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Venus Pipeline#

Venus is a clinical tumor variant calling pipeline built on oxo-flow. It is included as a workspace crate (crates/venus/) and ships with pre-defined workflow files, environment specs, and report templates.

Overview#

Venus implements a complete somatic variant detection workflow for tumor samples. It is designed for clinical genomics laboratories that need:

  • Validated, reproducible analysis
  • Structured clinical reports
  • Audit trails for regulatory compliance
  • Container-packaged execution

Pipeline Steps#

graph TD
    A[Quality Control] --> B[Read Trimming]
    B --> C[Alignment]
    C --> D[Duplicate Marking]
    D --> E[Base Recalibration]
    E --> F[Variant Calling]
    F --> G[Variant Filtering]
    G --> H[Annotation]
    H --> I[Clinical Report]
Step Tools Description
Quality Control FastQC Raw read quality assessment
Read Trimming fastp Adapter removal and quality filtering
Alignment BWA-MEM2 Read alignment to reference genome
Duplicate Marking GATK MarkDuplicates PCR duplicate identification
Base Recalibration GATK BQSR Base quality score recalibration
Variant Calling GATK Mutect2 Somatic variant detection
Variant Filtering bcftools Quality-based variant filtering
Annotation VEP / SnpEff Functional variant annotation
Clinical Report oxo-flow report Structured report generation

Project Structure#

pipelines/venus/
├── rules/           # Individual step definitions
├── envs/            # Conda/container environment specs
├── schemas/         # Validation schemas for config
└── report/          # Report templates

The pipeline definitions live in pipelines/venus/ while the Rust crate at crates/venus/ provides programmatic access.

Running Venus#

With the CLI#

# Validate the pipeline
oxo-flow validate pipelines/venus/venus.oxoflow

# Dry-run
oxo-flow dry-run pipelines/venus/venus.oxoflow

# Execute
oxo-flow run pipelines/venus/venus.oxoflow -j 16

Configuration#

Venus expects a configuration file with sample and reference information:

[config]
reference = "/data/references/hg38/hg38.fa"
known_sites = "/data/references/hg38/known_sites.vcf.gz"
tumor_sample = "TUMOR_001"
normal_sample = "NORMAL_001"
results = "results/venus"

Clinical Reporting#

Venus generates clinical-grade reports using oxo-flow's reporting system:

oxo-flow report pipelines/venus/venus.oxoflow -f html -o patient_report.html

Reports include:

  • Patient/sample metadata — sample IDs, sequencing date, reference genome
  • Quality metrics — read counts, coverage depth, duplication rates
  • Variant summary — total variants, filtered variants, variant types
  • Variant table — gene, position, consequence, allele frequency
  • Methodology — tools used, versions, parameters

Container Packaging#

Package Venus into a self-contained container:

# Docker
oxo-flow package pipelines/venus/venus.oxoflow -o Dockerfile
docker build -t venus:1.0.0 .

# Singularity
oxo-flow package pipelines/venus/venus.oxoflow -f singularity -o venus.def
singularity build venus.sif venus.def

Customization#

Venus is designed to be customized for specific laboratory needs:

Add a new analysis step#

  1. Create a new rule in pipelines/venus/rules/
  2. Add the environment spec to pipelines/venus/envs/
  3. Include the rule in the main .oxoflow file
  4. Add report sections for the new step

Modify variant filters#

Edit the filtering rule parameters in the workflow file to adjust quality thresholds, minimum depth, or allele frequency cutoffs.

Custom report templates#

Add Tera templates to pipelines/venus/report/ for custom report sections or layouts.

See Also#