nf-core Pipelines Skills Index

Identify and access nf-core pipelines for omics analysis workflows.

478|62|Updated Jul 30, 2025

Search Tags:#workflow #documentation #bioinformatics #pipelines #omics #nf-core #nextflow

Ready to run

npx skills add https://github.com/aristoteleo/PantheonOS --skill nf-core-pipelines-skills-index

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: nf-core Pipelines Skills Index
Source: https://github.com/aristoteleo/PantheonOS/tree/main/pantheon/factory/templates/skills/omics/upstream_processing/nfcore
Command: npx skills add https://github.com/aristoteleo/PantheonOS --skill nf-core-pipelines-skills-index

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

nf-core pipelines offer standardized, community-curated workflows for omics data analysis, and this skill index helps users quickly locate and understand those pipelines.

Core Features & Use Cases

Discover pipelines across genomics, transcriptomics, epigenomics, spatial omics, and more.
Access installation guidance, parameter references, usage examples, and official docs for each pipeline.
Use as a learning resource to bootstrap nf-core workflows in research projects.

Quick Start

Browse the nf-core skills index to locate a pipeline and open its docs to begin using nf-core.

Frequently Asked Questions about nf-core Pipelines Skills Index

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

FAQPage Schema

How do I find nf-core pipelines for specific omics analysis workflows?▼

The nf-core skills index helps you locate standardized omics pipelines by exposing pipeline metadata. You can discover workflows across transcriptomics, epigenomics, spatial omics, and variant calling, then access their documentation to understand their capabilities.

What is nf-core used for in bioinformatics?▼

nf-core provides community-curated, standardized workflows for bioinformatics and omics data analysis. It is used to process data across domains like genomics and transcriptomics, ensuring reproducible research through community-curated pipelines.

How do I get installation guidance and usage examples for nf-core pipelines?▼

You can access installation guidance, parameter references, and usage examples for nf-core pipelines by opening the Markdown documentation paired with each pipeline entry in the skills index, which covers usage, parameters, and outputs.

Does the nf-core skills index support spatial omics and epigenomics workflows?▼

Yes, the nf-core skills index supports spatial omics and epigenomics workflows. It allows you to discover and access pipelines across a broad range of omics categories including transcriptomics and variant calling.

Can I use nf-core pipelines as a learning resource to bootstrap research projects?▼

Yes, you can use the nf-core skills index as a learning resource to bootstrap workflows in research projects. The index provides access to official docs, parameter references, and usage examples to help you get started with Nextflow.