nextflow-development

Automate sequencing data analysis with nf-core bioinformatics pipelines.

10|1|Updated Feb 19, 2026

Search Tags:#analysis #bioinformatics #pipelines #omics #nextflow

Ready to run

npx skills add https://github.com/giadaf-boosha/claude-code --skill nextflow-development-giadaf-boosha

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: nextflow-development
Source: https://github.com/giadaf-boosha/claude-code/tree/main/skills/bio-research-nextflow-development
Command: npx skills add https://github.com/giadaf-boosha/claude-code --skill nextflow-development-giadaf-boosha

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires nextflow, nf-core, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill streamlines the process of running nf-core bioinformatics pipelines, reducing the manual effort and expertise required for complex analyses like RNA-seq, WGS/WES, and ATAC-seq data processing.

Core Features & Use Cases

Pipeline Automation: Automates the execution of nf-core pipelines (e.g., rnaseq, sarek, atacseq) for processing sequencing data.
Data Acquisition: Facilitates data acquisition from local FASTQ files or public datasets from GEO/SRA.
Workflow Management: Provides a structured workflow with steps for data acquisition, environment check, pipeline selection, and execution.
Use Case: Ideal for bench scientists and researchers who need to perform large-scale omics analyses without specialized bioinformatics training.

Quick Start

Use the nextflow-development skill to run the 'rnaseq' pipeline on your local RNA-seq data by providing the directory containing your FASTQ files.

Frequently Asked Questions about nextflow-development

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

FAQPage Schema

How do I automate RNA-seq analysis using nf-core pipelines?▼

You can automate RNA-seq analysis by using this Skill to run the nf-core rnaseq pipeline, which handles data acquisition, environment checks, and execution on your local FASTQ files automatically.

Can I process WGS or ATAC-seq data with nf-core pipelines?▼

Yes, this Skill automates the execution of nf-core pipelines for WGS/WES and ATAC-seq data processing. It performs pipeline selection and execution to handle these specific sequencing workflows.

Do I need Nextflow installed to run nf-core bioinformatics pipelines?▼

Yes, you must have Nextflow and nf-core pipelines installed and configured in your environment before using this Skill to automate your sequencing data analysis workflows.

How do I acquire public sequencing data for nf-core pipeline execution?▼

This Skill facilitates data acquisition from local FASTQ files or public datasets from GEO/SRA, preparing the input needed to execute nf-core bioinformatics pipelines.

What is the best way to run bioinformatics pipelines without specialized training?▼

Bench scientists can use this Skill to perform large-scale omics analyses through a structured workflow that automates environment checks, pipeline selection, and execution of nf-core tools.

Are there limitations when automating omics analyses with Nextflow?▼

This Skill is limited to automating nf-core pipelines for RNA-seq, WGS/WES, and ATAC-seq data, and requires proper installation and configuration of Nextflow and nf-core to function.