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Added the ability to transfer NovaSeq X runs and runs that have been uploaded to ICA Storage.
When creating or editing a reference file for run planning, the compatible DRAGEN versions are displayed next to each genome option.
Uploading a reference file now shows a progress bar and gives the ability to cancel the upload.
Improved emptying the trash to be more robust.
Updated the DELETE v2/trash endpoint to return a 409 when a previous delete request is still in progress.
Added two new fields to items returned by the GET v2/trash response, TrashStatus and CompletedChildEvents.
Fixed an issue that could prevent logs and other output files from being returned when an autolaunched analysis did not complete successfully.
Fixed an issue where FASTQ Datasets were not being created for unindexed reads after running BCL Convert.
Fixed an issue that prevented requeue of NovaSeq X manual mode runs.
Fixed an issue that could cause requeued NovaSeq X analyses to fail.
Fixed a rare issue that could lead to incorrect billing when an analysis times out.
Fixed an issue that affected certain analyses where the "Ica Workflow Session Id" was incorrectly referred to as the "Ica Analysis Id" in the analysis log.
Fixed an issue in Microarray Analysis Setup where threshold values were being reset after selecting a project.
Fixed an issue in Microarray Analysis Setup where only the latest analysis version of an analysis was selectable.
Fixed an issue in Run Planning where a duplicate Index ID error was not clearing after resolving the issue.
Fixed an issue when creating a custom Library Prep Kit that prevented the Compatible Index Adapter Kits dropdown from displaying correctly.
Fixed an issue in Run Planning that could prevent the addition of new configurations before the limit was reached.
Features
None.
Bugs Fixed
Native App Engine update - stability and performance improvements.
Features
None.
Bugs Fixed
Stability and performance improvements.
Added support for deleting Projects that are Biosample default projects. Deleting or transferring a default project will remove the association from all related Biosamples. Staged rollout complete January 4 2024.
Improved performance of moving data to the trash:
Moving a project to the trash is now an asyncronous operation.
Added a "Trash Status" column to items in the trash. The percentage indicates how much of the data has been moved into the trash.
Added support for FASTQ Dataset copy when the source FASTQ file is in ICA Storage.
Updated the 'Analysis Has Succeeded' email to include a warning if any nodes were unsuccessful.
Updated the pricing and cost for apps that run on ICA to link to the iCredit pricing page.
When using Run Planning to requeue an analysis, uploading a sample sheet now has the option to skip validations and submit as-is.
Added support in Run Planning for uploading reference files directly from the analysis configuration page.
Fixed a rare issue that could incorrectly charge compute for a timed-out analysis.
Fixed an issue that could cause NextSeq 1000/2000 autolaunched analysis to fail shortly after launching.
Improved the error message when sharing or transferring a project or run containing archived files.
Fixed an issue where Run Planning could not load a NextSeq 1000/2000 planned run created in Clarity LIMS.
Fixed an issue in Run Planning that could prevent the configuration page from displaying properly.
Fixed an issue in Run Planning that could cause a selected reference genome to carry over when creating a new configuration.
Fixed an issue in Run Planning that occured when switching from a standard kit to 'Not Specified'.
Fixed an issue in Run Planning where Local analysis planned runs with periods in the run name would not download.
Added support for sharing NovaSeq X Runs and autolaunched Analyses.
Added the option to upload a new sample sheet when requeueing from a planned run.
Added the ability to archive runs in "Needs Attention" status.
Updated the look and feel of the Analysis list and the Analysis Files tab.
Native App engine update - Staged roll out.
Improved error handling and performance.
Fixed a confusing error message when uploading a NovaSeqX manual mode run without a sample sheet.
Fixed an issue that caused CLI uploads to incorrectly display "Report is still being generated" on the Reports tab.
Fixed an issue where a new biosample could not be created when uploading FASTQ files to a Project.
Fixed an issue where a read 2 FASTQ file uploaded without a corresponding read 1 file wouldn't cause a warning.
Fixed an issue when requeueing a planned run where the Lane Usage checkbox could be incorrectly unchecked.
Fixed an issue that could cause certain apps to get stuck in Running.
Fixed an issue on the Search page where a long search term runs off screen.
Starting in August, uploads from instruments running Windows versions 7 or earlier will no longer be supported.
After uploading files, BaseSpace displays a blank analysis page. Reload the page to see upload information and files.
Performance Improvements and Fixes.
Fixed an issue in Run Planning where Next button remains disabled after copy-pasting data into Sample Table.
Fixed an issue in Run Planning where Application name is not displayed when editing a planned run's configuration.
Fixed an issue that prevented downloading files from analyses launched with the Microarray Analysis Setup tool.
Features
None.
Bugs Fixed
Performance and stability fixes.
Native App Engine update - stability and performance improvements.
Added the ability to unlock multiple biosamples at a time from the biosample list.
Updated the Import Samples feature in Run Planning with "Add" or "Replace" options when importing.
Added a warning message in Run Planning when a Sample ID is reused with different indexes.
Added the ability to specify thresholds for Microarray Analysis Setup Configurations.
Improved samplesheet validations for Microarray Analysis Setup.
Fixed an issue that prevented NovaSeq X Series from showing as an option in the Run Insights tool.
Fixed an issue that could prevent index QC metrics from populating for NovaSeq X runs following BCL Convert analysis.
Fixed an issue that would display a blank Report page after uploading files.
Fixed an issue that could cause Biosamples to get stuck in Sequencing status with no yield.
Fixed an issue that could cause the Analysis Reports tab to be incorrectly enabled or disabled.
Fixed an issue that could result in an error when navigating to the Analysis Reports tab.
Fixed an issue that could enable the Download option for an empty project.
Fixed an issue where attempting to delete a shared appsession redirected to a 403 page rather than displaying an error message.
Fixed an issue that affected the menu actions available on the Project Biosamples tab.
Fixed an issue where filters were missing on FASTQ Dataset lists.
Fixed an issue that could cause a Run to briefly update to Needs Attention after initiating a requeue.
Fixed an issue that prevented showing a warning when a read 2 FASTQ file was uploaded without a corresponding read 1 file.
Fixed an issue that could cause Project transfers to get stuck in a transferring state.
Fixed an issue that could prevent available products from being displayed in the Microarray Analysis Planning tool.
Fixed an issue in Run Planning tool where clearing the selection in the Application field causes the page to freeze.
Fixed an issue in Run Planning tool where the Application + Genome field does not display the selected value.
Fixed an issue where the template could not be downloaded when creating a custom Library Prep Kit for Prep Tab.
When performing certain actions on more than one item (eg, updating FASTQ QC statuses), the dialog box briefly displays before closing on its own when an error is returned.
Features
None.
Bugs Fixed
Fixed an issue that could cause delays when monitoring runs, loading run charts, and downloading run data.
Fixed an issue that could cause the Project size value to be higher than actual. This only affected the displayed project size; billing remained accurate.
Features
None.
Bugs Fixed
Performance and stability fixes.
Features
None.
Bugs Fixed
Performance and stability fixes.
Added the ability to requeue runs using the Run Planning tool. Currently supports requeue of analyses from Illumina DRAGEN Apps v4.1 and higher and DRAGEN TruSight Oncology 500 Apps 2.1 and higher. Staged rollout.
Added two new applications categories to the App Store: Illumina and Dragen. The App Store now filters for the Dragen category by default.
Renamed the application category "Synthetic Long Reads" to "Long Reads".
Improved the performance of post-processing analysis results from NovaSeq X.
Added copyright information to each page.
Fixed an issue that prevented download of NovaSeq X runs using the BaseSpace CLI.
Fixed an issue that could cause the Analysis Inputs tab to not load for NovaSeq X autolaunched analyses.
Fixed an issue that could affect deletion of analysis data generated from a NovaSeq X auto-launched app.
Fixed an issue that could prevent launch of the Reference Builder (Instruments) application.
Fixed an issue in the Run Planning tool where index uniqueness validation is not performed after importing samples from a Sample Sheet.
Fixed a rare issue that could cause FASTQ Generation to launch twice after run upload completes.
The following operations cannot be performed for NovaSeq X sequencing runs or analysis results: share, transfer, archive, and editing the run name.
Beginning with BSSH v7.12.0, uploads from instruments running Windows versions 7 or earlier will no longer be supported.
The Lane Usage toggle in Run Planning is not displayed when planning a run on NovaSeq X.
Improved error logging for NovaSeq X autolaunched analyses.
Improved the sample sheet viewer in the Analysis Inputs tab for apps that use a run or sample sheet as input.
Added Lane Usage checkbox in Run Planning's Configuration page, as an alternative way to configure for the use case where samples are loaded across all lanes. When this option is enabled, lane column will not be included in the sample sheet.
Added filter support in Application, Library Prep Kit, Index Adapter Kit, and Reference Genome dropdown fields in Run Planning
Fixed an issue where certain paid apps could be launched regardless of subscription status or iCredit balance.
Fixed an issue that could cause BCL Convert analyses to complete before Biosample yield was finalized. Note that this fix may cause slightly longer analysis durations due to increased post-processing time, but billing will only be for the analysis running time.
Fixed an issue that could cause a status summary message of "in progress" to appear for a completed analysis.
Fixed an issue that could incorrectly transition the status of a run from Needs Attention to Complete.
Fixed an issue where an invalid combination of standard Library Prep Kit Index and Not Specified Adapter Kit is allowed in Run Planning
Fixed an issue that could cause sample sheets with custom names to be ignored when uploaded using the CLI.
Fixed an issue in the list files API that could cause sort parameters to be ignored.
Combined New and Classic modes into a single view.
Removed the New/Classic application switch from Settings.
Allow Biosample/Sample selection from the app launch pages.
Run and Project pages now display both Biosample and Sample tabs.
For more information, see the and the
Updated the look and feel of the Project list, Project details, file upload, trash, and search pages.
Improved error messages when importing samples into the Run Planning tool.
The Usage page in Settings now includes a link to the Admin Console for domain admins.
Added support for IDAT file upload in Microarray Analysis Planning.
Fixed an issue that could cause NovaSeq X auto-launched analyses to get stuck in "Running".
Fixed an issue where 'Created' and 'Updated' columns were using incorrect date formats.
Fixed an issue that could cause biosample workflow uploads to launch duplicate analyses.
The following operations cannot be performed for NovaSeq X sequencing runs or analysis results: share, transfer, archive, and editing the run name.
Starting in August, uploads from instruments running Windows versions 7 or earlier will no longer be supported.
The Lane Usage toggle in Run Planning is not displayed when planning a run on NovaSeq X.
When uploading FASTQ files, no warning is shown when an R2 file is uploaded without a corresponding R1 file.
When uploading FASTQs, the biosample chooser does not display the option to create a new biosample.
BCL Convert does not generate Samples. To use FASTQ data from BCL Convert, use Biosamples.
Features
None.
Bugs Fixed
Fixed a bug where radio buttons could become disabled on application input forms.
Fixed an issue on the run share dialog that incorrectly suggested runs could be shared with write access.
Fixed an issue in the Run Planning tool where trailing spaces in Run Name were not trimmed on saving.
Added application version filtering in Run Planning. For instruments that support multiple analysis configurations, selecting an initial application will filter subsequent configuration application options to ensure compatibility with the BCL Convert version used.
Analyses auto-launched after NovaSeq 6000 and NextSeq 500/550 runs are uploaded to ICA storage will be placed in a folder named "ilmn-analyses" within the ICA project.
Analyses auto-launched after uploading a NovaSeq X run using the CLI will be placed in a folder named "ilmn-analyses" within the ICA project.
Added a link on the Analysis Files tab to the corresponding Analysis in ICA, when applicable. This link appears for users with an active ICA subscription.
Added support for persisting selections across pages in data tables.
AppSessions running longer than 1 week have been manually timed out. This will not result in any iCredit charges.
Fixed an issue when launching the Illumina Complete Long Reads (ICLR) app from the CLI. To use files when launching ICLR, upgrade to the CLI version 1.5.4 or later here.
Fixed an issue that could set a Run to Needs Attention status when more than one 'SampleSheet.csv' files are present in the run folder.
Fixed an issue that could occur during CLI upload of a Run folder where the --sample-sheet parameter is ignored.
Fixed an issue that prevented Runs from moving to Needs Attention status if the FASTQ Generation analysis timed out.
Fixed an issue that could cause a dialog box to briefly display before closing on its own when an error is returned.
Fixed an issue in Microarray Analysis Planning where the launch analysis button is available after removing the sample sheet.
Fixed an issue that prevented errors from displaying when updating metadata for a custom reference file.
Features
None.
Bugs Fixed
Fixed an issue where uploaded runs incorrectly had status 'Needs Attention' with an error indicating a custom samplesheet is missing.
Fixed an issue where some genomes in Resources page cannot be downloaded.
Added additional support for NovaSeqX instruments.
Improved integration for datasets, biosamples, reports, and metrics generated by analyses run in ICA.
Moved the Run Planning pages for viewing and creating kits, genomes, and reference files out of Settings and into a new Resources page. This page can be accessed through the Account drop-down list, by clicking "Resources".
Run Planning additions and improvements:
Added the ability to configure multiple secondary analysis configurations, for supported instrument types.
Added a "fill down" function for the Lane column in the Sample Table. Doing so will copy the first row's value to all other rows.
Improved the performance of pages displaying large tables and lists.
Fixed a bug in Run Planning where error messages would refer to Well Position instead of Index ID.
Features
None.
Bugs Fixed
Fixed an issue that could cause BCL Convert appsessions to stall during post-processing in cases where a sample was sequenced across multiple lanes.
Fixed an issue that caused reports from certain apps to fail to load for completed analyses.
Known Issues
When multiple datasets with the same name are generated from an analysis, only one for each name is displayed on the Analysis Files tab.