This page contains the documentation release notes for the current release. See the subpages for historic release notes.
New Functionality
Documented that multi-user workspaces now require an API key to use the CLI for authentication. This also applies to previously configured workspaces.
Updated Functionality
Updated default version to 25.10
Updated basic example
General Documentation updates
Added the --s3-no-check-bucket flag to rclone commands when copying across regions to avoid S3 bucket access errors.
Improved documentation on using your .
Added information that will not allow to copy a folder onto itself.
Updated import of images
Added new version
Various small GUI updates were documented
Added note on possible differences in table size, depending on how the information was written by Snowflake.
Improved information on rerunning jobs.
General
Added guidance about modifying existing Tools already added to a Pipeline
Updated for building a DRAGEN pipeline using Nextflow
Notifications
Updated list of system event notifications
Flow
Clarified expected behavior and recommended order of steps when connecting input to Tools and editing Input Details when building graphical CWL pipelines
Added information about details for monitoring Batch Jobs in Project Activity Screen
Storage
Added guidance on expected behavior when configuring user-managed AWS Buckets with Projects
General
Added for using scatter/gather for CWL graphical pipelines
Added information about Documentation tab in Nextflow pipelines
General
Added for building DRAGEN pipeline using Nextflow on ICA
Added for building DRAGEN pipeline using CWL on ICA
General
Added Quick Registration Guide
Added documentation for metadata models
Data Management
Provided list of ICA-supported data file formats
API
Included guidance on creating custom events for projects via the API
Added metadata model documentation
Updated supported ICA regions
Updated fields and descriptions under Tool Settings
Data Management
Added data privacy recommendations regarding uploading data files
Added guidance on supported characters in file/folder names
Added documentation for linking bundles to a project
Cohorts
Added ICA Cohorts Module documentation, including summary of features and example walk-throughs
Storage
Added instructions for setting up ICA v2 Bring Your Own Bucket (BYOB) with SSE-KMS key
Updated bucket name character length constraints
Added end-to-end tutorial highlighting DRAGEN Germline pipeline
Data Management
Added documentation for reference data
Flow
Added documentation for analysis output mappings
Added documentation for Nextflow configuration
General
General updates and improvements
Updated organization of Table of Contents
API
Documented how to archive or delete files programmatically using API endpoints
Added information about how the sort parameter is used to choose the default pagination
Flow
Added guidance about the ica_logs subfolder in the analysis output folder
Updated default scratch space reference documentation
Cohorts
Updated documentation to reflect OMOP ingestion and UI search for Procedures. The documentation changes also reflect instruction on the simplified ingestion and comparison sharing
Storage
Added explanation of the impact of billing mode when users bring their own S3 storage
General
General updates and improvements
Sequencer Integration: Added information that auto-launch from instrument is not currently compatible with MiSeq systems
General
General updates and improvement
Added link to resource
General
General updates and improvements
Added page to Reference
General
General improvements and fixes
User Management: Added details about how users can manage an overview of their Projects
General
General updates and improvements
User Management: Improved explanation of Team functionality
General
General updates and improvements
Updated guidance for selecting Project Location and availability of Storage Bundles when configuring a new Project
General
General updates and improvements
Refined and expanded reference documents for sequencer integration and analysis autolaunch, including new pages for sequencer reference and troubleshooting
General
Added reference documentation for deep links to a folder
Updated to include details about how to obtain access to the docker image on ICA
Added documentation for Analysis auto launch
General
Updated reference docs for workflow session events
Provided details about price-per-sample and zero-cost pipelines
Data Management
Documented an alternate method of adding files to samples and explained how to remove files from samples
Provided more guidance on data transfer options
Updated reference documentation for Data Copy functionality
Added a message to inform users that folder copy can be impacted in cases where a folder with the same name already exists in the target project
Added reference documentation for data integrity recommended practices
CLI
Updated CLI release history
Notifications
Updated Filtering section of Notifications page
Flow
Described analysis runtime environment used to execute user-defined pipeline tasks, steps, and processes
Updated ‘CWL: Scatter-Gather’ tutorial
Added documentation for analysis timeout
Base
Added a new tutorial for creating a Python dashboard to access Base metrics via API
Added information about Snowflake user/role setup
Included sample TSV file in Base Basics tutorial
Bench
Updated Fuse Driver troubleshooting
Updated the NovaSeq 6000 analysis auto-launch tutorial
SDK: Included new reference to Illumina's ICA Python SDK resource available on GitHub.com
Data Management
Add documentation around storage configuration synchronization behavior
Documented the new Data Copy functionality
Provided more guidance on data transfer options
Added a section describing Data Catalogue functionality
Added guidance about not using file names beginning with '/'
Service Connector: Added troubleshooting guidance for service connector
API
Added tip for users experiencing API rate limiting
Added troubleshooting guide for GetTemporaryUploadCredentialsAsync failure error scenario
CLI
Updated the CLI release history page with all required build files
Base
Improved descriptions and scenarios of Base tables and queries
Cohorts
Documented Cohorts Diagnosis Concept attribute search box functionality
Data Management
Document how to change Project owner
Updated Storage Size table for Compute on Pricing page to include XL, 2XL, 3XL
Improved explanation of hiding Projects when connecting to your own S3 bucket for data storage
Added default and shared explanation to storage documentation
Updated documentation to reflect the temp credentials returned for AWS datastore is for 36 hours
CLI
Added documentation for CLI config settings
Flow
Documented event for Analysis status transition
Added Nextflow best practices to reduce Analysis failures
Updated Pipeline activation code behavior explanation
Added documentation for specifying external docker images (i.e. Docker Hub)
Base
Added a tutorial for using Base via the CLI
Updated documentation to mention that Schema does not contain type ‘variant’
Documented Base query which joins to tables can result in duplicate columns
Documented SnowSQL show view vs show grants
Bench
Documented Bench permission changes
Cohorts
RNASeq ingestion
Applicable user-supplied RNASeq visualizations – Raw Expression Values in GTEx-like table
NeedlePlot
Structure Variant list
Data Management
Clarified the visibility of Batch jobs for different users in a Tenant
Bundles: Provided more details about Bundle linking and unlinking with data in folders
CLI
Updated the CLI command index
Updated the CLI release history page with all required build files
Added link to legacy ICA v1 CLI release history page
Flow
Described Analysis runtime environment used to execute user-defined pipeline tasks, steps, and processes
Added an explanation for how external S3 files can be used as inputs to Pipelines
Bench
Added an explanation that Project/Tenant Administrators can stop running Workspaces
Added guidance for downloading data when using JupyterLab Notebooks
Cohorts
Added instructions for RNA-Seq data ingestion into Cohorts
Added reference documentation for multi-cohort marker frequency and needle plot comparisons
Network Settings
Updated the list of whitelisted URLs on https://help.ica.illumina.com/reference/r-networksettings
Added guidance on versioning Bring Your Own storage buckets
Improved explanation on linking to data from other projects
Described functionality of Secondary Data
Updated guidance for file upload size
Updated configuration guidance for Bring Your Own Storage bucket using S3
Updated list of supported Data formats
Added a for mounting project data using the CLI
API
Added information to launch analysis API spec on output mappings overwrite behavior when files already exist on the target project during analysis output
CLI
Added CLI authentication best practices for setting up, validating, and resetting the configuration of a user's profile
Network Settings
Updated Network Settings regional S3 URLs list
Flow
Added a tutorial for building and running a CWL graphical pipeline
Included best practices for minimizing errors in Nextflow pipelines by adding retry logic
Base
Updated the Base schedule descriptions to include information about Metadata and Administrative schedules, as well about frequency of scheduled ingestions
Bench
Updated restrictions of available features when in the FUSE mount in a Workspace
Updated descriptions about Bench restrictions, including details about whitelisted URLs
Refined and expanded guidance for sequencer integration and analysis auto-launch, including adding a new tutorial for NovaSeq 6000 and expanding the sequencer reference table
Added tutorial for using scatter/gather for Nextflow pipeline
Updated information about data archive pricing
Updated software registration guide
Data Management
Added guidance that a sample must be complete to be linked to a Bundle
Included information about receiving and using Entitled Bundles
CLI
Updated CLI command index
Updated CLI binary and checksum files
Flow
Refined Pipelines documentation around clone function
Base
Added information that Base Tables must not contain reserved Snowflake terms in their definition
Added description for Copy Number Variants and Structural Variants tables now viewable in ICA Base for Cohorts
Cohorts
Added description for hg19 support as an alternative during ingestion for Cohorts
Included guidance for setting override behavior for file output of advanced output mappings
Described selection of entitlements when creating a Project
Updated FAQ with guidance on analysis run times
Updated explanation for adding Terms of Use to a Bundle
Included details for the Event Log
Data Management
Explained how to unlink a folder from a project
CLI
Updated CLI command index
Fixed a bug in the CLI release history files and updated integrity check instructions
Flow
Described limitation on amount of input files for analyses
Base
Added tutorial for accessing Base databases and tables via snowSQL
Refined and expanded description of Base Activity screen
Bench
Expanded description of Bench Activity screen
Explained multi-factor authentication compatibility with Bench and provide workaround suggestion
Cohorts
Added instructions to remove specific subjects from a cohort
Documented cohort needle plot enhancements: List of subjects and specific frequency data entry
Updated cohorts ingestion instruction including metadata documents, GWAS ingestion, OMOP ingestion, Structural Variant ingestion, and hg19 lift-over information
Added reference documentation for using Cohorts attributes metadata template
Added instruction for cohorts attribute query enhancement on numeric data
Storage
Clarified details about S3 bucket behavior and Bring Your Own Storage bucket (BYOB) compatibility
Network Settings
Updated documentation about network settings for pipelines
Provided guidance about deleting old versions of Bring Your Own Storage buckets
Explained limit of number of projects and bundles allowed per tenant
Data Management
Created new page for and updated list of available data file formats
Updated guidance for requirements for adding assets to a bundle
Updated service connector reference docs
Explained progress details for service connector
Added information about archiving or unarchiving a file
API
Added descriptions of cursor and offset pagination when using the API
CLI
Expanded explanation of default settings for the CLI
Base
Added guidance for Base JSON export
Updated supported formats for Base table/query export
Updated description of Base Activity screen
Added guidance for Base schedule's optional parameters
Bench
Provided documentation for available Bench compute types
Data Management
Service Connector: Updated information in the service connector screen to reflect the name change from "Type of Files" to the more accurate "Assign Format"
Added details about which data formats are compatible with UI Preview
Added details about syntax for linking to individual analyses and workflow sessions
Explained how to add assets to a bundle
CLI
Provided a command index for the ICA v2 CLI
Expanded explanation on default settings for the CLI
Clarified details about hidden metadata files behavior during CLI copy for MacOS users
Flow
Added information about standard and economy tier selection for compute types
Expanded guidance for XML-based input form required of pipelines defined using the "Code" mode
Expanded guidance on importing external docker images in ICA when running a pipeline
Included information about tile/grid view for analysis logs
Added guidance about balancing analysis queuing priorities when setting up a Project
Updated information about Batch Jobs
Added guidance about overriding CWL workflow requirements
Base
Added guidance on using Cohorts data in ICA Base
Cohorts
Included video overview of Cohorts Multiomics Cancer workflow
Updated steps for Cohorts ingestion
Updated steps for Cohorts analysis
Updated Functionality * Added information on the base sync button for synchronization with Snowflake.
Added ORA compression pipeline pricing details
Documented that new workspaces are now created with single-user as default.
General Documentation updates * Explained pipeline naming conventions
Consolidate way of compute pricing
Updated JSON event payload matching example on the notifications page.
Documented for DRAGEN map align pipeline on FPGA2
Explained the numberOfExpectedUploadedFiles parameter on the page.
The resource requirements FPGA1, FPGA2, GPU and software-only have been removed from the Analysis configuration screen as the transition period for which it was needed has ended. These settings were reset during this update, ensuring your pipeline will continue working.
New Functionality
Documented how pipeline deprecation and archival work.
The logs folder can now be selected when starting an analysis.
Documented that now show the used resource type.
now has an option to enable/disable ephemeral storage.
Updated Functionality
Resource requirements have been deprecated and removed from configuration.
Added that project contributor can now also delete data.
General Documentation updates
Added that external s3 inputs only support file inputs, not folders.
Added on the 2 minutes spot instance termination window.
New Functionality
Documented multinode configuration of Bench instances
Updated Functionality
Updated pipeline examples to FPGA2
Added YAML formatting for custom input example.
Documented the source column for images.
The section has been updated to the new interface design.
Documented that only the first 200 chars of a string, record or variant field are included in the results grid. The complete value is available through clicking the "show details" link.
General Documentation updates
Added that DRAGEN Iterative gVCF Genotyper (iGG) will incur a license of 0.6216 iCredits per gigabase.
Added note that will be sunset by AWS and replaced with FPGA2.
New Functionality
-
Updated Functionality
The legacy run report management tab "analysis report" present in /analyses details has been removed in favor of the recently introduced "report" tab.
Added how to parse JSON into tables for .
color descriptions have been updated.
Documented file 10 MB size limit and 200 fields limit. You can no longer use the parameter 'emptyValuesAllowed' with the field type "fieldgroup" on a JSON-based input form
General update to documentation.
section has been updated in accordance with user interface update.
Replaced generation instructions with links to the relevant documents.
General Documentation updates
Added explanation of how to out of externally-managed projects.
Added information on protection against public access.
This release (2.37.0) contains major changes to how workspaces operate.
By default, existing workspaces will have a 7 day automatic shutdown, so once started, they will shut down after 7 days to help save costs. If you need to keep your workspaces running longer than 7 days, change the automatic shutdown of your workspace to a longer period. You can still manually stop your workspace when you are not using it.
Currently running workspaces will shut down after 7 days after the upgrade to 2.37.0
Workspaces will restart every 30 days for security reasons, regardless of the automatic shutdown setting.
New Functionality
Documented that you can now specify if rare resources (F1, F2 and GPU) must be available on your pipeline.
Documented the new automatic bench shutdown feature. Default shutdown after 7 days, reboot after 30 days.
Updated Functionality
Added information on how to upload multiple files with the as wildcards are not supported.
Documented that unknown file types are considered to be binary to prevent them being displayed as text.
Documented how to create a nested folder structure when creating an .
General Documentation updates
Updated version support lifecycle
Added information to contact your Intrusion Detection System vendor when actions performed by ICA trigger warnings.
DRAGEN pipelines running on fpga2 compute type will incur a DRAGEN license cost of 0.10 iCredits per gigabase of data processed, with additional discounts as shown below.
80 or less gigabase per sample - no discount - 0.10 iCredits per gigabase
> 80 to 160 gigabase per sample - 20% discount - 0.08 iCredits per gigabase
> 160 to 240 gigabase per sample - 30% discount - 0.07 iCredits per gigabase
> 240 to 320 gigabase per sample - 40% discount - 0.06 iCredits per gigabase
> 320 and more gigabase per sample - 50% discount - 0.05 iCredits per gigabase
If your DRAGEN job fails, only the compute cost is charged, no DRAGEN license cost will be charged.
DRAGEN Iterative gVCF Genotyper (iGG) will incur a license cost of 0.6216 iCredits per gigabase. For example, a sample of 3.3 gigabase human reference will result in 2 iCredits per sample. The associated Compute costs will be based on the compute instance chosen.
New Functionality
Added information on pipeline pricing when running DRAGEN on FPGA2 which now offers discounts.
Documented the dropValueWhenDisabled flag for JSON input forms.
Added information on how to create the output folder when starting an .
Documented how to share with another user
Documented that a is now also shown when the analysis is aborted
Added .yml to documentation
Updated Functionality
Various updates to the chapter
Raised report limit from 20 to 200
General Documentation updates
Changed from 96 cores to 92 and from 768 GiB to 700 GiB to factor in overhead.
Improved documentation on
DRAGEN pipelines running on fpga2 compute type will incur a DRAGEN license cost of 0.10 iCredits per gigabase of data processed, with additional discounts as shown below.
80 or less gigabase per sample - no discount - 0.10 iCredits per gigabase
> 80 to 160 gigabase per sample - 20% discount - 0.08 iCredits per gigabase
> 160 to 240 gigabase per sample - 30% discount - 0.07 iCredits per gigabase
> 240 to 320 gigabase per sample - 40% discount - 0.06 iCredits per gigabase
> 320 and more gigabase per sample - 50% discount - 0.05 iCredits per gigabase
If your DRAGEN job fails, only the compute cost is charged, no DRAGEN license cost will be charged.
DRAGEN Iterative gVCF Genotyper (iGG) will incur a license cost of 0.6216 iCredits per gigabase. For example, a sample of 3.3 gigabase human reference will result in 2 iCredits per sample. The associated Compute costs will be based on the compute instance chosen.
Navigational change. The Projects navigation item moved from the left-side navigation to the top of the Project details.
New Functionality
Reports now have an option to define patterns for detecting report files in the analysis output. On opening an analysis result window of this pipeline, an additional tab will display these report files.
Added information on sorting and filtering behavior when sharing links. These are now retained when sharing or navigating away from an inventory.
Updated Functionality
Documented changes.
The navigation menu is now collapsible
The Product overview selection menu moved from top left to top right
General Documentation updates
Replaced directory with folder where possible for consistency
Added information that cloned pipelines and externally linked pipelines can coexist in a project even if they have the same name.
New Functionality
New documentation on Pipeline Development in Bench has been added. (Experimental Feature)
Added documentation on non-indexed folders to the data section
Added /api/projects/{projectId}/analyses/{analysisId}/usage as API endpoint for analysis price on the page
Documented the single-user option of
Updated Functionality
Documented the move of from System Settings > Storage > Credentials to System Settings > Credentials.
Updated that editing is now done at Projects > your_project > Project Settings > Details > Edit
General Documentation Updates
Improved description of roles in
Added information that you can only link to a project if that project belongs to a tenant who has access to the bundle.
General
Added experimental feature: Streamable inputs for JSON-based input forms. Adding "streamable":true to an input field of type "data" makes it a streamable input.
Documented version updates with removal of support for Java version 8 and added note on decommissioning of Nextflow 20.10.0 in the near future
Removed section on showing current workspace user as the functionality has been removed
Added information to to incorporate a failsafe mechanism by polling long-running analysis states when integrating with external software
Added : The event for analysis status changes with event code ICA_EXEC_028 is generated but not shown in the event log for ICA Projects with billing mode tenant. Notifications for this event will keep working
Flow
Added information how to see the price of an Analysis at Projects > your_project > Flow > Analyses > your_analysis > Details tab. See for details.
Documented that aborting an analysis is now also possible from the details screen
CLI
Added links to version 2.33
Data management
Documented updates to legal screen and tenant invite of .
Storage
Extended documentation on Activity - Data transfers screen
Added emphasis on not using the root folder of your .
General
Extended documentation on Activity - Data transfers screen
Verified and updated the project navigation structure in the online help
Flow
Documented the "display failed steps" option of failed
Documented the ongoing actions column from the column list in the view which allows to see if there are any ongoing actions on data
Documented the additional actions which are now possible with
CLI
Improved for Nextflow JSON project pipelines start nextflowjson example
Bench
Added to bench workspace sizes
Added information on downloading images
Cohorts
Updates to Spinner and information
Analysis outputs moved to a separate tab.
field is superseded by short description .
Added information that Bench uses project billing, not tenant billing.
Fixed syntax error in ICA XML form instructions.
Improved key prefix section for storage section.
Added information to retrying on
Added information on how to run in Bench.
Minor updates to
Minor typographical updates
Clarified that individual user rights override rights assigned as workgroup on the page.
The concurrent limit of 50 was incorrectly documented, in practice this is 20 or less, depending on a number of factors.
Added advice to use the process-time process when designing proceses.
Added FPGA2 large
General improvements to for better indexing.
Improved documentation.
Update on accessing for Dragen 4.3+
Updated the usage of the term workflow to be more consistent.
Added information on how to unblock deleting when there are undelivered notifications.
Removed the Anonymize via Schedule functionality documentation as the feature has been removed from the application.
Improved descriptions of data filtering for forms
Updated detail screen to the latest version
page documentation has been improved
The back button has been replaced by a breadcrumb menu
The Projects overview moved from top left to top center-left
Updates to documentation
Added on /api/projects/{projectId}/analysis:nextflowWithCustomInput
Improvements to chapter .
Added information that you can only link bundles to a project if that project belongs to a tenant who has access to the bundle
Added that when changing project owner, the project owner will automatically get all necessary permissions.
Added prerequisite that both the CLI and the service connector require x86 architecture or emulation.
Improved information on Pipeline linking
Added ICA_DATA_105 to
Updates to section
Documented that DRAGEN pipelines (> 4.3.13) are no longer cloneable as they contain proprietary information
Documented version updates with Added support of Nextflow version 24.10.2 (Experimental) and removal of support for Java version 8
Updated descriptions
Added information that exporting float values from base will result in different formats between JSON and CSV formats
Clarified that uploaded files are in status partial until upload is complete, when they become available
Documented that metadata is no longer searchable in the project search panel
Various updates to documentation
Added TX- Ramp certification to
Added background information on tags
Updated example to be in sync with latest software version.
Update OAuth access token lifespan from 2 to 12 hours in
Documented that it is now possible to navigate from analysis results to the data of that analysis
Added information on functionality which offers more protection for sensitive information than using the ICA teams page to invite other users to use your assets
Update to -form emptyValuesAllowed parameter description. When maxValues is greater than 1 or and emptyValuesAllowed is true, the values may contain null entries. Default is false
Added information that is only available in region US-east-1 and both FPGA-large and himem-X-large have limited availability
Documented resource types for compute
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
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
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
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
General
Transferred cloud-analysis auto-launch content to
Updated CLI release history with new build
General
General updates and improvements
Transferred cross-product content, such as cloud-analysis auto-launch, to
General
Added for how to manually launch pipelines on NovaSeq X data by linking data from externally-managed project to ICA projects
Data Management
General
General updates and improvements
Added mention of the collapsible menu bar in a brief overview of the GUI
General
Added for Oncology Walkthrough guided example
Added for how to connect an AWS S3 bucket to ICA
General
General updates and improvements
Updated the table of contents to match the Connected Analytics sidebar
General
General updates and improvements to reflect changes in graphical user interface
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
General
General updates and improvements
Clarified that bundle assets can only be linked once to the same data set
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
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
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
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
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
Replaced all instances of "volume configuration" with "storage configuration" for consistency, as they have the same definition
Created a new page in the "Reference" section for Document Revision History, separating it from Software Release Notes
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
Added a video to demonstrate how to connect an AWS S3 bucket with SSE-KMS Encryption enabled
Network Settings
Updated network setting URLs
Added network settings for Israel region
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
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
Added a tutorial to demonstrate how to create and launch a Nextflow pipeline using the ICA CLI
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
Corrected the example for cursor-based pagination, which was using offset-based parameters
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
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
Updated sequencer reference guide to reflect support for DRAGEN Amplicon autolaunch analysis using the NextSeq 1000/2000
Added link to ICA YouTube channel which contains video demos to Resources page
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
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
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 preliminary beginner's tutorial for ICA API usage
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
Updated the to account for no default scratch space
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