🚀 Acceleration Toolbox for Bioinformatics Pipelines

A hands-on workshop for building fast, reproducible, and portable bioinformatics pipelines.

Topics

• 📂 Git & GitHub
• 📦 Docker containers
• ⚡ CI/CD with GitHub Actions
• 🔄 Nextflow workflows
• 🧬 nf-core pipelines
• changed

Workshop Roadmap

1. Introduction
   • Why modern bioinformatics tools and workflow managers matter?
   • Reproducibility, scalability, and automation
2. Git & GitHub
   • Create a repository
   • Clone, commit, push, and pull
   • Organize a bioinformatics project
3. Docker
   • Build a container
   • DockerHub
   • Run bioinformatics tools in a reproducible environment
4. CI/CD
   • Automatically test workflows with GitHub Actions
5. Nextflow
   • Build an RNA-seq pipeline
   • Learn processes, channels, and configuration
   • Run on HPC (PULI)
6. nf-core
   • Run the nf-core/rnaseq pipeline
   • Explore standardized best practices

Goal

By the end of the workshop you'll have a complete RNA-seq workflow managed with Git, packaged with Docker, automated with CI/CD, and orchestrated with Nextflow.

Contents

• 1. Git & GitHub
• 2. Containers
• 3. Workflow Manager
• 4. Nextflow
• 6. nf-core

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From manual scripts → reproducible bioinformatics pipelines.