synthetic-sciences/openscience is an AI workbench that carries out scientific research by reading papers, forming hypotheses, writing and running code, conducting experiments, analyzing results, and preparing reports. Researchers use it for work in machine learning, biology, physics, and chemistry with remote or local models. Catalogue add-ons extend its scientific workflows through skills and 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 synthetic-sciences/openscience --skill nextflowgit clone --depth 1 https://github.com/synthetic-sciences/openscienceWrote 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/synthetic-sciences/openscience/nextflow)<a href="https://agentmods.dev/skills/synthetic-sciences/openscience/nextflow"><img src="https://agentmods.dev/badge/skills/synthetic-sciences/openscience/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/synthetic-sciences/openscience/nextflow"><img src="https://agentmods.dev/badge/skills/synthetic-sciences/openscience/nextflow.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 | $0.00181 | $0.03389 |
| Opus 5.5 | $0.00072 | $0.01356 |
| Sonnet 5.5 | $0.00036 | $0.00678 |
| Haiku 4.5 | $0.00018 | $0.00339 |
Grade A, and why
nextflow 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 1mo 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.
This is a copy
97% identical to nextflow — 70 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 219 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: per-task containers (Docker/Singularity/Apptainer/Conda/Wave) +
-resumecaching + pinned pipeline revisions. - 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.
- Build a reproducible scientific/bioinformatics workflow (even if "Nextflow" is not named).
- Understand processes, channels, operators,
take/emit,publishDir,ext.args, meta maps.
Setup
Nextflow needs Bash and Java 17 or newer (17–25 supported). Verify with java -version.
# Install Nextflow: prefer the package manager (conda below); the launcher
# script is at https://get.nextflow.io, to download, inspect, then run.
nextflow info # verify
# Or via conda/bioconda (also gets a managed Java)
conda create -n nf -c bioconda -c conda-forge nextflow nf-core
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.
- 1mo ago Changed · +5 lines 01cafd4fab62
- 1mo ago First seen · 214 lines · 181 tokens per session scan A 96e5b04a2705
nextflow is a skill published in the GitHub repository synthetic-sciences/openscience (4,025 stars, last pushed today), licensed Apache-2.0. It adds 181 tokens to every session and 3,389 once invoked, about $0.0007 per session on Opus 5.5. A static security scan graded it A with 0 findings. It is 97% identical to nextflow, differing in 70 lines, and is treated as a copy.
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