Bio Viromics
Detect, classify, and QC viral contigs.
Instructions
- Run virus detection (geNomad).
- Run CheckV for completeness/contamination.
- Assign taxonomy and cluster genomes (vConTACT3 for hierarchical classification and gene-sharing network analysis).
Quick Reference
| Task | Action |
|---|---|
| Run workflow | Follow the steps in this skill and capture outputs. |
| Validate inputs | Confirm required inputs and reference data exist. |
| Review outputs | Inspect reports and QC gates before proceeding. |
| Tool docs | See docs/README.md. |
| References | - See ../bio-skills-references.md |
Input Requirements
Prerequisites:
- Tools available in the active environment (Pixi/conda/system). See
docs/README.mdfor expected tools. - Reference DB root: set
BIO_DB_ROOT(default/media/shared-expansion/db/on WSU). - Input contigs are available. Inputs:
- contigs.fasta
Output
- results/bio-viromics/viral_contigs.fasta
- results/bio-viromics/checkv_results/
- results/bio-viromics/vcontact3_results/
- results/bio-viromics/viral_taxonomy.tsv
- results/bio-viromics/genome_clusters.tsv
- results/bio-viromics/viromics_report.md
- results/bio-viromics/logs/
Quality Gates
- CheckV quality thresholds meet project standards.
- Contamination flags are below thresholds.
- On failure: retry with alternative parameters; if still failing, record in report and exit non-zero.
- Verify contigs.fasta is non-empty.
- Verify viral reference DBs exist under the reference root.
Examples
Example 1: Expected input layout
contigs.fasta
Troubleshooting
Issue: Missing inputs or reference databases Solution: Verify paths and permissions before running the workflow.
Issue: Low-quality results or failed QC gates Solution: Review reports, adjust parameters, and re-run the affected step.