Latest improvements for QIAGEN CLC Main Workbench early access

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These are the draft release notes for CLC Main Workbench 24.0, due for release on January 9, 2024.

Installers for this product are available as “early access” via links at the bottom of this page. These products are not supported, and we recommend they are not used in production during the early access period.

To download a commercial license for this product, you must have a license covered for Maintenance, Upgrades and Support (MUS) until on or after January 9, 2024. A two week evaluation license is available via the License Manager within the software.

New features and improvements

Workflows

• Branch on Sequence Count – a new workflow control flow element for controlling the downstream processing of a sequence list depending on the number of sequences in that list.
• The workflow build id is included in the Workflow details section of the History view for data elements generated using installed workflows. Previously only the workflow name and workflow version were reported.
• Workflow inputs can be preconfigured with files stored on AWS S3. This is of particular relevance when using reference data stored on AWS S3.
• Options have been added to jump to the workflow element at the source or destination of a connection between elements.

Usability

• A View Settings menu has replaced the “Save View” functionality at the bottom of Side Panels of elements open for viewing. The updated functionality makes it simple to save, apply and manage view settings for elements and element types.
• The font size of the Navigation Area, Toolbox tab and Favorites tab can be increased and decreased.
• Drag-and-drop can be used for selecting files in import tools.
• Non-CLC format files can be directly saved to disk from the Navigation Area using the “Save to disk…” option in the right-click menu or by dragging and dropping from the Navigation Area to a file browser.
• Non-CLC format files in a CLC File Location can be opened in a relevant program by dragging them from the Navigation Area to a program icon in a toolbar, or similar, on systems that support this. This adds to the existing functionality where double clicking on such files in the Navigation Area leads these to be opened in a relevant program on systems that support this.

Table related

• Column order can be adjusted by moving the corresponding column names up or down in the Side Panel. Previously re-ordering could be done only by dragging a column to the desired location within the table view.
• The column order for most table types can be saved and applied as view settings. Previously, column order could be adjusted when viewing tables, but the revised order could not be saved for later use or for use with other tables of the same type.
• Sets of criteria used to filter tables can be saved as Filter Sets. These can be reapplied to other tables in a single click, or exported and imported, for sharing purposes.
• When exporting an element with no contents to Excel format (.xlsx, .xls), the sheet created contains column headers. Previously, column headers were not included in this case.
• Expression data tables containing more than 1 million rows can now be sorted.

BLAST

• The list of databases available using BLAST at NCBI has been expanded, including the addition of the experimental taxonomic nt databases ‘Eukaroyta nt (nt_euk)’, ‘Prokaryota (bacteria and archaea) nt (nt_prok)’ and ‘Viruses nt (nt_viruses)’.
• Spaces in the names of BLAST database locations and folders in the path are supported.

Report processing

• Combine Reports has the following improvements:
  • A summary section can be included.
  • Content is customizable. Sections to include and their order can be specified.
  • Configurations can be re-used in future runs of Combine Reports.
  • Modify Report Type A tool for changing the type of a report, affecting where the contents of that report will be included in a combined report.
  • Reports generated by Homology Based Cloning are supported.

Other new features and improvements

• Custom color gradients can be defined, including specifying the type and number of boundaries in the gradient, and colors to use at those boundaries.
• Extract from Selection has the following improvements:
  • Reads can be extracted from read mappings based on the orientation they were mapped in.
  • Reads can be extracted from read mappings as broken pairs when only one read of a pair matches the extraction criteria.
  • The organization of the options in the wizard has been updated accordingly.
• The names of outputs generated by Homology Based Cloning now contain the name of each of the sequences included in the cloning reaction.
• Data in public AWS S3 buckets can be accessed.
• Export history to PDF includes information about the workflow that produced the data element.
• When connected to a CLC Server, subfolders of CLC Server File System Locations that you have access to are listed at the top of the containing folder in the Workbench Navigation Area. Previously subfolders were not ordered according to access level.
• The history for elements created using an external application includes the version of the external application used.
• CLC File Locations can be removed and re-indexed when the Workbench is being run in Viewing Mode.
• Fixed a rare issue that would result in an error dialog being shown during a drag and drop operation in the Navigation Area.
• New policy property: ‘run_on_workbench_when_server_is_available’ When set to ‘deny’, server-enabled tools, and workflows, cannot be run locally on the CLC Genomics Workbench when it is connected to a CLC Genomics Server. The default is set to ‘allow’.
• Various minor improvements

Bug fixes

• Fixed an issue where paired reads with unaligned ends overlapping within an insertion were not shown in different colors for forward and reverse reads after the option to show the strands was selected in the Side Panel view settings.
• Fixed an issue where the axis scale range for plots in reports exported to PDF format could sometimes differ from the range seen when viewing that plot in a CLC Workbench.
• Fixed an issue where infinite values were included in report plots when the report was exported to pdf format.
• Fixed an issue where providing incomplete metadata (e.g. a column name missing) when launching a workflow containing an Iterate element would lead to the analysis stalling, instead of failing with an error.
• Sorting Local Search results based on sized sorts in numerical order. Previously, the sorting was alphabetical.
• Fixed an issue in Download BLAST Databases that caused part of the description of the available databases to be hidden in the launch wizard.
• Fixed an issue in the Workflow Manager where multiple workflow installer files (.cpw) could be selected at the same time. Selection is now restricted to a single workflow file per installation action.
• Various minor bug fixes

Changes

• Combine Reports has been moved in the Toolbox to Utility Tools | Reports. It was previously under Sanger Sequencing Analysis.
  
• When reports that are not supported by Combine Reports are provided as input, the tool will fail. Previously, the tool would run, but would ignore the unsupported reports. In practice, this change is most likely to be noticed in the context of workflows where output channels for unsupported reports have been connected to the input channel of a Combine Reports workflow element. Unsupported reports cannot be entered as input in the tool launch wizards.
• The SRA blast database can no longer be used with BLAST at NCBI, because NCBI no longer supports blasting against that database via their API.
• BLAST has been upgraded to BLAST+ 2.14.0. BLAST+ changes can be viewed at http://www.ncbi.nlm.nih.gov/books/NBK131777.
• The Java version bundled with CLC Main Workbench 24.0 is Java 17.0.8.1, where we use the JRE from the Azul OpenJDK builds.
• Dedicated installers for Intel and ARM-based mac systems are available.

General information

Important: For network licenses, CLC Network License Manager 5.5.2 or above is needed. See the latest improvements page for release notes. Upgrading the software is described in the manual. Get the CLC Network License Manager installers for the latest version via the website. The version running on a system can be found in the VERSION.txt file in the installation folder of the CLC Network License Manager.

Advanced notice

The Sequence Representation functionality, allowing the display name for sequence elements in the Navigation Area to based on the accession, latin name or common name of that sequence has been marked as legacy functionality. Setting the display name for sequence elements in the Navigation Area to the accession, latin name or common name in a sequence record using the Sequence Representation functionality, via a right-click menu or in Preference settings, will be retired in a future release.

Early Access installers

Early access products are not supported, and we recommend they are not used in production during the early access period.

• CLC Main Workbench 24.0 early access for Windows
• CLC Main Workbench 24.0 early access for Linux
• CLC Main Workbench 24.0 early access for macOS Apple Silicon
• CLC Main Workbench 24.0 early access for macOS Intel