EGAPx is NCBI's publicly accessible Eukaryotic Genome Annotation Pipeline, implemented as a Nextflow DSL2 workflow with a Python CLI entry point. The pipeline takes a genome assembly plus RNA-seq and/or protein evidence, aligns evidence with tools like STAR, minimap2, and miniprot, runs Gnomon gene model prediction and filtering, and produces ASN.1 annotation data, summary files, and MultiQC reports. The main entry point is ui/egapx.py, which validates inputs, resolves taxonomy IDs, fetches protein/HMM files, and orchestrates the Nextflow run. The workflow is organized into reusable subworkflows under nf/subworkflows/ncbi/, with checkpointing and parameter-merging patterns for reproducibility and environment flexibility across AWS, Slurm, SGE, and container runtimes.