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Updated 3d ago

by nextflow-io

agent-skills

Agent skills for building and running Nextflow pipelines.

  • Active — Updated in the last 14 days
  • Multi-agent — Targets three or more agents
Works with
  • Claude
  • Codex
  • Cursor
View on GitHub (opens in a new tab)

24 GitHub stars (24)

+3 in 16 days

Stars gained per day · daily snapshots since Sep 30
Stars gained per day, Sep 30 to Oct 16: +3 in total; the busiest day was Oct 15 with +2 stars.Oct 1: 0 starsOct 2: 0 starsOct 3: 0 starsOct 4: 0 starsOct 5: 0 starsOct 6: 0 starsOct 7: 0 starsOct 8: 0 starsOct 9: 0 starsOct 10: 0 starsOct 11: 0 starsOct 12: 0 starsOct 13: 0 starsOct 14: 0 starsOct 15: +2 starsOct 16: +1 stars
Stars gained between daily snapshots
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  • 5 skills (5 skills found in its SKILL.md files)
  • 1 forks (1 forks)
  • 3d ago last update (Last updated 3d ago)

Install

Skills CLI

npx skills add nextflow-io/agent-skills

Asks which skills and agents to install. Just one: npx skills add nextflow-io/agent-skills --skill create-workflow — add -g for every project.

Claude Code

git clone https://github.com/nextflow-io/agent-skillscp -r "agent-skills/skills/create-workflow" ~/.claude/skills/

Copies the create-workflow skill into ~/.claude/skills/ for every project (use .claude/skills/ for one project). Repeat for the other skills listed below.

Plugin

/plugin marketplace add nextflow-io/agent-skills

Run inside Claude Code if the repository ships a plugin marketplace, then pick plugins from /plugin.

Skills can run code on your machine — read the SKILL.md first.

What it does

In the author's own words, from each skill's SKILL.md.

  • create-workflow

    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 from the Nextflow Registry. This skill handles all Nextflow workflow creation tasks.

    skills/create-workflow/SKILL.md on GitHub (opens in a new tab)

  • install-nextflow

    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.

    skills/install-nextflow/SKILL.md on GitHub (opens in a new tab)

  • 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.

    skills/launch-workflow/SKILL.md on GitHub (opens in a new tab)

  • migrate-nextflow-code

    Migrate Nextflow pipeline code to newer language requirements. Use when fixing strict syntax errors, replacing versions channels with topic channels, migrating from `publishDir` to workflow outputs (the `output {}` block), or adding static typing (typed processes/workflows, records, typed params).

    skills/migrate-nextflow-code/SKILL.md on GitHub (opens in a new tab)

  • run-module

    Run Nextflow Registry modules natively using `nextflow module` commands. Use when running, listing, or getting info about Nextflow modules.

    skills/run-module/SKILL.md on GitHub (opens in a new tab)

Review before you install

A skill is a set of instructions and scripts your agent will follow, and it can run code on your machine. Read the SKILL.md and any scripts first — this listing is not a security review.