Bundles

Bundles are curated data sets which combine assets such as pipelines, tools, and Base query templates. This is where you will find packaged assets such as Illumina-provided pipelines and sample data. You can create, share and use bundles in projects of your own tenant as well as projects in other tenants.

For data-management reasons, there is a combined limit of 30 000 projects and bundles per tenant.

The following ICA assets can be included in bundles:

• Base tables (read-only)

• Base query templates

• Bench docker images

• Data

• Pipelines

• Reference data

• Sample data

• Tools and Tool images

Assets must meet the following requirements before being added to a bundle:

• For Samples and Data, the project the asset belongs to must have data sharing enabled.

• The region of the project containing the asset must match the region of the bundle.

• You must have permission to access the project containing the asset.

• Pipelines and tools need to be in released status.

• Samples must be available in a complete state.

The main Bundles screen has two tabs: My Bundles and Entitled Bundles. The My Bundles tab shows all the bundles that you are a member of. This tab is where most of your interactions with bundles occur. The Entitled Bundles tab shows the bundles that have been specially created by Illumina or other organizations and shared with you to use in your projects. See Access and Use an Entitled Bundle.

As of ICA v.2.29, the content in bundles is linked in such a way that any updates to a bundle are automatically propagated to the projects which have that bundle linked.

If you have created bundle links in ICA versions prior to ICA v2.29 and want to switch them over to links with dynamic updates, you need to unlink and relink them.

Linking an Existing Bundle to a Project

1. From the main navigation page, select Projects > your_project > Details.

2. Click the Edit button at the top of the Details page.

3. Click the + button, under LINKED BUNDLES.

4. Click on the desired bundle, then click the +Link Bundles button.

5. Click Save.

The assets included in the bundle will now be available in the respective pages within the Project (e.g. Data and Pipelines pages). Any updates to the assets will be automatically available in the destination project.

Bundles and projects have to be in the same region in order to be linked. Otherwise, the error The bundle is in a different region than the project so it's not eligible for linking will be displayed.

Create a New Bundle

To create a new bundle and configure its settings, do as follows.

1. From the main navigation, select Bundles.

2. Select + Create Bundle.

3. Enter a unique name for the bundle.

4. From the Bundle Location drop-down list, select where the assets for this bundle should be stored.

5. [Optional] Configure the following settings.

   • Categories—Select an existing category or enter a new one.

   • Status—Set the status of the bundle. When the status of a bundle changes, it cannot be reverted to a draft or released state.

     • Draft—The bundle can be edited.

     • Released—The bundle is released. Technically, you can still edit bundle information and add assets to the bundle, but should refrain from doing so.

     • Deprecated—The bundle is no longer intended for use. By default, deprecated bundles are hidden on the main Bundles screen (unless non-deprecated versions of the bundle exist). Select "Show deprecated bundles" to show all deprecated bundles. Bundles can not be recovered from deprecated status.

   • Short Description—Enter a description for the bundle.

   • Metadata Model—Select a metadata model to apply to the bundle.

6. Enter a release version for the bundle and optionally enter a description for the version.

7. [Optional] Links can be added with a display name (max 100 chars) and URL (max 2048 chars).

   • Homepage

   • License

   • Links

   • Publications

8. [Optional] Select the Documentation tab and enter any information you would like to attach to the bundle.

9. Select Save.

There is no option to delete bundles, they must be deprecated instead.

Edit Existing Bundle

To make changes to a bundle, do as follows.

1. From the main navigation, select Bundles.

2. Select a bundle.

3. Select Edit.

4. Modify the bundle information and documentation as needed.

5. Select Save.

When the changes are saved, they also become available in all projects that have this bundle linked.

Adding Assets to a Bundle

To make changes to a bundle, do as follows.

1. Select a bundle.

2. On the left-hand side, select the asset type under Flow (such as pipeline or tool) you want to add to the bundle.

3. Depending on the asset type, select add or link to bundle.

4. Select the assets and confirm.

When you link folders to a bundle, a warning is displayed indicating that, depending on the size of the folder, linking may take considerable time. The linking process will run in the background and the progress can be monitored on the Bundles > your_bundle > activity > Batch Jobs screen. To see more details and the progress, double-click the batch job and then double-click the individual item. This will show how many individual files are already linked.

You can not add the same asset twice to a bundle. Once added, the asset will no longer appear in the selection list.

Which batch jobs are visible as activity depends on the user role.

Project Creator	Project Collaborator same tenant	Project Collaborator different tenant
All batch jobs	All batch jobs	Only batch jobs of own tenant

Create a New Bundle Version

When creating a new bundle version, you can only add assets to the bundle. You cannot remove existing assets from a bundle when creating a new version. If you need to remove assets from a bundle, it is recommended that you create a new bundle.

1. From the main navigation, select Bundles.

2. Select a bundle.

3. Select Create new Version.

4. Make updates as needed and update the version number.

5. Select Save.

Manage Bundle Users

To manage bundle users and their permissions, do as follows.

1. From the main navigation, select Bundles > your_bundle > Team.

2. To invite a user to collaborate on the bundle, do as follows.

   • To add a user from your tenant, select Someone of your tenant and select a user from the drop-down list.

   • To add a user by their email address, select By email and enter their email address.

   • To add all the users of an entire workgroup, select Add workgroup and select a workgroup from the drop-down list.

   • Select the Bundle Role drop-down list and choose a role for the user or workgroup. This role defines the ability of the user or workgroup to view or edit bundle settings.

   • Repeat as needed to add more users.\

   Users are not officially added to the bundle until they accept the invitation.

3. To change the permissions role for a user, select the Bundle Role drop-down list for the user and select a new role.

4. To revoke bundle permissions from a user, select the trash icon for the user.

5. Select Save Changes.

Add Terms of Use to a Bundle

1. From the main navigation, Select Bundles > your_bundle > Legal.

2. To add Terms of Use to a Bundle, do as follows:

   • Select New Version.

   • Use the WYSIWYG editor to define Terms of Use for the selected bundle.

   • Click Save.

   • [Optional] Require acceptance by clicking the checkbox, Acceptance required. Acceptance required will prompt a user to accept the Terms of Use before being able to use a bundle or add the bundle to a project.

3. To edit the Terms of Use, repeat Steps 1-3 and use a unique version name. If you select acceptance required, you can choose to keep the acceptance status as is or require users to reaccept the terms of use. When reacceptance is required, users need to reaccept the terms in order continue using this bundle in their pipelines. This is indicated when they want to enter projects which use this bundle.

Access and Use an Entitled Bundle

Entitled bundles are bundles created by Illumina or third parties for you to use in your projects. Entitled bundles can already be part of your tenant when it is part of your subscription. You can see your entitled bundles at Bundles > Entitled Bundles.

To use your shared entitled bundle, add the bundle to your project via Project Linking. Content shared via entitled bundles is read-only, so you cannot add or modify the contents of an entitled bundle. If you lose access to an entitled bundle previously shared with you, the bundle is unlinked and you will no longer be able to access its contents.