nextflow-development

Configures and runs nf-core pipelines on local FASTQ inputs or public GEO/SRA accessions, writing pipeline outputs to a user-specified directory.

   
Type Claude Skill
Supplier Anthropic
Availability GA — distributed via anthropics/life-sciences (Oct 2025); positioned by Anthropic as a prototype / educational example
Pricing Free / OSS
Capabilities Read/Write

How to install

  • Also packaged in the SciAgent-Skills collection (jaechang-hits (community OSS, CC BY 4.0)): clone jaechang-hits/SciAgent-Skills and run /plugin install sciagent-skills in Claude Code (or copy skills/scientific-computing/nextflow-workflow-engine into ~/.claude/skills/).
  • Claude Code — plugin marketplace: 
    /plugin marketplace add anthropics/life-sciences
/plugin install nextflow-development@life-sciences
  • Claude.ai — Settings → Capabilities → Skills → Upload skill, using the skill bundle from the anthropics/life-sciences repo.
  • Alternative — K-Dense skill: npx skills add K-Dense-AI/scientific-agent-skills, then enable the nextflow skill. A community-maintained skill (MIT collection) covering the same Nextflow / nf-core workflows; use it if you don’t have anthropics/life-sciences marketplace access.

What it does

Skill instructions for nf-core rnaseq (v3.22.2), sarek (v3.7.1), and atacseq (v2.1.2) — including the standard -profile test,docker smoke commands and pointers to expand support to other nf-core pipelines.

Primary use cases: Bench-scientist orchestration of bulk RNA-seq, germline/somatic variant calling, and ATAC-seq analyses without bespoke bioinformatics tooling.

Notes

Requires Nextflow and Docker (or another supported container engine) on the host. Users are responsible for compute capacity and result validation — Anthropic flags this skill as not production-ready without domain validation.

Sources

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