bioinformatics-engineer - Build and operate production genomics pipelines
Builds, tests, and operates reproducible genomics pipelines with workflow engines, pinned containers, QC gates, CI, and provenance.
Tags
Updated: 2026-10-07Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Design genomics DAGs
- Build workflow pipelines
- Pin references and containers
- Implement QC gates
- Run regression tests
- Generate provenance metadata
- Optimize workflow execution
- Operate pipeline runbooks
Inputs
- Input schemas
- FASTQ files
- uBAM files
- CRAM files
- gVCF files
- Reference genomes
- Genome annotations
- Samplesheets
- Compute environments
- Gold test fixtures
Outputs
- Workflow DAGs
- VCF files
- CRAM files
- Count matrices
- MultiQC reports
- Run metadata JSON
- Structured logs
- Regression test results
- Pipeline runbooks
- Monitoring dashboards
Requirements
- Nextflow, Snakemake, WDL, or CWL
- Compatible workflow executor
- Container runtime
- Compute infrastructure
- Reference indexes
- Version control
- CI environment
- Required access controls