$ show ncbi/egapx
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.
The LLM identified 3 files worth highlighting for reuse:
Python CLI entry point containing isolated, reusable functions for taxonomy ID resolution, protein set selection, SRA query building, URL parsing, and input validation. These functions are self-contained enough to be extracted into a standalone library for interacting with NCBI APIs and preparing annotation pipeline inputs.
Nextflow subworkflow for long-read RNA-seq alignment and reporting. It encapsulates a complete alignment-and-report process chain that can be reused in other Nextflow pipelines needing long-read transcript evidence processing, with clear process boundaries and output reporting.
Nextflow subworkflow that extracts protein products from gene models for orthology analysis. It demonstrates a reusable pattern for model-to-protein conversion in annotation pipelines, decoupled from the specific upstream model source and suitable for integration into other eukaryotic annotation or comparative genomics workflows.