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Co-Scientist in the Seqera CLI

Co-Scientist combines self-service bioinformatics, interactive intelligence, and autonomous execution into one unified experience.

You can use the Seqera CLI to build, run, and manage bioinformatics workflows in an interactive terminal experience for working with Nextflow pipelines and Seqera Platform.

Co-Scientist has access to:

  • Your Seqera Platform workspace: View and manage workflows, pipelines, and data through your authenticated account
  • Your local environment: Execute commands and edit files in your working directory (with configurable approval controls)
  • AI capabilities: Natural language understanding, code generation, and intelligent suggestions

Co-Scientist features​

Skills​

Co-Scientist supports reusable skills for common workflows. Backend skills are exposed as slash commands in the / command palette and /help, and project or user SKILL.md files are discovered automatically from standard skill directories.

Natural language interface​

Interact with Seqera Platform using plain English. Ask questions, launch workflows, and manage pipelines through conversational commands.

Build and plan modes​

Switch between build and plan modes during an interactive session with Shift+Tab. Build mode is the default for execution and file changes, while plan mode is optimized for analysis, implementation planning, and read-only investigation.

Goal mode​

Use /goal <task> to set a persistent goal. Co-Scientist will keep working toward that goal across multiple model attempts until it is complete or the goal attempt limit is reached.

Workflow management​

Launch, monitor, and debug Nextflow workflows directly from your terminal. Get real-time status updates, view logs, and analyze run metrics.

Pipeline development​

Generate Nextflow configurations, create pipeline schemas, and convert scripts from other workflow languages (WDL, R) to Nextflow.

nf-core integration​

Search and discover nf-core modules, get detailed execution information, and access ready-to-run Nextflow commands for over 1,000 standardized bioinformatics tools.

Data management​

Browse cloud storage through data links, manage datasets, generate download and upload URLs, and access reference genomes and sequencing data.

Wave containers​

Build containerized environments on-the-fly with conda packages, pip packages, or custom Docker images. Create reproducible containers for your bioinformatics tools without writing Dockerfiles.

Local file operations​

Edit files, run commands, and manage your local development environment with AI assistance and configurable approval modes.

LSP code intelligence​

Real-time error detection and AI-powered code navigation for Nextflow, Python, and R files in your workspace.

Session management​

Resume previous sessions to continue your work. Use seqera ai -c to continue your most recent session or seqera ai -s <id> to resume a specific session.

Seqera Platform integration​

Full access to Platform capabilities including compute environments, datasets, data links, and workspace management.

Projects​

Organize a workspace into projects by applying Seqera Platform labels prefixed with project_. Each project scopes the pipelines, datasets, workflow runs, and chat context the AI sees — without needing a separate CRUD surface in Co-Scientist.

Learn more​

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