Translation Comparison - bio-viromics

Run virus detection (geNomad).
Run CheckV for completeness/contamination.
Assign taxonomy and cluster genomes (vConTACT3 for hierarchical classification and gene-sharing network analysis).

运行病毒检测（geNomad）。
运行CheckV以评估完整性/污染情况。
分配分类学信息并对基因组进行聚类（使用vConTACT3进行层级分类和基因共享网络分析）。

Quick Reference

快速参考

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

任务	操作
运行工作流	遵循本技能中的步骤并保存输出结果。
验证输入	确认所需输入和参考数据已存在。
审核输出	在继续下一步前检查报告和QC关卡。
工具文档	查看 `docs/README.md` 。
参考文献	- 参见../bio-skills-references.md

Input Requirements

输入要求

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

前提条件：

活动环境（Pixi/conda/系统）中已安装所需工具。预期工具列表请查看
```
docs/README.md
```
。
参考数据库根目录：设置
```
BIO_DB_ROOT
```
（华盛顿州立大学（WSU）默认路径为
```
/media/shared-expansion/db/
```
）。
输入contigs已准备就绪。输入文件：
contigs.fasta

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/

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

质量关卡

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.

CheckV质量阈值符合项目标准。
污染标记低于阈值。
若失败：使用替代参数重试；若仍失败，将情况记录在报告中并以非零状态退出。
验证contigs.fasta不为空。
验证病毒参考数据库存在于指定的参考根目录下。

Example 1: Expected input layout

示例1：预期输入结构

text

contigs.fasta

text

contigs.fasta

Troubleshooting

故障排除

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.

问题：缺少输入文件或参考数据库 解决方案：运行工作流前验证路径和权限。

问题：结果质量低或未通过QC关卡 解决方案：查看报告，调整参数，重新运行受影响的步骤。

bio-viromics

Original

Translation

Bio Viromics

生物病毒组学

Instructions

操作说明