Genebuild Metadata

ensembl-genes-metadata is a repository that centralizes Nextflow pipelines and other helper tools for managing metadata within Genebuild.

Nextflow Pipelines

• Assembly Metadata Registry: Nextflow pipeline to update the MySQL Genebuild assembly metadata database.
• Assembly Metadata Updates: Nextflow pipeline to check existing assemblies against NCBI and update their metadata.

Prefect Orchestrator

• Genebuild Metadata Prefect: Prefect flows that submit the Nextflow pipelines above (and other scripts) as SLURM jobs.

Web App

• Genebuild Web App: coming soon

src

• MySQL schema: DDL for the Genebuild assembly metadata database — assembly, species, taxonomy, organism, bioproject, genebuild_status, and related tables.
• Python (gb_metadata): shared Python package used by both pipelines' bin/ scripts (DB connection helpers, species/taxonomy checking, DB write logic), plus a standalone reference-assembly checker.

Requirements

• Nextflow >= 24.10.0
• Singularity >= 3.7.0
• Java 11 or later
• Access to a SLURM cluster
• Access to a MySQL instance for the Genebuild assembly metadata database
• Python 3.9+ and Prefect (for the Prefect flows)

Installation

git clone https://github.com/Ensembl/ensembl-genes-metadata.git
cd ensembl-genes-metadata

See each pipeline's own README (e.g. assembly_metadata, assembly_metadata_update) for pipeline-specific setup and configuration.

Contributing

Contributions are welcome. Please open an issue to discuss significant changes before submitting a pull request, and make sure any new pipeline includes its own README.

License

This project is licensed under the Apache License 2.0