A workflow for identifying novel viruses in Virtool.
- Eliminate sample reads that map to any default (representative) isolate of any OTU.
- Eliminate sample reads that map to the configured subtraction.
- Repair paired reads if some pair members were lost in elimination.
- Assemble the remaining reads using SPAdes.
- Calculate ORFs from the assembled contigs.
- Use ORFs as input for HMMER to detect viral motifs using profile hidden Markov models derived from the vFAM project.
Set environment variables for proper file permissions:
export USER_ID=$(id -u) GROUP_ID=$(id -g)
Build the test container:
docker compose build
Run all tests:
docker compose run --rm app poetry run pytest
Run specific tests:
docker compose run --rm app poetry run pytest tests/test_workflow.py
- No rebuilds: Uses bind mounts to get latest code without rebuilding
- No permission issues: Container runs as your user via USER_ID/GROUP_ID
- Fast iterations: Only Poetry and pytest execution, no Docker build time
Read our guide on writing commits for Virtool repositories.