Seqera AI Enterprise deployment docs

.pre-commit-config.yaml

@@ -9,4 +9,4 @@ repos:
   - id: check-yaml
     args:
       - --allow-multiple-documents
-  - id: check-added-large-files
+#  - id: check-added-large-files

docusaurus.config.js

@@ -232,12 +232,13 @@ export default async function createConfigAsync() {
     onBrokenAnchors:
       process.env.FAIL_ON_BROKEN_LINKS === "true" ? "throw" : "warn",
 
-    markdown: {
-      hooks: {
-        onBrokenMarkdownLinks:
-          process.env.FAIL_ON_BROKEN_LINKS === "true" ? "throw" : "warn",
-      },
-    },
+    // TODO: markdown.hooks not supported in Docusaurus 3.8.1 - upgrade Docusaurus or remove
+    // markdown: {
+    //   hooks: {
+    //     onBrokenMarkdownLinks:
+    //       process.env.FAIL_ON_BROKEN_LINKS === "true" ? "throw" : "warn",
+    //   },
+    // },
 
     customFields: {
       // Put your custom environment here

netlify.toml

@@ -15,6 +15,8 @@
 
 [context.deploy-preview.build.environment]
   INCLUDE_NEXT="true"
+  EXCLUDE_PLATFORM_API="true"
+  EXCLUDE_PLATFORM_OPENAPI="true"
 
 # Seqera API docs are too large to host / build on netlify on their own.
 # The appropriate ENVVAR is set to disable the API Builds on Netlify for the main docs site.

platform-cloud/cloud-sidebar.json

@@ -125,6 +125,19 @@
           "launch/advanced"
         ]
       },
+     {
+      "type": "category",
+      "label": "Seqera AI CLI",
+      "link": {"type": "doc", "id": "seqera-ai/index"},
+      "collapsed": true,
+      "items": [
+        "seqera-ai/get-started",
+        "seqera-ai/installation",
+        "seqera-ai/authentication",
+        "seqera-ai/command-approval",
+        "seqera-ai/use-cases"
+      ]
+    },
      {
         "type": "category",
         "label": "Studios",
@@ -158,19 +171,6 @@
           "administration/credit-management"
           ]
       },
-     {
-      "type": "category",
-      "label": "Seqera AI CLI",
-      "link": {"type": "doc", "id": "seqera-ai/index"},
-      "collapsed": true,
-      "items": [
-        "seqera-ai/get-started",
-        "seqera-ai/installation",
-        "seqera-ai/authentication",
-        "seqera-ai/command-approval",
-        "seqera-ai/use-cases"
-      ]
-    },
       {
         "type": "category",
         "label": "Developer tools",

platform-cloud/docs/seqera-ai/authentication.md

@@ -33,46 +33,34 @@ This will:
 1. Display a success message in your terminal
 
    ```
-   Opening browser for authentication...
-   Successfully authenticated as user@example.com
+   [Login] Starting Seqera CLI authentication...
+   [Login] ✓ Authentication successful!
+   [Login] ✓ Organization set: <org_name>
    ```
 
 ### View session status
 
-To view your current authentication status, run:
+To view your current session status, use the `/status` command inside the TUI:
 
-```bash
-seqera status
 ```
-
-You should see output similar to:
-
-```console
-Logged in as: user@example.com
-Session expires: 2025-12-16 14:30:00
+/status
 ```
 
-### Add access tokens for automation
-
-For automated environments, you can provide a Seqera Platform access token directly:
+This shows your authentication status and organization details.
 
-```bash
-seqera ai --token <PLATFORM_ACCESS_TOKEN>
-```
+### Add access tokens for automation
 
-You can also set the token via environment variable:
+For automated environments, you can provide a Seqera Platform access token directly using the `SEQERA_ACCESS_TOKEN` environment variable:
 
 ```bash
-export TOWER_ACCESS_TOKEN=<PLATFORM_ACCESS_TOKEN>
+export SEQERA_ACCESS_TOKEN=<PLATFORM_ACCESS_TOKEN>
 seqera ai
 ```
 
-This shows your login status, authenticated email, and session details.
+When this environment variable is set, the CLI skips the OAuth login flow and uses the provided token directly.
 
 ### Log out
 
-#### Standard logout
-
 To sign out from the current session, run:
 
 ```bash
@@ -81,15 +69,33 @@ seqera logout
 
 This command revokes your current authentication token and removes locally stored credentials. You will need to re-authenticate on next use.
 
-#### Clear all sessions
+## Organization management
 
-To remove all profiles and completely reset authentication, run:
+Seqera AI CLI supports managing your organization selection for billing. Use the `seqera org` command to view and switch organizations.
+
+**View current organization**:
 
 ```bash
-seqera logout --all
+seqera org
 ```
 
-This command removes all stored credentials and session data.
+**List all organizations**:
+
+```bash
+seqera org list
+```
+
+**Switch organization**:
+
+```bash
+seqera org switch
+```
+
+**Clear organization selection**:
+
+```bash
+seqera org clear
+```
 
 ## Token refresh
 

platform-cloud/docs/seqera-ai/command-approval.md

@@ -17,27 +17,24 @@ Seqera AI can execute local commands and edit files in your environment. This pa
 
 ## Approval prompts
 
-When a command requires approval, you will see output similar to:
+When a command requires approval, you will see a prompt similar to:
 
 ```
-⚠ Approval required (default mode)
+APPROVAL REQUIRED (default mode)
+Command: rm -rf ./build/
 
-╭──────────────────────────────────────╮
-│ rm -rf ./build/                      │
-╰──────────────────────────────────────╯
+[1] Yes, approve this command
+[2] Always approve this session
+[3] No, reject
 
-  1 Yes, run this command
-  2 Yes, and don't ask again this session
-  3 No, cancel and stop
-
-Select [1/2/3]:
+Press 1, 2, or 3 to choose
 ```
 
 You can:
 
-- **1**: Run the command as shown
-- **2**: Run the command and switch to `full` approval mode for the rest of the session
-- **3**: Cancel the command and stop the current operation
+- **1**: Run the command once (or press Enter)
+- **2**: Run the command and auto-approve all commands for the rest of the session
+- **3**: Reject the command (or press Escape)
 
 ## Approval modes
 
@@ -51,6 +48,18 @@ There are three approval modes:
 | **default** | Safe commands and workspace file edits run automatically | Typical development |
 | **full** | Everything except dangerous commands runs automatically | Experienced users |
 
+You can set the approval mode when starting the CLI:
+
+```bash
+seqera ai --approval-mode full
+```
+
+Or change it during a session using the `/approval` TUI command:
+
+```
+/approval basic
+```
+
 ### Basic
 
 **Rule**: Only safe, read-only commands run automatically. Everything else requires approval.
@@ -82,17 +91,12 @@ This is the most restrictive mode. The assistant can only auto-execute commands
 ```
 > Create a new file called test.txt with "hello world"
 
-⚠ Approval required (basic mode)
-
-╭──────────────────────────────────────╮
-│ Write ./test.txt                     │
-╰──────────────────────────────────────╯
+APPROVAL REQUIRED (basic mode)
+Command: Write ./test.txt
 
-  1 Yes, run this command
-  2 Yes, and don't ask again this session
-  3 No, cancel and stop
-
-Select [1/2/3]:
+[1] Yes, approve this command
+[2] Always approve this session
+[3] No, reject
 ```
 
 ### Default
@@ -131,17 +135,12 @@ File creation in the workspace runs automatically.
 ```
 > Edit /etc/hosts
 
-⚠ Approval required (default mode)
-
-╭──────────────────────────────────────╮
-│ Edit /etc/hosts                      │
-╰──────────────────────────────────────╯
+APPROVAL REQUIRED (default mode)
+Command: Edit /etc/hosts
 
-  1 Yes, run this command
-  2 Yes, and don't ask again this session
-  3 No, cancel and stop
-
-Select [1/2/3]:
+[1] Yes, approve this command
+[2] Always approve this session
+[3] No, reject
 ```
 
 Editing outside the workspace requires approval.
@@ -194,17 +193,12 @@ Most operations run without prompts.
 ```
 > Delete the build directory
 
-⚠ Approval required (full mode)
-
-╭──────────────────────────────────────╮
-│ rm -rf ./build/                      │
-╰──────────────────────────────────────╯
+APPROVAL REQUIRED (full mode)
+Command: rm -rf ./build/
 
-  1 Yes, run this command
-  2 Yes, and don't ask again this session
-  3 No, cancel and stop
-
-Select [1/2/3]:
+[1] Yes, approve this command
+[2] Always approve this session
+[3] No, reject
 ```
 
 Dangerous commands still require approval.
@@ -216,15 +210,12 @@ In **default** mode, the "workspace" is your current working directory and its s
 - **Inside workspace**: `/path/to/workspace/src/file.txt` - auto-executes
 - **Outside workspace**: `/etc/config` or `~/other-project/file.txt` - requires approval
 
-The workspace is set when you start the assistant:
+The workspace is set to your current directory when you start the CLI:
 
 ```bash
 # Workspace is /home/user/my-project
 cd /home/user/my-project
 seqera ai
-
-# Or explicitly set the workspace
-seqera ai -w /home/user/my-project
 ```
 
 ## Best practices

platform-cloud/docs/seqera-ai/get-started.md

@@ -20,7 +20,7 @@ To get started with Seqera AI:
 1. Install the Seqera AI CLI:
 
     ```bash
-    pip install seqera
+    npm install -g seqera
     ```
 
     See [Installation](./installation.mdx) for a comprehensive installation guide.
@@ -40,6 +40,12 @@ To get started with Seqera AI:
     seqera ai
     ```
 
+    You can also start with an initial query:
+
+    ```bash
+    seqera ai "list my pipelines"
+    ```
+
 1. Run your first prompt:
 
     ```

platform-cloud/docs/seqera-ai/index.md

@@ -51,6 +51,14 @@ Build containerized environments on-the-fly with conda packages, pip packages, o
 
 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.