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nextflow-development

Run nf-core Nextflow pipelines for RNA-seq, variant, and ATAC-seq analyses.

7|Updated Feb 6, 2026
Search Tags:#bioinformatics#genomics#nf-core#nextflow#rna-seq#variant calling#fastq
One-click install
npx skills add https://github.com/Epiphytic/ai-plugin-translator --skill nextflow-development-epiphytic
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: nextflow-development
Source: https://github.com/Epiphytic/ai-plugin-translator/tree/main/packages/core/test/fixtures/regression-output/knowledge-work-plugins/bio-research/skills/nextflow-development
Command: npx skills add https://github.com/Epiphytic/ai-plugin-translator --skill nextflow-development-epiphytic

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill simplifies running complex nf-core bioinformatics workflows by guiding researchers through data acquisition, environment setup, pipeline selection, execution, and result validation.

Core Features & Use Cases

  • Pipeline Deployment Guidance: Runs nf-core Nextflow pipelines for RNA-seq, WGS/WES variant calling, and ATAC-seq analyses with structured validation steps.
  • Sequencing Data Preparation: Helps acquire GEO/SRA datasets, generate samplesheets, detect data types, and configure reference genomes.
  • Use Case: A researcher with FASTQ files can use this Skill to prepare and execute an RNA-seq analysis workflow and verify the resulting quality control and expression outputs.

Quick Start

Use the nextflow-development skill to analyze my FASTQ sequencing data with the appropriate nf-core pipeline.

Frequently Asked Questions about nextflow-development

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

FAQPage Schema
How do I run an RNA-seq pipeline on FASTQ files using Nextflow?▼

To run an RNA-seq pipeline on FASTQ files, this Skill guides you through generating samplesheets, configuring reference genomes, and executing validated nf-core workflows to produce quality control and expression analysis outputs.

What's the best way to automate variant calling for whole genome sequencing data?▼

Automating variant calling for whole genome sequencing is achieved by deploying validated nf-core Nextflow pipelines, which streamline workflow execution from FASTQ input through to final variant detection and result validation.

How do I retrieve GEO or SRA datasets and generate a samplesheet for bioinformatics analysis?▼

Retrieving GEO or SRA datasets and generating a samplesheet involves using guided sequencing data preparation steps to acquire raw files, detect data types, and format inputs for reproducible omics analysis.

Do I need Docker or an HPC environment to execute nf-core pipelines?▼

Yes, executing nf-core pipelines requires Docker or an HPC execution environment, alongside Nextflow and validated workflow configurations, to ensure reproducible bioinformatics sequencing data analysis.

Can I use this nf-core workflow setup for ATAC-seq data analysis?▼

Yes, you can use this setup for ATAC-seq data analysis, as the Skill supports deploying and running validated nf-core pipelines specifically tailored for ATAC-seq alongside RNA-seq and WGS workflows.

How does Nextflow handle reproducibility for genomics workflows?▼

Nextflow handles reproducibility for genomics workflows by applying validated workflow configurations, standardized reference genomes, and containerized execution environments to ensure consistent omics analysis outputs.

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