Bio Viromics

Detect, classify, and QC viral contigs.

Instructions

1. Run virus detection (geNomad).
2. Run CheckV for completeness/contamination.
3. 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.md for 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.