Nextflow Managed Services Infrastructure & Operations

Nextflow is an open-source workflow management system designed for scalable, reproducible computational pipelines. It enables you to write pipelines once and run them anywhere: local machines, HPC clusters, AWS, Azure, or Kubernetes. This portability eliminates infrastructure lock-in and makes your research reproducible across environments.

nf-core is a community-driven collection of 100+ peer-reviewed, production-ready Nextflow pipelines. We deploy, customize, and support all nf-core pipelines including rnaseq, sarek (variant calling), atacseq, and many others. We also build custom modules following nf-core best practices.

Costs depend on scope and complexity. AWS Batch setup or Azure Batch deployment typically starts at $3,000-$8,000. nf-core pipeline deployment ranges from $2,000-$5,000 per pipeline. Ongoing Nextflow support services range from $2,000-$10,000/month based on support level and infrastructure complexity. Book a free consultation for a custom estimate.

Yes, HPC to cloud migration for bioinformatics is one of our core services. We migrate Nextflow, Snakemake, and custom pipelines from Slurm, SGE, PBS, or LSF to AWS Batch, Azure Batch, or Kubernetes. Typical results include 10x faster processing through elastic scaling and 50-70% cost reduction with Spot instances.

AWS Batch is the most popular choice among our clients due to mature Nextflow integration, Spot instance support (up to 90% cost savings), and the extensive AWS genomics ecosystem. Azure Batch is excellent for organizations with Microsoft agreements. We support both, plus Google Cloud and on-premise Kubernetes.

We implement security best practices including encrypted storage (S3 with SSE, Azure Blob encryption), VPC isolation, IAM least-privilege access, and audit logging. For regulated environments, we configure HIPAA-eligible services on AWS/Azure and implement BAA requirements. Data remains within your infrastructure; we never access raw genomic data without explicit authorization.

Seqera Platform (formerly Nextflow Tower) provides a web interface for launching, monitoring, and managing Nextflow pipelines. We deploy and configure Seqera Platform for enterprise clients, or implement open-source alternatives using Grafana dashboards and custom monitoring for teams preferring self-managed solutions.

Basic AWS Batch or Azure Batch setup with storage and networking takes 1-2 weeks. Full production infrastructure with monitoring, CI/CD, and Seqera Platform integration typically takes 3-6 weeks. nf-core pipeline deployment and configuration takes 1-2 weeks. We provide detailed timelines during discovery based on your specific requirements.

Yes. We audit existing pipelines for performance bottlenecks, optimize resource allocation (CPU, memory, disk), implement caching strategies, and tune cloud configurations. Common improvements include parallel execution optimization, Spot/preemptible instance usage, and storage I/O optimization. Typical results: 30-60% cost reduction and 2-5x faster execution.

Yes. Our managed services include pipeline monitoring, failure investigation, software updates (Nextflow, tools, containers), cloud infrastructure management, and on-call support for production issues. We offer tiered support plans from business-hours email support to 24/7 critical response depending on your operational requirements.

All are workflow managers for bioinformatics. Nextflow excels in cloud portability and has the largest community (nf-core). Snakemake is Python-based with strong HPC support. WDL/Cromwell is popular in clinical genomics (Broad Institute origin). We help teams choose the right tool and can migrate between platforms if needed.

Yes. Nextflow has native Kubernetes executor support for EKS, GKE, and AKS. This is ideal for organizations with existing Kubernetes infrastructure or needing fine-grained resource control. We configure Kubernetes deployments with proper storage classes, resource quotas, and autoscaling for genomics workloads.