Tired of basic Bash prompts and repetitive typing? Discover how upgrading to Zsh (Z Shell) can transform your terminal experience with smart autocomplete, plugins, and beautiful themes. Install it without admin access using Pixi!
In Part 1, we built a complete 16-step GATK variant calling pipeline in bash—perfect for academic research and 1-10 samples. But what happens when you need to scale to 100+ samples? This is where Nextflow becomes essential.
📁 Repository: All code from this tutorial is organized in the variant-calling-gatk-pipeline-best-practice-from-scratch repository. The structure follows best practices with separate directories for bash (
workflows/bash/) and Nextflow (workflows/nextflow/) implementations.
Before you can transform a bash workflow to Nextflow, you need a solid, reproducible bash baseline. This hands-on guide walks through building a complete 16-step GATK variant calling workflow using bash scripts and Pixi for environment management—following GATK best practices with GVCF mode and hard filtering. While this traditional approach works for academic research and proof-of-concept work, scaling to thousands of samples in industry requires the reproducibility and reliability of workflow managers like Nextflow, which we'll cover in Part 2.
Whether your lab uses bash scripts, Python workflows, Snakemake pipelines, or custom solutions—your in-house pipeline works fine locally. It's been running for years. But as your research scales, you face a hard truth: in-house pipelines don't scale, aren't reproducible across teams, and require constant manual fixes.