2023
2023 December 05 - ICA v2.21.0
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
2023 October 31 - ICA v2.20.0
General
General updates and improvements
Sequencer Integration: Added information that auto-launch from instrument is not currently compatible with MiSeq systems
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
2023 October 3 - ICA v2.19.0
General
General updates and improvement
Added link to Illumina Knowledge resource
Updated analysis autolaunch reference docs
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
2023 August 31 - ICA v2.18.0
General
General updates and improvements
Added ICA Terminology page to Reference
Logging: Documented event logging transfer of ownership
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
2023 June 27 - ICA v2.17.0
General
General improvements and fixes
User Management: Added details about how users can manage an overview of their Projects
Included a new reference to Illumina’s ICA Python SDK resource available on Github
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
2023 May 31 - ICA v2.16.0
General
General updates and improvements
User Management: Improved explanation of Team functionality
Data Management
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 tutorial 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
2023 April 25 - ICA v2.15.0
General
General updates and improvements
Updated guidance for selecting Project Location and availability of Storage Bundles when configuring a new Project
Updated details about paging in the Event Log
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
2023 March 28 - ICA v2.14.0
General
General updates and improvements
Refined and expanded reference documents for sequencer integration and analysis autolaunch, including new pages for sequencer reference and troubleshooting
Added tutorial for setting up a notification service and Lambda function in AWS for chaining pipelines
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
2023 February 28 - ICA v2.13.0
General
Added reference documentation for deep links to a folder
Updated Nextflow DRAGEN tutorial to include details about how to obtain access to the docker image on ICA
Improved documentation about pipeline activation codes
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
2023 February 13 - ICA v2.12.1
Added documentation for Analysis auto launch
2023 January 31 - ICA v2.12.0
General
Updated reference docs for workflow session events
Provided details about price-per-sample and zero-cost pipelines
Described pipeline Proprietary flag available
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
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