2024
Last updated
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Last updated
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General
Updated decimal separators from commas to dots
Values can be filtered with ‘equal to’ and ‘different from’ operators
Transferred Account Management information to help site
Flow
Nextflow reports are now visible
Inactive Nextflow versions cannot be selected when cloning or saving a pipeline
The pipeline details screen now has a ‘Start analysis’ button
Re-running an analysis reuses a limited number of characters to build the user reference
Added information that re-running analysis keeps only the first 231 characters of the name
Added information on ‘Data found for parameter [parameter_name], but status is Partial instead of Available’ when running analysis
Documented new pipeline file size limit of 20 Megabytes
CLI
Added command-line interface details to ‘Bring your own Bench image’ chapters
CLI updates to the project pipeline start commands for JSON-based pipelines
Added CLI files for 2.31.0
Base
Updated information on Base billing
Storage
Updated the documentation for adding an S3 bucket policy to clarify which fields in the policy must be replaced with user’s account information
Added a video to demonstrate how to connect S3 buckets with SSE-KMS encryption enabled
Updated JSON documentation with support for storage size validation and creating tree structures.
Bench
Removed gpu-large from list of supported Bench instances
Cohorts
Added Measurement search, Disease search and Needle Plot information.
Data Management
Added information to indicate that the action to link data is now only possible from the root level of your project. Previously, this was possible on all levels, but the data was always linked on root level which was not in line with user expectations
Improved description of linked folders, now indicating that linking in linked folder and creating subfolders in linked folders is not possible
Added note explaining that there is a discrepancy between the API specification and the actual response for the GET /api/projects/{projectId}/analyses/{analysisId}/outputs endpoint because analysisData is retained for backward compatibility
Clarified that adding a "New folder name" when moving data to another folder does NOT rename a folder. Instead, it creates a new folder to move data to. You can rename a folder by moving files to a new folder, then deleting the original contents
Added information about which AWS storage classes are supported and how they map to statuses for ICA data
Added note to advise users to use Intelligent tiering without the Archive and Deep Archive tiers, as these tiers are currently not supported
If data is modified in the source or destination folder of a Move job before the Move job is complete, this will lead to the job aborting. Added documentation for how to fix this issue if it occurs
Added information that move jobs will fail if any files being moved are in the "Partial" or "Archived" state. For copy jobs, files in the "Partial" or "Archived" state will be skipped
Flow
Added information about JSON based pipeline input forms
Improved descriptions of scratch space
Documented possible causes of exit code 55 for analysis failure (external event such as spot termination, node draining, ...)
Bench
Updated Bench workspace documentation to indicate the storage size can be between 1GB and 16TB
Updated information on bring your own bench image software volumes
General
Updated CLI release history with new build
Data Management
Added information that "Has access + archive" should not be used as permission in IAM
Updated storage settings for Indonesia, Israel, and UAE regions
Added troubleshooting information on "Unable to generate credentials from the objectstore as the requested path is too long."
Documented that storage credential actions are now integrated with the grid view
Added information on how dynamic linking works. This replaces static linking
Flow
Fixed broken link on Basic Nextflow Tutorial page
Bench
Added explanation on how to use bring-your-own-bench-image functionality
Added information on how to open Jupyter notebook workspaces in a new tab
General
General updates and improvements
Replaced all instances of "volume configuration" with "storage configuration" for consistency, as they have the same definition
Data Management
Added information on how the Service Connector determines when files can be transferred to prevent partial files from being processed
Documented the new 100 concurrent file upload limit on GUI-side upload
CLI
New version of the CLI documentation
Notifications
Corrected configuration explanation error in the configure notifications section for Amazon SQS
Flow
Added information on how to resubmit an analysis with modified values
Added information that setting the Nextflow XML to multiValue="true" will result in ICA treating it as a list
Documented the limitation of tags. The limit is 500 characters per tag and no more than 250 tags per tag type
Sorting on duration is not supported and has been removed from the GUI as duration is dynamically calculated when it is requested
Documented how the user is now able to write a pipeline which executes files located in the /data/bin folder of the runtime environment
Updated a screenshot in the CWL Dragen pipeline creation section
Documented the new files tab on the pipeline screen which provides an easier overview of files related to your pipeline
Base
Added an example query for how to obtain the costs incurred by the individual steps of an analysis
Bench
Corrected file path in Jupyter Notebooks section
Added hint that using the option "latest" for public docker images increases the likelihood of errors
Improved explanation of how workspace permissions work
Cohorts
Updated Cohorts information
Storage
Added information on storage credentials and how to configure them
Network Settings
Updated network setting URLs
Workgroups
Documented that there is now an "all workgroup" option to easily reset workgroup filtering
Added a hint that your BaseSpace workgroup needs access to ICA if you want to use BSSH-managed projects
General
Data Management
Added information on allowed search field characters when searching for projects or data
Added a note to clarify that data is always linked to the root folder of the project
Documented that single files can now be directly downloaded without the need to open them first
API
Added guidance on how to prevent excessive API requests from exceeding the ICA API rate limit
Added a description to the API guide of how to copy multiple files with an API request
CLI
Added a warning to not use the CP -f command to copy or move data to a mounted location, as this will result in data loss
Updated CLI Command Index
Notifications
The data unarchived event ICA_DATA_114 has been added to the list of notification codes
Flow
Documented how the user is now able to write a pipeline which executes files located in the /data/bin folder of the runtime environment
General
General updates and improvements
Added mention of the collapsible menu bar in a brief overview of the GUI
Moved content in the Troubleshooting Guide from References section to relevant sections in the docs
Data Management
Added information on copying Docker images and reference data to different regions
Added hint that the service connector or CLI should be used for uploading large files
Added information about how bundles and projects need to be in the same region in order to be linked
Documented how there will no longer be a status displayed when adding an external docker image, as the status would always be shown as active even when the external image could not be reached
Added data formats: adat, zarr, tiff and wsi to the list of supported file types
API
Added information on how to set API keys
CLI
Updated command index with new commands
Updated the CLI release history with new build
Notifications
Added how to create SNS notifications in a region different from where the control plane is installed
Flow
Corrected the statement that, for CWL pipelines, creating a scratch space has to be done as part to the requirement section instead of a hint
Included how the analysis-details URL now points to the correct information when sharing the URL from your browser with other users
Added information for three new transfer compute types: transfer-small, transfer-medium, and transfer-large
Documented system capacities to reflect that there is a maximum of 50 concurrent runs per tenant
Bench
Updated URL whitelist expression for restricted bench workspaces
Updated Bench reference docs with details about when workspace will be stopped if not accessed for long duration
Cohorts
Added information on sharing a Cohort as a Bundle
Storage
Added guidance on using key prefixes when setting up an S3 storage configuration
Added a list of common issues encountered when connecting an AWS S3 bucket through a storage configuration to the Troubleshooting Guide
General
Removed obsolete Instrument Run Upload tutorial, now replaced with Sequencer Integration tutorial
Updated sequencer integration guide
Improved the description for “Tenant” billing mode
Data Management
Added information about how to create a new service connector from the “Schedule for Download” screen
Added information about the character limit for links in bundles and pipelines
CLI
Documented the new CLI environment variable ICA_NO_RETRY_RATE_LIMITING, which disables the retry mechanism
Updated the CLI release history with new build
Flow
Added information on how ICA compute type will be determined based on CPU and Memory
Bench
Updated documentation to reflect how paths can be added to allowed URLs on restricted setting for Bench
General
General updates and improvements
Updated the table of contents to match the Connected Analytics sidebar
Updated region named "Europe" to "Germany" for consistency with other regions named by country
Updated sequencer reference guide to reflect support for DRAGEN Amplicon autolaunch analysis using the NextSeq 1000/2000
Data Management
Documented how folders cannot include a backslash in their name
Documented how you can copy data between folders within the same project
API
Added information on how to start a pipeline with the API to the ICA API Beginner Guide
When using the Sample Creation Batch API endpoint to link nested files with the same name, the duplicate file on the root level will be ignored instead of resulting in an error. The API documentation has been updated to reflect this.
CLI
Updated the CLI release history with new build
Flow
Documented how additional files related to your Nextflow or CWL pipeline will be displayed alphabetically
Updated the CWL CLI Workflow tutorial to include a description of the behavior for how `runtime.ram` and `runtime.cpu` are evaluated
Updated analysis lifecycle documentation to include all analysis statuses
Base
Updated the Base Tables documentation to reflect how defining the precision of numbers when creating tables with SQL is not supported as this will result in a rounding issue
Updated Base Tables documentation to reflect how you can now see the Load Status of files uploaded to the table
Updated the Base Query documentation to inform users how to find the correct capitalization to use when querying the ICA reference data, which is case sensitive
Bench
Updated documentation to reflect how paths can be added to allowed URLs on restricted settings for Bench
Storage
Updated the AWS S3 help guide to include information about S3 bucket policies
Revised the Storage Configuration Troubleshooting Guide to be a general Troubleshooting Guide and included a section for data transfer issues
Network Settings
Updated the "Network Settings" reference page with URLs for Indonesia and UAE
General
General updates and improvements to reflect changes in graphical user interface
Updated the list of auto-launch analysis workflows in the Sequencer Reference table
Data Management
Updated the list of addresses which need to be whitelisted for the service connector
Notifications
Updated the list of Notification Subscriptions to include all possible notifications
CLI
Updated the CLI Command index to reflect addition of --exclude-source-path flag for ‘project data download’ command
Flow
Added information on how to add scratch space to all processes in a pipeline
Added note stating that batch jobs which have a final state such as Failed or Succeeded are removed from the activity list after 7 days
For Nextflow version 20.10.10, using the ‘copy’ method in thepublishDir directive for uploading output files that consume large amounts of storage may cause workflow runs to complete with missing files. Added information on workarounds to prevent this from occurring.
Bench
Added the 500GB limit per file for the FUSE driver
General
General updates and improvements
Clarified that bundle assets can only be linked once to the same data set
Removed outdated information about creating new tabs from workspace description
Added information about stopping Workspaces and removed information about pausing Workspaces, as pausing is no longer an option
Added information about creating an OAuth access token
Clarified that upload and download rights act independent of user roles
Updated the table which shows the regions ICA is hosted on to include all the available regions in alphabetical order
Added language specifying that folders with the name '.' are not supported
API
Added information about how to use data stored in Basespace as an input when starting an analysis via the API
CLI
Updated the CLI release history
Flow
Added information on how to define scratch space in CWL workflows
Described analysis runtime environment used to execute user-defined pipeline tasks, steps, and processes
Base
Added explanation of how to query arrays in table data
Added information about how to query views from Data Catalogues using the Snowflake FLATTEN function
Storage
Made it more explicit that the custom bucket name needs to be entered in the IAM configuration
Updated instructions for creating an AWS IAM user policy to remove a permission which is not correct
Transferred cloud-analysis auto-launch content to
Added warning that when you from one location to another, you should not change the source data while the Move job is in progress, as this will result in jobs getting stuck in progress
Transferred cross-product content, such as cloud-analysis auto-launch, to
Updated the link for software registration from ICA to the cross-product
Created a new page in the "Reference" section for , separating it from Software Release Notes
Added a video to demonstrate
Added for Israel region
Added for how to manually launch pipelines on NovaSeq X data by linking data from externally-managed project to ICA projects
Added a to demonstrate how to create and launch a Nextflow pipeline using the ICA CLI
Corrected the example for , which was using offset-based parameters
Added for Oncology Walkthrough guided example
Added for how to connect an AWS S3 bucket to ICA
Added link to which contains video demos to
Added a to demonstrate the end-to-end user flow for planning a NovaSeq X run with BaseSpace Run Planner and performing the run with data storage and automated analysis in ICA
Added preliminary
Updated the to account for no default scratch space