From laptop scripts to a production pipeline
When the only computational scientist left, nobody could reproduce last quarter's results. We rebuilt the analysis as a tested, versioned pipeline the team owns.
- Client
- Series A biotech
- Data
- Weekly scRNA-seq and bulk RNA-seq runs
- Timeline
- 6 weeks build, then monthly maintenance
- Outcome
- Turnaround cut from 2 weeks to 2 days per run
Anonymized composite case. Details are combined and altered to protect client confidentiality.
The problem
Analysis lived in undocumented R scripts on one laptop, with hard-coded paths and package versions that no longer installed. After that scientist left, the team could not reproduce figures shown to its board, and new data piled up.
What we found
- No version control, no environment pinning, and no record of which parameters produced which results.
- Inconsistent QC thresholds between runs made comparisons across experiments meaningless.
How we rescued it
- Built a modular Nextflow pipeline on nf-core components, with pinned containers, for both scRNA-seq and bulk RNA-seq.
- Deployed on AWS Batch with cost controls, and storage lifecycle rules for raw data.
- Added automated QC reports, data versioning and a results catalog so every figure traces back to inputs and code.
- Wrote tests on small reference datasets and continuous integration so updates cannot silently change results.
- Moved to monthly flat-rate maintenance: version upgrades, new modules, monitoring, and a duo team on call for analysis.
The result
Each new sequencing run now produces a QC report and standard analysis within two days, without manual work. The team reproduced its historical results and passed due diligence for its next financing round.
| Measure | Result |
|---|---|
| Turnaround per run | 2 weeks to 2 days |
| Reproducibility | Every figure traceable |
| Ownership | Client owns all code |
Have a project like this?
We audit failed or questioned analyses, explain what went wrong, and rebuild them reproducibly, often within days of a reviewer deadline.
- Service
- Pipeline build and maintenance
- Price
- From $79/h