nextflow-io/agent-skills

nextflow-io profile

Latest recorded source activity: October 13, 2026 at 11:55

SkillsMP catalog refreshed: October 26, 2026 at 11:37

skills collected: 5

GitHub stars: 24
GitHub forks: 1

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Repository README source: README.md

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# Nextflow Agent Skills Agent skills for building and running Nextflow pipelines with modules from the [Nextflow Registry](https://registry.nextflow.io). The Nextflow Registry is the central place to discover and share Nextflow modules and plugins. Modules are published under namespaces — [nf-core](https://nf-co.re) is the most prominent — and these skills work with modules from any of them. These skills follow the [Agent Skills](https://agentskills.io/specification) specification, so they can be used by any skills-compatible agent, including Claude Code, Codex CLI, OpenCode, and Cursor. ## Skills - [`install-nextflow`](./skills/install-nextflow) — Install or upgrade Nextflow (and Java 17+ via SDKMAN if needed) - [`create-workflow`](./skills/create-workflow) — Create Nextflow pipelines by composing modules from the Nextflow Registry - [`run-module`](./skills/run-module) — Run Nextflow Registry modules (process and workflow modules) natively using the `nextflow module` command - [`launch-workflow`](./skills/launch-workflow) — Launch pipeline executions on Seqera Platform - [`migrate-nextflow-code`](./skills/migrate-nextflow-code) — Migrate pipeline code to new language features ## Installation ### Claude Code ``` /plugin marketplace add nextflow-io/agent-skills /plugin install nextflow@nextflow-io-agent-skills ``` When prompted, approve the Seqera MCP server connection to enable the skills. Claude Code automatically keeps your skills up to date. ### GitHub CLI If you use the [GitHub CLI](https://cli.github.com/) (v2.90.0+), you can install skills with [`gh skill`](https://github.blog/changelog/2026-04-16-manage-agent-skills-with-github-cli/): ```bash gh skill install nextflow-io/agent-skills ``` Pick the skills you want and the coding agents you want to install them on. The installer supports Claude Code, Codex, Cursor, and other agents that follow the skills convention. For skills that require the Seqera MCP (e.g. `launch-workflow`), make sure the [Seqera MCP server](https://mcp.seqera.io/mcp) is configured for your agent. You can update installed skills using `gh skill update`: ```bash # Check for updates interactively gh skill update # Update all installed skills gh skill update --all ``` ## Local Development To test the plugin locally without installing: ```bash claude --plugin-dir /path/to/agent-skills ``` ## Requirements - A coding agent that supports agent skills (e.g. Claude Code, Codex, Cursor) - [Nextflow](https://nextflow.io) **26.04 or later** (you can use the `install-nextflow` skill to install it); **26.10 or later** for workflow modules ## License Apache-2.0

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Skills in this repository

Network & Computer Systems Administrators

1 occupation categories · 20% classified

skill

occupation

description

updated

migrate-nextflow-code

unclassified

Migrate a Nextflow pipeline to new language patterns.

2026-10-13

create-workflow

unclassified

INVOKE THIS SKILL IMMEDIATELY when user asks to: write/create/build a Nextflow pipeline or workflow, create any bioinformatics pipeline (RNA-seq, DNA-seq, variant calling, ChIP-seq, etc.), or compose/chain Nextflow modules (process or workflow modules) from…

2026-10-13

install-nextflow

unclassified

Install or upgrade Nextflow on the user's machine. Use when the user wants to install Nextflow, check their current Nextflow version, upgrade Nextflow, or set up the prerequisites (Java 17+) needed to run Nextflow.

2026-10-13

run-module

unclassified

Run Nextflow Registry modules natively using `nextflow module` commands. Use when running, listing, or getting info about Nextflow modules, including process modules (a single tool) and workflow modules (subworkflows that chain several modules).

2026-10-13

launch-workflow

Network & Computer Systems Administrators

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…

2026-06-09

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