Bioinformatics pipeline
Bioinformatics Pipeline Monitoring Software
StrixFlow watches every pipeline run in real time, diagnoses failures down to the step that broke, and tracks compute cost per sample. It connects to existing Nextflow, Snakemake, WDL, and CWL pipelines without a rewrite, and runs self-hosted.
Engineered for self-hosted deployment, with no change to existing orchestration.
A pipeline run dies overnight, and nobody knows until morning
A lab running Nextflow or Snakemake across HPC and cloud rarely has a single place to see what is running, what failed, and why. A run fails at two in the morning; the first sign of it is a clinician asking where a result has gone, and the bioinformatician then spends the day hunting for the failure instead of fixing it. Compute cost is just as hidden, because it stays unbudgeted until the cloud bill arrives.
That blind spot is expensive, because genomics pipelines are among the heaviest consumers of cloud and HPC, and a failed or runaway run costs money long before anyone sees it.
What StrixFlow includes
StrixFlow arrives as a working observability layer that a lab connects to its own pipelines.
- Real-time alerting that flags a failure the moment a run breaks
- Step-level diagnosis down to the process that failed, with the actual error output
- Cost-per-sample tracking that brings HPC and cloud spend into one view
- Multi-framework support across Nextflow, Snakemake, WDL, and CWL, connected without rewrites
- Reproducibility manifests that record tool versions, container digests, and parameters per run, supporting CLIA/CAP and 21 CFR Part 11 traceability
- Slack and Teams alerts, so the right person hears about a failed run first
What's ready to run, and what the lab tailors
The observability layer, the failure diagnosis, and the cost tracking already exist, so a project starts around the halfway mark rather than at zero.
| Already built | Customized for the lab |
|---|---|
| Observability layer, failure diagnosis, cost tracking, multi-framework connectors, alerting | The specific pipelines and parameters, the cost thresholds and budgets, the alert routing and on-call rules |
Because that foundation is in place, NonStop estimates a build reaches production 40 to 50 percent faster than starting from scratch, and the lab owns the result when the engagement ends.
Over your existing pipelines, without changing them
StrixFlow connects to the pipelines a lab already runs and watches them, so there is no need to replace the orchestration or rewrite a workflow.
| Connects to | Nextflow, Snakemake, WDL, and CWL |
| Runs across | HPC and cloud, in one view |
| Feeds | Clean pipeline output into LIMS |
| Deploys | Self-hosted, inside the lab's environment |
Hours of debugging, returned to the science
| Manual monitoring | With StrixFlow |
|---|---|
| 4–8 hrs a day debugging failed runs, with cost invisible | Failures caught in real time, with cost visible per sample |
* Figures are NonStop estimates and vary by engagement scope.
Those are hours of skilled bioinformatics time that go back to the work that actually needs judgment.
Frequently Asked Questions
Does it work with Nextflow and Snakemake without rewriting pipelines?
How does it give compute cost visibility?
Can it alert the team when a run fails?
Is StrixFlow an off-the-shelf product?
Can it run self-hosted?
Book a call
See your pipelines in one view
Book a 15-minute scoping call and tell us which frameworks and compute the lab runs. We will show where observability fits and what the team would still own.
Book a call →