Projects

Introduction

When looking at the main ICA navigation, you will see the following structure:

• Projects are your primary work locations which contain your data and tools to execute your analyses. Projects can be considered as a binder for your work and information. You can have data contained within a project, or you can choose to make it shareable between projects.

• Reference Data are reference genome sets which you use to help look for deviations and to compare your data against.

• Bundles are packages of assets such as sample data, pipelines, tools and templates which you can use as a curated data set. Bundles can be provided both by Illumina and other providers, and you can even create your own bundles. You will find the Illumina-provided pipelines in bundles.

• Audit/Event Logs are used for audit purposes and issue resolving.

• System Settings contain general information susch as the location of storage space, docker images and tool repositories.

Projects are the main dividers in ICA. They provide an access-controlled boundary for organizing and sharing resources created in the platform. The Projects view is used to manage projects within the current tenant.

Create new Project

To create a new project, click the Projects > + Create button.

On the project creation screen, add information to create a project. See Project Details page for information about each field.

Required fields include:

• Name

  • 1-255 characters

  • Must begin with a letter

  • Characters are limited to alphanumerics, hyphens, underscores, and spaces

• Project Owner Owner (and usually contact person) of the project. The project owner has the same rights as a project administrator, but can not be removed from a project without first assigning another project owner. This can be done by the current project owner, the tenant administrator or a project administrator of the current project. Reassignment is done at Projects > your_project > Project Settings > Team > Edit.

• Region Select your project location. Options available are based on Entitlement(s) associated with purchased subscription.

• Analysis Priority (Low/Medium(default)/High) This is balanced per tenant with high priority analyses started first and the system progressing to the next lower priority once all higher priority analyses are running. Balance your priorities so that lower priority projects do not remain waiting for resources indefinitely.

• Billing Mode Select if the costs of this project are to be charged to the tenant of the Project owner or the tenant of the user who is using the project.

• Storage Bundle (auto-selected based on user selection of Project Location)

Click the Save button to finish creating the project. The project will be visible from the Projects view.

Create with Storage Configuration

Refer to the Storage Configuration documentation for details on creating a storage configuration.

During project creation, select the I want to manage my own storage checkbox to use a Storage Configuration as the data provider for the project.

With a storage configuration set, a project will have a 2-way sync with the external cloud storage provider: any data added directly to the external storage will be sync'ed into the ICA project data, and any data added to the project will be sync'ed into the external cloud storage.

Managing Projects

Several tools are available to assist you with keeping an overview of your projects. These filters work in both list and tile view and persist across sessions.

1. Searching is a case-insensitive wildcard filter. Any project which contains the characters will be shown. Use * as wildcard in searches. Be aware that operators without search words are blocked and will result in Unexpected error occurred when searching for projects. You can use the brackets, AND, OR and NOT operators, provided that you do not start the search with them (Monkey AND Banana is allowed, AND Aardvark by itself is invalid syntax)

2. Filter by Workgroup : Projects in ICA can be accessible for different workgroups. This drop-down list allows you to filter projects for specific workgroups. To reset the filter so it displays projects from all your workgroups, use the x on the right which appears when a workgroup is selected.

3. Hidden projects : You can hide projects (Projects > your_project > Details > Hide) which you no longer use. Hiding will delete data in base and bench and will thus be irreversible.

   • You can still see hidden projects if you select this option and delete the data they contain at Projects > your_project > Data to save on storage costs.

   • If you are using your own S3 bucket, your S3 storage will be unlinked from the project, but the data will remain in your S3 storage. Your S3 storage can then be used for other projects.

   • Hiding projects is not possible for externally-managed projects.

4. Favorites : By clicking on the star next to the project name in the tile view, you set a project as favourite. You can have multiple favourites and use the Favourites checkbox to only show those favourites. This prevents having too many projects visible.

5. Tile view shows a grid of projects. This view is best suited if you only have a few projects or have filtered them out by creating favourites. A single click will open the project.

6. List view shows a list of projects. This view allows you to add additional filters on name, description, location, user role, tenant, size and analyses. A double-click is required to open the project.

Externally-managed projects

Illumina software applications which do their own data management on ICA (such as BSSH) store their resources and data in a project much in the same was as manually created projects work in ICA. For ICA, these projects are considered to be externally-managed projects and from ICA, there are a number of restrictions on which actions are allowed on externally-managed projects. For example, you can not delete or move externally-managed data. This is to prevent inconsistencies when these applications want to access their own project data.

What you can do is add files and data such as samples to externally managed projects. Separation of data is ensured by only allowing additional files at the root level or in dedicated subfolders which you can create in your projects. Data which you have added can be moved and deleted again.

You can add bundles to externally managed projects, provided those bundles do not come with additional restrictions for the project.

You can start bench workspaces in externally-managed projects. The resulting data will be stored in the externally-managed project.

Tertiary modules such as cohorts are not supported for externally-managed projects.

When you create a folder with a name which already exists as externally-managed folder, your project will have that folder twice. Once ICA-managed and once externally-managed as S3 does not require unique folder names.

Externally-managed projects protect their notification subscriptions to ensure no user can delete them. It is possible to add your own subscriptions to externally-managed projects, see notifications for more information.

Projects are indicated as externally-managed in the projects overview screen by a project card with a light grey accent and a lock symbol followed by "managed by app".

Tutorial

For a better understanding of how all components of ICA work, try the end-to-end tutorial.

Sharing

You can share links to your project and content within projects to people who have access to it. Sharing is done by copying the URL from your browser. This URL contains both the filters and the sort options which you have applied.