nextflow-development

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Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core, Nextflow, FASTQ analysis, variant calling, gene expression, differential expression, GEO reanalysis, GSE/GSM/SRR accessions, or samplesheet creation.

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#references#pipelines#Pipeline#GEO#troubleshooting.md#DECISION POINT#SRA#nf-core

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Installation for Agentic Skill

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Claude Code (CLI) Fast

skilz install anthropics/life-sciences/nextflow-development

OpenCode (CLI) Fast

skilz install anthropics/life-sciences/nextflow-development --agent opencode

OpenAI Codex (CLI) Native

skilz install anthropics/life-sciences/nextflow-development --agent codex

Gemini CLI (Project) Project

skilz install anthropics/life-sciences/nextflow-development --agent gemini

First time? Install Skilz: pip install skilz

Works with 22+ AI coding assistants

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For Claude Desktop Easy

Download Agent Skill ZIP

Extract and copy to ~/.claude/skills/ then restart Claude Desktop

Manual Installation

1. Clone the repository:

git clone https://github.com/anthropics/life-sciences

2. Copy the agent skill directory:

cp -r life-sciences/nextflow-development ~/.claude/skills/

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AI-Detected Topics

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references pipelines Pipeline GEO troubleshooting.md DECISION POINT SRA nf-core troubleshooting.md references variant calling

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