Improvements

• Improved the stability and performance when using tools that communicate with the NCBI. This will provide noticeable improvements when retrieving large numbers of search results or downloading large numbers of sequences using tools like Search for Sequences at NCBI.
• Improved the placement of figures when reports are exported to PDF.
• Improved the stability of workflow execution when the data is placed on a Network File System (NFS).

Bug fixes

• Fixed an issue where a large nucleotide sequence could be detected as a protein sequence when being extracted from a BLAST database.

Advanced notice

The PPfold plugin will be retired  as of the next major release of the CLC Workbenches and Servers.

The TRANSFAC plugin will be retired as of the next major release of the CLC Workbenches and Servers.

If you are concerned about this proposed change, please contact our Support team by emailing [email protected].

Bug fixes

• Fixed an issue where an error could occasionally arise during workflow validation when adding or connecting workflow elements in the workflow editor.

• Fixed an issue where the installation of large plugins occasionally failed.

Advanced notice

The PPfold plugin will be retired  as of the next major release of the CLC Workbenches and Servers.

The TRANSFAC plugin will be retired as of the next major release of the CLC Workbenches and Servers.

If you are concerned about this proposed change, please contact our Support team by emailing [email protected].

Improvements

• In tracks/track lists, entering "chr4" or "4:" in the location field now searches for a chromosome named "4", "chr4" or "chromosome_4", instead of selecting the 4th chromosome in the drop-down menu. 
• Columns in variant tables are now ordered more consistently.

Bug fixes

• The BLAST Selection Against NCBI and BLAST Selection against Local Data options are once again available in the right-click context menu for sequence selections in a sequence view.  
• Fixed a bug where the Download BLAST Databases tool sometimes failed with an error during download.
• Fixed an issue where the table from Create Pairwise Comparison would not update correctly when the number of decimals to be shown was changed.
• Fixed an issue causing the Workbench to freeze when showing a heat map where all entries are identical. 
• Fixed an issue where the PDF export of reports did not contain column headers if the first header was empty.
• Fixed an issue where text files did not have the expected ".txt" extension after a "Tab delimited text" export with the "Output as a single file" option selected. 
• Fixed an issue where the Excel and PDF export of reports failed for reports that contained empty tables.
• Fixed an issue with the Search for Sequences at NCBI tool, where the search could fail when the Workbench had been configured to use a proxy server.
  
• Fixed a bug where numeric columns with at least five "?" would be left aligned instead of right aligned.
• Fixed a bug where, when launching a CLC Workbench using a CLC URL pointing to a data element stored on a CLC Server location, the data element was not opened automatically inside the Workbench after startup.
• Fixed an issue caused by a bug in Java 10 where files resulting from an analysis were occasionally corrupted. Often this affected analysis log files, but could affect other outputs. This affected GPFS file systems, and could affect other distributed file systems. CLC Main Workbench 8.1, and any versions released with the version 8.1.x, use Java 10. While we have worked around this issue so that analysis results files should no longer be affected by it, we recommend that the software itself not be installed directly on a GPFS file system.

Advanced notice 

The PPfold plugin will be retired  as of the next major release of the CLC Workbenches and Servers.

The TRANSFAC plugin will be retired as of the next major release of the CLC Workbenches and Servers.

If you are concerned about this proposed change, please contact our Support team by emailing [email protected].

New features

• A folder called Utility Tools has been introduced, which contains the tools Batch Rename and Extract Annotations tools. The folder under Molecular Biology Tools called Sequencing Data Analysis is now called Sanger Sequencing Analysis. The Toolbox | Workflows folder has been renamed Installed Workflows.
• The Batch Rename tool allows sets of data elements, or members of a data element (e.g. sequences in an alignment or reads within a read mapping) to be renamed. Changes can be simple, like adding text to the start or end of names, or more complex changes, using regular expressions or custom options. This tool was formerly delivered in the Batch Rename plugin, but is now integrated into the Workbench.
• An item called CLC Server Connection has been introduced under the File menu. This launches a dialog for connecting from the Workbench to a CLC Server. This functionality was formerly delivered in the CLC Workbench Client Plugin, but is now integrated into the Workbench.

Improvements

• Data created in CLC Main Workbench 8.1 will be internally compressed by default. Options are available for for exporting data without this compression or for disabling it entirely.
• A new option allows users to "Export table as currently shown" - including all filter settings and potential additional columns selected using the Side Panel.
• Tooltips on data elements in the Navigation Area show the following additional information: type of the element (e.g. Sequence List), file size, and compression status.
• It is now easier to reorder items in the Navigation Area. It was not previously possible to change the order of adjacent folders.
• Searching in the Navigation Area is now available when using the workbench in Viewing Mode.
• When starting the workbench with a "clc://" argument, the requested element is now selected in the Navigation Area.
• On macOS, the standard file browser is now used for browsing files. Previously, a third-party library was used.
• A new filtering button in all tables allows users to display in the table view only pre-selected rows.
• The 'is in list' table filter now supports tabs as a list separator. This makes it possible to paste rows from Excel into the search field.
• The Import tool allows for entering folder paths in the File name field.
• NCBI API keys for E-utilities can now be entered under Preferences | Advanced | NCBI API Key. This may be of particular interest where multiple machines with CLC Workbenches installed use the same IP address. If an NCBI API key is provided, it is used when running the following tools: Search for Sequences at NCBI, Search for PDB Structures at NCBI.
• The Search for Sequences in UniProt tool is now available in Viewing Mode.
• The Search for Sequences in Uniprot tool has been updated to use the HTTPS protocol which is now required by UniProt.
• When using Search for Sequences at NCBI or Search for Sequences in UniProt to download sequences, the name of the searched database is now reported in the History view. If multiple sequences are downloaded, the resulting Sequence List now also has details in the History view.
• The Download BLAST Databases tool now requires less disk space when downloading and installing BLAST databases.
• The history information associated with results from the BLAST and BLAST at NCBI tools now includes the version of the BLAST software used for the search.
• When right-clicking a CDS annotation on a stand-alone sequence, the option "Translate CDS/ORF..." gives a choice between translating using a selected code translation table or by extracting the translation code from the annotation itself if this information is available.
• The Show History View no longer has a restriction on the number of elements shown.
• A message now warns if a bug report fails to reach Support using Help | Contact Support.
• The Create installer for workflows dialog has additional fields for specifying information about the workflow's author.
• A "Check for updates" functionality is now available from the Help menu.
• Improved error message when attempting to save a file that is not the newest copy.
• The tool called Replace Selection With Sequence which appears in context menus for sequences in the cloning tool will now be disabled when the sequence is linear but a selection spanning the end to start position has been made. Reasons why sequences cannot be marked as circular or linear are now described more clearly in the tooltip.
• The format of the serverinfo.properties file has been changed. The new format supports up to 8 servers.
• The "Whole Genome shotgun-reads (wgs)" database has been removed from the BLAST at NCBI tool. Growth in the database means that specialized variants of BLAST are now required for search. More details on these can be found here.
• Track lists now display additional information about an annotation when hovering on it with the mouse cursor: the name and strand of the annotation, which exon is currently being hovered over and the position of the mouse cursor relative to the start of the annotation. This information is available in the ruler shown in the reference track of a track list, as well as in the lower right corner of the workbench.
• Sequence annotations where the strand is not known are now drawn without an arrow to distinguish them from annotations on the plus strand.
• The Reverse Sequence tool now names the output sequence name with the input sequence name followed by "-R" .
• Various minor improvements.

Bug fixes

• Fixed a problem introduced in CLC Main Workbench 8.0 where launching a tool from the Quick Launch window after sorting led to the wrong tool being started.
• Fixed an issue where the Motif Search tool would incorrectly update the input file.
• Fixed an issue where it was possible to create an empty alignment editor, causing the Workbench to crash.
• Fixed bug that caused import of empty text files to stall.
• Fixed an issue found in the History of a result generated by the Extract Annotations tool, that would incorrectly show that a reference sequence track was used when it was not.
• Fixed the links to the AmiGO Gene Ontology website used for GO annotations.
• Fixed the links to the HGNC (HUGO Genome Nomenclature Consortium).
• On Windows 10 and Windows Server 2016, the default BLAST database location will now be either 'C:\Users\USERNAME\My Documents\CLCdatabases' or 'C:\Users\USERNAME\Documents\CLCdatabases'. Previously it was 'C:\Users\USERNAME\CLCdatabases'.  When upgrading from earlier versions, an existing BLAST database location will not be modified and will continue to work.
• On some Windows 10 and Windows Server 2016 systems, the log files, user settings file, and workflow files, normally stored in 'C:\Users\USERNAME\AppData\Roaming\CLC bio\Workbench' were installed in 'C:\Users\USERNAME\Application Data\CLC bio\Workbench'. Now we instead store these files in '%APPDATA%\CLC bio\Workbench'. User settings and workflow files will be automatically copied to the new location if they were previously stored in 'C:\Users\USERNAME\Application Data\CLC bio\Workbench'.

Plugin notes

Plugin retirements

• CLC Workbench Client Plugin The CLC Server Connection item under the File menu has replaced the need for this plugin.
• Batch Rename  The Batch Rename tool, formerly delivered by this plugin, is now available directly in the Workbench under the Utility Tools folder.

Advanced notice

Improvements

• NCBI API keys for E-utilities can now be entered under Preferences | Advanced | NCBI API Key. This may be of particular interest where multiple machines with CLC Workbenches installed use the same IP address. If an NCBI API key is provided, it is used when running the following tools: Search for Sequences at NCBI, Search for PDB Structures at NCBI 

• The Search for Sequences in Uniprot tool now uses the HTTPS protocol.
  

Bug fixes

• Links to the HGNC (HUGO Genome Nomenclature Consortium) website are now working again. 

• Fixed the links to the AmiGO Gene Ontology website used for GO annotations. 
  

Notice

 Only 64 bit versions of the CLC Main Workbench are available for CLC Main Workbench 8.1, released November 28, 2018, and above. 

Bug fixes

• Fixed an issue where domain annotations added by the Pfam Domain Search tool started one amino acid later than expected. The corresponding start position in the table produced by the tool was correct.
• Fixed an issue with the advanced table filter functionality that prevented the removal of empty entries from columns expected to contain text.
• Fixed an issue where Excel formatted files (.xls, .xlsx) could not be imported as Trim Adapter Lists.
• Fixed a license issue causing workbenches to not start properly on Turkish Operating Systems.
• Fixed issue causing the license assistant dialog and EULA dialog to be too big for smaller screens. 
• Fixed an issue where weblinks to Uniprot sequences led to the homepage.

Advanced notice

With a release planned for late 2018, only 64 bit versions of the CLC Main Workbench will be made available. 32 bit versions will be discontinued from that time.

If you are concerned about this change, please contact our Support team ([email protected]).

Improvements and new features

• Workbenches without a license can now be run in Viewing Mode. In this mode, data can be viewed, imported and exported. Plugins needed for viewing certain data types can be installed. Viewing mode, with its added functionalities, replaces Limited Mode.
• A dialog is now presented on startup if there are installed workflows that need to be updated before they can be run. The information about what to do to when a workflow needs to be updated has been improved.
• The history of a data element can now be exported as a CSV format file.
• Changed amino acids colors to better suit users with various forms of color blindness.
• The Download Pfam Database tool now downloads version 31. Updates can now be made independently of the release of CLC Main Workbench, so the version available for download could change over time from the one recorded here.
• In table views, it is now possible to filter columns with the filters "Is in list" and "Is not in list" when the values are numbers.
• Importing a GO annotation file with the Standard Import tool, specifying the format "Generic annotation file for expression data", now fails with an informative warning if any of the GO annotations are truncated.
• Warnings are now reported if truncated GO annotations are found when opening data created by the Create Expression Browser tool.
• The 'Expression Browser Table' (output from the Create Expression Browser tool) now preserves sorting when changing the grouping, if sorting is not on any of the grouped columns.
• All wizard steps are now shown in the wizard sidebar when starting a tool or workflow.
• Visualization of features that wrap around the origin of circular sequences has been improved for sequences.
• Table filtering and search now interpret thousands and decimal separators in the same manner as the displayed table. Previously US punctuation was always used. This change means that if a table displays numbers in the form "123.456,7" then it is possible to find numbers less than ten by searching for "< 10,0" or "<10", but not "<10.0". If the table displays numbers in the form "123,456.7" then it is possible to find numbers less than ten by searching for "<10.0" and "<10", but not "<10,0".
• When a tool is disabled in a right-click context menu, hovering the mouse over the tool name will now reveal why a tool was disabled in most cases.
• The help window can now be closed by pressing the escape key.
• HTML formatting tags are now removed during export of data to Excel .xlsx or .xls format. This change does not affect the export of hyperlinks.
• A warning message is now presented when the tool Extract Sequences is run with the "Extract to single sequences option" selected and more than 100 sequences would result.

Changes

• The Search for Sequences at NCBI tool now uses accession.version identifiers instead of GI numbers, as GI numbers are being phased out by NCBI (see https://ncbiinsights.ncbi.nlm.nih.gov/2016/07/15/ncbi-is-phasing-out-sequence-gis-heres-what-you-need-to-know/. )
• Scrolling in a table now scrolls a fixed number of pixels, and not a fixed number of rows or columns.
• The "Help" and "Reset" buttons in pop-up dialogs are now buttons with text labels. They were previously buttons with icons.
• The GCG sequence exporter has been removed. The GCG alignment exporter is unaffected by these changes.
• Upgraded NCBI blast executables to version 2.6.0 for 64-bit systems. 32-bit systems still use version 2.2.30.

Bug fixes

• Fixed an issue where filtering a log for a job that was still running would result in error dialogs.
• Fixed an issue that had previously prevented configuration of the export option "Output as single file" in workflows.
• Fixed an issue where data exported with gzip or zip compression did not have the .gz or .zip suffix appended to the filename when earlier exports had been made with the same name and export location specified.
• Fixed an issue that could cause exports of reports with line graphs to fail.
• Fixed a bug where a cell containing multiple hyperlinked URLs caused export to Excel 2010 or Excel 97-2007 format to fail. Such cell contents are now written in plain text.

Plugin Notes

• Licenses for commercial modules are no longer required to install a module on a Workbench nor to view data generated by tools of a commercial module.
• The flexibility associated with network module licenses has been improved. Workbench module licenses provided via a CLC License Server are now initially loaded only when a tool provided by that module is launched. Such licenses are returned when 4 hours lapses since the last module tool was launched from that Workbench.

Advanced Notice