Development Requirements

Requirements

These were the considerations considered essential when developing this workflow:

1. It should run sistr to generate the serotype calls.
2. It should implement rules and filters to modify the sistr output where identified as appropriate during the validation -- these are detailed in the SOP and validation documents.
3. Document over each run how these rules and filters are applied.
4. For each run of the software, ensure positive and negative controls are run, and the results documented.
5. Produce, when appropriate, an output that can be uploaded directly in to LIMs.
6. Have a process in place for self-validation of any changes to the code. This should produce a PDF that can be filed with Quality demonstrating that the characteristics of the test have not changed with modifications to the code.
7. Have an easy way of introducing and documenting new rules and filters.
8. Be deployed in a Singularity container.
9. Output must report sistr version, as well as container version.
10. Workflow should be in Snakemake, and be able to work on an HPC running SLURM.