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.

The following ICA assets can be included in bundles:

Linking an Existing Bundle to a Project

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

To unlink a bundle from a project,

1. Select Projects > your_project > Project Settings > Details.

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

3. Click the (-) button, next to the linked bundle you wish to remove.

Create a New Bundle

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

1. From the main navigation, select Projects > your_project > Bundles.

2. Select + Create .

3. Enter a unique name for the bundle.

4. From the Region 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] Enter any information you would like to distribute with the bundle in the Documentation section.

9. Select Save.

Edit an Existing Bundle

To make changes to a bundle:

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.

Adding Assets to a Bundle

To make changes to a bundle:

1. Select a bundle.

2. On the left-hand side, select the type of asset 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.

Assets must meet the following requirements before they can be 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.

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.

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

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. All users wich currently have access to a bundle will automatically have access to the new version as well.

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.

When you create a new version of a bundle, it will replace the old version in your list. To see the old version, open your new bundle and look at Bundles > your_bundle > Details > Versioning. There you can open the previous version which is contained in your new version.

Assets such as data which were added in a previous version of your bundle will be marked in green, while new content will be black.

Add Terms of Use to a Bundle

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

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

   • Select + Create New Version.

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

   • Click Save.

   • [Optional] Require acceptance by clicking the checkbox next to 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.

Collaborating on a Bundle

If you want to collaborate with other people on creating a bundle and managing the assets in the bundle, you can add users to your bundle and set their permissions. You use this to create a bundle together, not to use the bundle in your projects.

1. From the main navigation, select Bundles > your_bundle > Bundle Settings > 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.

     • Viewer: view content without editing rights.

     • Contributor: view bundle content and link/unlink assets.

     • Administrator: full edit rights of content and configuration.

   • 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.

Sharing a Bundle

Once you have finalized your bundle and added all assets and legal requirements, you can share your bundle with other tenants to use it in their projects.

Your bundle must be in released status to prevent it from being updated while it is shared.

1. Go to Bundles > your_bundle > Edit > Details > Bundle status and set it to Released.

2. Save the change.

Once the bundle is released, you can share it. Invitations are sent to an individual email address, however access is granted and extended to all users and all workgroups inside that tenant.

1. Go to Bundles > your_bundle > Bundle Settings > Share.

2. Click Invite and enter the email address of the person you want to share the bundle with. They will receive an email from which they can accept or reject the invitation to use the bundle. The invitation will show the bundle name, description and owner. The link in the invite can only be used once.

You can follow up on the status of the invitation on the Bundles > your_bundle > Bundle Settings > Share page.

• If they reject the bundle, the rejection date will be shown. To re-invite that person again later on, select their email address in the list and choose Remove. You can then create a new invitation. If you do not remove the old entry before sending a new invitation, they will be unable to accept and get an error message stating that the user and bundle combination must be unique. They can also not re-use an invitation once it has been accepted or declined.

• If they accept the bundle, the acceptance date will be shown. They will in turn see the bundle under Bundles > Entitled bundles. To remove access, select their email address in the list and choose Remove.

Entitled Bundles

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.

Illumina® Connected Analytics is a cloud-based software platform intended to be used to manage, analyze, and interpret large volumes of multi-omics data in a secure, scalable, and flexible environment. The versatility of the system allows the platform to be used for a broad range of applications. When using the applications provided on the platform for diagnostic purposes, it is the responsibility of the user to determine regulatory requirements and to validate for intended use, as appropriate.

The platform is hosted in regions listed below.

The platform hosts a suite of RESTful HTTP-based application programming interfaces (APIs) to perform operations on data and analysis resources. A web application user-interface is hosted alongside the API to deliver an interactive visualization of the resources and enables additional functionality beyond automated analysis and data transfer. Storage and compute costs are presented via usage information in the account console, and a variety of compute resource options are specifiable for applications to fine tune efficiency.

Getting Started

Getting Help

Use the search bar on the top right to navigate through the help docs and find specific topics of interest.

If you have any questions, contact Illumina Technical Support by phone or email:

Illumina Technical Support | techsupport@illumina.com | 1-800-809-4566

For customers outside the United States, Illumina regional Technical Support contact information can be found at www.illumina.com/company/contact-us.html.

To see the current ICA version you are logged in to, click your username found on the top right of the screen and then select About.

Other Illumina Products

To view a list of the products to which you have access, select the 9 dots symbol at the top right of ICA. This will list your products. If you have multiple regional applications for the same product, the region of each is shown between brackets.

The More Tools category presents the following options

• My Illumina Dashboard to monitor instruments, streamline purchases and keep track of upcoming activities.

• Link to the Support Center for additional information and help.

• Link to the order management from where you can keep track of your current and past orders.

Release Notes

Illumina Connected Analytics allows you to create and assign metadata to capture additional information about samples.

Each tenant has one root metadata model that is accessible to all projects in the tenant. This allows an organization to collect the same piece of information for every sample in every project in the tenant, such as an ID number. Within this root model, you can configure multiple metadata submodels, even at different levels.

Illumina recommends that you limit the amount of fields or field groups you add to the root model. If there are any misconfigured items in the root model, it will carry over into all other metadata models in the tenant. Once a root model is published, the fields and groups that are defined within it cannot be deleted. You should first consider creating submodels before adding anything to the root model. When configuring a project, you have the option to assign one published metadata model for all samples in the project. This metadata model can be the root model, a submodel of the root model, or a submodel of a submodel. It can be any published metadata model in the tenant. When a metadata model is selected for a project, all fields configured for the metadata model, and all fields in any parent models are applied to the samples in the project.

❗️ Illumina recommends that you limit the amount of fields or field groups you add to the root model. You should first consider creating submodels before adding anything to the root model.

Metadata concepts

The following terminology is used within this page:

• Metadata fields = Metadata fields will be linked to a sample in the context of a project. They can be of various types and could contain single or multiple values.

• Metadata groups = You can identify that a few fields belong together (for example, they all are related to quality metrics). That would be the moment to create a group so that the user knows these fields belong together

• Root model = Model that is linked to the tenant. Every metadata model that you link to a project will also contain the fields and groups specified in this model as this is a parent model for all other models. This is a subcategory of a project metadata model

• Child/Sub model = Any metadata model that is not the root model. Child models will inherit all fields and groups from their parent models. This is a subcategory of a project metadata model

• Pipeline model = Model that is linked to a specific pipeline and not a project

Metadata in the context of ICA will always give information about a sample. It can be provided by the user, the pipeline and via the API. There are 2 general categories of metadata models: Project Metadata Model and Pipeline Metadata Model. Both models are built from metadata fields and groups. The project metadata model is specific per tenant, while the pipeline metadata model is linked to a pipeline and can be shared across tenants. These models are defined by users.

Each sample can have multiple metadata models. Whenever you link a project metadata model to your project, you will see its groups and fields present on each sample. The root model from that tenant will also be present as every metadata model inherits the groups and fields specified in the parent metadata model(s). When a pipeline is executed with sample and the pipeline contained a metadata model, the groups and fields will be present as well for each analysis that comes out of a pipeline execution.

Groups & fields

The following field types are used within ICA:

• Text: Free text

• Keyword: Automatically complete value based on already used values

• Numeric: Only numbers

• Boolean: True or false, cannot be multiple value

• Date: e.g. 23/02/2022

• Date time: e.g. 23/02/2022 11:43:53, saved in UTC

• Enumeration: select value out of drop-down list

The following properties can be selected for groups & fields:

• Required: Pipeline can’t be started with this sample until the required group/field is filled in

• Sensitive: Values of this group/field are only visible to project users of the own tenant. When a sample is shared across tenants, these fields won't be visible

• Filled by pipeline: Fields that need to be filled by pipeline should be part of the same group. This group will automatically be multiple value and values will be available after pipeline execution. This property is only available for groups

• Multiple value: This group/field can consist out of multiple (grouped) values

❗️ Fields cannot be both required and filled by pipeline

Project vs. Pipeline Metadata Models

Project metadata model has metadata linked to a specific project. Values are known upront, general information is required for each sample of a specific project, and it may include general mandatory company information.

Pipeline metadata model has metadata linked to a specific pipeline. Values are populated during the pipeline execution and it requires an output file with the name 'metadata.response.json'.

❗️ Field groups should be used when configuring metadata fields that are filled by a pipeline. These fields should be part of the same field group and be configured with the Multiple Value setting enabled

Metadata Actions

Publish a Metadata Model

Newly created and updated metadata models are not available for use within the tenant until the metadata model is published. When a metadata model is published, fields and field groups cannot be deleted, but the names and descriptions for fields and field groups can be edited. A model can be published after verifying all parent models are published first.

Retire a Metadata Model

If a published metadata model is no longer needed, you can retire the model (except the root model).

1. First, check if the model contains any submodels. A model cannot be retired if it contains any published submodels.

2. When you are certain you want to retire a model and all submodels are retired, click on the three dots in the top right of the model window, and then select Retire Metadata Model.

Assign a Metadata Model to a Project

To add metadata to your samples, you first need to assign a metadata model to your project.

1. Go to Projects > your_project > Project Settings > Details.

2. Select Edit.

3. From the Metadata Model drop-down list, select the metadata model you want to use for the project.

4. Select Save. All fields configured for the metadata model, and all fields in any parent models are applied to the samples in the project.

Add Metadata to Samples Manually

To manually add metadata to samples in your project, do as follows.

1. Precondition is that you have a metadata model assigned to your project

2. Go to Projects > your_project > Samples > your_sample.

3. Double-click your sample to open the sample details.

4. Enter all metadata information as it applies to the selected sample. All required metadata fields must be populated or the pipeline cannot start.

5. Select Save

Populating a Pipeline Metadata Model

To fill metadata by pipeline executions, a pipeline model must be created.

1. In the Illumina Connected Analytics main navigation, go to Projects > your_project > Flow > Pipelines > your_pipeline.

2. Double-click on your pipeline to open the pipeline details.

3. Create/Edit your model under Metadata Model tab. Field groups should be used when configuring metadata fields that are filled by a pipeline. These fields should be part of the same field group and be configured with the Multiple Value setting enabled.

In order for your pipeline to fill the metadata model, an output file with the name metadata.response.json must be generated. After adding your group fields to the pipeline model, click on Generate example JSON to view the required format for your pipeline.

❗️ The field names cannot have . in them, e.g. for the metric name Q30 bases (excl. dup & clipped bases) the . after excl must be removed.

Pushing Metadata Metrics to Base

Populating metadata models of samples allows having a sample-centric view of all the metadata. It is also possible to synchronize that data into your project's Base warehouse.

1. In the Illumina Connected Analytics main navigation, select Projects.

2. In your project menu select Schedule.

3. Select 'Add new', and then click on the Metadata Schedule option.

4. Type a name for your schedule, optionally add description, and select whether you would like the metadata source would be the current project or the entire tenant. It is also possible to select whether ICA references would be anonymized and if sensitive metadata fields would be included. As a reminder, values of sensitive metadata fields would not be visible to other users outside of the project.

5. Select Save.

6. Navigate to Tables under BASE menu in your project.

7. Two new table schemas should be added with your current metadata models.

The event log shows an overview of system events with options to search and filter. For every entry, it lists the following:

• Event date and time

• Category (error, warn or info)

• Code

• Description

• Tenant

Up to 200,000 results will be be returned. If your desired records are outside the range of the returned records, please refine the filters or use the search function at the top right.

Export is restricted to the amount of entries shown per page. You can use the selector at the bottom to set this to up to 1000 entries per page.

In order to create a Tool or Bench image, a Docker image is required to run the application in a containerized environment. Illumina Connected Analytics supports both public Docker images and private Docker images uploaded to ICA.

Importing a Public External Image (Tools)

1. Navigate to System Settings > Docker Repository.

2. Click Create > External image to add a new external image.

3. Add your full image URL in the Url field, e.g. docker.io/alpine:latest or registry.hub.docker.com/library/alpine:latest. Docker Name and Version will auto-populate. (Tip: do not add http:// or https:// in your URL)

Note: Do not use :latest when the repository has rate limiting enabled as this interferes with caching and incurs additional data transfer.

1. (Optional) Complete the Description field.

2. Click Save.

3. The newly added image will appear in your Docker Repository list.

Verification of the URL is performed during execution of a pipeline which depends on the Docker image, not during configuration.

External images are accessed from the external source whenever required and not stored in ICA. Therefore, it is important not to move or delete the external source. There is no status displayed on external Docker repositories in the overview as ICA cannot guarantee their availability. The use of :stable instead of :latest is recommended.

Importing a Private Image (Tools + Bench Images)

In order to use private images in your tool, you must first upload them as a TAR file.

1. Navigate to Projects > your_project .

3. Select your uploaded TAR file and click in the top menu on Manage > Change Format .

5. Navigate to System Settings > Docker Repository (outside of your project).

6. Click on Create > Image.

7. Click on the magnifying glass to find your uploaded TAR image file.

8. Select the appropriate region and if needed, filter on project from the drop-down menus to find your file.

9. Select that file.

11. The newly added image should appear in your Docker Repository list. Verify it is marked as Available under the Status column to ensure it is ready to be used in your tool or pipeline.

Copying Docker Images to other Regions

1. Navigate to System Settings > Docker Repository.

2. Either

   • Select the required image(s) and go to Manage > Add Region.

   • OR double-click on a required image, check the box matching the region you want to add, and select update.

3. In both cases, allow a few minutes for the image to become available in the new region (the status becomes available in table view).

To remove regions, go to Manage > Remove Region or unselect the regions from the Docker image detail view.

Downloading Docker Images

You can download your created Docker images at System Settings > Docker Images > your_Docker_image > Manage > Download.

In order to be able to download Docker images, the following requirements must be met:

• The Docker image can not be from an entitled bundle.

• Only self-created Docker images can be downloaded.

• The Docker image must be an internal image and in status Available.

• You can only select a single Docker image at a time for download.

File Size Considerations

Docker image size should be kept as small as practically possible. To this end, it is best practice to compress the image. After compressing and uploading the image, select your uploaded file and click Manage > Change Format in the top menu to change it to Docker format so ICA can recognize the file.

Software Registration

Tenant Setup

The platform requires a provisioned tenant in the Illumina account management system with access to the Illumina Connected Analytics (ICA) application. Once a tenant has been provisioned, a tenant administrator will be assigned. The tenant administrator has permission to manage account access including add users, create workgroups, and add additional tenant administrators.

Each tenant is assigned a domain name used to login to the platform. The domain name is used in the login URL to navigate to the appropriate login page in a web browser. The login URL is https://<domain>.login.illumina.com, where <domain> is substituted with the domain name assigned to the tenant.

New user accounts can be created for a tenant by navigating to the domain login URL and following the links on the page to setup a new account with a valid email address. Once the account has been added to the domain, the tenant administrator may assign registered users to workgroups with permission to use the ICA application. Registered users may also be made workgroup administrators by tenant administrators or existing workgroup administrators.

API Keys

For security reasons, it is best practice to not use accounts with administrator level access to generate API keys and instead create a specific CLI user with basic permission. This will minimize the possible impact of compromised keys.

Generate an API Key

Click the button to generate a new API Key. Provide a name for the API Key. Then choose to either include all workgroups or select the workgroups to be included. Selected workgroups will be accessible with the API Key.

Click to generate the API Key. The API Key is then presented (hidden) with a button to show the key to be copied and a link to download to a file to be stored securely for future reference. Once the window is closed, the key contents will not be accessible through the domain login page, so be sure to store it securely for future reference if needed.

After generating an API key, save the key somewhere secure to be referenced when using the command-line interface or APIs.

Access via Web UI

• On the left, you have the navigation bar which will auto-collapse on smaller screens. When collapsed, use the ≡ symbol to expand it.

• The central part of the display is the item on which you are performing your actions.

• At the top right, you have icons to refresh the screen for information, status updates, and access to the online help.

Access via the CLI

Access via the API

Object Identifiers

The object data models for resources that are created in the platform include a unique id field for identifying the resource. These fixed machine-readable IDs are used for accessing and modifying the resource through the API or CLI, even if the resource name changes.

JSON Web Token (JWT)

Accessing the platform APIs requires authorizing calls using JSON Web Tokens (JWT). A JWT is a standardized trusted claim containing authentication context. This is a primary security mechanism to protect against unauthorized cross-account data access.

A JWT is generated by providing user credentials (API Key or username/password) to the token creation endpoint. Token creation can be performed using the API directly or the CLI.

A storage configuration provides ICA with information to connect to an external cloud storage provider, such as AWS S3. The storage configuration validates that the information provided is correct, and then continuously monitors the integration.

Refer to the following pages for instructions to setup supported external cloud storage providers:

Credentials

The storage configuration requires credentials to connect to your storage. AWS uses the security credentials to authenticate and authorize your requests. On the System Settings > Credentials > Create, you can enter these credentials. Long-term access keys consist of a combination of the access key ID and secret access key as a set.

Fill out the following fields:

• Type—The type of access credentials. This will usually be AWS user.

• Name—Provide a name to easily identify your access key.

• Access key ID—The access key you created.

• Secret access key—Your related secret access key.

Create a Storage Configuration

1. In the ICA main navigation, select System Settings > Storage > Create.

2. Configure the following settings for the storage configuration.

   • Type—Use the default value, eg, AWS_S3. Do not change.

   • Region—Select the region where the bucket is located.

   • Configuration name—You will use this name when creating volumes that reside in the bucket. The name length must be in between 3 and 63 characters.

   • Description—Here you can provide a description for yourself or other users to identify this storage configuration.

   • Bucket name—Enter the name of your S3 bucket.

   • Key prefix [Optional]—You can provide a key prefix to allow only files inside the prefix to be accessible. The key prefix must end with "/".

   • If a key prefix is specified, your projects will only have access to that folder and subfolders. For example, using the key prefix folder-1/ ensures that only the data from the folder-1 directory in your S3 bucket is synced with your ICA project. Using prefixes and distinct folders for each ICA project is the recommended configuration as it allows you to use the same S3 bucket for different projects.

   • Using no key prefix results in syncing all data in your S3 bucket (starting from root level) with your ICA project. Your project will have access to your entire S3 bucket, which prevents that S3 bucket from being used for other ICA projects. Although possible, this configuration is not recommended.

   • Secret—Select the credentials to associate with this storage configuration. These were created on the Credentials tab.

   • Server Side Encryption [Optional]—If needed, you can enter the algorithm and key name for server-side encryption processes.

3. Select Save.

With the action Set as default for region, you select which storage will be used as default storage in a region for new projects of your tenant. Only one storage can be default at a time for a region, so selecting a new storage as default will unselect the previous default. If you do not want to have a default, you can select the default storage and the action will become Unset as default for region.

The System Settings > Credentials > Share action is used to make the storage available to everyone in your tenant. By default, storage is private per user so that you have complete control over the contents. Once you decide you want to share the storage, simply select it and use the Share action. Do take into account that once shared, you can not unshare the storage. Once your storage is used in a project, it can also no longer be deleted.

Storage Configuration Verification

Every 4 hours, ICA will verify the storage configuration and credentials to ensure availability. When an error is detected, ICA will attempt to reconnect once every 15 minutes. After 200 consecutively failed connection attempts (50 hours), ICA will stop trying to connect.

When you update your credentials, the storage configuration is automatically validated. In addition, you can manually trigger revalidation when ICA has stopped trying to connect by selecting the storage and then clicking Validate on the System Settings > Storage > Manage.

Supported Storage Classes

A Tool is the definition of a containerized application with defined inputs, outputs, and execution environment details including compute resources required, environment variables, command line arguments, and more.

Create a Tool

Tools define the inputs, parameters, and outputs for the analysis. Tools are available for use in graphical CWL pipelines by any project in the account.

1. Select System Settings > Tool Repository > + Create.

2. Configure tool settings in the tool properties tabs. See Tool Properties.

3. Select Save.

Tool Properties

The following sections describe the tool properties that can be configured in each tab.

Information Tab

Tool Status

The release status of the tool. can be one of "Draft", "Release Candidate", "Released" or "Deprecated".

Documentation Tab

The Documentation tab provides options for configuring the HTML description for the tool. The description appears in the Tool Repository but is excluded from exported CWL definitions.

General Tool Tab

The General Tool tab provides options to configure the basic command line.

The Hints/Requirements include CWL features to indicate capabilities expected in the Tool's execution environment.

• Inline Javascript

  • The Tool contains a property with a JavaScript expression to resolve it's value.

• Initial workdir

  • The workdir can be any of the following types:

    • String or Expression — A string or JavaScript expression, eg, $(inputs.InputFASTA)

    • File or Dir — A map of one or more files or directories, in the following format: {type: array, items: [File, Directory]}

    • Dirent — A script in the working directory. The Entry name field specifies the file name.

• Scatter feature — Indicates that the workflow platform must support the scatter and scatterMethod fields.

Tool Arguments Tab

The Tool Arguments tab provides options to configure base command parameters that do not require user input.

Tool arguments may be one of two types:

• String or Expression — A literal string or JavaScript expression, eg --format=bam.

• Binding — An argument constructed from the binding of an input parameter.

The following table describes the argument input fields.

Example

Tool Inputs Tab

The Tool Inputs tab provides options to define the input files and directories for the tool. The following table describes the input and binding fields. Selecting multi value enables type binding options for adding prefixes to the input.

Tool Settings Tab

The Tool Settings tab provides options to define parameters that can be set at the time of execution. The following table describes the input and binding fields. Selecting multi value enables type binding options for adding prefixes to the input.

Tool Outputs Tab

The Tool Outputs tab provides options to define the parameters of output files.

The following table describes the input and binding fields. Selecting multi value enables type binding options for adding prefixes to the input.

Tool CWL Tab

The Tool CWL tab displays the complete CWL code constructed from the values entered in the other tabs. the CWL code automatically updates when changes are made in the tool definition tabs, and any changes to the CWL code are reflected in the tool definition tabs.

❗️ Modifying data within the CWL editor can result in invalid code.

Edit a Tool

1. From the System Settings > Tool Repository page, select a tool.

2. Select Edit.

Update Tool Status

1. From the System Settings > Tool Repository page, select a tool.

2. Select the Information tab.

3. From the Status drop-down menu, select a status.

4. Select Save.

Import Tool

In addition to the interactive Tool builder, the platform GUI also supports working directly with the raw definition when developing a new Tool. This provides the ability to write the Tool definition manually or bring an existing Tool's definition to the platform.

A simple example CWL Tool definition is provided below.

#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: CommandLineTool
label: echo
inputs:
  message:
    type: string
    default: testMessage
    inputBinding:
      position: 1
outputs:
  echoout:
    type: stdout
baseCommand:
- echo

When creating a new Tool, navigate to System Settings > Tool Repository > your_tool > Tool CWL tab to show the raw CWL definition. Here a CWL CommandLineTool definition may be pasted into the editor. After pasting into the editor, the definition is parsed and the other tabs for visually editing the Tool will populate according to the definition contents.

Creating Your First Tool - Tips and Tricks

• General Tool - includes your base command and various optional configurations.

  • The base command is required for your tool to run, e.g. python /path/to/script.py such that python and /path/to/script.py are added in separate lines.

  • Inline Javascript requirement - must be enabled if you are using Javascript anywhere in your tool definition.

  • Initial workdir requirement - Dirent Type

    • Your tool must point to a script that executes your analysis. That script can either be provided in your Docker image or using a Dirent. Defining a script via Dirent allows you to dynamically modify your script without updating your Docker image. In order to define your Dirent script define your script name under Entry name (e.g. runner.sh) and the script content under Entry. Then, point your base command to that custom script, e.g. bash runner.sh.

❗ What's the difference between Settings and Arguments?

Settings are exposed at the pipeline level with the ability to get modified at launch, while Arguments are intended to be immutable and hidden from users launching the pipeline.

• How to reference your tool inputs and settings throughout the tool definition?

  • You can either reference your inputs using their position or ID.

    • Settings can be referenced using their defined IDs, e.g. $(inputs.InputSetting)

    • All inputs can also be referenced using their position, e.g. bash script.sh $1 $2

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.

Note that there is a combined limit of 30,000 projects and bundles per tenant.

Create new Project

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

Required fields include:

• Name

  • 1-255 characters

  • Must begin with a letter

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

• 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.

• 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.

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

• 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

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.
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.

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.

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