EBP Assemblies Tracker

A GitHub Actions workflow that automatically tracks genome assemblies by cross-referencing eukaryote taxon data with the Earth BioGenome Project (EBP).

Observable Notebook

See the TSV file as a data table here

🎯 Purpose

This repository contains an automated pipeline that:

• Monitors genome assemblies from the Earth BioGenome Project (EBP)
• Cross-references eukaryote assemblies with specific project accessions
• Creates a tracking matrix with new assemblies

🔄 GitHub Actions Workflow

Overview

The workflow runs automatically every day at midnight UTC and performs the following steps:

1. Retrieve Eukaryote Assemblies: Gets all genome assemblies under eukaryote taxon ID 2759
2. Retrieve Project Assemblies: Gets assemblies from specific EBP project accession PRJNA533106
3. Cross-reference: Finds common assemblies between eukaryotes and the project
4. Get Metadata: Retrieves detailed metadata for the cross-referenced assemblies
5. Create Matrix: Creates the matrix

Workflow File: .github/workflows/main.yml

Schedule

schedule:
  - cron: '0 0 * * *'  # Runs every day at midnight UTC

🔧 Configuration

Environment Variables

The workflow uses environment variables loaded from a .env file:

• MATRIX_PATH: Path to the output matrix file
• TSV_FIELDS: Fields to extract from NCBI datasets
• PROJECT_ACCESSION: NCBI project accession to track
• DATASET_EXTRA_ARGS: Additional arguments for NCBI datasets queries

Example .env file:

PROJECT_ACCESSION=PRJNA533106
ROOT_TAXON=2759
TSV_FIELDS=organism-name,organism-tax-id,accession,assminfo-name,assminfo-release-date,assminfo-biosample-accession,assminfo-bioproject,assminfo-bioproject-lineage-parent-accessions,source_database
MATRIX_PATH=./data/ebp-eukaryotes.tsv

🧪 Testing

Local Testing

Use the included test script to validate the pipeline locally:

chmod +x test_pipeline.sh
./test_pipeline.sh