Secrets

Secrets store the keys and tokens used by workflow tasks to interact with external systems, such as a password to connect to an external database or an API token. Seqera Platform relies on third-party secret manager services to maintain security between the workflow execution context and the secret container. This means that no secure data is transmitted from your Seqera instance to the compute environment.

AWS, Google Cloud, and HPC compute environments are currently supported. See AWS Secrets Manager and Google Secret Manager for more information.

Pipeline secrets

To create a pipeline secret, go to a workspace (private or shared) and select the Secrets tab in the navigation bar. Available secrets are listed here and users with appropriate permissions (maintainer, admin, or owner) can create or update secret values.

Multi-line secrets must be base64-encoded.

Select Add Pipeline Secret and enter a name and value for the secret. Then select Add.

User secrets

Listing, creating, and updating secrets for users is the same as secrets in a workspace. You can access user secrets from Your secrets in the user menu.

Secrets defined by a user have higher priority and will override any secrets with the same name defined in a workspace.

Use secrets in workflows

When you launch a new workflow, all secrets are sent to the corresponding secrets manager for the compute environment. Nextflow downloads these secrets internally when they're referenced in the pipeline code. See Nextflow secrets for more information.

Secrets are automatically deleted from the secret manager when the pipeline completes, successfully or unsuccessfully.

In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a custom job definition.

AWS Secrets Manager integration

Seqera and associated AWS Batch IAM Roles require additional permissions to interact with AWS Secrets Manager.

Seqera instance permissions

Augment the existing instance permissions with this policy:

IAM Permissions

Augment the permissions given to Seqera with the following Sid:

    {
        "Version": "2012-10-17",
        "Statement": [
            {
                "Sid": "AllowTowerEnterpriseSecrets",
                "Effect": "Allow",
                "Action": [
                    "secretsmanager:DeleteSecret",
                    "secretsmanager:ListSecrets",
                    "secretsmanager:CreateSecret"
                ],
                "Resource": "*"
            }
        ]
    }

ECS Agent permissions

The ECS Agent uses the Batch Execution role to communicate with AWS Secrets Manager.

• If your AWS Batch compute environment does not have an assigned execution role, create one.
• If your AWS Batch compute environment already has an assigned execution role, augment it.

IAM permissions

1. Add the AmazonECSTaskExecutionRolePolicy managed policy.
2. Add this inline policy (specifying <YOUR_COMPUTE_REGION>):

    {
        "Version": "2012-10-17",
        "Statement": [
            {
                "Sid": "AllowECSAgentToRetrieveSecrets",
                "Effect": "Allow",
                "Action": "secretsmanager:GetSecretValue",
                "Resource": "arn:aws:secretsmanager:<YOUR_COMPUTE_REGION>:*:secret:tower-*"
        }
      ]
    }

Including tower-* in the Resource ARN above limits access to Platform secrets only (as opposed to all secrets in the given region).

IAM trust relationship

    {
        "Version": "2012-10-17",
        "Statement": [
            {
                "Sid": "AllowECSTaskAssumption",
                "Effect": "Allow",
                "Principal": {
                    "Service": "ecs-tasks.amazonaws.com"
                },
                "Action": "sts:AssumeRole"
            }
        ]
    }

Compute permissions

The Nextflow head job must communicate with AWS Secrets Manager. Its permissions are inherited either from a custom role assigned during the AWS Batch CE creation process, or from its host EC2 instance.

Augment your Nextflow head job permissions source with one of the following policies:

EC2 Instance role

Add this policy to your EC2 Instance role:

    {
        "Version": "2012-10-17",
        "Statement": [
            {
                "Sid": "AllowNextflowHeadJobToAccessSecrets",
                "Effect": "Allow",
                "Action": "secretsmanager:ListSecrets",
                "Resource": "*"
            }
        ]
    }

Custom IAM role

Add this policy to your custom IAM role (specifying YOUR_ACCOUNT and YOUR_BATCH_CLUSTER):

        {
            "Version": "2012-10-17",
            "Statement": [
                {
                    "Sid": "AllowNextflowHeadJobToAccessSecrets",
                    "Effect": "Allow",
                    "Action": "secretsmanager:ListSecrets",
                    "Resource": "*"
                },
                {
                    "Sid": "AllowNextflowHeadJobToPassRoles",
                    "Effect": "Allow",
                    "Action": [
                        "iam:GetRole",
                        "iam:PassRole"
                    ],
                    "Resource": "arn:aws:iam::YOUR_ACCOUNT:role/YOUR_BATCH_CLUSTER-ExecutionRole"
                }
            ]
        }

Add this trust policy to your custom IAM role:

        {
            "Version": "2012-10-17",
            "Statement": [
                {
                    "Sid": "AllowECSTaskAssumption",
                    "Effect": "Allow",
                    "Principal": {
                        "Service": "ecs-tasks.amazonaws.com"
                    },
                    "Action": "sts:AssumeRole"
                }
            ]
        }

Google Secret Manager integration

You must enable Google Secret Manager in the same project that your Google compute environment credentials have access to. Your compute environment credentials require additional IAM permissions to interact with Google Secret Manager.

IAM permissions

See the Google documentation for permission configuration instructions to integrate with Google Secret Manager.

Seqera Platform requires roles/secretmanager.admin permissions in the project where it will manage your secrets. Ensure that your compute environment contains credentials with this access role for the same project_id listed in the service account JSON file.