7.40.0 - BaseSpace Downloader 3.1
November 18, 2025
Adapter Read 1 and 2 can now be edited during run setup for easier customisation.
Fixed an issue that prevented downloads when system certificates could not be verified.
Fixed an issue that could cause an 'Apple could not verify' warning to appear when installing the BaseSpace Downloader on Mac.
Downloader UI improvements and fixes.
The copy and merge features are currently unavailable for samples generated by BCL Convert.
Fixed an issue that could update lane-library mappings when analysis completes on a shared run.
Fixed an issue that could prevent the Analysis Inputs tab from loading.
7.32.0 - File Preview in Search
Improved the behavior when viewing files in the search feature. Clicking a file name will now open the file preview modal, allowing the file to be viewed and/or downloaded.
Clarified the different options available when moving runs and datasets to the trash.
Security updates and fixes.
Fixed an issue that could cause some files to be retained following the deletion of a run.
Fixed an issue that occurred after updating the owner of a workgroup that continued to charge the original owner's storage to the workgroup.
Fixed an issue that allowed a project to be transferred when it contained analyses in statuses that are not eligible for transfer (e.g., running).
7.37.0 - Analysis Details "Orchestrated Analyses" Section
7.34.0 - Deletion of Custom Reference Genomes
7.39.0 - BaseSpace Downloader 3.0
7.38.0 - App Deprecations
7.33.0 - Shared BCL Convert Section
Fixed an issue that could cause run and project transfers to become stuck.
Added an "ICA Orchestrated Analyses" section to the Analysis Details page for autolaunched analyses. The section displays the status and details of each individual analysis launched.
Added a link to Usage Explorer in the header waffle menu.
Switching to the Usage Explorer now retains the current workgroup context. Only admins can see workgroup or domain-level usage.
Fixed an issue in the Analysis Files tab that occurred when multiple datasets with the same name existed, causing only one to be displayed.
Fixed an issue that could prevent pricing information from displaying on the App details page.
Fixed an issue that could prevent an app from transitioning to 'Complete' when no output datasets were produced.
Fixed an issue on the Analysis Details page that could display a link to a Project the user does not have access to, resulting in a 403 Forbidden page when clicked.
The copy and merge features are currently unavailable for samples generated by BCL Convert.
Added the ability to delete custom reference genomes from the Genomes page in the Resources section.
Added 'Archiving' and 'Unarchiving' file statuses for runs and datasets in the process of being archived or restored.
Fixed an issue that prevented the creation of samples following completion of BCL Convert 4.3.13.
Fixed an issue that caused analysis post-processing to fail when a sample sheet contained the same project name multiple times with different casings.
Fixed an issue that prevented sharing of a run that had been archived and subsequently files-only deleted.
Fixed an issue in Run Planning that stalled the page after selecting a custom fixed-layout kit containing only a single index.
Updated the BaseSpace Downloader to version 3.0. For more details, see What's New.
Added the 'DRAGEN Server' analysis location in Run Planning. Use this option to export the sample sheet to analyze sequencing data on a standalone DRAGEN server.
Manual mode runs from NovaSeq X and MiSeq i100 instruments without a sample sheet will now transition to 'complete' following upload. Previously these runs were marked as 'needs attention'.
Improved performance when loading the Microarray Analysis Setup tool.
Fixed an issue that could cause a "Separator must begin with the + sign" error when uploading a FASTQ file.
Fixed an issue that could cause a run or project transfer to become stuck.
Fixed an issue with the Analysis file browser that could cause files to display under the incorrect folder.
Fixed an issue that could cause a run status to stay 'Pending Analysis' after analysis aborts.
Fixed an issue in Microarray Analysis Setup where file upload was silently failing.
Fixed an issue in the Analysis list page Application filter that showed duplicated application names.
Fixed the Application filter in the Analysis list page to include the ICA Workflow Session Tracking app.
Fixed an issue when launching an analysis from the CLI where the default analysis name is not generated correctly.
The copy and merge features are currently unavailable for samples generated by BCL Convert.
We are deprecating a significant number of applications on BaseSpace. See Release Notifications for more information.
Updated Run Planning so that Adapter sequence reads are always displayed regardless of the instrument type.
Clarified the allowable values for the redirect URI field in the Developer Portal.
Fixed an issue that could cause a run or project transfer to become stuck.
Improved the message for a permissions error that can occur when launching an app.
The copy and merge features are currently unavailable for samples generated by BCL Convert.
BaseSpace Ground Control 2.31.1 - October 9, 2025
Bugs Fixed
Fixed an error that could occur during BaseSpace login on sequencing instruments.
Updated Run Planning to display a "Shared BCL Convert" section for platforms supporting multiple analysis configurations. The section shows on the Run Review page and displays the BCL Convert version and the settings that will be used.
Added notifications in Run Planning when changes to the planned run affect the version or settings of the shared BCL Convert configuration.
Added support to import settings from an Analysis Configuration Template directly into Run Planning.
Combined the Pillar ONCO/Revealâ„¢ library prep kits into a single Pillar oncoRevealâ„¢ kit, and added three new compatible index adapter kits.
Clicking a file on the Analysis Inputs tab now opens the file preview modal, allowing the file to be viewed and/or downloaded.
Improved the process of timing out analyses that become stuck during post-processing.
Fixed an issue on the Analysis details page that would incorrectly display a compute charge of 0 iCredits for certain applications. This issue was in the display only and did not affect billing.
Fixed an issue in the CLI where an error message would not list the correct scopes required.
Fixed an issue in storage-related emails where the storage limit unit (TB) was not displayed.
Release 7.33.1 - April 28, 2025
Bugs Fixed
Stability and performance improvements.
7.31.0 - Usage Explorer
February 18, 2025
Combined the Usage and Storage tabs into a single tab on the Settings page.
Removed the usage table and added a link to the new Usage Explorer tool.
Storage now shows a single chart with the proportion of data across Runs, Projects, and Trash. Shared data is no longer displayed.
Updated the terms and conditions. The new agreement must be accepted before browsing the BaseSpace website.
Improved the look and feel of the Terms of Service page.
Runs in 'Needs Attention' status can now be renamed and transferred.
Added a project link to the Analysis Reports and Analysis Inputs tabs.
Added a checkbox in Run Planning to use samples across all lanes, removing the need to set lane numbers.
Fixed a rare issue that could create duplicate biosamples when running sides A and B simultaneously on NovaSeq X instruments.
Fixed an issue that could cause analysis autolaunch to fail after uploading the run with a CLI version older than 1.5.2.
Fixed an issue that allowed certain analyses to be aborted during post-processing.
7.41.0 - Run Planning Improvements
December 16, 2025
Enhanced Run Planning to display warnings, e.g. for deprecated apps
Updated "Local" Analysis Location label in Run Planning to "On Instrument (Local)"
Enhanced Run Planning to retain BCL Convert per-sample settings imported from sample sheet
Improved performance of deletes with large number of items
Better cleanup of background processes preventing project transfer
Fix login from certain instruments where user needs to accept agreements
Prevent users from seeing and deleting hidden analyses
Fixed issue where QC recalculation could fail if appsession wasn’t complete, causing downstream workflows to misfire. QC update now occurs only after appsession completion to ensure correct status transitions.
The copy and merge features are currently unavailable for samples generated by BCL Convert.
7.36.0 - Analysis Size Display
7.35.0 - Display Cost for Completed ICA Analyses
Fixed an issue in Run Planning that prevented the Sample Table columns from updating correctly when changing kit selection from a standard or custom kit to "Not Specified".
Fixed an issue that prevented setting the custom reference file field when creating an Analysis Configuration Template for the DRAGEN Microbial Enrichment application.
Fixed an issue that prevented error messages from displaying on the Archive dialog box.
Improved billing for some older apps
Security and performance fixes
Updated the analysis size display to only reflect datasets the user has permissions to view.
Fixed an issue that could cause an autolaunched analysis to be marked as complete before all downstream analyses finished.
Fixed an issue that could cause samples produced by the FASTQ Generation app to appear twice in the Analysis Reports tab, and to download duplicate FASTQ files when downloaded.
Fixed an error that could occur when attempting to delete a project using the CLI or API.
Fixed an issue that caused timed out runs to get stuck in 'Pending Analysis' after launching an analysis.
Fixed an issue on the Analysis Reports tab that displayed a summary link when no summary report existed.
Fixed an issue that caused PDF files to immediately download when opening them in a preview window.
The copy and merge features are currently unavailable for samples generated by BCL Convert.
Release 7.36.1 - August 11, 2025
Bugs Fixed
Stability and performance improvements.
Final compute cost is now displayed for analyses that execute in ICA.
Added the ability to delete an analysis when data is partially owned by another user (i.e., following a project transfer). Only data owned by the user will be deleted, and other users with analysis data will retain access to the analysis details.
Updated the file preview modal to include a link to the analysis files tab. The link appears when viewing a file without the analysis context, such as in search results.
Added a note on the Microarray Analysis Setup sample selection page to indicate when a sample sheet with additional information is recommended for the selected analysis.
Added an info icon with an explanatory tooltip when a run's data status is 'Zipped' or 'Zipping'.
Fixed an issue that could cause an analysis details page to get stuck while loading.
Fixed an issue that could result in an error when attempting to empty the trash or restore items.
Fixed an issue that could cause 'analysis completed' emails to be erroneously sent immediately after launching certain apps.
7.30.0 - Prep Tab Deprecation
January 21, 2025
Prep functionality is officially deprecated. All run planning and sequencer integration is available through the Run Planning tool.
Added the ability to export a Sample Sheet from the Run Planning Review page when the secondary analysis location is set to BaseSpace.
Improved performance when moving large projects to the trash.
Increased the size of the file preview modal.
Fixed an issue that could cause biosample workflows to time out during post-processing.
Fixed an issue that caused analysis post-processing to fail when a dataset name was too long.
Fixed an issue that prevented errors from displaying in Run Planning when using the Import Samples feature.
Improved the error message when importing sample data in Run Planning from a sample sheet with a different application version that what is currently selected.
Clarified a warning message when downloading FASTQ or SAV files from a run whose BCL files were deleted.
Clarified instructions in the Run Planning custom index adapter kit .tsv template.