Add annotation-database project and GFF3-to-Iceberg HealthOmics workflow#85
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wisech-aws wants to merge 1 commit intoaws-samples:mainfrom
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Add annotation-database project and GFF3-to-Iceberg HealthOmics workflow#85wisech-aws wants to merge 1 commit intoaws-samples:mainfrom
wisech-aws wants to merge 1 commit intoaws-samples:mainfrom
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- annotation-database/: Standalone project for loading GFF3 files into
Apache Iceberg tables on AWS S3 Tables using PyIceberg
- Schema 1 (normalized): features, sources, feature_relationships tables
- Schema 2 (denormalized): single genomic_annotations table
- GFF3 parser with URL-decoding, reserved attribute extraction,
parent-child relationship tracking, and FASTA section handling
- Metadata schema for GFF3 directives and pragmas
- templates/gff3-to-iceberg/: HealthOmics WDL workflow template
- 7-stage pipeline: validate, setup catalog, check connectivity,
check permissions, initialize tables, load GFF3, generate summary
- Supports S3 Tables and vanilla Iceberg (Glue catalog)
- Dockerfile, ECR build scripts, parameter template
- test_data/sample.gff3: Sample GFF3 with 30 features across chr1/chr2
(genes, mRNAs, exons, CDS) from Ensembl and Havana sources
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annotation-database/: Standalone project for loading GFF3 files into Apache Iceberg tables on AWS S3 Tables using PyIceberg
templates/gff3-to-iceberg/: HealthOmics WDL workflow template
test_data/sample.gff3: Sample GFF3 with 30 features across chr1/chr2 (genes, mRNAs, exons, CDS) from Ensembl and Havana sources
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