Run Nextflow pipelines on AWS without the infrastructure glue.

SeqFlux is the control plane for bioinformatics pipelines in the cloud. Launch pipelines, enforce cloud guardrails, and track every run — all in your own AWS account.

Built for teams running genomics workflows who want reproducibility, visibility, and cost control without maintaining custom DevOps tooling around Nextflow.

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Why not just use Nextflow?

Nextflow already runs pipelines across AWS Batch, Kubernetes, and HPC.

Nextflow runs the pipeline.
SeqFlux runs the infrastructure around it.

SeqFlux removes the operational work required to run those pipelines reliably in AWS.

Nextflow handles

process orchestration
retries and caching
workflow execution

SeqFlux handles

infrastructure provisioning
Batch configuration
IAM and environment setup
job submission
run monitoring
artifact tracking
cost guardrails

Nextflow defines pipelines. SeqFlux operates them in the cloud.

SeqFlux is infrastructure software for running pipelines, not a replacement for Nextflow.

Bioinformatics teams spend too much time on infrastructure

Established pipelines — nf-core/rnaseq, sarek, atacseq — run fine. But configuring Batch compute, managing IAM, and chasing artifacts across S3 eats into the work that matters. No lightweight option between "run it yourself on EC2" and enterprise platforms.

What SeqFlux does

Infrastructure for bioinformatics teams, computational biology groups, and platform/DevOps teams already running pipelines in the cloud.

Launch

Run standardized workflows from curated templates without stitching together cloud infrastructure by hand.

nf-core/rnaseq supported
Pinned revisions
One-click runs

Control

Apply cloud guardrails automatically, including compute caps, Spot-first execution, and timeout policies.

Hard vCPU cap
Spot-first compute
3-hour timeout
Lifecycle retention

Track

See status, logs, outputs, and reproducibility metadata in one place instead of chasing jobs and artifacts across AWS.

Live status
Logs & artifacts
Immutable run manifests

Trust

Your data stays in your AWS account.

BYOC agent model
IAM least privilege
No data egress

How It Works

From AWS connection to results in five steps.

Connect AWS

Provision SeqFlux into your AWS account using a Terraform module.

Connect Workspace

Choose Template

Select a curated pipeline such as nf-core/rnaseq.

Provide Inputs

Point SeqFlux to FASTQ files in S3 and provide a sample sheet.

Run & Review

Launch the run, monitor progress, and retrieve outputs without managing Batch configuration manually.

Architecture & flow

Explore how data flows through the system, how runs progress, and how BYOC differs from managed deployment.

In BYOC mode, all compute and data remains inside the customer AWS boundary.

BYOC vs Managed

In BYOC (Bring Your Own Cloud) mode, pipelines run inside your AWS account. Data stays in your S3 buckets. SeqFlux does not require moving sequencing data to a third-party platform.

IAM permissions are scoped using least privilege.
SeqFlux communicates with your environment through controlled APIs and queues.

This architecture allows teams to adopt SeqFlux without changing existing security, compliance, or data residency policies.

Choose how you deploy. Both options use the same product — the deployment model is the only difference.

BYOC	Managed
Data remains in your AWS account. Full ownership.	SeqFlux hosts infrastructure in our AWS account.
Compute billed directly by AWS. Use your Enterprise Discount Program (EDP) if you have one.	Single platform fee covers compute. Simpler billing.
IAM scoped to least privilege. No cross-account access.	Fast onboarding — no Terraform required.
Ideal for regulated environments (pharma, biotech).	Early-access only. Limited availability.
Required: AWS account and VPC.	No AWS account required to start.

BYOC is the recommended path for any team with data residency, compliance, or AWS Enterprise Discount Program requirements. Managed is the fastest way to evaluate SeqFlux.

Built-in controls, by default

SeqFlux enforces operational guardrails so pipelines run safely in the cloud.

Hard max vCPU cap

Enforced resource limits prevent runaway compute jobs and cost overruns.

Spot-first compute

Cost control through Spot instances. Configurable for dev environments.

3-hour job timeout

Prevents orphaned long-running jobs and surprise bills.

S3 lifecycle retention

Configurable retention. Keeps storage costs predictable.

Immutable pipeline revisions

Full reproducibility. Each run records exact pipeline version and configuration.

Run manifests

Operational visibility. Every run produces a manifest with inputs, parameters, and outputs.

Who it's for

SeqFlux is infrastructure for teams already running pipelines. Not a general bioinformatics tool — built for teams that use or plan to use Nextflow and do not want to maintain the surrounding cloud infrastructure themselves.

Bioinformatics teams. Computational biology groups. Platform/DevOps teams supporting R&D.

Head of Bioinformatics

Owns pipeline infrastructure decisions. Evaluates tools for the team. Cares about reproducibility and compliance.

Computational Biology Lead

Runs nf-core workflows daily. Frustrated by infra overhead. Wants to focus on analysis, not AWS config.

Platform / DevOps (R&D)

Responsible for cloud cost, security, and reliability of compute. Needs guardrails and visibility.

VP R&D

Budget authority. Needs BYOC and reproducibility story for compliance and audit.

CTO at biotech startup

Evaluating platforms. Cares about speed to value, cost, and avoiding vendor lock-in.

Frequently Asked Questions

Why not just use Nextflow directly?

Nextflow defines pipelines. SeqFlux operates them in the cloud. Nextflow handles workflow execution. SeqFlux handles the infrastructure around it — provisioning, configuration, monitoring, artifact tracking, and cloud guardrails.

Does data leave our AWS account?

In BYOC mode, no. Your FASTQ files, sample sheets, pipeline outputs, and MultiQC reports all stay in your S3 buckets. SeqFlux only communicates via SQS (to dispatch run requests) and HTTPS callbacks (for status updates). The control plane stores workspace metadata and run records, but never accesses your pipeline data.

Which workflows are supported?

nf-core/rnaseq is available at launch with pinned revision 3.19.0. Additional templates (sarek, atacseq, etc.) will be added based on demand. Submit a request via the early access form if you have a specific workflow in mind.

Is Spot instance use required?

Yes in the POC. Spot-only is a guardrail-driven cost control — it keeps compute costs predictable and prevents runaway spend. Spot interruptions are handled by Nextflow's retry logic. Configurable in enterprise deployments for teams that need on-demand capacity.

What about compliance?

SeqFlux is built with reproducibility and auditability in mind. Every run produces an immutable manifest with template hash, compute config, and timestamps. SOC 2 Type I is on the roadmap. BYOC supports existing compliance postures (e.g., pharma, post-acquisition biotech) without requiring data egress from your environment.

Who should use SeqFlux?

Bioinformatics teams, computational biology groups, and platform/DevOps teams supporting R&D. SeqFlux is infrastructure for teams already running pipelines who want operational control without maintaining custom tooling around Nextflow.

What stage is the product in?

SeqFlux is currently in early access with a small group of design partners. We're looking for teams with real workflow needs who want to help shape the product.

Request Early Access

We're onboarding a small group of design partners running real pipelines in the cloud.

If your team is running pipelines in the cloud and wants to help shape SeqFlux, tell us about your environment.