FAQ

Q: What is the No Access role when adding users to workgroups in the IAM console?

A: In the IAM Console, you can assign users in a workgroup Has Access or No Access roles for Illumina Connected Analytics (ICA). The No Access role prevents the users from performing operations in ICA, but still allows them access to other applications, such as BaseSpace Sequence Hub. The default role for each user is No Access. See the Illumina Connected Analytics Flow Help for information on granting users access. For information on granting users access to other software applications, see the documentation for the relevant software.

Q: Why are there two namespaces in the CWL definition?

A: At the beginning, it will be two namespaces because it's historical/combining.

Q: Can I use a sample in multiple projects?

A: Samples are multiple files that are related to one sample (eg, multiple lanes). You can link samples to multiple projects; however, a file can only be added to one sample.

Q: Can I use ENS to launch a pipeline?

A: Yes, see the Illumina Connected Analytics command-line interface documentation.

Q: What does it mean for files and samples to be linked to a project?

A: Files and samples linked to a project allow the data to be used when launching pipelines within that project.

Q: I have a private docker image that I want to upload to a tool and only work on in my project. Does anyone in workgroup have access to docker images?

A: Yes, docker images are available to the entire domain when added to the Docker Repository in ICA.

Q: When creating a tool, if I have my own CWL doc, can I just import it instead of building the tool using the UI?

A: Yes, you can take your CWL docs and paste it in instead of configuring a tool via the UI. However, might need to change the namespace. Best practice is to try it first locally, a good option is CWL "runner".

Q: What service connector methods are available in ICA Connectivity?

A: Only the local service connector is supported.

Q: Are there sample files or reference genomes available?

A: Yes, see the Illumina Connected Analytics user interface for available files or visit the BaseSpace Sequence Hub resources available.

Q: Can I create custom roles and permissions for my domain and applications?

A: For each project, project admins can assign a user the Viewer, Contributor, or Admin role. See the Illumina Connected Analytics documentation for more information.

Q: Can I add collaborative users from another domain?

A: es, whitelist the email address of the user to collaborate.

Q: What sequencing systems are compatible?

A: All sequencing systems that use a sample sheet in v2 format are compatible. See the Illumina Connected Analytics Product Compatibility page for more information.

Q: Can I add more than one domain admin?

A: Yes, see the BaseSpace Sequence Hub documentation for information on adding domain admins.

Q: How can I bring my S3 data into GDS?

A: You can connect your own S3 bucket to GDS using the Illumina Connected Analytics command-line interface. This option is only available via the CLI. See the Illumina Connected Analytics command-line interface documentation for more information.

Q: What are the file size limits when uploading/downloading data through the user interface compared to the CLI?

A: here are no file size limits; however, upload/download time depends on file size. The service connector runs in the background until data is uploaded. See the Illumina Connected Analytics documentation for more information.

Q: Since the inputs/outputs have already been configured in tools, why do I need to reconfigure in the pipeline?

A: Tools define the inputs and outputs available, and pipelines connect the inputs and outputs to other steps or the initial inputs/final output files. Pipelines can be shared across projects and tools, so you might want the behavior to differ.

Q: Can I run multiple pipelines at the same time?

A: Yes, see the Illumina Connected Analytics Flow documentation for information on running pipelines.

Q: Can I add SSO to my domain?

A: Yes, see the Illumina Connected Analytics documentation.

Q: If my tool has two configured outputs and I only specify one output when creating the pipeline, can I still run the pipeline?

A: You can run the pipeline successfully if output was marked as is required in the tool configuration. If the output was marked as optional, you cannot run the pipeline.

Q: Why can I specify a compute instance when building a tool, but again when running the tool?

A: When building the tool, you can specify the default compute instance at the pipeline level. When running the tool, you can override the default specified.

Q: If I upload a docker, which workgroups within the domain have access?

A: All workgroups have access. Docker images in ICA are available at the domain level.

Q: Can a task run independently from a workflow?

A: If using the Illumina Connected Analytics command-line interface, tasks can be created and run separately from a workflow. You cannot create tasks in the Illumina Connected Analytics user interface. See the Illumina Connected Analytics command-line interface documentation.

Q: In the CLI, can I create a task from the Docker repository in the user interface?

A: No

Q: Can I create multiple samples and upload the associated data in bulk?

A: You can use the local service connector to combine files into a sample after uploading. You can configure the option in the advanced settings for the local service connector's upload rules. See the Illumina Connected Analytics documentation for more information.

Q: Are pipelines created in the user interface available in the CLI?

A: Yes, pipelines created in the user interface are available as workflows in the CLI. However, you cannot edit pipelines created in the user interface in the CLI.

Q: Do tools created in the user interface act as tasks in the CLI?

A: No. Tools created in the GUI do not exist as tasks in the CLI. See the Illumina Connected Analytics command-line interface documentation for more information on tools and tasks.

Q: When configuring inputs/outputs for a tool, can I use a config file to set parameters instead of configuring in the user interface?

A: No, you cannot configure parameters for inputs/outputs outside the user interface when creating a tool inside the user interface.

Q: If I push to one tool, and then push to a second, are the tools run on the same compute node?

A: All tools are executed on independent compute nodes, regardless of the Machine Profile selected. Shared compute nodes are not supported.

Q: Will customers have the ability to specify resources for running tools?

A: Yes. The resources for running tools are configured when building pipelines, using the Machine Profiles menu.

Q: How does Illumina Connected Analytics Base work?

A: Base uses Snowflake and relational tables.

Q: Where do I configure docker resources?

A: You can configure machine profiles (docker resources) in each tool.

Q: Can I use the tools I create in bench in pipelines and version them?

A: Yes, in a workspace you can build a new docker image, create a tool process, and then the tool becomes a tool in your tool respository.

Q: Can I upload an Excel file?

A: Yes, all file types are supported.