Seqera MCP server

Connect Seqera to Claude, ChatGPT, Cursor, Claude Code, Codex, Gemini, GitHub Copilot and any other MCP client, for your whole team. Metorial adds security, governance, and tracing, and gives everyone one Magic MCP URL to connect.

What you can do with the Seqera MCP server

Ask your agent in plain language. Each of these maps to a real tool on the server.

  • Use the list workflow runs tool in Seqera
  • Use the list credentials tool in Seqera
  • Use the create pipeline tool in Seqera
  • Use the list compute environments tool in Seqera
  • Use the get workflow run tool in Seqera
  • Use the list workspace participants tool in Seqera

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 and pagination.

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.

list_workflow_tasks

List Workflow Tasks

List a page of tasks for a workflow run, with search, process filtering, and sorting. Call list_workspaces to discover workspace IDs when using a workspace context.

get_current_user

Get Current User

Get the authenticated Seqera user and their default workspace ID.

manage_pipeline

Manage Pipeline

Update a saved pipeline configuration or delete a pipeline. Use list_workspaces to discover workspace IDs, then list_pipelines to find pipeline IDs.

Connect Seqera to your AI client

Every client uses the same Magic MCP URL, and so does any other MCP client. Add it once and sign in with SSO.

  1. Enable Seqera in Metorial. In your Metorial portal, enable the Seqera MCP server and sign in with the account that owns the data. Access stays governed by your team policies.
  2. Add a custom connector. Open Customize, then Connectors. Select Add, then Custom, then Web.
  3. Paste your Metorial MCP URL. Name it Metorial, paste your Magic MCP URL (<your-magic-mcp-url>) and continue.
  4. Sign in. Select Add and sign in to load Seqera tools.

Run Seqera through the Metorial gateway

One governed layer for every app your agents reach, not a separate connector per tool.

  • Give Seqera and every other app to your whole team through one MCP gateway, behind your SSO.
  • Scope which teams and agents can use Seqera tools with role-based access control, and trace every call.
  • Prefer to run it yourself? Metorial is open source and self-hostable.

More integrations teams use with Seqera

Notion

Create, read, update, and archive pages and databases in a Notion workspace. Manage blocks (paragraphs, lists, headings, embeds, etc.) within pages. Query databases with filters and sorts across rich property types including text, numbers, dates, selects, relations, and formulas. Search across pages and databases by title. Add and read comments on pages and blocks. Upload files to pages. Manage workspace users and retrieve user profiles.

Google Sheets

Create, read, and update spreadsheets and their cell data. Read and write values to individual cells, ranges, or multiple ranges using A1 notation or named ranges. Apply cell formatting including text styles, backgrounds, borders, number formats, and conditional formatting. Manage sheets (tabs) within a spreadsheet—add, delete, copy, rename, and reorder them. Create and manage embedded charts, pivot tables, filter views, data validation rules, protected ranges, named ranges, and merged cells. Perform batch operations to apply multiple updates atomically.

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.

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. Manage org metadata including custom objects, fields, layouts, and workflows. Query data using GraphQL for precise data retrieval across related objects.

Sharepoint

Manage SharePoint sites, document libraries, lists, and files. Create, read, update, and delete lists and list items with custom columns. Resolve site users to numeric Person/Group LookupId values. 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. Retrieve site properties and search for sites across Microsoft 365.

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. Support for Focused Inbox, @-mentions, mail tips, send-on-behalf, and send-as capabilities.

Technical notes for Seqera

Manage Nextflow pipelines and workflow runs in Seqera Platform. Create, update, and delete saved pipelines; launch, monitor, and cancel runs; inspect task pages and logs; manage datasets, pipeline secrets, and resource labels; discover organizations and workspaces; list credential metadata and inspect compute environments; manage existing pipeline actions; and list workspace participants.

Frequently asked questions

Common questions about connecting Seqera to AI agents with Metorial.

  1. How many tools does the Seqera MCP server have?
    The Seqera MCP server exposes 21 tools, including List Workflow Runs, List Credentials, Create Pipeline. Each one is governed and traced through Metorial.
  2. Seqera exposes tools your agents call on demand; it does not publish event triggers yet. Everything still runs through one governed MCP URL.
  3. Any MCP client, including VS Code, Windsurf, Zed, OpenCode and Grok. Each one reaches the Seqera MCP server through the same Metorial URL.
  4. Use role-based access control to decide which teams, users, and agents can use Seqera and which of its tools they can call.
  5. Yes. Metorial is open source, so you can run the Seqera MCP server yourself or use the hosted gateway.

Connect Seqera to production AI agents

See how Metorial gives your team governed access to Seqera, with tracing and security controls built in.