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A workflow for identifying novel viruses in Virtool.

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 usingSPAdes.
5. Calculate ORFs from the assembled contigs.
6. Use ORFs as input forHMMER to detect viral motifs using profile hidden Markov models derived from the vFAM project.

To run the tests for this package, use the following command:

docker run$(docker build -q .) pytest

If you want to run specific tests, you can specify the test file or directory as anargument topytest:

docker run$(docker build -q .) pytest tests/test_workflow.py

If you get an error like:

Unable to find image 'pytest:latest' locally

Your build is likely failing. Run the build separately to make sure it works:

docker build.

Readour guide onwriting commits for Virtool repositories.