Connect Seqera to AI agents

Connect Seqera to Claude, Codex, Cursor, or other AI agents for your entire team. Metorial security, governance, observability, and gives your team a unified Magic MCP url to connect.

Supported Tools

list_workflows

List Workflow Runs

List workflow runs (pipeline executions) in a workspace. Returns run status, duration, metadata, and basic execution details. Supports search, pagination, and sorting.

list_credentials

List Credentials

List credentials stored in a workspace. Credentials are encrypted access keys for compute environments, code repositories, and external services. Does not expose credential values.

create_pipeline

Create Pipeline

Create a new pre-configured pipeline in the workspace. A pipeline bundles a workflow repository with a compute environment and launch parameters for easy repeated execution.

list_compute_envs

List Compute Environments

List compute environments in a workspace. Compute environments define the execution platform (AWS Batch, Google Cloud, Azure, Kubernetes, etc.) where pipelines run.

get_workflow

Get Workflow Run

Get detailed information about a specific workflow run, including execution status, progress, metrics, and task-level details. Optionally includes the list of tasks and execution log.

list_participants

List Workspace Participants

List participants (users and teams) with access to the current workspace. Shows role assignments and membership details for access control management.

launch_workflow

Launch Workflow

Launch a new Nextflow workflow run. Can launch from a pipeline repository URL directly or use a pre-configured pipeline's compute environment and settings. Returns the workflow run ID for monitoring.

manage_compute_env

Manage Compute Environment

Get details about, set as primary, or delete a compute environment. Use **action** to specify the operation to perform.

list_organizations

List Organizations

List organizations accessible to the authenticated user. Organizations are top-level entities containing workspaces, teams, and members.

list_datasets

List Datasets

List datasets in a workspace. Datasets are versioned CSV/TSV samplesheets used as pipeline inputs. Supports searching by name and pagination.

cancel_workflow

Cancel Workflow

Cancel an active workflow run. Only running or submitted workflows can be cancelled.

manage_dataset

Manage Dataset

Create, update, delete, or upload a new version to a dataset. Datasets are versioned, structured data (CSV/TSV samplesheets) used as pipeline inputs.

get_pipeline

Get Pipeline

Get detailed information about a specific pipeline, including its repository, compute environment, launch configuration, and labels.

manage_labels

Manage Resource Labels

List, create, update, or delete resource labels. Labels are used to tag pipelines, workflow runs, and compute environments for cost tracking and organizational purposes across teams and workspaces.

list_workspaces

List Workspaces

List workspaces in an organization. Workspaces contain pipelines, compute environments, credentials, runs, and datasets. Each workspace has its own access controls and resource isolation.

manage_actions

Manage Pipeline Actions

List, describe, trigger, pause, or delete pipeline actions. Actions enable event-based pipeline execution via GitHub webhooks or Tower launch hooks. Triggering an action launches its pre-configured pipeline.

list_pipelines

List Pipelines

List pre-configured pipelines in a Seqera workspace. Supports searching by name, pagination, and sorting. Returns pipeline configuration details including repository, compute environment, and labels.

manage_secrets

Manage Pipeline Secrets

List, create, update, or delete pipeline secrets. Secrets are secure keys used by workflow tasks to interact with external systems (e.g., database passwords, API tokens). Secrets are available to workflows launched in the workspace.

More integrations teams use with Seqera

Linear

Create, read, update, and delete issues across teams with support for priorities, labels, assignees, due dates, and workflow states. Manage projects that group related issues, and organize work into time-boxed cycles (sprints). Create and manage documents, comments, and file attachments. Search issues using vector similarity or rich filters. Configure teams, workflow states, and labels. Track customers and link them to issues. Subscribe to real-time webhooks for changes to issues, projects, cycles, comments, documents, and more.

GitHub

Manage repositories, issues, and pull requests. Create and configure branches, star repositories, review code, and merge changes. Automate CI/CD workflows with GitHub Actions, manage workflow runs, secrets, and artifacts. Track issues with labels, milestones, and assignees. Search across code, repositories, issues, and users. Manage organizations, teams, and memberships. Create and manage projects, gists, packages, deployments, and environments. Access security alerts including code scanning, secret scanning, and Dependabot alerts. Read and write file contents in repositories. Manage webhooks, notifications, and codespaces.

Sharepoint

Manage SharePoint sites, document libraries, lists, and files. Create, read, update, and delete lists and list items with custom columns. Upload, download, move, copy, and version files in document libraries. Search across sites, files, folders, lists, and list items using Microsoft Search. Manage permissions at site, list, and item levels with granular access control. Define and manage content types and site columns. Subscribe to webhooks for list and library change notifications. Retrieve site properties and search for sites across Microsoft 365.

Salesforce

Manage CRM data including Accounts, Contacts, Leads, Opportunities, Cases, and custom objects. Create, read, update, and delete records. Query data using SOQL and search across objects using SOSL. Perform bulk data operations for large-scale imports, exports, and migrations. Execute composite requests to batch multiple operations in a single API call. Access analytics, reports, and dashboards. Manage files and attachments associated with records. Interact with Chatter feeds, posts, and groups for social collaboration. Subscribe to real-time change events via Change Data Capture and Platform Events. Manage org metadata including custom objects, fields, layouts, and workflows. Query data using GraphQL for precise data retrieval across related objects.

Microsoft Outlook

Send, read, reply to, forward, and manage email messages in user mailboxes. Organize messages into folders, apply categories, flags, and importance levels. Manage file and item attachments. Create, update, delete, and respond to calendar events and meetings. Find available meeting times, manage attendees, handle recurrence, and work with shared or delegated calendars. Create, read, update, and delete contacts, organize them into contact folders, and manage contact photos. Manage tasks and task lists via Microsoft To Do, including due dates, reminders, recurrence, and checklist items. Subscribe to webhook notifications for changes to messages, calendar events, and contacts. Support for Focused Inbox, @-mentions, mail tips, send-on-behalf, and send-as capabilities.

Airtable

Create, read, update, and delete records in Airtable bases and tables. Manage base schemas including creating tables and fields. Filter records using formulas, sort by fields, and scope queries to specific views. Upsert records to find, create, or update in a single call. Upload attachments to records, read and write record comments, list accessible bases, and receive real-time base change events through webhooks.

Technical notes for Seqera

Manage and orchestrate Nextflow data pipelines across cloud and on-premises environments. Launch, monitor, and cancel workflow runs with detailed task-level status, resource metrics, and execution logs. Create and configure compute environments for AWS Batch, Google Cloud, Azure, and Kubernetes. Manage pipelines, datasets (CSV/TSV samplesheets), credentials, and pipeline secrets within workspaces. Organize resources across organizations, workspaces, and teams with role-based access control. Set up automated pipeline triggers via GitHub webhooks or custom launch hooks. Create and manage interactive Studio sessions (Jupyter, RStudio, VS Code). Browse cloud storage and data links through Data Explorer. Apply resource labels for cost tracking and organization. Manage API access tokens programmatically.

Connect Seqera to production AI agents

See how Metorial gives Seqera access the governance, tracing, and security controls teams need.

Frequently asked questions

Common questions about connecting Seqera to AI agents with Metorial.

  1. Can Metorial connect Seqera to AI agents?
    Yes. Metorial connects AI agents to Seqera through a governed integration layer, so teams can use the provider while keeping access controlled and observable.
  2. Metorial is MCP compatible and lets teams expose approved provider tools to MCP-capable agents and clients through a controlled access layer.
  3. Metorial applies policies across users, groups, providers, agents, and individual tools, then records the context around every agent interaction.
  4. Yes. Metorial records provider activity so teams can inspect tool calls, troubleshoot integrations, and give security teams the visibility they need.