docs(seqera-ai): align Enterprise Co-Scientist docs for 26.1 #1381
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| --- | ||||||
| title: "Command approval" | ||||||
| description: "Control which local commands require user approval in Co-Scientist" | ||||||
| date created: "2025-12-15" | ||||||
| tags: [seqera-ai, co-scientist, cli, approval, security] | ||||||
| --- | ||||||
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| Co-Scientist can execute local commands and edit files in your environment. This page explains approval modes that control which operations run automatically versus which require your permission, including dangerous commands, workspace boundaries, and best practices. | ||||||
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| :::info | ||||||
| Starting a persistent task with `/goal <task>` switches the session to `full` approval mode automatically so Co-Scientist can continue working without repeated prompts. | ||||||
| ::: | ||||||
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| ## Approval prompts | ||||||
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| When a command requires approval, you will see a prompt similar to: | ||||||
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| ## Approval modes | ||||||
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| Approval modes control which local commands Co-Scientist can execute automatically and which require your explicit approval. This provides a balance between convenience and safety when working with local files and commands. | ||||||
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| There are three approval modes: | ||||||
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| ## Learn more | ||||||
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| - [Co-Scientist CLI](index.md): Co-Scientist CLI overview | ||||||
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| - [Installation](./installation): Detailed installation instructions | ||||||
| - [Authentication](./authentication): Log in, log out, and session management | ||||||
| - [Use cases](./use-cases.md): Co-Scientist use cases | ||||||
| - [Usage and cost](./usage-and-cost.md): Co-Scientist usage in Enterprise deployments | ||||||
| - [Troubleshooting](../troubleshooting_and_faqs/seqera-ai.md): Troubleshoot common errors | ||||||
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| --- | ||||||
| title: "Get started" | ||||||
| description: "AI-powered assistant for bioinformatics workflows and Seqera Platform" | ||||||
| date created: "2026-03-11" | ||||||
| tags: [seqera-ai, co-scientist, cli, ai] | ||||||
| --- | ||||||
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| ## Get started | ||||||
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| To get started with Co-Scientist: | ||||||
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| 1. Install the Co-Scientist CLI: | ||||||
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| ```bash | ||||||
| npm install -g seqera | ||||||
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| See [Authentication](./authentication.md) for a comprehensive authentication guide. | ||||||
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| For Enterprise deployments, set `SEQERA_AI_BACKEND_URL` to your organization's agent backend before you start Co-Scientist. Your administrator should provide this URL; it maps to `global.agentBackendDomain` in the [Seqera AI install guide](../enterprise/install-seqera-ai.md). See [Authentication](./authentication.md#connect-to-an-enterprise-backend) for the full environment variable reference. | ||||||
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| 1. Start Co-Scientist: | ||||||
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| ```bash | ||||||
| seqera ai | ||||||
| ``` | ||||||
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| 1. Open the command palette and review the available built-in commands and skills: | ||||||
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| ``` | ||||||
| /help | ||||||
| ``` | ||||||
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| You can also type `/` to open command autocomplete. | ||||||
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| 1. Try build mode and plan mode: | ||||||
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| - Press `Shift+Tab` to switch between **build** and **plan** | ||||||
| - Check the current mode in the composer footer | ||||||
| - Run `/status` if you want a full status readout | ||||||
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| Example plan-mode prompt: | ||||||
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| ``` | ||||||
| Compare whether I should add FastQC or fastp as the first QC step in this RNA-seq pipeline, including the workflow changes each option would require | ||||||
| ``` | ||||||
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| 1. Run your first workflow-focused prompt: | ||||||
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| ``` | ||||||
| /debug-last-run-on-seqera | ||||||
| ``` | ||||||
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| 1. Try goal mode for a longer task: | ||||||
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| ``` | ||||||
| /goal update this pipeline for AWS Batch and add nf-tests | ||||||
| ``` | ||||||
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| See [Use cases](./use-cases.md) for more examples. | ||||||
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| ## Learn more | ||||||
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| - [Installation](./installation.mdx): Detailed installation instructions | ||||||
| - [Authentication](./authentication.md): Log in, log out, and session management | ||||||
| - [Skills](./skills.md): Discover, create, and install skills | ||||||
| - [Modes](./modes.md): Work in build mode, plan mode, and goal mode | ||||||
| - [Command approval](./command-approval.md): Control which commands run automatically | ||||||
| - [Use cases](./use-cases.md): Co-Scientist CLI use cases | ||||||
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| - [Usage and cost](./usage-and-cost.md): Co-Scientist usage in Enterprise deployments | ||||||
| - [Troubleshooting](../troubleshooting_and_faqs/seqera-ai.md): Troubleshoot common errors | ||||||
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,39 +1,48 @@ | ||
| --- | ||
| title: "Co-Scientist in the Seqera CLI" | ||
| description: "AI-powered assistant for bioinformatics workflows and Seqera Platform" | ||
| date created: "2026-03-11" | ||
| last updated: "2026-04-29" | ||
| tags: [seqera-ai, co-scientist, cli, ai] | ||
| --- | ||
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| Co-Scientist combines self-service bioinformatics, interactive intelligence, and autonomous execution into one unified experience. | ||
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| 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. | ||
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| Co-Scientist has access to: | ||
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| - **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 | ||
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| Co-Scientist can load local project context, including instruction files such as `AGENTS.md`, `CLAUDE.md`, and `CONTEXT.md`, project skills, and files under `.seqera/docs` and `.seqera/memory`. Review local context files before starting a session in a repository that contains sensitive instructions or private run history. | ||
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| ## Co-Scientist features | ||
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| ### Skills | ||
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| 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. | ||
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| ### Natural language interface | ||
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| Interact with Seqera Platform using plain English. Ask questions, launch workflows, and manage pipelines through conversational commands. | ||
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| ### Build and plan modes | ||
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| 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. | ||
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| ### Goal mode | ||
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| 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. | ||
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| ### Workflow management | ||
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| Launch, monitor, and debug Nextflow workflows directly from your terminal. Get real-time status updates, view logs, and analyze run metrics. | ||
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| ### Pipeline development | ||
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| Generate Nextflow configurations, create pipeline schemas, and convert scripts from other workflow languages (WDL, R) to Nextflow. | ||
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| ### nf-core integration | ||
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| ### Projects | ||
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| 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. | ||
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| ## Learn more | ||
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| - [Installation](./installation.mdx): Detailed installation instructions | ||
| - [Authentication](./authentication.md): Log in, log out, and session management | ||
| - [Skills](./skills.md): Discover, create, and install skills | ||
| - [Modes](./modes.md): Work in build mode, plan mode, and goal mode | ||
| - [Command approval](./command-approval.md): Control which commands run automatically | ||
| - [Working with Claude Code](./skill-claude-code.md): Install Co-Scientist as a skill for Claude Code | ||
| - [Working with Codex](./skill-codex.md): Install Co-Scientist as a skill for Codex | ||
| - [Working with GitHub Copilot](./skill-github-copilot.md): Install Co-Scientist as a skill for GitHub Copilot | ||
| - [Working with other coding agents](./skill-other-agents.md): Install Co-Scientist for other coding agents | ||
| - [Code intelligence](./nextflow-lsp.md): Language-server support in Co-Scientist | ||
| - [Use cases](./use-cases.md): Seqera CLI use cases | ||
| - [Projects](./projects.md): Organize workspace resources into projects using Platform labels | ||
| - [Usage and cost](./usage-and-cost.md): Co-Scientist usage in Enterprise deployments | ||
| - [Troubleshooting](../troubleshooting_and_faqs/seqera-ai.md): Troubleshoot common errors | ||
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