Multi-Organism Support

sr2silo supports processing samples from multiple organisms with organism-specific reference sequences.

Supported Organisms

Organism	Identifier	Description
COVID-19	covid	SARS-CoV-2 / Severe acute respiratory syndrome coronavirus 2
RSV-A	rsva	Respiratory Syncytial Virus A

Reference Resolution

sr2silo resolves reference sequences in the following priority order:

1. Local References (fastest): resources/references/{organism}/
2. LAPIS Instance: Fetched from specified --lapis-url if available
3. Fallback: Local references as final fallback if LAPIS fetch fails

This allows for both static local references and dynamic references from a LAPIS instance.

Usage

For detailed usage, see:

sr2silo process-from-vpipe --help

The --organism parameter specifies which organism to process. Can also be set via ORGANISM environment variable (CLI argument takes precedence).

Adding New Organisms

To add support for a new organism:

1. Add reference files to resources/references/{organism_id}/:
2. nuc_ref.fasta - Nucleotide reference sequence(s)

3. aa_ref.fasta - Amino acid reference sequences for gene annotations

4. Use GenBank parser (if starting from GenBank format):

   python scripts/extract_gbk_references.py \
       reference.gbk \
       --nuc-output resources/references/{organism_id}/nuc_ref.fasta \
       --aa-output resources/references/{organism_id}/aa_ref.fasta
   

5. Update configuration (optional):

6. Update workflow config.yaml with your new organism ID

7. Update documentation with organism details

8. Test (optional):

9. Add test fixtures in tests/conftest.py
10. Add parameterized tests in tests/test_main.py

Workflow Integration

Specify organism in workflow/config.yaml:

ORGANISM: "covid"  # or "rsva"

Troubleshooting

Reference files not found: - Verify files exist: ls resources/references/{organism}/ - Check organism identifier spelling - Use --lapis-url to fetch from LAPIS - Generate from GenBank: python scripts/extract_gbk_references.py --help