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