October 19, 2017 - 5.6 - New Biosample-Centric Data Model and Data Automation Features

Classic Updates

  • Features

    • Updated the look of the apps page

    • Added ability to toggle between classic mode and new mode (see full notes on the new BaseSpace Sequence Hub below)

  • Bugs Fixed

    • Fixed issue with some access tokens unexpectedly changing workgroup contexts

    • Fixed issue with multi-select of libraries on the Create Pool page of Prep Tab

    • Fixed broken navigation links to analysis info, inputs, and outputs in Internet Explorer browsers

New Updates

Our v5.6 release provides a new Biosample-centric data model and other changes to support Automation of previously time-consuming tasks. To try the new features, select New on the Dashboard page toggle button, or contact your workgroup owner to turn on the new features for you. Visit our updated Help site for more information on the new features and updates.

The new features will be rolling out over the next few days.

  • UI Changes

    • Relocated Projects, Biosample, Runs, and Analyses under My Data in the navigation bar

    • Added an action toolbar throughout the app, where all functions like requeues, status changes, downloading, and sharing are accessed from

    • Added a Lane & QC Status to Runs and added the new status to the Filters widget

    • Added a Delivery Status to Analyses in order to manually track delivery of files to customers

    • Renamed Run & Lane Metrics to Metrics in the Run section

    • Renamed "Fix Sample Sheet and Requeue" to Requeue > Sample Sheet in the action toolbar

    • Renamed "Regenerate FASTQ" to Requeue > FASTQ Generation in the action toolbar

    • Added the ability to view details about an Analyses via a tooltip in the status column

    • Updated the Filter widget on the Analyses list

    • Updated the layout of applications on the BaseSpace Apps storefront screen

    • Added the filter widget to more lists so you can quickly narrow down to results that are relevant to you

    • Added inline tooltips throughout the application to provide additional helpful information

    • Added guided tutorials that demonstrate how to perform common actions via the Help menu

    • Added the ability to switch between the Classic and New versions of BaseSpace Sequence Hub via a toggle switch to the dashboard (only workgroup admins and owners of accounts can see this toggle). During the transition period you can switch to and from New and Classic as many times as you want. Please use the Email button on the bar containing the toggle switch to provide feedback if you experience any issues.

  • New Screens

    • Added separate screens that list all your Biosamples and Analyses

    • Added a Summary screen for each Biosample, along with dedicated screens for all associated Libraries, Runs, Requeues, Analyses, and Datasets for each Biosample

    • Replaced Samples with Biosamples in the Projects and Runs sections

    • Launched a new Help section to document all the new application features and make discovery of help topics easier

  • New Actions

  • New Automation

    • Added a new v2 version of the REST API for the new entities. The v1 API is still completely supported too.

    • Added the automatic collection of FASTQ data for the same biosamples put in different runs and lanes

    • Added the ability to automate app launch through the creation and use of app templates called Analysis Workflows

    • Added the ability to set Run Lane Thresholds for automatically setting a run lane to passed or failed

    • Added calculations on sequencing yield for each biosample

    • Added a Missing Yield status on biosamples to indicate it fell short of its required sequencing yield

  • Existing Features Updated

    • Replaced samples with Biosamples on app input forms

    • Replaced Appresults with Datasets on app input forms

    • Updated the File Import screen to save FASTQ files as a FASTQ datasets linked to a new biosample, rather than a new sample

    • Updated the File Import screen to save VCF files as a General dataset, optionally linked to a new Biosample

    • Updated the global search to support finding Biosamples and Datasets

  • New Capabilities

    • FASTQ Generation speed dramatically increased when processing NovaSeq runs by running parallel processes for each flowcell lane

  • Downloader New Features

    • Updated the downloader client for Windows to work with new BaseSpace Sequence Hub features

    • Updated the downloader client for Mac to work with new BaseSpace Sequence Hub features

    • Improved consistency of automatically generated folder names when downloading runs

    • Improved notifications about download status

    • Added support for downloading using a proxy server

    • Added capability to download datasets from the Biosample details Datasets tab

  • Downloader Bugs Fixed

    • Fixed an issue that could prevent download of SAV data from NovaSeq Runs (fix requires that new BaseSpace Sequence Hub features are enabled for account)

    • Fixed an issue where a file that exceeded available disk space was still allowed do be downloaded

    • Fixed an issue in the the Mac downloader client where the progress bar for queued downloads appeared to show they had already completed

  • Known Issues

    • In rare cases, app launch may create a duplicate set of output files for the same appsession. In the case of FASTQ Generation, this produces an additional FASTQ dataset. BaseSpace Sequence Hub prevents subsequent app launches with the related Biosample in these cases. If this occurs, check the Biosample datasets tab for duplicates, and QC fail one set of duplicates.

    • In some cases, the Run button in app error messages does not launch the app. The app can be launched manually from the GUI.

    • Sample IDs with the same name are aggregated to a single Biosample of the same name. Automatic data aggregation enables merging of the same sample run across multiple flow cells for downstream processing, however this may result in inaccurate app results if data from different samples with the same sample ID are aggregated to a biosample in error. To prevent unintended aggregation, use unique sample names across all runs. If BaseSpace Sequence Hub detects aggregation upon launching an app, the biosample is locked and must be reviewed and manually unlocked to allow it to proceed with app launch.

    • Selecting biosamples from the biosamples list before launching an app will not carry over the selected biosamples in to the app form. Instead, re-select the biosamples on the app launch page.

    • If you get certain biosample related warning triangles when launching an app from the New mode launch page, the normal behavior of being able to override and launch anyway may not work, preventing launching of the app. If this occurs, switch to Classic mode and launch from the corresponding samples.

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