Base

• Minor updates to the Base UI

Bench

• Multi-user bench will no longer authenticate automatically.

• Created images will always be owned by the creating user, regardless of which domain the user is in

Flow

• Improved guardrails to reduce bugs when users interact with pipeline statuses

Cohorts

• -

Analysis and workflow details now appropriately show in the UI.

Validation errors on invalid email entries for analysis notifications no longer persist after the email is corrected

Refreshing an analysis input form no longer automatically fills the email notification field with the last used email address

Base

• -

Bench

• -

Data Management

• Fixed an issue that caused copy and paste of URL to not show filtered results when combining folders with filters

• Data copy now prevents recursive copying of data with the "copy from" command

Cohorts

• -

[CLI] Fix folder upload "panic: close of closed channel" error

[API] Fix API for project creation returning success with invalid storage configuration provided

[Bench] Fix for docker build logs not showing when build is interrupted

Fix population of sample metadata from multiple analyses on the same sample

Fix error message for missing docker image on tool creation

[CLI] Fix pipeline create command to make pipeline code an argument instead of a flag parameter

Fix UI element for tags to remove active button appearance

Fix error when attempting to link pipeline with no pipeline selected

Fix error message when attempting to add field to Base table schema with invalid characters

Fix issue with analysis outputs files and logs not showing after analysis completion

Fix UI issue with pipeline selection in the Generated by Pipelines field of the view to create a Base s

Fix issue with a duplicate workspace being created while editing a workspace

Fix issue for table creation using schedule for metadata

Fix Base viewer role when applied to workgroups

Fixed Issue: optional parameters for Nextflow pipeline cause error when value not provided

Fixed issue when selecting data records to export from the Data overview page on a Bundle

Fix for Base saved queries not visible in shared project

Fix minor price calculation error (rounding) for Base storage

OpenAPI v3 API Spec published at https://ica.illumina.com/ica/api/swagger/index.html

Added sort parameter to several APIs

Custom event payload is defined as a json

Separate call to retrieve metadata model fields available

Add rclone temporary credentials support in the API to retrieve folder upload session details

Tokens API POST also contains basic authentication

Activation code endpoints are aligned with start analysis endpoints

Base templates cannot be deleted

Information can be written from Bench to Base

Viewer/Contributor permissions are introduced in Snowflake

Saved Template details can be edited

Access via Illumina authentication is available

Snowflake access token can be created

Added new Bundles feature for sharing data with other users

ICA allows the user to connect an S3 bucket as storage instead of an Illumina managed storage

An overview of all storage configurations is available

Secrets can be managed for the storage configuration

A new storage configuration can be added

The health status of a configuration can be monitored

A storage configuration can be deleted when not used in a project

Storage type and health are displayed in the overview

When selecting own storage ICA will return you a list of all BYOBs in the chosen region

A default bucket can be selected for every region

Data is automatically archived/deleted when the grace period (if present) is over

Data is archived/deleted automatically by a housekeeping mechanism

An admin user can change the date to be archived/deleted at any time

Data has a status

Data format is automatically detected at creation

Files can be grouped in a sample

Data can have additional linked projects

The data screen shows project data and data linked via a bundle

3 new columns are present in the data grid: "Owning Project", "Linked Projects" and "Linked Bundles"

The record is displayed in the data grid depending on the data being linked or not

Filter on Status with checkboxes on status values is possible

Total Data Size is available

Data can be linked/unlinked to/from a project

Only root parent files and folders are shown when opening the data grid

Deleted status does not exist anymore

Data from projects with Data Sharing disabled cannot be linked

Project is hidden instead of (soft-)delete

Metadata models can be created for linking to a project

Add support for Nextflow pipeline language

A pipeline input can have multiple formats

Output JSON for CWL analysis is shown

Ongoing logfiles are available for the user

You have two options to define a CWL pipeline: Graphical editor or code

Test connection button is available for SQS

Checkbox is added to toggle view between all rules or only your own rules

Notification channels can be validated

Subscription can be edited

Custom subscriptions are possible

Notifications can be received via SQS, SNS, Mail, and Webhook

All users have an overview of all the notifications used in their tenant

Notification channels are only visible for tenant admins

Notifications can have a filter expression to only receive specific events

A project administrator can grant permission to a single user on a project

A project administrator can invite somebody unknown to ICA to his project

A contributor can manage reference data

A project administrator can define who pays for using my project

A project administrator can invite a workgroup to a project

When multiple project roles are given to a user/workgroup the correct project role is applied

Team-page in projects and bundles are aligned

Reference data can exist in multiple regions

Species and type are being populated per tenant

Data can become reference data

Data tree shows all the regions in which the reference data is available

FAILED and PARTIALLY_SUCCEEDED are increased to 90 days

Data Management

• Data can now be uploaded into the BaseSpace-managed project

Flow

• Analyses can now be started from the pipeline details screen

• The analysis details now contain two additional tabs displaying timeline and execution reports for Nextflow analyses to aid in troubleshooting errors

• Introduced a start command for starting a Nextflow pipeline with a JSON-based input form

• Added new API endpoints to create a new CWL pipeline and start an analysis from a CWL pipeline with JSON-based input forms:

  • POST/api/projects/{projectId}/pipelines:createCwlJsonPipeline

  • POST/api/projects/{projectId}/analysis:cwlJson

• Pipelines with JSON-based input forms can now pre-determine and validate storage sizes

• Added support for tree structures in dropdown boxes on JSON-based input forms to simplify searching for specific values

• Introduced a new filtering option on the analyses gid to enable filtering for values which differ from, or do not equal (!=), a given value (such as exit codes in the pipeline steps in the analysis details screen)

• The analysis output folder format will now be user reference-analysis id

Cohorts

• The side panel now displays the Boolean logic used for a query with ‘AND’, ‘OR’ notations

• The needle plot visualization now drives the content of the variant list table below it. By default, the list displays variants in the visualization and can be toggled to display all variants with subsequent filtering

• For diagnostic hierarchies, concept children count and descendant count for each disease name is displayed

• The measurement/lab value can be removed when creating query criteria

Fixed a data synchronization issue when restoring an already restored object from a project configured with S3 storage

Flow

• Corrected the status of deleted Docker images from incorrect ‘Available’ to ‘Deleted’

• The reference for an analysis has changed to userReference-UUID, where the UUID matches the ID from the analysis. (The previous format was userReference-pipelineCode-UUID.)

• Pipeline files are limited to a file size of 20 Megabytes

Bench

• Fixed an issue which caused ‘ICA_PROJECT_UUID not found in workspaceSettings.EnvironmentVariables’ when creating a new Workspace

Cohorts

• Fixed an issue where the system displays ALL/partial filter chips when the top level tree node is selected in a hierarchical search

• Fixed an issue where the system displays 400 bad request error despite valid input of metadata files during import jobs

• Fixed an issue where the system displays inconsistent hierarchical disease filter results

• Fixed an issue where the system changes the layout when displaying the p-value column

• Fixed an issue where the system disables the next blutton when there is no study available in the dropdown menu

• Fixed an issue where studies could not be selected when a project has one study to ingest data into

Flow

• Users can now access json-based pipeline input forms for both Nextflow and CWL pipelines. API access is not yet available for CWL pipelines

• Added GPU compute types (gpu-small, gpu-medium) for use in workflows

• Users can now sort analyses by request date instead of start date, which was not always available

• The analysis details page has been upgraded with the following features:

  • The progress bar which could be found on the analyses overview page will now also appear in the details page

  • A maximum of 5 rows of output are shown for each output parameter, but the output can be displayed in a large popup to have a better overview

Cohorts

• Users can now use the Measurement concept API to create cohorts based on lab measurement data and harmonize their values to perform downstream analysis

• Users can now access the Hierarchical concept search API to view the phenotype ontologies

Made file and folder selection more consistent

Fixed an issue with the CLI where using the “projectsamples get” command to retrieve a sample shared via an entitled bundle in another tenant failed

Fixed filtering so you can only see subscriptions and channels from your own tenant

Improved GUI handling for smaller display sizes

Fixed the workflow session user reference and output folder naming to use BaseSpace Experiment Name when available

Data Management

• The unlink action is now greyed out if data not linked is in the selection

• Fixed an issue that when deleting folders, the parent folders were deleted first, giving the impression that the parent folder is deleted but not the subfolders and files

• Fixed an issue where the connector downloads only downloaded the main folder, not the folder contents

• For consistency, it is no longer possible to link to folders or files from within subfolders. Previously, you could link, but the files and folders are always linked to top level instead of the subfolder from where linking was done

• Updated error handling for dataUpdateBatch API endpoint

• Moving small files (>8Mb) will not trigger a "moving" event, only that the move has completed as out-of-order events caused issues and moving small files happens fast enough to not need the status of being moved, only the completion of the move

• Improved error handling when encountering issues during cancellation of data copy/move

• Improved error message when trying to unlink data from a project via the API when this data is native to that project and not linked

• Fixed issue where analysis can proceed to download input data when any of the inputs are in status other than AVAILABLE, including records within folder data inputs

Flow

• Redesigned UI component to prevent issues with Analysis summary display

• Fixed an issue where the field content was not set to empty when the field input forms have changed between the original analysis and a rerun

• Replaced retry exhaustion message, "External Service failed to process after max retries 503 Unique Reference ID: 1234" with a more useful message to end users that advises them to contact Illumina support: "Attempt to launch ICA workflow session failed after max retries. Please contact Illumina Tech Support for assistance. Unique Reference ID: 1234". This does not replace more specific error messages that provide corrective advice to the user, such as "projectId cannot be null"

• For efficiency reasons, pipeline files are limited to a file size of 100 Megabytes

Bench

• Fixed an issue which caused .bash_profile to no longer source .bashrc

• Fixed the status of deleted docker images which previously were displayed as available

• After creating a tool, the Information tab and Create Tool are now no longer accessible to prevent erroneous selection

Cohorts

• Fixed layout issue where buttons were moved up when the user selected the option

• Fixed issue where user was not able to view PheWas plot when multiple cohorts are open and same gene is searched

• Fixed issue where the user was not able to view GWAS plot when multiple cohorts are open and user switched forth and back between cohorts

• Fixed issue where users were not able to see the cryogenic map in the gene summary page for gene associated with the chromosome

The user can now manually, dynamically link a folder

The icav2 project data mount command now supports the “--allow-other” option to allow other users access to the data

The user can now set a time to be archived or deleted for files and folders with the “timeToBeArchived” and “timeToBeDeleted” parameter on the “POST/api/projects/{projectId}/dataUpdateBatch” command

Added 4 new API endpoints which combine the create and retrieve upload information

• POST​/api​/projects​/{projectId}​/data:createFileWithTemporaryCredentials Creates a file in this project, and retrieves temporary credentials for it

• POST​/api​/projects​/{projectId}​/data:createFileWithUploadUrl Creates a file in this project, and retrieves an upload url for it

• POST Creates a folder in this project, and and retrieves temporary credentials for it

• POST Creates a folder in this project, and creates a trackable folder upload session

Flow

• The default Nextflow version is now 22.04.03, from 20.10.0

• The user can now specify the Nextflow version when deploying a pipeline via the CLI with the “--nextflow-version” flag

Bench

• The user now has the option to choose either a tool or bench as a docker image when adding new docker images

• It is now possible to open contents of a Bench workspace in a new tab from the Bench details tab > access section

Removed the "Edit storage credential" button. The user can now edit the column directly in the open dialog when clicking on the name

Performance improvements to scheduled data download

Fixed an issue where data records were shown more than once when updating the tags\

The data details were erroneously labeled with "size in bytes" while the size was in a variable unit

Fixed an issue where trying to download files could result in the error "Href must not be null" when the file was not available

Fixed an issue where existing data catalog views would return an empty screen caused by a mismatch in role naming

Flow

• Fixed an issue that caused opening a pipeline in the read-only view to incorrectly detect there were unsaved changes to the pipeline

• Fixed an issue when having different pipeline bundles with the same (name) resource models would result in duplicate listing of these resources

• Improved error handling when encountering output folder creation failure, which previously could result in analysis being stuck in REQUESTED status

  • By default Nextflow will no longer generate the trace report. If you want to enable generating the report, add the section below to your userNextflow.config file:

    trace.enabled = true

    trace.file = '.ica/user/trace-report.txt'

    trace.fields = 'task_id,hash,native_id,process,tag,name,status,exit,module,container,cpus,time,disk,memory,attempt,submit,start,complete,duration,realtime,queue,%cpu,%mem,rss,vmem,peak_rss,peak_vmem,rchar,wchar,syscr,syscw,read_bytes,write_bytes,vol_ctxt,inv_ctxt,env,workdir,script,scratch,error_action'

• Fixed the issue where users not allowed to run or rerun workflows could start them from the API or BaseSpace SequenceHub. Now, users that cannot start workflows cannot rerun them.

Cohorts

• Fixed issue where the users can select the lower needles despite the overlap of multiple needles at the same location in the needle plot

• Fixed issue where the user would not be able to view the cryogenic map in the gene summary page for gene associated with the chromosome

• Fixed issue where the user would not be able to view the PheWas plot when multiple cohorts are open and same gene is searched

Added a 25,000-item limit to the v3 endpoint for batch data linking. Using the v4 endpoint, which does not have this limitation, is recommended

Flow

• Analyses and workflow sessions can now be resubmitted, and parameters can be updated upon resubmission

• Changed the default image used for CWL pipeline processes with undefined image from docker.io/bash:5 to public.ecr.aws/docker/library/bash:5

• Updated the choice of default nextflow docker image which is used when no docker image is defined. It is now public.ecr.aws/lts/ubuntu:22.04_stable

• The analysis logs in the analysis details page can be refreshed

• The user is now able to write a pipeline which executes files located in the /data/bin folder of the runtime environment

• Pipeline files are now shown in a tree structure for easier overview

Cohorts

• Updated GWAS UK Biobank data base gives users access to more phenotype information

• Users can now incrementally ingest their molecular data for germline, CNV, structural variants, and somatic mutation data

Fixed an issue where 'Copy to Clipboard' button did not work anymore

After searching for a folder in the search box and going into that folder, the search box is now cleared

Improved the project permissions API to correctly handle empty values

Previously, when attempting to save and send a message from the Websolutions section without a unique subject, the system would report an error and still send the message. Now the non-unique message subject error is reported and no message is sent

Fixed an issue where linking samples in the sample screen would result in receiving the same "sample(s) linked" message twice

Improved error handling for CLI FUSE driver

Hardened log streaming for ongoing runs to better handle network issues which previously would result in missing log streaming

Add retries for "connected reset by peer" network-related errors during analysis upload tasks

Fixed an issue where inviting a user to collaborate on a project containing base would result in the error "entity not managed" if that user did not have base enabled in any project or if base was not enabled in the project tenant

Data Management

Fixed an issue where data could be moved to a restricted location called /analyses/ and no longer be visible after the move. Please contact Illumina Support with your data move job information to recover your data if you have encountered this issue

Fixed an issue where sorting on data format did not work correctly

Copying empty folders no longer results in a partially copied status

ICA now performs an automatic refresh after unlinking or deleting a sample

Improved handling of file path collisions when handling linked projects during data copy / move

Fixed an issue where, even though uploading a file in a linked folder is not permitted, this would erroneously present a success message without copying the file

Analysis-events which are too large for SQS (256KB) are now truncated at the first 1000 characters when using SQS

Improved error handling when trying to upload files which no longer exist

Fix system degradation under load by introducing rate limit for spawning tasks for a given analysis to 25 per 1 min

The createUploadUrl endpoint can now be used to upload a file directly from the region where it is located. The user can create both new files and overwrite files in status "partial"

Improved the project data list command with wildcard support. For example:

• / or /* will return the contents of the root

• /folder/ will return the folder

• /folder/* will return the contents of the folder

To optimize performance, a limit has been set to prevent concurrent uploading of more than 100 files

Fixed an issue where folder syncing functionality would sometimes result in “Unhandled exception in scheduling worker”

Flow

• Fixed an issue where writing a pipeline which executes files in the /data/bin folder wasn't functioning properly with larger storage classes

• Nextflow pipelines no longer require pipeline inputs when starting them via the CLI

• Improved error handling when using an unsupported data format in the XML input forms during pipeline creation

• Fixed the issue where it was not possible to add links in the detail page for pipelines and bundles

• Sorting is no longer supported on duration and average duration columns for analysis grids

• In situations where the user would previously get the error "zero choices with weight >= 1" after the first attempt, additional retries will execute to prevent this from occurring

Cohorts

• Fixed an issue resulting in a blank error when a cohort with hundreds of diagnostic concepts was created

Data Management

• New DataFormats YAML (.yaml, .cwl), JAVASCRIPT (.js, .javascript), GROOVY (.groovy, .nf), DIFF (.diff), SH (.sh), SQL (.sql) to determine the used syntax highlighting when displaying/editing new pipeline files in the UI

• ICAv2 CLI supports moving data both between and within projects

• Added an alert to notify users when data sharing or data move is disabled for the project

• A new version of the Event Log endpoint has been developed to support paging, retrieval of previous events, and resolution of inconsistencies in date formats. This new endpoint introduces the EventLogListV4 data transfer object

• The user is now able to select a single file and download it from the browser directly. This does not apply for folders and multiple files selected at once

• User can subscribe to notifications when data is unarchived

• The BaseSpace Sequencing Run Experiment name will now be added to the technical tags when a workflow session is launched

Flow

• Fastqs with the .ora extension are now supported when staging these for secondary analysis, either as a list of fastqs or as fastq_list_s3.csv files

• Before, users had to click on the pipeline on the pipeline overview screen to start a new analysis. Now, you will enter the pipeline in edit mode when you click on the pipeline name. If you want to select a pipeline to start an analysis, you need to check the checkbox

Data Management

• Fixed a bug so folders copied from another previously copied folder no longer results in a corrupted file

• Fixed an issue where creating a new bundle would result in an error if a project with the same name already exists

• Data move between projects from different tenants is now supported

• Fixed an issue where not selecting files before using the copy or move commands would result in EmptyDataId errors

• For the CLI, Improved notifications when files can not be downloaded correctly

• Fixed an issue where scheduled downloads of linked data would fail without warning

• Corrected an issue where the tenant billing mode would be erroneously set to Illumina after a data copy

• Fixed an issue where BatchCopy on linked data did not work

Flow

• Resolved an issue to ensure that when a user creates a pipeline using a docker image shared from an entitled bundle, their analyses utilizing that pipeline can pull the docker image without errors

• Removed superfluous options from the analysis status filter

• Awaiting input

• Pending request

• Awaiting previous unit

• Fixed an issue where writing a pipeline which executes files in the /data/bin folder wasn't functioning properly with larger storage classes

• Fixed an issue where many-step analyses are getting stuck in "In Progress" status

• Fixed an issue where the wrapper scripts when running a CommandLineTool in CWL would return a warning

• Fixed the issue which caused the "Save as" option not to work when saving pipelines

Base

• Fixed an issue where the ICA reference fields in the schema definition had the wrong casing. As a result of this update you might end up with 2 different versions of the reference data (one with keys written with an uppercase letter at the start, another one with keys written entirely in lowercase letters). To fix this:

• Update your queries and use the Snowflake function : GET_IGNORE_CASE (ex: select GET_IGNORE_CASE( to_object(ica) , 'data_name' ) from testtableref)

• Update the 'old' field names to the new ones (ex: update testtableref_orig set ica = object_delete(object_insert(ica, 'data_name', ica:Data_name), 'Data_name'))

• Fixed an issue where using an expression to filter the "Base Job Success" event is not working

Flow

• New compute types (Transfer Small, Transfer Medium, Transfer Large) are supported and can be used in upload and download tasks to significantly reduce overall analysis runtimes (and overall cost)

• API: All the endpoints containing pipeline information now contain the status from the pipeline(s) as well

Bench

• External Docker images will no longer display a status as they consistently showed 'Available,' even when the URL is not functional

Cohorts

• Performance improvements to needle plot by refactoring its API endpoint to return only sample IDs

• Users now click a cancel button that returns them to the landing page

• Users can now perform time series analysis for a single patient view

• Refresh of PrimateAI data now drives data in variant tables

• Users can now access the structural variant tab in the Marker frequency section

Flow

• The analysis is no longer started from the API if error 400 ( 'Content-Type' and 'Accept' do not match) occurs

Base

• Fixed an issue where the Base schedule would not run automatically in some cases when files are present in the schedule

Bench

• Improved error handling when trying to create a tool with insufficient permissions

• Fixed an issue where the user is unable to download docker-image with adhoc-subscription

• The "version":"string" field is now included in the API response GET /api/referenceSets. If no version is specified, the field is set to "Not Specified"

• Fixed an issue where, under some conditions, fetching a job by id would throw an error if the job was in pending status

Flow

• New CLI environment variable ICA_NO_RETRY_RATE_LIMITING allows users to disable the retry mechanism. When it is set to "1”, no retries are performed. For any other value, http code 429 will result in 4 retry attempts after 0.5, 2, 10, and 30 seconds * Code-based pipelines will alphabetically order additional files next to the main.nf or workflow.cwl file

• When the Compute Type is unspecified, it will be determined automatically based on CPU and Memory values using a "best fit" strategy to meet the minimum specified requirements

Bench

• Paths can be whitelisted to allowed URLs on restricted settings

Fixed an issue with the service connector where leading blanks in the path of an upload/download rule would result in errors. It is no longer possible to define rules with leading or trailing blanks

Fixed an issue where a folder copy job fails if the source folder doesn't have metadata set

Linking data to sample has been made consistent between API and GUI

Improved resource handling when uploading large amounts of files via the GUI

Fixed an issue where the API endpoint to retrieve input parameters for a project pipeline linked to a bundle would fail when the user is not entitled on the bundle

Fixed an issue where deleting and adding a bundle to a project in one action does not work

Flow

• The event sending protocol was rewritten to limit prematurely exhausting event retries and potentially leaving workflows stuck when experiencing high server loads or outages

• Fixed an issue where specifying the minimum number of CPUs using coresMin in a CWL workflow would always result in the allocation of a standard-small instance, regardless of the coresMin value specified

• Fixed an issue in the API endpoint to create a Nextflow analysis where tags were incorrectly marked as mandatory inputs in the request body

• Fixed an issue with intermittent failures following completion of a workflow session

Base

• Improved syntax highlighting in Base queries by making the different colors more distinguishable

Bench

• Fixed an issue where the Bench workspace disk size cannot be adjusted when the workspace is stopped. Now, the adjusted size is reflected when the workspace is resumed

• Fixed an issue where regions were not populating correctly for Docker images

• Fixed an issue where API keys do not get cleaned up after failed workspace starts, leading to unusable workspaces once the API key limit is reached

The card or grid view selected will become the default view when navigating back to the Projects or Bundles views

Added a new API endpoints to retrieve and accept the Terms & Conditions of an entitled bundle:

• /api/entitledbundles{entitledBundleId}/termsOfUse

• /api/entitledbundles/{entitledBundleId}/termsOfUse/userAcceptance/currentUser

• /api/entitledbundles/{entitledBundleId}/termsOfUse:accept

Flow

• Added a new API endpoint to retrieve orchestrated analyses of a workflow session

  • GET /api/projects/{ProjectID}/workflowSessoins/{WorkflowSessionID}/analyses

• Code-based pipelines will alphabetically order additional files next to the main.nf or workflow.cwl file

Bench

• New JupyterLab - 1.0.19 image published for Bench using the Ubuntu 22.04 base image

• Resources have been expanded to include more options for compute families when configuring a workspace. See ICA help documentation for more details

Cohorts

• Sample count for an individual cohort may be viewed in the variants table

• Filter the variants list table through the filter setting in the needle plot

• Execute concurrent jobs from a single tenant

• Improved the display of error and warning messages for import jobs

• Structural variant tab may be accessed from the Marker frequency section

The counter is now accurately updated when selecting refresh in the Projects view

Fixed an issue resulting in one job to succeed and one to fail when running two or more file copy jobs at the same time to copy files from same project to same destination folder

Fixed an issue resulting in an error in a sample when linking nested files with the same name

Added a new column to the Source Data tab of the Table view which indicates the upload status of the source data

Removed the unused ‘storage-bundle’ field from the Data details window

Fixed an issue where the Project menu does not update when navigating into a Project in Chrome browsers

(CLI) Fixed an issue where deleting a file/folder via path would result in an error on Windows CLI

Base

• Improved schedule handling to prevent an issue where some files were not correctly picked up by the scheduler in exceptional circumstances

• Fixed an issue where an incorrect owning tenant is set on a schedule when running it before saving

• The number of returned results which is displayed on the scheduler when trying to load files now reflects the total number of files instead of the maximum number of files which could be displayed per page

• Fixed an issue where Null Pointer Exception is observed when deleting Base within a Project

Bench

• Fixed an issue where users were unable to delete their own Bench image(s) from the docker repository

Cohorts

• Fixed an issue where the value in the tumor_or_normal field, in the phenotype table in database, would not set properly for germline and somatic mutation data

• Fixed an issue where large genes with subjects containing large sets of diagnostic concepts caused a 503 error

Notifications

• Added support for multi-version notification event payloads corresponding to versioned API response models

Flow

• (API) Improved the analysis-dto by adding a new POST search endpoint as a replacement for the search analysis GET endpoint. The GET endpoint will keep working but we advise using the new POST endpoint.

• Improved analysis statuses to reflect the actual status more accurately

• Parallelized analysis input data downloads and output data uploads to reduce overall analysis time

• No scratch size is allocated if tmpdirMin is not specified

Cohorts

• Performance improvements of the ingestion pipeline

• Performance improvements to subject list retrieval

• Increased the character limit of ingestion log messages to the user

Fixed an issue where the GET API call with the ‘Sort’ parameter returns an error when multiple values are separated by commas followed by a space

Fixed an issue where adding the –eligible-link flag to the ‘projectdata list’ API endpoint caused other flags to not work correctly

Added cursor-based pagination for the ‘projectdata list’ API endpoint

Fixed an issue with the entitled bundles cards view where the region is cut off when the Status is not present

Fixed an issue where bundle filtering on categories did not work as expected

Fixed an issue where file copy across tenants did not work as expected

Added a cross-account permission check so that file copy jobs fail when the cross-account set up is missing instead of being retried indefinitely

Fixed an issue where ‘Get Projects’ API endpoint returns an error when too many projects are in the tenant

Fixed an issue where the UpdateProject API call (PUT /api/projects/{projectId}) returns an error when technical tags are removed from the request

Fixed an issue where users need to confirm they want to cancel an action multiple times when clicking the back button in the graphical UI

Fixed an issue where clicking into a new version of a bundle from the details view does not open the new version, and instead directs to the bundle card view

Flow

• Fixed an issue where the analysis logs are returned in the analysis screen “outputs” section and included in the getAnalysisOutputs API response. The log output is no longer considered as part of the analysis outputs

• Analysis history screen has been removed

• Fixed an issue resulting in inability to retrieve pipeline files via the API when the pipeline is shared cross-tenant

• Fixed an issue where the API endpoint to retrieve files for a project pipeline would not return all files for pipelines created via CLI or API

• Fixed an issue where the API does not check the proprietary flag of a pipeline before retrieving or downloading the pipeline files

Base

• The ‘Download’ button is available to download Base activity data locally (and replaces the non-functional ‘Export’ button for restricted bundles)

• Fixed an issue resulting in missing ICA reference fields in table records if the file was loaded into the table with no metadata

• Improved consistency of the references included in the scheduler

Bench

• Users are now logged out from a terminal window opened in a workspace after a period of inactivity

• Fixed an issue where permissions could not be enabled after a workspaces has been created

• Fixed an issue where a Contributor could not start/stop a workspace

Cohorts

• Fixed an issue where large genes with subjects with large sets of diagnostic concepts cause a 503 error

• Fixed an issue where the value in tumor_or_normal field in the phenotype table in the database is not set properly for germline and somatic mutation data

• Resolved a discrepancy between the number of samples reported when hovering over the needle plot and the variant list

Improved existing endpoints and added new endpoints to link and unlink data to a bundle or a project in batch:

• POST /api/projects/{projectId}/dataUnlinkingBatch

• GET /api/projects/{projectId}/dataUnlinkingBatch/{batchId}

• GET /api/projects/{projectId}/dataUnlinkingBatch/{batchId}/items

• GET /api/projects/{projectId}/dataUnlinkingBatch/{batchId}/items/{itemId}

Flow

• Analyses started via the API can now leverage data stored in BaseSpace Sequence Hub as input

• ICA now supports auto-launching analysis pipelines upon sequencing run completion with run data stored in BaseSpace Sequence Hub (instead of ICA)

• Updated the API for creating pipelines to include "proprietary" setting, which hides pipeline scripts and details from users who do not belong to the tenant which owns the pipeline and prevents pipeline cloning.

Cohorts

• Added support for partial matches against a single input string to the “Search subjects” flexible filtering logic

• Users can now view an overview page for a gene when they search for it or click on a gene in the marker frequency charts

• ICA Cohorts includes access to both pathogenic and benign variants, which are plotted in the “Pathogenic variants” track underneath the needle plot

• Ingestion: UI notifications and/or errors will be displayed in the event of partially completed ingestions

• Users can share cohort comparisons with any other users with access to the same project

Flow

• Input parameters of pipelines are now displayed in the "label (code)" format unless there is no label available or the label equals the code, in which case only the code is shown

• Fixed an issue where multiple folders were created upon starting new analyses

• Fixed an issue preventing analyses from using inputs with BaseSpace v1pre3 APIs

• Fixed an issue causing analyses with a specified output path to incorrectly return an error stating that the data does not exist

• The following endpoint "/api/projects/{projectId}/workflowSessions/{workflowSessionId}/inputs" now supports using external data as input

• Any value other than "economy" or "standard" for submitted analysis jobs will default to "standard" and use "standard"

• The parameter to pass an activationcode is now optional for start-analysis API endpoints

Base

• Improved the display of errors in the activity jobs screen if a Meta Data schedule fails

• If an error occurs when processing metadata a failed job entry will be added in the Base Activity screen

• Fixed an issue where records ingested via schedules from the same file could be duplicated

• Fixed an issue where exporting the view shared via bundle would show an error 'Could not find data with ID (fol. ....)'

• Resolved a NullPointerException error when clicking on Format and Status filters in the details screen of a Schedule in the Results tab

• Fixed an issue where a schedule download would fail when performed by different user than the initial user

Bench

• Fixed an issue when trying to query a Base table with a high limit within a workspace

• Fixed an apt-get error when building images due to an outdated repository

• Fixed an issue where a stopped workspace would display "Workspace paused" instead of "Workspace stopped"

• Fixed an issue where large files (e.g., 150GB+) could not be downloaded to a fuse-driver location from a Workspace, and set the new limit to 500GB

Cohorts

• Fixed an issue where split Nirvana JSON files are not recognized during ingestion

• Fixed an issue causing the UI hangs on large genes and returns a 502 error

• Fixed an issue where OMOP files are not correctly converted to CAM data model, preventing OMOP data ingestions

• Fixed an issue where OMOP large drug ingestions led to memory issues and preventing further drug data ingestion

• Fixed an issue where users from a different tenant accessing a shared project could not ingest data

Move data which is in the first level of the destination folder

Move data to a destination folder which would create a naming conflict such as a file name duplicate

Move data across regions

Externally-managed projects are no longer greyed out

Favorites icon in list view

Indication of Analysis in progress

Folder size is displayed in project details

General accessibility fixes for users using screen readers

Bench

• When creating a new workspace, the default is now single-user workspace instead of multi-user workspace.

Flow

• -

Cohorts

• -

Base

• Added support to abort “Prepare Data” jobs that get stuck in the “Creation Pending” state.

• Exporting data from a query to a new table now correctly shows the data size in the new table.

• Fixed an issue which caused the prepare data step to fail with the error "Failed to access remote file: access denied. Please check your credentials" when adding json.gz files to a table.

Bench

• Fixed an issue where default storage size would default to PB instead of GB when deselecting and selecting "include ephemeral storage".

Data Management

• -

Cohorts

• -

Bench

• When you have multiple Bench entitlements, all their related resources are now taken into account for Bench usage. You no longer have to select the appropriate entitlement.

Flow

• Output files are now displayed on a separate tab after completion of your analysis.

• The resource requirements FPGA1, FPGA2, GPU and software-only have been removed from Analysis configuration as the transition period for which it was needed has ended. If it has been configured, it is reset during this update, ensuring your pipeline will continue working.

• It is now possible to choose during analysis configuration, where the logs from your analysis should be stored.

• New lifecycle controls for pipelines are introduced, allowing pipeline developers to mark pipelines as deprecated or archived.

  • Deprecated pipelines remain usable but display a banner message to signal their upcoming retirement, helping users transition smoothly.

  • Archived pipelines are fully retired and can no longer be used to run analyses.

Cohorts

• -

Bench

• When creating Bench clusters, the default ephemeral storage size is 0. If you want to use ephemeral storage, you select the checkbox next to ephemeral storage on the Bench workspace configuration and provide a storage size.

• A verification has been added to see if a Docker image supports web access in order to set the allowed options from which you can choose in Bench when creating your workspace with that Docker image.

Data Management

• Project contributors can now delete data from the project via the UI. Previously, this was already possible from the API/CLI.

Flow

• Added validation if output/logs folders already exist when entering a folder name in analysis.

• Fixed an issue where a -1 would appear in the sample column after linking and unlinking data.

• Improved information on API usage on the page.

Cohorts

• -

Data Management

• -

Bench

• You can now choose clusters in addition to single nodes for your workspaces for better performance with Bench Images that support this feature. You can have a dedicated cluster and for the cluster members, you can choose to use a static number of nodes or dynamic scaling.

• FPGA2 instances are now also available in workspaces.

• DRAGEN is now available to all users in Bench.

• Users can now edit running workspaces to update the shutdown timer, shutdown reminder and auto restart reminder.

Flow

• New bench images are provided for Spark, SunGrid Engine and clusters.

• ICA will display a message in the analysis status field when the system's underlying cloud provider is at low capacity for storage resources

• A limit of 100 report configurations per API pipeline creation call has been introduced.

Cohorts

• Promoter AI scores are now integrated into the Cohort Analysis Module, providing additional insights in the variants table alongside existing scores like PrimateAI and SpliceAI.

• Updated data ingestion rules so that the sex/gender attribute is now optional for all nonCNV data types, simplifying metadata requirements and reducing ingestion errors.

Base

• -

Bench

• Corrected input validation for storage size during workspace configuration.

Data Management

• -

Flow

• Improved input form validations for Pipelines.

• Improved pipeline development in Bench when importing a flow pipeline.-

Cohorts

• The system now provides clear error messages in JSON format—rather than confusing HTML—when project link notifications fail, making it easier to understand and troubleshoot issues.

• Fixed an issue in the Correlation tab where the scatter plot failed to update when switching between cohorts after applying filters.

• Corrected the axis titles in RNA expression scatter plots within the Correlation tab to ensure accurate mathematical representation of log-transformed expression ratios.

• Fixed an issue where gene lists in Gene Expression, Somatic Mutation, and Copy Number Variation tabs failed to sort correctly by gene name, improving data navigation in cohort comparisons.

• Resolved an issue where legend colours in gene expression, somatic mutation, and copy number variation charts did not match across cohort comparison views, ensuring consistent and accurate visual interpretation

An application field has been added to Job entities to track the originating application.

An application field has been added to Workflow Session entities to track the originating application.

To prevent downstream issues, a new constraint has been added that disallows the use of dots (.) in the names of metadata models, fields, and groups. This ensures better consistency and system stability when managing metadata.

Data Management

• The API endpoint /projects/{projectId}/dataUpdateBatch now supports explicitly clearing willBeArchivedAt and willBeDeletedAt dates using dedicated boolean flags.

Bench

• -

Flow

• The legacy run report management tab "analysis report" present in graphical CWL pipelines/analyses details has been removed in favor of the recently introduced "report" tab.

• Performance improvements for opening pipeline-views in a project.

Cohorts

• Added support in the API and UI for filtering cohorts by name on the cohort list page, including partial matches, to make searching easier.

• Extended support for additional filename patterns for germline, CNV, and SV molecular data to improve compatibility and ease of auto-upload during ingestion.

• Redesigned the Comparison View page to match the Cohort View layout, adding collapsible panels for details and charts, and improving access to key actions.

• Updated the GWAS Manhattan plot to use canvas for smoother performance and better responsiveness when switching tabs.

Fixed an issue where the create pipeline API (V3) incorrectly returned an empty field in the response; now, reportConfigs are only included in the V4 create pipeline endpoint, ensuring consistent and streamlined responses across versions.

Fixed an issue when creating or modifying a Base Table, the newly added fields could not be removed.

Base

• Fixed an issue which caused using the same name for a project and bundles to negatively impact base usage.

Data Management

• Fixed an issue where .yml files were not recognized as yaml files in the pipeline file editor.

• Fixed an issue where some users experienced inconsistent access when transferring data between projects, caused by their administrator status unexpectedly switching on and off. This was due to how the system interpreted login details in certain cases and has now been fixed.

• Fixed an issue where downloading the files via the service connector would not look for matching files after the first 1000 entries.

• Fixed an issue where read-only credentials for volume and folder would return delete permissions.

Flow

• Json Input Form now has validation to ensure input form file itself is not larger than 10 MB.

• Improved Swagger documentation regarding the date format for the API endpoint POST /api/projects/{projectId}/dataUpdateBatch

• When nextflow pipeline analysis with JSON input is created with null data value, it will now correctly return a 400 response instead of a 500.

• You are no longer allowed to use the parameter 'emptyValuesAllowed' with the field type "fieldgroup" on a json based input form.

• Made behavior for fields in pipelines more consistent as these would sometimes be shown as mandatory while they were optional. When on a parameter minValues=1 and maxValues=1 it will be rendered as a required field: so a value needs to be entered to be able to start the analysis. In all other minValues and maxValues setups the fields are rendered as optional, as before.

Bench

• -

Cohorts

• Fixed an issue where clicking the Finish button during file import could trigger duplicate job submissions.

• Fixed an issue where large count values in cohort and comparison widgets were getting visually truncated in charts.

• Fixed an issue where navigating to the next page in the Cohorts list could automatically select a cohort without user action.

• Fixed an issue where the subject count in the bookmark tab was incorrectly updated when filtering by phenotype.

• Fixed an intermittent issue where a valid API call to compare CNV data could fail with a “Failed to deserialize” error.

• Fixed an issue where somatic mutation data ingestion jobs using the "Append" type showed misleading error messages and could fail to clean outdated data.

• Improved the Genes tab in comparison view to show a loading spinner instead of a misleading “No variants data” message while data is still loading.

• Fixed a bug where closing one cohort in a multi-cohort view could unintentionally close another open cohort.

Bench

• To save costs, there is a new automatic bench shutdown feature. Default shutdown happens after 7 days and can be changed per workspace, reboot happens after 30 days for security reasons.

• Switched from Miniconda to Miniforge in Bench JupyterLab images to avoid failures caused by Anaconda’s new license terms and restricted access to default channels. If your use case is not in line with the with the license terms, stop the workspace and use the new 1.2.4 JupyterLab bench image.

• Fixed an issue in JupyterLab 1.2.4 (inherited from JupyterLab 1.2.3) where the system used an outdated Java version from /usr/bin instead of the correct conda-installed version, causing pipeline failures.

Flow

• The default Nextflow version has changed from v22.04.3 to v24.10.2. Nextflow v22.04.3 is still available to create new pipelines.

• Due to AWS's F1 to F2 migration, you will temporarily be able to specify the resource requirements (FPGA1/FPGA2/GPU) when creating a pipeline. This allows you to explicitly choose instance types as availability shifts across regions during the migration. If the hardware is not available, the analysis will be cancelled.

• JSON-Based Input Forms now support nameFilter on Directory-type inputs

Cohorts

• -

Data Management

• -

Flow

• Improved handling of CWLTool Expressions

• Fixed an issue where graphical CWL pipelines could not be saved as a new version of the pipeline.

• When starting an analysis of a JSON-form based pipeline via the API, default values are now correctly taken into account.

Bench

• -

Cohorts

• -

Data Management

• .yml extension is now recognized as YAML format.

Flow

• The limit of analysis reports has been increased from 20 to 200 per analysis report pattern.

• Added “dropValueWhenDisabled” as an optional field attribute; if set to true and the field is disabled, its values are excluded from the submitted result.

• The endpoint GET /api/projects/{projectId}/analyses/{analysisId}/reports now returns report configs with optional titles and matching data. These configs can be used in all POST /api/projects/{projectId}/pipelines:create<pipelinetype>Pipeline endpoints.

• Added support for searching pipelines by ID in the pipeline grid.

• The price of aborted analyses is now visible in the UI.

• New endpoint: POST /api/projects/{projectId}/pipelines/{pipelineId}/generalAttributes to update general attributes of a project pipeline.

• Users can now create a new output folder directly from the pipeline output selection screen.

• Added “Standard 3Xlarge” as a new compute type for Flow & Bench.

Cohorts

• Cohorts view page now has collapsable items for "show charts" and "query details" on the right corner as an icon thus creating more real estate for cohort subject list.

Improved searching on size of Docker images.

Updated tool repository screen to new standard:

• The selection window for docker images while creating a new tool has been updated to be in line with the new layout.

• Removed the unnecessary "Technical" option from the tool inputs tab when editing tools.

When linking a bundle which includes base to a project that does not have base enabled, the following scenarios apply:

• Base is not allowed due to entitlements: The bundle will be linked, and you will be given access to the data, pipelines, samples, ... but you will not see the base tables in your project.

• Base is allowed, but not yet enabled for the project. The bundle will be linked and you will be given access to the data, pipelines, samples, ...but you will not see the base tables in your project and base remains disabled until you enable it.

API: /api/projects/{projectId} returns a new attribute projectOwner to identify the current project owner in addition to the existing ownerid of the project creator.

Owners of notifications are now able to delete those notification subscriptions. Previously, only the project administrator could do this.

Improved error message when trying to share storage credentials from another user.

Data Management

• Performance improvement when creating a data copy in batch in the GUI

• Improved connector resilience when downloading data elements with billing mode project.

• There will be a change in one of the upcoming releases where users are no longer able to edit connectors of other users through the API. This will be made consistent with the UI.

• Improved navigation in the edit connector screen.

Flow

• The currently selected report file is now highlighted on the reports tab.

• Fixed an issue which caused show failed steps to fail when opening in an analysis

• Corrected API documentation for /api/projects/{projectId}/analyses/{analysisId}/outputs

• Fixed an issue which caused files and folders to not appear correctly when using the grid's search field in the dialog when selecting input files

Bench

• Fixed issue which caused object references an unsaved transient instance during preview of new tools in bench workspaces

Cohorts

• Fixed issue where RNASeq data ingestions are failing.

• Fixed issue where UI elements are scrambled upon opening subject timeline view.

• Fixed issue where PRKN gene not properly loading pertinent information on the variant needle plot

• Fixed issue where phenotype tabs plot is missing when loading molecular breakdown plot on molecular breakdown tab first. \

  \

The back button has been replaced by a breadcrumb menu.

The Projects overview back button is now part of the breadcrumb menu.

Sorting and filtering parameters are now part of the URL meaning they are retained

when sharing a link, or when entering the details of an object in the grid and going

back to the grid screen.

Moved the Export button to the left side of the footer of the grid as a small tertiary

button for more consistency and ease of use.

Improved error message when a duplicate request is sent to create credentials via the

API.

Improved link sharing so that user is brought to the correct page after logging in.

When creating a project with only one storage bundle available, that storage bundle is

now automatically selected.

Data Management

• Made the contributor role for bundles more consistent by removing edit rights for

  details and terms of use from the role.

• Bundle sharing is now limited to users with bundle administrator role.

• It is now possible to download one or more files from the data grid and details, even

  when the format has no viewer associated.

Flow

• Pipelines now have an option to define patterns for detecting report files in the analysis

  output. On opening the analysis result window of this pipeline, an additional tab will

  display these report files.

• New API endpoint POST/api/projects/\{projectId}/analysis:nextflowWithCustomInput

  for starting a Nextflow pipeline which uses both YAML and JSON as custom input.

• For advanced output mapping the timelines and execution reports are now available for

  Nextflow pipelines.

• Performance improvement in the response times for analyses with high number of

  inputs.

• Improved aborting running analyses by faster process cancellation.

• Analyses prices are rounded to two decimals for easier reading. More decimals are

  retained for calculations and invoicing.

Cohorts

• Handing previously unrecognized consequence term protein_altering_variant during

  somatic mutation JSON ingestion to support TSO data inputs.

• Users can now input a comma-separated list of up to 100 subject identifiers to filter

  cohorts directly by subject ID. This new filter is optional and integrates with existing

  filters using AND logic across filters and OR logic within the list. Subject counts update

  dynamically as IDs are added or removed.

• Improved Needle Plot and Comparison Needle Plot filtering by making key variant filters

  (% gnomAD frequency, Sample Count, primateAI score) simultaneously and updating

  layout for better usability and alignment.

• Cohorts phenotypic data available in base tables after input of user data as data sets in

  Cohorts. Tables will also accompany a data set when shared through a bundle.

• Replaced Angular Material tab components with ILMN standard tab components in the

  Cohorts UI.

• Added missing consequence values for somatic variants from TSO.

• Cohorts reference database for PrimateAI includes previously not included genes.

During docker image creation 'Name' and 'Version' are now mandatory to fill in.

Fixed an issue in the API so it now returns the error in the appropriate dto format when

an incorrect or invalid dockerDataProjectId is provided in the request body

Data Management

• Fixed an issue which caused user who already had permission to a project or bundle to

  still appear in the list of users without permissions when trying to add more users.

• Improved user verification when modifying the project owner.

• Fixed an issue where the old project owner was not granted upload and download

  permissions when a new project owner was chosen for his project.

• Fixed an issue which resulted in error 400/500 when encountering data connection

  problems. Retries have been implemented and if it still fails it will now show a 503

  instead of a 400 or 500.

• Improved error handling during storage configuration creation.

• Fixed an issue where cloned pipelines would appear to override externally linked

  pipelines with the same name. Both are now present in the list of pipelines.

• Fixed an issue which caused the ica_logs folder to not always be present

• Fixed an issue where sample metadata would not immediately be shown.

Flow

• The project connector would incorrectly label samples from BSSH as being linked from

  another app, thus preventing their removal. This has been fixed.

• Improved handling of database issues when analysis is stuck in progress.

Cohorts

• Fixed issue where Firefox users could not export results.

• Fixed issue where the [DELETE] /v1/study/{studyId} API returned a 500 error when

  deleting a valid and existing study.

• Fixed issue where the spinner would remain indefinitely in the import wizard after a

  backend 500 error, instead of displaying an error message.

• Fixed issue where using the dropdown for project information on a single subject was

  not working in Fire Fox.

• Fixed an issue where modifying variant and phenotype category filters after searching

  in the PheWAS table caused the filters to stop applying to the table.

Autolaunch and BCLConvert now support dots and spaces in project names

Data Management

• Users are now able to create non-indexed folders. These are special folders which cannot be accessed from the UI with some specific actions blocked (such as moving or copying those folders)

• Enhanced visibility for data transfers by clearly marking those that do not match any download rule as 'ignored' in the UI. This helps users quickly identify transfers that won't start, preventing confusion and improving troubleshooting.

• In bundles it is now possible to open the details for docker and tool images by clicking on the name in the overview

• User managed storage configurations now allow for the copying of tags when copying/moving/archiving files and folders

Bench

• For fast read/write access in Bench, you can now, link non-indexed folders with the CLI command workspace-ctl data create-mount --mode read-write

• Bench can now be started in a single-user mode allowing only one user to work in the workspace. All assets generated in bench (e.g. pipelines) are owned by the Bench user instead of a service account

• UI Changes made to Workspace configuration and splash pages

Fixed duplicate project detection to handle the new 400 error response format, ensuring consistency with other unique constraint violations

Changes made to advanced scheduler options that are not applicable any longer

Removed erroneous Link/Unlink buttons in Tool and Docker Images of shared bundles

Fixed issue where project with large number of analyses loads slowly

Data Management

• There will be a change in one of the upcoming releases where users are no longer able to edit connectors of other users through the API. This will be made consistent with the UI.

• Fixed an issue where the sample list did not automatically refresh after deleting samples using the 'Delete input data and unlink other data' or 'Delete all data' options

• Made display color of Bundle-related data more consistent

• Removed on-click behavior off an added Cohorts dataset in a bundle that caused a yellow-bar warning

• Fixed an issue preventing project creation with user managed storage when specifying a bucket name and prefix in the Storage Config without a subfolder

• Fixed an issue where managing tags on data could result in a TransactionalException error, causing long load times and failed saves

• When a project data download CLI command returned an error for a file, the command returned status 0, while it should have returned 1. This has now been fixed

• Brought API in line with UI for detection of duplicate folder path already existing outside of your project

• Fixed local version detection affecting automatic service connector upgrades

Flow

• Improved error messaging when developing pipeline JSON based input forms

• Fixed an issue where in some case Nextflow logs are too big but are still copied into the notification which causes the notification to fail. The log behind 'Show more' button is now truncated to a size which is accepted by SQS

• Updated API behavior for JSON-based CWL and Nextflow pipelines to prevent unintended rounding of 'number' fields with values greater than 15 digits. Added a warning to advise users to pass such values as strings to maintain precision

• Each analysis step attempt is now recorded as a separate entry, ensuring accurate billing and providing end users access to stdout/stderr logs for every retry

• Fixed an issue when retries or duplicate step names caused improper entity_id identification

• Clicking 'Open in Data' from analysis details now correctly redirects users to the file's parent folder in the project data view instead of the root

• Refreshing the pipeline/workflow detail view now correctly updates the UI to reflect the latest version, ensuring any changes are displayed

Base

• Fixed issue where columns filtering on a number in base activity producing an error

Bench

• Improved protection against concurrent status changes when stopping workspaces

• Added refresh button to Bench workspaces

• Improved error handling when special characters are added to the storage size of bench workspaces

• Made the behavior when running and stopping workspaces more consistent

• Fixed an issue where the UI did not refresh automatically during long workspace initialization times, causing the workspace status to remain outdated until manually refreshed

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.

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.

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

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)