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workflow-nuvs

A workflow for identifying novel viruses in Virtool.

Steps

  1. Eliminate sample reads that map to any default (representative) isolate of any OTU.
  2. Eliminate sample reads that map to the configured subtraction.
  3. Repair paired reads if some pair members were lost in elimination.
  4. Assemble the remaining reads using SPAdes.
  5. Calculate ORFs from the assembled contigs.
  6. Use ORFs as input for HMMER to detect viral motifs using profile hidden Markov models derived from the vFAM project.

Contributing

Running Tests

Setup (one-time)

Set environment variables for proper file permissions:

export USER_ID=$(id -u) GROUP_ID=$(id -g)

Build the test container:

docker compose build

Running Tests

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

Why This Approach?

  • 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

Commits

Read our guide on writing commits for Virtool repositories.

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A workflow for identifying novel viruses in Virtool

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