/workflow-pathoscope

A workflow for detecting known viruses in Virtool

Primary LanguagePython

workflow-pathoscope

An analysis workflow for detecting known OTUs (viruses) by matching reads against a reference of known virus genomes.

Steps

  1. Map default isolates. Identify potentially present OTUs by mapping against representative (default) isolates of each OTU.
  2. Build isolate index. Build a mapping index of all isolates of the previously identified OTUs.
  3. Map all isolates. Map sample reads against all isolates of OTU candidates.
  4. Map and eliminate subtractions. Map reads with alignment in previous step against the user-selected subtraction to eliminate contaminating reads (usually host).
  5. Reassignment. Use Pathoscope 2.0 to statistically reassign read weight to the most likely reference genomes of origin. Minimize the impact of multi-mapping and similar reference genomes on the analysis.

Contributing

Commits

All commits must follow the Conventional Commits specification.

These standardized commit messages are used to automatically publish releases using semantic-release after commits are merged to main from successful PRs.

Example

feat: add API support for assigning labels to existing samples

Descriptive bodies and footers are required where necessary to describe the impact of the commit. Use bullets where appropriate.

Additional Requirements

  1. Write in the imperative. For example, "fix bug", not "fixed bug" or "fixes bug".
  2. Don't refer to issues or code reviews. For example, don't write something like this: "make style changes requested in review". Instead, "update styles to improve accessibility".
  3. Commits are not your personal journal. For example, don't write something like this: "got server running again" or "oops. fixed my code smell".

From Tim Pope: A Note About Git Commit Messages