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nextflow-development

Automate nf-core pipeline deployment and execution for omics data analysis.

23.4k|2.8k|Updated Jan 23, 2026
Search Tags:#data analysis#bioinformatics#nf-core#nextflow#rna-seq#atac-seq#variant calling
One-click install
npx skills add https://github.com/anthropics/knowledge-work-plugins --skill nextflow-development-anthropics
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: nextflow-development
Source: https://github.com/anthropics/knowledge-work-plugins/tree/main/bio-research/skills/nextflow-development
Command: npx skills add https://github.com/anthropics/knowledge-work-plugins --skill nextflow-development-anthropics

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill automates the execution of complex bioinformatics pipelines (like nf-core RNA-seq, Sarek, ATAC-seq) for researchers who may not have deep bioinformatics expertise, simplifying the analysis of omics data.

Core Features & Use Cases

  • Pipeline Execution: Runs nf-core pipelines for RNA-seq, variant calling (Sarek), and ATAC-seq.
  • Data Acquisition: Fetches public data from GEO/SRA.
  • Environment Validation: Checks for necessary software (Docker, Nextflow, Java).
  • Use Case: A researcher needs to analyze RNA-seq data from a public GEO dataset. This Skill can download the data, validate the environment, generate the necessary samplesheet, and run the nf-core/rnaseq pipeline, providing the final gene expression counts.

Quick Start

Use the nextflow-development skill to analyze RNA-seq data from the GEO accession GSE110004.

Frequently Asked Questions about nextflow-development

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I run nf-core RNA-seq pipelines from a GEO accession?▼

To run nf-core RNA-seq pipelines, this Skill automates fetching public data via a GEO accession, validates your software environment, generates the required samplesheet, and executes the pipeline to produce final gene expression counts.

What software dependencies are required to execute Nextflow pipelines?▼

Executing Nextflow pipelines requires Docker, Nextflow, and Java to be installed in your environment. This Skill validates the presence of these necessary software dependencies before deploying and running the bioinformatics workflows.

Can I use this to automate data acquisition from SRA for ATAC-seq analysis?▼

Yes, you can automate data acquisition from SRA for ATAC-seq analysis. The Skill fetches public omics data from GEO/SRA and subsequently runs the nf-core ATAC-seq pipeline to process your sequencing samples.

What is the best way to run variant calling pipelines without deep bioinformatics expertise?▼

The best way to run variant calling pipelines without deep bioinformatics expertise is using this Skill to automate Sarek deployment. It simplifies environment validation, samplesheet generation, and pipeline execution for omics data analysis.

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