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Version: 24.1

Git integration

Data pipelines are composed of many assets, including pipeline scripts, configuration files, dependency descriptors (such as for Conda or Docker), documentation, etc. When you manage complex data pipelines as Git repositories, all assets can be versioned and deployed with a specific tag, release, or commit ID. Version control and containerization are crucial to enable reproducible pipeline executions, and provide the ability to continuously test and validate pipelines as the code evolves over time.

Seqera Platform has built-in support for Git and several Git-hosting platforms. Pipelines can be pulled remotely from both public and private Git providers, including the most popular platforms: GitHub, GitLab, and BitBucket.

Public repositories​

Launch a public Nextflow pipeline by entering its Git repository URL in the Pipeline to launch field.

When you specify the Revision number, the list of available revisions are automatically pulled using the Git provider's API. By default, the default branch (usually main or master) will be used.

nf-core is a great resource for public Nextflow pipelines.

The GitHub API imposes rate limits on API requests. You can increase your rate limit by adding GitHub credentials to your workspace as shown below.

Private repositories​

To access private Nextflow pipelines, add the credentials for your private Git hosting provider to Seqera.

Credentials are encrypted with the AES-256 cypher before secure storage and are never exposed in an unencrypted way by any Seqera API.

Multiple credential filtering​

When you have multiple stored credentials, Seqera selects the most relevant credential for your repository in the following order:

  1. Seqera evaluates all the stored credentials available to the current workspace.

  2. Credentials are filtered by Git provider (GitHub, GitLab, Bitbucket, etc.)

  3. Seqera selects the credential with a Repository base URL most similar to the target repository.

  4. If no Repository base URL values are specified in the workspace credentials, the most long-lived credential is selected.

Credential filtering example

Workspace A contains four credentials:

Credential A

Type: GitHub

Repository base URL:

Credential B

Type: GitHub

Repository base URL: https://github.com/

Credential C

Type: GitHub

Repository base URL: https://github.com/pipeline-repo

Credential D

Type: GitLab

Repository base URL: https://gitlab.com/repo-a

If you launch a pipeline with a Nextflow workflow in the https://github.com/pipeline-repo, Seqera will use Credential C.

For the application to select the most appropriate credential for your repository, we recommend that you:

  • Specify the Repository base URL values as completely as possible for each Git credential used in the workspace.

  • Favor the use of service account type credentials where possible (such as GitLab group access tokens).

  • Avoid storing multiple user-based tokens with similar permissions.

Azure DevOps repositories​

You can authenticate to Azure Devops repositories using a personal access token (PAT).

Once you have created and copied your access token, create a new credential in Seqera using these steps:

Create AzureDevOps credentials

  1. From an organization workspace: Select Credentials > Add Credentials. From your personal workspace: Go to the user menu and select Your credentials > Add credentials.

  2. Enter a Name for the new credentials.

  3. Select Azure DevOps as the Provider.

  4. Enter your Username and Access token.

  5. (Recommended) Enter the Repository base URL for which the credentials should be applied. This option is used to apply the provided credentials to a specific repository, e.g., https://dev.azure.com/<your organization>/<your project>.

GitHub​

Use an access token to connect Seqera to a private GitHub repository. Personal (classic) or fine-grained access tokens can be used.

A user's personal access token (classic) can access every repository that the user has access to. GitHub recommends using fine-grained personal access tokens (currently in beta) instead, which you can restrict to specific repositories. Fine-grained personal access tokens also enable you to specify granular permissions instead of broad scopes.

For personal (classic) tokens, you must grant access to the private repository by selecting the main repo scope when the token is created. See Creating a personal access token (classic) for instructions to create your personal access token (classic).

For fine-grained tokens, the repository's organization must opt in to the use of fine-grained tokens. Tokens can be restricted by resource owner (organization), repository access, and permissions. See Creating a fine-grained personal access token for instructions to create your fine-grained access token.

After you've created and copied your access token, create a new credential in Seqera:

Create GitHub credentials

  1. From an organization workspace: Select Credentials > Add Credentials. From your personal workspace: Go to the user menu and select Your credentials > Add credentials.

  2. Enter a Name for the new credentials.

  3. Select GitHub as the Provider.

  4. Enter your Username and Access token.

  5. (Recommended) Enter the Repository base URL for which the credentials should be applied. This option is used to apply the provided credentials to a specific repository, e.g., https://github.com/seqeralabs.

GitLab​

GitLab supports Personal, Group, and Project access tokens for authentication. Your access token must have the api, read_api, and read_repository scopes to work with Seqera. For all three token types, use the token value in both the Password and Access token fields in the Seqera credential creation form.

After you have created and copied your access token, create a new credential in Seqera with these steps:

Create GitLab credentials

  1. From an organization workspace: Select Credentials > Add Credentials. From your personal workspace: Go to the user menu and select Your credentials > Add credentials.

  2. Enter a Name for the new credentials.

  3. Select GitLab as the Provider.

  4. Enter your Username. For Group and Project access tokens, the username can be any non-empty value.

  5. Enter your token value in both the Password and Access token fields.

  6. Enter the Repository base URL (recommended). This option is used to apply the credentials to a specific repository, e.g. https://gitlab.com/seqeralabs.

Gitea​

To connect to a private Gitea repository, use your Gitea user credentials to create a new credential in Seqera with these steps:

Create Gitea credentials

  1. From an organization workspace, go to the Credentials tab and select Add Credentials. From your personal workspace, select Your credentials from the user menu, then select Add credentials.

  2. Enter a Name for the new credentials.

  3. Select Gitea as the Provider.

  4. Enter your Username.

  5. Enter your Password.

  6. Enter your Repository base URL (required).

Bitbucket​

To connect to a private BitBucket repository, see the BitBucket documentation to learn how to create a BitBucket App password. Then, create a new credential in Seqera with these steps:

Create BitBucket credentials

  1. From an organization workspace: Select Credentials > Add Credentials. From your personal workspace: Go to the user menu and select Your credentials > Add credentials.

  2. Enter a Name for the new credentials.

  3. Select BitBucket as the Provider.

  4. Enter your Username and Password.

  5. Enter the Repository base URL (recommended). This option can be used to apply the credentials to a specific repository, e.g., https://bitbucket.org/seqeralabs.

AWS CodeCommit​

To connect to a private AWS CodeCommit repository, see the AWS documentation to learn more about IAM permissions for CodeCommit. Then, use your IAM account access key and secret key to create a credential in Seqera with these steps:

Create AWS CodeCommit credentials

  1. From an organization workspace: Select Credentials > Add Credentials. From your personal workspace: Go to the user menu and select Your credentials > Add credentials.

  2. Enter a Name for the new credentials.

  3. Select CodeCommit as the Provider.

  4. Enter the Access key and Secret key of the AWS IAM account that will be used to access the target CodeCommit repository.

  5. Enter the Repository base URL for which the credentials should be applied (recommended). This option can be used to apply the credentials to a specific region, e.g., https://git-codecommit.eu-west-1.amazonaws.com.

Self-hosted Git​

Seqera Platform Enterprise supports Git server endpoints. For more information, see Git configuration in the Enterprise installation guide.