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2024

2024 December 2 - ICA v2.31.0

  • General

    • Updated decimal separators from commas to dots

    • Values can be filtered with ‘equal to’ and ‘different from’ operators

    • Transferred Account Management information to Illumina Connected Software 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.

2024 October 30 - ICA v2.30.0

  • 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

2024 September 25 - ICA v2.29.0

  • General

  • 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

    • Added warning that when you move data 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

2024 August 28 - ICA v2.28.0

  • General

    • General updates and improvements

    • Transferred cross-product content, such as cloud-analysis auto-launch, to Illumina Connected Software help site

    • Updated the link for software registration from ICA to the cross-product ICS software registration page

    • 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

  • Network Settings

  • 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

2024 June 25 - ICA v2.27.0

  • General

    • Added tutorial in ICS docs for how to manually launch pipelines on NovaSeq X data by linking data from externally-managed project to ICA projects

  • 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

2024 June 5 - ICA v2.26.0

  • 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

    • 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

2024 April 24 - ICA v2.25.0

  • General

    • Added video demo for Oncology Walkthrough guided example

    • Added video demo for how to connect an AWS S3 bucket to ICA

    • 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

2024 March 27 - ICA v2.24.0

  • 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

    • 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

2024 February 28 - ICA v2.23.0

  • General

    • General updates and improvements to reflect changes in graphical user interface

    • Added a tutorial 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

    • 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

2024 January 31 - ICA v2.22.0

  • 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

  • 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 Nextflow DRAGEN tutorial 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

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