Automating Reporting Pipelines

Software engineering solved the problem of reliable deployment years ago with CI/CD (Continuous Integration / Continuous Deployment). Clinical genomics needs to adopt these same principles.

Infrastructure as Code

Your bioinformatics pipeline should not be a collection of shell scripts on a server. It should be defined in code (e.g., Nextflow, WDL) and version controlled. This ensures that every patient sample is processed identically.

Automated QC

Instead of a human checking coverage plots, automated scripts should flag samples that fail QC metrics (e.g., low coverage, contamination) before they ever reach the interpretation queue.