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Nextflow Development

Official
anthropics·vlatest·other

This skill helps you develop Nextflow workflows for scalable bioinformatics pipelines, accelerating data analysis and reproducibility.

Repository

Install on your platform

Showing Claude Code. One command installs this skill into any of the agents below.

  1. 1

    Run this in your project

    terminal
    $ npx skills add anthropics/life-sciences --skill nextflow-development -a claude-code

  2. Uses the open-source skills CLI and needs Node.js. Add -g to install it for your user instead of this project.

What we know about this skill

Publisher

anthropics

Matched to the vendor's own GitHub organisation.

Install target

Live repository

Not pinned. Installing fetches whatever the repository holds at the time you run the command.

No human has reviewed this code. The checks below are a static scan of the files at one commit — nobody has run this skill or judged whether it works. A skill runs with whatever access you give your agent, so read the source before you install it.

Automated safety checks

scanned

This skill failed 2 of 6 checks. A failure is not proof of bad intent; it means something in the code needs a human to look at it before you run it.

  • No undeclared network calls: failed

    Contacts 6 hosts that are neither well-known infrastructure nor declared in the skill's frontmatter: docs.docker.com, eutils.ncbi.nlm.nih.gov, ftp.ncbi.nlm.nih.gov, get.nextflow.io, nf-co.re….

    Every host the skill dials — from its scripts, its config endpoints or the commands it tells the agent to run — is either well-known package and API infrastructure or declared in its own frontmatter. Links in documentation are not counted.

    Hosts contacted

    get.nextflow.ioundeclareddocs.docker.comundeclaredhub.docker.compackage registrynf-co.reundeclaredeutils.ncbi.nlm.nih.govundeclaredftp.ncbi.nlm.nih.govundeclaredwww.ebi.ac.ukundeclared

    What it found (3 of 22)

    • nextflow-development/references/installation.md:15contacts get.nextflow.io
      curl -s https://get.nextflow.io | bash
    • nextflow-development/scripts/check_environment.py:120contacts get.nextflow.io
      fix="curl -s https://get.nextflow.io | bash && mv nextflow ~/bin/ && export PATH=$HOME/bin:$PATH"
    • nextflow-development/scripts/check_environment.py:54contacts docs.docker.com
      fix="Install Docker: https://docs.docker.com/get-docker/"

  • No pipe-to-shell installers: failed

    Runs code fetched at install time in 3 places.

    No `curl … | sh` pattern, in the code or in the instructions, that runs code fetched at run time.

    What it found

    • nextflow-development/references/installation.md:15remote script piped into a shell
      curl -s https://get.nextflow.io | bash
    • nextflow-development/scripts/check_environment.py:120remote script piped into a shell
      fix="curl -s https://get.nextflow.io | bash && mv nextflow ~/bin/ && export PATH=$HOME/bin:$PATH"
    • nextflow-development/SKILL.md:75tells the user to run: remote script piped into a shell(in the instructions, not code)
      | Not installed | `curl -s https://get.nextflow.io \| bash && mv nextflow ~/bin/` |

  • Declares what it does: passed

    SKILL.md parses and declares a name and a description.

    SKILL.md exists, its frontmatter parses, and it declares a name and a description.

  • No obfuscated payloads: passed

    No encoded or obfuscated payloads.

    No base64, hex or compressed blob is decoded and then executed, and no encoded shell commands.

  • No credential access: passed

    Reads no keys, tokens, keychains or credential files.

    Neither the code nor the SKILL.md instructions read SSH keys, cloud credentials, keychains, token stores, browser cookie databases or dotfiles that hold secrets.

  • Pinned to a commit: passed

    Scanned anthropics/life-sciences at e96556b637.

    The exact upstream commit SHA that was scanned is recorded, so the result refers to specific bytes.

Commit
e96556b637
Manifest
nextflow-development/SKILL.md
Scanned
22 files, 5,994 lines
This is a static scan, not a review. It reads the skill's files; it does not run them, and it cannot tell you whether the skill is any good or whether the code does what its description says. A skill runs with whatever access you give your agent.
What each check looks for →

About this skill

What it does

This skill enables AI agents to develop and manage Nextflow pipelines. Nextflow is a workflow management system commonly used in bioinformatics for automating complex data processing tasks. It allows users to define, execute, and share reproducible workflows with ease.

When to use it

  • Automating genomic analysis pipelines: Quickly set up and run analyses on large datasets of genetic information.
  • Creating reproducible research workflows: Ensure that your scientific experiments can be easily replicated by others.
  • Managing complex bioinformatics projects: Organize and streamline the various steps involved in a data-intensive project.
  • Sharing and collaborating on workflows: Facilitate teamwork and knowledge sharing within a research group or across institutions.

Key capabilities

  • Nextflow pipeline definition
  • Workflow execution management
  • Reproducible workflow creation
  • Pipeline sharing and collaboration

Example prompts

  • "Create a Nextflow pipeline for RNA-seq analysis."
  • "Run my existing Nextflow pipeline with these input parameters."
  • "Help me debug an error in my Nextflow workflow definition."
  • "Share this Nextflow pipeline with my team."

Tips & gotchas

This skill requires some familiarity with Nextflow concepts and syntax. While the agent can assist, a basic understanding of bioinformatics workflows will be beneficial for effective use.