December 11, 2018 - 5.29 - FASTQ Filename Validation and App Bookmarking

• Features

  • Added bookmarks to the app landing page. Bookmarked apps are listed in the sidebar adjacent to the apps list.

  • Added filename validation to uploaded FASTQ files. To prevent potential downstream app failure, the web uploader does not allow filenames that contain special characters.

  • A confirmation email is now sent when an inactive user reactivates their account by logging in.

  • Improved UI

    • Tabbed pages no longer display a subheader if the subheader is a duplicate of the tab name.

    • Initial Lane & QC Status label on the runs page is listed as Initial. Initial status was originally displayed as --.

  • The creation and updated dates for all resources in BaseSpace Sequence Hub are now formatted according to ISO-8601.

• Bugs Fixed

  • Fixed an issue that caused problem when attempting to switch workgroups when the window size is small.

  • Fixed an issue that prevented some users from downloading project files when in New mode.

  • Fixed some display issues in Safari.

August 13, 2018 - 5.25 - ISO Date Display and Improved Project Master Page Appearance

• Features

  • Dates and times are now displayed in ISO-compatible formats on the Dashboard, Runs list, Run Summary, and Run Files pages.

  • Removed folder icons from the projects master list to improve appearance. The Owner column lists the owner of projects shared with you. To view a list of collaborators in projects you own, select Share | Send Invitation from the project.

  • Biosample pages have been corrected to remove the term Registry, which is no longer used.

• Bugs Fixed

  • Fixed a slow page loading issue in projects with large numbers of analyses.

  • Fixed Timed Out runs to allow requeues.

  • Fixed an issue that caused analysis workflow metrics and QC data to be removed if the associated analysis was deleted.

  • Fixed the default file sorting on run and analysis file pages.

June 26, 2018 - 5.23 - Publishing Apps to your Enterprise and Faster SAV Downloads

• Features

  • Added the ability for Enterprise users to publish apps to their domain. Apps published in a domain through the Developer Portal will only show up for users in the domain.

  • The performance of SAV download of run InterOp files has been improved by only downloading aggregated files when available. When aggregated files are not available, per cycle files will downloaded.

• Bugs Fixed

  • Fixed an issue where a user could be prompted with the window to accept an app's EULA after accepting it already.

  • Fixed an issue with workflow analyses getting stuck in "Pending Execution".

Release 5.23.1 - June 28, 2018

• Bugs Fixed

  • Fixed an issue displaying reports for multi-node apps.

November 8, 2018 - 5.28 - Improvements to File Upload, Run Data Display, and Search

• Features

  • Added more run, status, and QC data to the Run Summary page.

  • Improved file upload to support encrypted manifest (*.emf) files and AmpliSeq for Illumina manifests.

  • Improved the Analysis Master List display. Column data is automatically resized when the filter widget is activated so that table columns are not obscured.

  • Improved the search function to include flow cell ID. Searching by flow cell ID now returns associated runs even if the run name does not contain the flow cell ID.

  • Updated www.basespace.illumina.com to redirect to the BaseSpace Sequence Hub login page at https://basespace.illumina.com/auth/logon.

• Bugs Fixed

  • Fixed sample pair selection to allow more than one pair to be created via drag and drop.

  • Improved Runs list page loading times. Pages with a large number of rows now load content continuously as you scroll.

  • Fixed sample pair selection to allow more than one sample pair to be created using drag and drop.

  • Fixed minor page display issues.

Release 5.28.1 - November 15, 2018

• Features

  • Internal release, no changes in functionality

• Bugs Fixed

  • None

October 2, 2018 - 5.27 - Analysis List Filters and UTC Timestamps

• Features

  • Added Delivery Status and Project filters to Analyses List Page.

  • Added messaging to the Transfer Ownership dialog to clarify that the Optional Message text field supports 140 characters.

  • Added UTC-formatted timestamps to the Dashboard, Runs list, Run Summary tab, and Run Files tab.

• Bugs Fixed

  • Fixed an issue that caused free apps to be disabled for Basic account users.

  • Fixed an issue with the app input form returning an error. If a FASTQ data set associated with an input biosample had been deleted, the app failed to launch. This issue occurred in New mode only.

  • Fixed slow loading times on Runs list pages.

  • Disabled the Reports tab for apps that do not include report output. Application results are available on the Files tab.

  • Changed the Prep tab index edit icon to a pencil.

Release 5.27.1 - October 29, 2018 - staged roll out complete

• Features

  • Changed the compute instance type used by default for apps because AWS is deprecating the existing type. Thew new type is a more powerful instance with more cores and typically faster run times and lower costs. Please note that we have not been able to test all the apps, but have not seen issues with the illumina apps that we were able to test with the new instance type. Affected illumina apps (not labs apps) have an updated "What's New" section.

• Bugs Fixed

  • Fixed an issue running DESeq2 with blank entries in sample matcher.

  • Coverage files are no longer created from indexed bam files, resulting significantly shorter run times for apps that produce them.

• 5.29.0

• 5.28.0

• 5.27.0

• 5.26.0

• 5.25.0

• 5.24.0

• 5.23.0

• 5.22.0

• 5.21.1

• 5.21.0

• 5.20.0

• 5.19.0

• 5.18.0

• 5.17.0

• 5.16.0

• 5.15.0

• 5.14.0

• 5.13.0

• 5.12.0

• 5.11.0

July 17, 2018 - 5.24 - Display and Filtering Bug Fixes

• Bugs Fixed

  • Fixed an issue with the applications API returning an incorrect total count when getting a list of applications.

  • Fixed an issue with the Classic/New banner information icon in the Frankfurt/EU instance incorrectly linking to the US help files.

  • Fixed an issue with the My Illumina selection redirecting to the last-visited Illumina page instead of the account settings page.

  • Fixed a display issue with data point tooltips in Run Charts not displaying on screen.

  • Fixed a display issue with the FASTQ file upload library prep kit dropdown. The list of the display is widened to fit long prep kit names.

  • Fixed a filtering issue in New mode. The .bed filter in the app input file chooser incorrectly returned .txt files in addition to .bed files.

May 1, 2018 - 5.19 - Updated Run ID API

• Features

  • Updated Run ID API for v2

• Bugs Fixed

  • Fixed an issue with the Launch Apps dropdown on the Projects page failing to load a list of apps.

  • Fixed an API performance issue which previous caused unexpected down time.

  • Fixed an issue that caused the Set Project option to be disabled on the Prep Tab's Libraries page.

  • Fixed an issue with the loading spinner animation disappearing while lists are still loading.

  • Fixed an issue with the Run Files page displaying only the first 500 files for a run. The page now displays up to 2000 run files.

Release 5.19.1 - May 2, 2018

• Bugs Fixed

  • Fixed an issue with access via OAuth.

  • If a run has failed to complete after 90 days, we now automatically change its status to Timed Out. The storage associated with the run may increase when this happens. Timed Out runs can be deleted..

May 15, 2018 - 5.20 - New Run Chart Options and v2 APIs

• Features

  • Added new % PF option to Flow Cell chart for all sequencing instruments, and % occupancy to Flow Cell charts and Data by Lane plot for iSeq100 and MiniSeq.

  • Added v2 API endpoint to provide default workgroup storage location information for a user or workgroup.

  • Now automatically timing out existing runs sitting in an active status for 90 days or more.

• Bugs Fixed

  • Fixed an issue with auto-logout logging out users before the 30 minute mark.

  • Fixed an issue with login sessions expiring during large project file imports.

  • Fixed issue with project file upload sessions failing to auto-complete when the user is inactive for a few minutes.

  • Fixed issue with the run summary page initially scrolling down below the navigation tabs upon loading.

  • Fixed incorrect sum in TotalCount of the v2 applications API.

April 5, 2018 - 5.17 - NovaSeq S4 Flow Cell Multi-Node FASTQ Generation

• Features

  • Changed NovaSeq S4 flow cells processed in BSSH New mode to use multi-node FASTQ Generation by default.

  • Added a setting to specify the number of items shown per page in the runs master list, project biosamples list, and pool libraries list.

  • Updated the look of the run's file browser, including switching the Last Modified date and time column to a Created date and time column.

• Bugs Fixed:

  • Fixed broken hyperlink for general datasets on the biosample's datasets page.

  • Removed inherited permissions from tokens generated by the BaseSpace CLI to limit access token scope to a specific resource.

March 22, 2018 - 5.16 - UX Improvements and Bug Fixes

• Features

  • Added a setting to change the number of results shown per page on the biosample and analysis master lists.

  • Updated look of project chooser information in app input form.

• Bugs Fixed

  • Fixed an issue that prevented sharing runs from the Run details page.

  • Fixed an issue with the biosample runs tab not displaying updated FASTQ dataset statuses.

  • Fixed issue with missing Edit button on Libraries tab for some new Prep Tab kits.

  • Fixed an issue that created duplicate library names for the same biosample when separate runs containing the biosample completed at the same time.

May 30, 2018 - 5.21 - Improved Yield Status Information on Biosample Summary Page

• Features

  • Updated Latest Yield section of the biosample summary page to display more relevant yield values.

• Bugs Fixed

  • Fixed an issue with the file downloader failing to find multi-node FASTQ analysis files.

  • Fixed an issue with the loading spinner on the analysis metrics page continuously displaying after sorting by column header.

  • Fixed an issue that caused miscellaneous (ie, non-manifest) .txt files to be treated as manifest file type instead of misc file type when uploading to a project, resulting in rejection due to failed validation.

June 12, 2018 - 5.22 - Associate Biosamples With Uploaded Files and Show/Hide Columns on Runs Page

• Features

  • Added an option to associate a file (or dataset of files uploaded together) with a new or existing biosample during file upload.

  • Added an option to show or hide columns on the runs page, and added sort function to additional columns.

• Bugs Fixed

  • Fixed an issue with library prep kits not appearing in the Multiple Kits drop-down list when selecting a biosample in the app input form.

Release 5.22.1 - June 14, 2018

• Bugs Fixed

  • Fixed an issue with BaseSpace menu navigation to different software products. The links have been restored and you are now successfully transferred to the selected product.

January 25, 2018 - 5.12 - Improvement to Biosample Workflow, Analysis Fixes

• Features:

  • Changed biosample workflow validation to allow duplicate biosamples for analysis.

  • Added dataset file dependency for analysis workflow auto-app launch.

  • Moved analysis details tabs from side to the top of the page.

  • Improved performance and stability for native apps (staged roll out completed: Jan 31, 2018).

• Bugs Fixed:

  • Fixed issue where files from aborted FASTQ Generation analyses could be used as inputs to downstream analyses.

  • Fixed display issue with Stats tab in Developer Portal.

  • Fixed issue with prep tab library creation unexpectedly showing "User container ID is required" error.

  • Fixed missing pool link on the run settings page for planned runs.

February 6, 2018 - 5.13 - Improved Run Metrics and Analysis Input Pages

• Features:

  • Improved Run Metrics page with reorganized layout, lane status color-coding, and run summary section.

  • Added ability to select setting to show or hide the phasing/pre-phasing columns on the Run Metrics page.

  • Improved styling of the analysis inputs page.

• Bugs Fixed:

  • Fixed issue with the library prep kit dropdown showing an incomplete list of kits when uploading FASTQ files to a new library.

  • Fixed issue with apps being able to launch when the sample inputs had no files.

  • Fixed issue with launch simulation buttons not appearing in FormBuilder.

  • Fixed missing error message for selecting inactive workgroups.

  • Fixed error message language for requesting lab requeue for a canceled biosample.

  • Fixed messaging on app details page to correctly identify the latest version of the app.

  • Fixed issue with text running horizontally off the analysis inputs page when showing inputs from tabular fieldsets.

January 10, 2018 - 5.11 - New Run Details Charts Measurements and AmpliSeq for Illumina Support

• Features:

  • Added new measurements to the Charts section of the Run details page: additional Phasing and Pre-Phasing metrics, % No Call, and Median QScore.

  • Added Occupied Count (K) and % Occupied measurements for compatible instrument types to the Charts section of the Run details page.

  • Updated menus in the Charts section of the Run details page to show only data types available for the current cycle during the instrument run.

  • The Run details page now provides Extracted, Called, and Scored cycles as a minimum-maximum range during an instrument run.

  • A parent analyses is now marked as Aborted when all child analyses have aborted.

  • Added AmpliSeq Library PLUS for Illumina kit to Prep Tab.

• Bugs Fixed:

  • Fixed missing display field text on app input forms

  • Fixed issue with Analysis Details page not showing all analysis reports

  • Fixed issue with Prep Tab pools showing only the first 20 samples

  • Fixed issue with Cancel Analysis from Biosample analysis page

  • Fixed an issue that could cause missing Indexing QC results for NovaSeq S4 flow cells

  • Fixed issue with scheduled analyses from workflows not being moved to the trash when the corresponding project is moved to the trash

###Release 5.11.1 - January 15, 2018

• Bugs Fixed:

  • Fixed issue with Internet Explorer browser running slowly when opening an app input form

  • Fixed issue that prevented the creation of a new project from the project chooser window

  • Fixed issue that could cause the Run details page for NovaSeq S4 runs to show Indexing QC data for Lane 1 only

March 6, 2018 - 5.15 - Optional Thresholds for Automatic QC

• Features

  • Automatic QC of analysis workflow metrics can now be configured to QC only when the metric is calculated.

• Bugs Fixed

  • Fixed issue with Shift+select of multiple plate wells when pooling libraries together in Prep Tab.

  • Fixed broken links in run and project share notification emails.

  • Fixed an issue with the Integrative Genomics Viewer (IGV) failing to launch in the EU instance of BaseSpace Sequence Hub.

  • Fixed "Value cannot be null" error on analyses inputs pages.

Release 5.15.1 - March 7, 2018

• Fixed an issue that caused Indexing QC information to not display for runs.

Release 5.15.3 - March 20, 2018

• Native App engine update - Staged roll out Completed March 22

  • Fixed an issue where FASTQ Generation and other apps could fail while saving results.

  • Fixed a rare issue where some apps failed to start.

May 30, 2018 - 5.21 - Improved Yield Status Information on Biosample Summary Page

• Features

  • Updated Latest Yield section of the biosample summary page to display more relevant yield values.

• Bugs Fixed

  • Fixed an issue with the file downloader failing to find multi-node FASTQ analysis files.

  • Fixed an issue with the loading spinner on the analysis metrics page continuously displaying after sorting by column header.

  • Fixed an issue that caused miscellaneous (ie, non-manifest) .txt files to be treated as manifest file type instead of misc file type when uploading to a project, resulting in rejection due to failed validation.

September 11, 2018 - 5.26 - Storage Limit Banner Notifications

• Features

  • Added banner notifications for Basic accounts that have exceeded data storage limits.

  • Improved text formatting in the screens for uploading miscellaneous file types.

  • Improved design of the available app selection list for launching apps.

• Bugs Fixed

  • Fixed an issue with FASTQ Generation failure when processing NovaSeq data with 384 samples per lane. FASTQ Generation can now process up to 1000 samples per lane for NovaSeq. Staged roll out complete.

  • Fixed an issue that caused Analysis summary pages to hang.

  • Fixed the dashboard widget and usage reports to correctly display the number of iCredits used for app purchases.

  • Fixed the runs list display of run sizes larger than 1 TB. The run size is now rounded to two decimal places.

  • Fixed an issue that caused chart displays to load slowly. As a result, the InterOp folder now includes a cache subfolder that contains additional files.

  • Improved the usability of the BaseSpace app launch pages. Some input fields have been widened to increase legibility.

  • Fixed the display of the settings page loading icon, which was appearing in duplicate.

April 19, 2018 - 5.18 - Upload Any File Type to a Project

• Features

  • Added ability to upload any file type to a project.

• Bugs Fixed

  • Fixed an issue that caused analysis summary pages to display miscalculated duration for users in time zones ahead of UTC time. This was a display issue only; billing amounts were calculated correctly.

  • Fixed an issue that prevented download of FASTQ data from a run details page if the sample data was originally output to multiple projects and one of the projects was transferred to a new owner.

  • Fixed personal account settings page with corrected edit profile link and new change password link.

  • Fixed an issue with sample data generated from multi-node FASTQ Generation not appearing in the Run Samples tab when viewed in Classic mode.

Release 5.18.1 - April 20, 2018

• Bugs Fixed

  • Fixed an issue that reduced system performance.

• Known Issue

  • The v5.18 fix for the multi-node FASTQ Generation display issue was reverted due to performance issues. It will be fixed in a later release.

Release 5.18.2 - April 23, 2018

• Bugs Fixed

  • Fixed an API issue that reduced overall system performance.

  • Fixed an issue where whitelisted beta apps were not shown available apps list.

February 20, 2018 - 5.14 - Bug Fixes

• Features:

  • Added capability to product switcher dropdown menu to dynamically update for available Illumina products

• Bugs Fixed:

  • Fixed issue with missing Metrics link on analyses pages for both imported files and FASTQ Generation runs.

  • Fixed rare issue with the Regenerate FASTQ where action could occur more than once for a run when button was clicked more than once.

  • Fixed issue where editing a project description did not lead to automatic refresh of the project page.

  • Fixed issue where the infinite scrolling on the apps list did not work properly when loading the page with large browser windows.

  • Fixed an issue where the summary metrics tooltip in the Runs list showed metrics for Index Read 1 instead of Data Read 2 for "R2"

  • Fixed issue with inconsistent dates for the billing cycle on the dashboard widget and the user settings storage page.