloud (AWS Batch, Google Batch, Azure Batch, Kubernetes) by changing config/profiles, not code.
- Reproducibility: pinned software environments and pipeline revisions, immutable inputs/references, recorded parameters and seeds.
-resumeis a computational cache, not scientific validation. Conda is an environment manager; Wave resolves/builds images rather than executing them. - DSL2 is the modern, required syntax: modular
process/workflow/includedefinitions.
This skill covers both running existing pipelines and developing your own (Nextflow language + nf-core conventions, testing with nf-test, configuration, and deployment).
When to Use This Skill
Use this skill when the user wants to:
- Run an nf-core or custom Nextflow pipeline, or debug a failing/resuming run.
- Write or modify
.nfscripts,nextflow.config, profiles, ornextflow_schema.json. - Author or test nf-core-style modules/subworkflows (
main.nf,meta.yml,tests/, nf-test). - Configure executors, containers, or resources; scale to HPC or cloud.
- Implement a scientific workflow in Nextflow or adapt an existing nf-core pipeline.
- Understand processes, channels, operators,
take/emit,publishDir,ext.args, meta maps.
Setup
This review targets stable Nextflow 26.04.6, nf-core tools 4.1.0, and nf-test 0.9.5. Nextflow needs Bash 3.2+ and Java 17–26; verify java -version (a launcher on PATH does not prove a runtime is installed). The strict parser is the default in 26.04. See release notes and the 26.04 migration guide. Stable and edge documentation can differ; do not use a preview feature without its version/flag.
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.
- 24d ago Changed · +10 lines · -107 tokens per session scan D → A daa37795b3fe
- 25d ago Changed f3b7c6ed124a
- 1mo ago First seen · 213 lines · 181 tokens per session scan D 4ef839f586a7
nextflow is a skill published in the GitHub repository K-Dense-AI/scientific-agent-skills (54,587 stars, last pushed 6d ago), licensed MIT. It adds 74 tokens to every session and 3,678 once invoked, about $0.0003 per session on Opus 5.5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
Other skills, from other repositories
discovery-toolbox
A routed repertoire of 90 scientific thinking operators for biological research agents - visual reasoning, detectability and information budgets, search reframing, causal identification, competing explanations, observation and selection processes, pipeline artifact diagnosis, effort allocation, and confirmation…
discovery-director
Operate as a research director making original discoveries from a given biological question and dataset. Use when the task is open-ended scientific research, exploring omics or experimental data for findings, hypothesis generation and testing, screening a large candidate space of genes, variants, features or…
alterlab-remote-compute
Dispatch long-running GPU/CPU jobs to remote compute with a provider-agnostic submit → poll → harvest pattern across SLURM/HPC (sbatch, squeue, sacct) and managed APIs (Modal, RunPod, GCP Batch / Vertex AI). Use when submitting a batch job to a cluster, polling job status, retrieving result artifacts from a scheduler…
go-tooling-security
Use when setting up Go modules/workspaces, configuring golangci-lint v2, running govulncheck, or building a Go CI quality gate. Not for app logic or non-Go audits.
launch-workflow
Launch Nextflow pipeline executions on cloud and HPC clusters via Seqera Platform. Use when the user wants to run/launch/submit a pipeline on a cloud or cluster compute environment, configure a compute environment, push pipeline changes to GitHub before launching, or sign in to Seqera Platform.
10-cloud-security
AWS/Azure/GCP security auditing, container and Kubernetes hardening, Infrastructure as Code scanning, and cloud compliance assessment.