Venus (启明星)

Venus (启明星 — "Morning Star") is a clinical-grade tumor variant detection pipeline built on oxo-flow.

Features

• Multiple Analysis Modes

  • experiment_only: Tumor-only somatic calling
  • control_only: Germline variant calling
  • experiment_control: Paired tumor-normal analysis

• Sequencing Support

  • Whole Genome Sequencing (WGS)
  • Whole Exome Sequencing (WES)
  • Targeted Panel Sequencing

• Core Tools

  • fastp/FastQC: Quality control and trimming
  • BWA-MEM2: Read alignment
  • GATK 4: MarkDuplicates, BQSR, Mutect2, HaplotypeCaller
  • Strelka2: Alternative somatic caller (paired mode)
  • VEP: Variant annotation

Installation

From Source

git clone https://github.com/WangLabCSU/oxo-flow-venus.git
cd oxo-flow-venus
cargo install --path .

Prerequisites

• Rust 1.75+ (for building)
• conda/mamba (for environments)
• oxo-flow CLI (cargo install oxo-flow)

Quick Start

1. Create a configuration file (config.toml):

name = "venus_pipeline"
mode = "experiment_control"
seq_type = "wes"
genome_build = "GRCh38"
reference_fasta = "/path/to/genome.fa"
target_bed = "/path/to/exome.bed"

[[samples]]
name = "TUMOR"
type = "tumor"
r1 = "TUMOR_R1.fq.gz"
r2 = "TUMOR_R2.fq.gz"
pair_id = "NORMAL"

[[samples]]
name = "NORMAL"
type = "normal"
r1 = "NORMAL_R1.fq.gz"
r2 = "NORMAL_R2.fq.gz"

2. Generate workflow:

venus generate config.toml -o venus.oxoflow

3. Run pipeline:

oxo-flow run venus.oxoflow -j 8

CLI Commands

Command	Description
venus generate <config>	Generate .oxoflow workflow file
venus validate <config>	Validate configuration
venus list-steps	List pipeline steps

Pipeline Steps

1. fastp — FASTQ QC and trimming
2. BWA-MEM2 — Read alignment
3. MarkDuplicates — PCR duplicate marking
4. BQSR — Base quality recalibration
5. Mutect2 — Somatic variant calling
6. FilterMutectCalls — Variant filtering
7. Strelka2 — Alternative somatic caller (paired mode)
8. VEP — Variant annotation
9. Clinical Report — Report generation

Output Structure

results/
├── trimmed/          # Trimmed FASTQ
├── aligned/          # Aligned BAM
├── dedup/            # Deduplicated BAM
├── recal/            # Recalibrated BAM
├── variants/         # VCF files
├── annotated/        # Annotated VCF
├── tmb/              # TMB calculations
└── reports/          # Clinical reports

License

Apache-2.0

Links

• oxo-flow
• GATK
• VEP