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

  • Updated Illumina Connected Software registration guide

• 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

• Flow

  • Improved the tutorial for Scatter-gather method in Nextflow

  • Improved tutorial for Nextflow: RNASeq Lift

  • Added a tutorial for converting open-source nf-core pipelines to ICA Nextflow pipelines

  • Updated reference docs for starting analyses

  • Improved tutorial for scatter-gather in CWL

• 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