Building a Reproducible GATK Variant Calling Bash Workflow with Pixi (Part 1)
· 30 min read
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.