Known Issues

• General:

  • Manual refresh on Data view required after archive/unarchive action to reflect new status

  • User Management: User with ‘Data Provider’ role cannot view the Data page in the UI

• Data Management:

  • Unable to add tags to sample during creation

  • Sample deleteDeep API fails with 500 error code when sample contains a linked folder in archived status

  • Unable to set file formats BedGraph, Bisulfite Converted Index, CNS.TAB, NextSeq/MiSeq/HiSeq RTA BCL, VCF.IDX - results in the UNKNOWN format when viewing file details

  • Some files in Data, including SampleSheets, will not export to Excel with error ‘void org.apache.poi.ss.usermodel.CellStyle.setAlignment(short)'

  • User receives incorrect error message via API/CLI/UI when trying to link a file from an externally managed project into a sample

  • The Project Connector is only triggered for actual file uploads, not file linking (where both work for samples)

  • Unable to create a Project Connector rule as a Viewer

  • After creating a sample with multiple files linked to it, the user does not see these files on the details page under the Files section. When clicking a sample in the table, the details are sometimes not shown to the user in the GUI. This does not impact sample creation.

  • User is unable to see details of bundles they have access to in the GUI

  • DELETE /api /connectors /{connectorId} /uploadRules /{uploadRuleId} does not delete the upload rules. Users can delete connector rules via the GUI

  • Service Connector: Unable to download a folder via 'Schedule for download' in Folder Details window

  • Sorting the new data grid can have an unexpected impact. Data will be sorted correctly, but if the user scrolls horizontally in the view, the user will be brought back to the first column

  • When a user tries to download more than 220,000 files via CLI, it is possible that content in some files will be lost during the download process

  • Analysis-events are sometimes too large for SQS, causing BSSH to miss events

• Flow:

  • Workflows attempting to provision nodes of instance types with capacity issues may result in prolonged waiting periods and/or pipeline run failures

  • Graphical CWL pipelines containing Tools with any Input file with a populated "format" will always fail

  • Incorrect failure cause reported through error logs when infrastructure fails to spin up nodes for pipeline steps

  • Issue handling special characters in input file/folder paths

  • Unable to specify secondaryFiles when launching CWL pipeline analyses via API

  • CWL file/directory pipeline inputs are not mounted when provided within nested structures (ie, CommandInputRecordSchema, CommandInputArraySchema)

  • Log streaming is not guaranteed to be in real time and may be minorly delayed

  • When a user reruns single or bulk workflows/analyses from the Analyses overview page, no notification is sent to the specified email address after completion

  • A “-” cannot be used for the ‘number’ and ‘integer’ fields of JSON pipeline input forms. Using a “-“ between numbers in these fields will result in a blank value

• Base:

  • In some exceptional cases the Save button may not be active

  • When a Bundle with a Base Table(s) is added to a Project with no Base permissions, Base is automatically enabled so users can see the Bundle’s Tables. However, access to the Tables is revoked upon deletion of Base, and not granted again if Base is re-enabled

  • The Activity/Base Jobs screen takes minutes to load when there are thousands of entries

• Bench:

  • Unable to enter a Bench workspace stuck in Starting status

  • No clear message in UI when invalid characters are entered when creating a new Workspace

  • The UI does not refresh in new workspaces during long initialization times

• Cohorts:

  • After unsuccessful data ingestion or ingestion with warnings, it is difficult to copy affected subject and sample IDs for verification. Please refer to the e-mail notification to obtain a list of all warnings and errors including subject and sample IDs.

  • Correlation plot can intermittently show no results in bubble plot while there are results in the scatter plot.

  • Bubble fails to load after viewing a correlation in a comparison.

  • Long sample names (30 characters and above) are causing a misalignment with other sample information in the grid.

  • The variant ID list under the needle plot is not displaying all study names where the variants are found.