Automated pipelines for reproducible omics workflows
Containerized, scalable workflows built with Nextflow, Docker, and industry-standard bioinformatics tools. Select your analysis type to get started.
Reproducible by construction
Every Floxgen pipeline is a versioned, containerized Nextflow workflow. Pin a release and you get bit-for-bit identical results across laptops, on-prem clusters and the cloud — no "works on my machine," no dependency drift.
Containerized
Docker / Singularity images per process — fully isolated, fully reproducible.
Scalable
From a single sample to population scale — the same workflow, auto-parallelised.
Validated tools
BWA-MEM2, GATK, DeepVariant, STAR, VEP — industry standards, benchmarked.
API-driven
Trigger runs, stream logs and pull results over a clean REST API.
Stack & tools
Open-source, benchmarked components orchestrated by Nextflow and packaged in Docker.
Run it
Launch any pipeline with a single command, or call the API from your own systems.
nextflow run floxgen/wgs-germline -r v2.4.1 \
--input samples.csv --genome GRCh38 \
-profile docker,cluster --outdir results/
Outputs
Every run emits analysis-ready artifacts plus a full provenance record.
Annotated VCF / gVCF
VEP-annotated calls, ready for the Aggregator and interpretation.
QC report
Interactive MultiQC across every sample and step.
Alignment metrics
Coverage, duplication and contamination summaries.
Provenance manifest
Versions, parameters and checksums for full reproducibility.