Build, Launch, Automate: Scaling Enterprise Bioinformatics with Seqera Co-Scientist

Seqera Co-Scientist is the collaborative agent that brings the power of Seqera’s secure, reproducible engine to every scientist. Developed for bioinformatics, Co-Scientist understands scientific context, reasons with you, and executes with intelligence. Last month, we hosted a webinar showing exactly what that means in practice, covering how Co-Scientist helps teams:

• →Build: Developers write, debug, and optimize pipelines.
• →Launch: Scientists execute, explore, and understand results.
• →Automate: Agents that run, fix, and improve pipelines on their own.

Why Co-Scientist, Why Now?

AI is changing the pace of science. Agents propose more experiments, more analyses, more iterations than any team could manually manage. Agents need to run reproducibly on real data and real compute.

Nextflow is the substrate for AI agents, bringing control and traceability to the volume and velocity agentic science demands. Nextflow is the de facto standard for modern bioinformatics because reproducibility and traceability became non-negotiable as data volumes exploded. By early 2025, AI was driving meaningful adoption in scientific teams, with daily Nextflow runs spiking toward 500,000 and the rolling average doubling.

But speed without infrastructure is chaos. This is what drove the decision to build an organizational layer on top. Seqera Platform is the intelligent engine that makes science reproducible, auditable, and production-ready for AI agents. Seqera Co-Scientist is built on this foundation, inheriting the enterprise security and governance that teams depend on. Co-Scientist puts organizations at the forefront of AI-driven bioinformatics, accelerating velocity through automation without sacrificing quality, security, or reproducibility.

Build, Launch, and Automate with Co-Scientist

Co-Scientist can take on the kind of bioinformatics tasks that slow teams down. Unlike general-purpose AI tools, it specializes in Nextflow, nf-core, and the broader bioinformatics ecosystem, giving it the kind of domain context that makes the difference between a suggestion and a correct answer. Co-Scientist is built for enterprise bioinformatics, with deep integration across your data, compute, and internally hosted models, complete visibility across your entire stack, and controls that let you move faster without compromising on reproducibility or security. With Co-Scientist, we're enabling teams to build better pipelines, launch them with confidence, and automate routine tasks that should not require manual intervention.

Build: Write, Debug, and Optimize Pipelines

Co-Scientist helps developers write, debug, and optimize Nextflow pipelines, handling the time-consuming bioinformatics tasks that slow teams down. In this webinar, we demonstrated how Co-Scientist migrated an RNA-seq pipeline written in Bash to Nextflow with high accuracy. The agent iterated autonomously through commits, runs, and output checks across 84 iterations until it achieved identical results.

Co-Scientist is also natively connected to the Nextflow Registry, reaching for nf-core modules first rather than generating code from scratch. This meaningfully reduces hallucination and keeps code quality high. For organizations with their own standards, there’s support for private module registries. Co-Scientist acts as the agent that reviews your codebase, promotes reusable components to that library, and refactors legacy code against it over time. On Seqera's internal benchmarks, Co-Scientist delivers a 20% improvement in code quality against comparable tools, at lower token cost.

For teams already using tools like Claude, Copilot, Cursor, or Codex, Co-Scientist is also accessible via the Seqera MCP, so AI builders can bring Seqera's bioinformatics intelligence and execution layer directly into the agents they are already building.

Launch: Execute, Explore, and Understand Results

Whether you are a developer wanting a tight feedback loop, a bioinformatician running ad-hoc analyses, or a bench scientist who just needs to get a pipeline running, Co-Scientist meets you where you are. There are 3 ways to work: Chat, CLI, scientist view.

Chat - Natural language pipeline runs

A conversational interface for ad-hoc pipeline runs. Describe what you want to run in plain language and Co-Scientist maps your request to the right pipeline and confirms parameters before launching on Seqera. In the webinar, we showed this with an RNA-seq pipeline (~170 parameters), configured and launched entirely through natural language.

💡 Best for: ad-hoc runs, exploration, and scientists unfamiliar with the command line.

CLI - Interaction from the terminal

With Co-Scientist in the CLI, you can edit code, promote it to a branch, and immediately test changes by launching directly on Seqera Platform in a single loop. In the webinar, we demonstrated this by converting a Snakemake pipeline to Nextflow from the terminal, with Co-Scientist iterating through the conversion autonomously.

💡 Best for: pipeline developers who prefer working from the command line.

Scientist view - Self-service for bench scientists

A simplified interface that removes platform complexity entirely, giving bench scientists three buttons: Launch, Explain, and Fix It. Launch kicks off a pipeline, Explain lets you reason over results with Co-Scientist, and Fix It automatically diagnoses and resolves a failed run. In the webinar, we showed how this enables non-bioinformatics users to self-serve without needing to understand the underlying infrastructure.

💡 Best for: bench scientists, repeatable assay workflows, and lab handoffs.

Automate: Agents that run, fix, and improve pipelines on their own.

The next frontier for Co-Scientist is automation: moving bioinformatics teams away from manual, sample-by-sample science toward a model where external events trigger intelligent responses. New samples arrive, pipelines launch. A run fails, an agent debugs and relaunches. A run completes, Co-Scientist reads the results and surfaces what matters. In the webinar, we previewed how this works through a set of composable triggers and responses:

• →Data arrival: When a sequencer drops a completed run, a deterministic pipeline launch fires automatically on Seqera, with full provenance preserved.
• →Failure recovery: When a pipeline fails, Co-Scientist reads the .nextflow.log, traces the failing process, proposes a fix, and relaunches, escalating to a human only when its confidence threshold or resource budget is hit.
• →Result interpretation: When a run completes, Co-Scientist reads the MultiQC report, generates a summary, flags QC concerns, and posts findings to the team.

Critically, none of this is ungoverned. Agents operate within your existing RBAC permissions, every code change goes through a pull request, and every action is logged. And with Nextflow data lineage now on Seqera, you'll be able to trace any output back through an agent's actions to the exact inputs and code that produced it. Co-Scientist gives you automation without giving up control.

Building for the Future of AI

Seqera Co-Scientist isn't a standalone AI product. It's the agentic layer of a platform that was already built for enterprise science at scale. The auditability, the security, the reproducibility were not retrofitted. They were there from the start. The result is a system that works across an entire organization: bioinformaticians move faster without the operational overhead; scientists run analyses without waiting; and teams building their own AI agents have a secure, governed execution layer to build on. As the AI acceleration continues to compound, the teams that will move fastest are those with infrastructure built to absorb that velocity without losing control. Co-Scientist is built for exactly that moment.