An analysis workflow for detecting known OTUs (viruses) by matching reads against a reference of known virus genomes.
- Map default isolates. Identify potentially present OTUs by mapping against representative (default) isolates of each OTU.
- Build isolate index. Build a mapping index of all isolates of the previously identified OTUs.
- Map all isolates. Map sample reads against all isolates of OTU candidates.
- Map and eliminate subtractions. Map reads with alignment in previous step against the user-selected subtraction to eliminate contaminating reads (usually host).
- 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.
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
- Write in the imperative. For example, "fix bug", not "fixed bug" or "fixes bug".
- 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".
- 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