2025

2025 March 13 - ICA v2.33.2

Fixed Issues

• Cohorts

  • Fixed an issue where users could not search the hierarchical disease concepts because of incorrect URL in the UI configuration.

2025 February 26 - ICA v2.33.0

New Features and Enhancements:

• General

  • The current tab (e.g. analysis details, analysis steps, pipeline details, pipeline XML config, ...) is now saved in the URL, making the back button bring the user back to the tab they were in

  • Users are now able to go from the analysis data details to their location in the project data view

  • Toggling the availability of the "Acceptance list" tab in the legal view by a tenant admin used to be possible in the "Restrictions of monitoring" tab when editing the bundle. It has been moved to the legal tab

• Data Management

  • New data formats available:

    • TRANSCRIPT: *.quant.sf, *.quant.sf.gz

    • GENE: *.quant.genes.sf, *.quant.genes.sf.gz

    • JSON.gz are now recognized as JSON format

  • New endpoint to create files POST /api​/projects​/{projectId}​/data:createFile

  • Endpoint POST ​/api​/projects​/{projectId}/data has been deprecated

  • The endpoint GET​/api​/projects​/{projectId}​/data​/{dataId}​/children now has more filters for more granular filtering

  • Users are now able to filter based on the owning project ID for the endpoint GET​/api​/projects​/{projectId}​/data

  • The links section in Bundle details and pipeline details now has proper URL validation and both fields are now required when adding links. In the case of editing an older links section of a bundle/pipeline, the user won't be able to save until the section is corrected

• Flow

  • The cost of a single analysis is now exposed on its details page

  • Users can now abort analysis while being in the analysis detail view

  • '.command.*' files from Nextflow WorkDir are now copied into ICA logs

• Base

  • Expanded the lifespan of Base OAuth token to 12h

• Bench

  • Removed display of the current user using a bench workspace

• Experimental Features

  • Streamable inputs for JSON-based input forms. Adding "streamable":true to an input field of type "data" makes it a streamable input.

Fixed Issues:

• General

  • Fixed an issue which would overgenerate event calls when an analysis would run into diskfull alert

  • Improved API error handling so that being unable to reach ICA storage will now result in error code 500 instead of error code 400

  • Added a full name field for users in various grids (Bench activity, Bundle share, ...) to replace the separate first and last name fields

  • In the event log, the event ICA_EXEC_028 is now shown as INFO, it was before displayed as ERROR which was not correct

• Data Management

  • Fixed an issue which would result in a null-pointer error when trying to open the details of a folder which was in the process of being deleted

  • Fixed an issue with bundle invites, now making it clear that you can only re-invite someone to that bundle if the previously rejected invites are removed

  • Various improvements to hardening data linking

  • Fixed an issue where the folder copy job would throw an Access Denied when copying file with _ in path

  • Fixed an issue that would produce a false error notification when changing the format from the data details window

  • Fixed an issue where an out of order event for Folder Deleting and Deleted would occur in rare scenarios

  • Fixed an issue regarding path too long error for Folder copy/Move operations for Managed bucket src and destination

• Flow

  • Improved API file handling to better handle post processing when downloading the results from a successful analysis which could previously result in failed analysis being reported as result

  • Fixed an issue which resulted in a null-pointer error when starting an XML based CWL pipeline with an input.json

  • Fixed an issue which caused user references with slashes to prevent errors in failed runs from being displayed

  • Fixed an issue where the value 0 was not accepted in pipeline's inputForm.json for fields of type number

  • Fixed an issue where users could not retrieve pipeline_runner.0 logs file while a pipeline is running

  • List fields in filter options are now saved if closing and reopening the filter panel

  • Fixed an issue where the start time of an analysis's step would be intermittently reported wrongly

  • Fixed an issue where retrieving outputs of analysis through API was not consistent between analysis with advanced output-mapping or without

  • Improvements to the handling of large file uploads to prevent token expiry from blocking uploads

• Base

  • Fixed an issue where shared database would not be visible in project Base, this was fixed in the newer version of Snowflake 9.3

• Bench

  • Removed the rollback failed operations function on docker images as it had little to no benefit for end-users and frequently caused confusion

  • Fixed issue where users without proper permissions could create a workspace

• Cohorts

  • Fixed issues where users doing large scale inputs of data received timeouts from the ICA API for file retrieval

  • Fixed issue with large OMOP data sets causing out of memory issues on input

  • Fixed issue where the 'Search Attributes' box in the 'Create Cohort' was not scrolling after typing a partial string.

  • Fixed issue with line-up of the exon values under exon track.

  • Fixed issue where subject attribute search box overlapped with other items when web browser zoom used.

  • Fixed issue where single subject view displayed concept codes and now shows concept names for diseases, drugs, procedures, and measurements.

2025 February 13 - ICA v2.32.2

Fixed Issues

• Flow

  • Added retries for analysis process infrastructure provisioning to mitigate intermittent (~1%) CWL analysis failures. This impacts analysis steps failing with error "OCI runtime create failed" in logs.

2025 January 29 - ICA v2.32.0

Features and Enhancements

• General

  • The End User License Agreement has been updated

  • New API endpoints for Docker Images management:

    • GET /api/dockerImages

    • GET /api/dockerImages/{imageId}

    • POST /api/dockerImages:createExternal

    • POST /api/dockerImages:createInternal

    • POST /api/dockerImages/{imageId}:addRegions

    • POST /api/dockerImages/{imageId}:removeRegions

  • Split up CWL endpoint (POST/api/projects/{projectId}/analysis:cwl) in 2:

    • CWL analysis with a JSON input (POST /api/projects/{projectId}/analysis:cwlWithJsonInput)

    • CWL analysis with a structured input (POST /api/projects/{projectId}/analysis:cwlWithStructuredInput)

• Data Management

  • Next to using the Teams page to invite other tenants to use your assets, a dedicated bundle-sharing feature is now available. This allows you to share assets while also shielding sensitive information from other users, such as who has access to these assets

  • Improved visibility on ongoing data actions move and copy on the UI

  • Users can now add/remove bundles in an externally managed project. It will not be possible to link a restricted Bundle to a project containing read-only, externally managed data

• Flow

  • JSON based input form now has a built-in check to make sure a tree does not have any cyclical dependencies

  • Added commands for creation and start of CWL JSON pipelines in the CLI

  • Users can now input external data into JSON based input forms from the API

• Bench

  • Bench workspaces can be used in externally managed project

• Cohorts

  • Users can now filter needles by customizable PrimateAI Score thresholds, affecting both plot and table variants, with persistence across gene views

  • The 'Single Subject View' now displays a summary of measurements (without values), with a link to the 'Timeline View' for detailed results under the section 'Measurements and Laboratory Values Available

Fixed Issues

• General

  • Fixed an issue which caused authentication failures when using a direct link

  • Actions which are not allowed on externally-managed projects are now greyed-out instead of presenting an error when attempting to use them

  • Improved handling of regions for Docker images so that at least one region must remain. Previously, removing all regions would result in deleting the Docker image

  • Improved filtering out Docker images which are not relevant to the current user

  • Tertiary modules are no longer visible in externally-managed projects as they had no functional purpose there

  • Fixed an issue where adding public domain users to multiple collaborative workgroups would result in inconsistent instrument integration results

  • Added verification on the filter expressions of notification subscriptions

  • Fixed an issue where generating a cURL command with empty field values on the Swagger page resulted in invalid commands

  • Added information in the API swagger page that the GET ​/api​/projects​/{projectId}​/data endpoint can not retrieve the list of files from a linked folder. To get this list, use parentfolderid instead of parentfolderpath

  • For consistency reasons, UUID has been renamed to ID in the GUI

  • The bundle administrator will now see all data present in the bundle, including all versions with older versions in a different color

• Data Management

  • Removed deprecated cloud connector from Activity/Data transfers option

  • Removed the erroneous 'Import' option from the direction filter which was present in Activity/Data transfers

  • Fixed an issue where entering multiple Download rules for a Service connector would result in not setting the correct unique sequence numbers

  • Improved the error message when erroneously trying to link data from an externally-managed subject to a sample. This is not allowed because data can only be linked to a single sample

  • Fixed an issue where filtering on file formats was not correctly applied when selecting files and folders for downloads with the service connector

  • Improved the download connector to fix Chrome compatibility issues

  • Fixed an issue where it was possible to update linked files if you had access to both the original file and the linked file

  • Fixed an issue where samples from externally-managed projects were not correctly linked to analyses

• Flow

  • Fixed a JSON validation error when attempting to have more than one default value for a field configured as single value which would result in index out of bounds error

  • Fixed an issue where numerical values with a scientific exponent would not be correctly accepted

  • Improved the API error validation for usage of duplicate group id fields

  • Improved error handling when starting analysis via API with an incorrect DATA-ID in the request body

  • Improved handling of incorrect field types for JSON-based input forms

  • Improved error handling when trying to use externally-managed data as reference data

  • Removed the superfluous "save as" button from the create pipelines screen

  • Fixed an issue where refreshing the analysis page would result in an error when more than 1 log file was opened

  • Upon clicking "start run" to launch a pipeline, ICA now redirects to the "Runs" view

  • Fixed an issue where the minimum and maximum numbers of high values were incorrectly rounded for JSON input forms

  • Fixed an issue where the user could pass a value with the "values" parameter instead of "dataValues" for the data field type

  • Fixed an issue which caused the "dataValues" parameter to be valid for the textbox field type instead of "values"

  • Improved timeout handling for autolaunch workflow

  • Fixed auto-launched TSO500 pipelines using the StartsFromFastq=false setting to direct analysis outputs to the ilmn-analyses folder within the ICA project data

  • Added JSON validation to ensure only a single radio button can be selected at the same time as part of a radio-type list

  • Removed the Simulate button from the View mode pipeline detail screen

  • The proprietary option can now be set via the CLI on create pipeline commands

  • Added a validation to prevent pipeline input forms from having the same value for 'value' and 'parent'

• Bench

  • Fixed an issue which caused bench workspaces to have incorrect last modified timestamps that were over 2000 years ago. They now will use the correct last updated timestamp

  • Adding or removing regions to bench images is now possible

  • Improvements to how workspaces handle deletion

• Cohorts

  • Fixed issue where the error message for invalid disease IDs did not disappear after selecting the correct ontology, and filter chips were incorrectly created as 'UNDEFINED

  • Fixed issue where the search functionality in the ingestion file picker was not working correctly in production, causing a long delay and no files to display after entering a filename or folder name

  • Fixed issue where the Clinvar significance track was not resetting properly, causing the resized track and pointer to not return to the original position, with triangle data points displaying empty whitespace

  • Fixed issue where the 'PARTIAL' status for HPO filter chips was incorrectly removed when multiple chips were selected

  • Fixed issue where the pagination on the Variant List Needle Plot incorrectly displayed 741 items across 75 pages, causing a discrepancy with the actual number of displayed variants

  • The 'Search Attributes' box in the 'Create Cohort' page now properly scrolls and filters results when typing substrings, displaying matching results as the user types

  • Fixed issue where the search spinner continued loading after the search results were displayed in the Import Jobs table

  • Fixed issue where the 'stop_lost' consequence in Needleplot is corrected to 'Frameshift, Stop lost,' and the legend updated to 'Stop gained|lost.' The 'Stop gained' filter now excludes 'Stop lost' variants when the 'Display only variants shown in the plot above' toggle is on

  • Fixed issue where intermittent 500 error codes occurred on USE1 Prod when running Needleplot/VariantList queries with the full AGD/DAC dataset (e.g., LAMA1 gene query)