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

Bug fixes

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

• Weblinks to UniProt sequences are now working again.

• 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.
  

Advanced notice

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

• Improved the information about what to do to when a workflow needs to be updated.
• Various minor bugfix.

Bug fixes

• Fixed an issue with the Cloning tool introduced in the CLC Main Workbench 7.9 where the tool could not be launched.

New features

• Added keyboard shortcuts to change editor views. Ctrl + Shift + PageUp and Ctrl + Shift + PageDown now changes the current view of the currently focused editor. 
• New keyboard shortcuts are available for navigation within the workbench:
  • Navigate between open tabs with Ctrl + Page Down and Ctrl + Page Up (Windows/Linux/Mac). On laptops without Page Up/Down keys, the shortcuts are Ctrl+fn+arrow up/down.
  • Return focus to the navigation area with Alt + Home.
• We have made the following improvements to tab presentation in the View area of the Workbench:
  • Tabs show more of the name of the opened object.
  • Tabs now open from the top left corner to the right and down.
  • Tabs always stay in the same position when another tab is selected or a new tab is opened.
  • A new sub menu has been added to the right click menu on tabs to select between the open tabs.
• Anonymous Workbench usage information can now be shared with us to help us improve our products and offerings. Information about what is collected and how to opt out is provided when the updated Workbench is launched. Further details are available in the manual.

Improvements

• New and improved Save View Settings dialog. This new dialog can be used for saving, applying, importing and exporting side panel views.
• Opening large pairwise comparisons generated by the the Create Pairwise Comparison tool is now faster.

Bug fixes

• Fixed an issue where the GFF3 Exporter could generate invalid GFF3 for features of length 0.

• Fixed a rare issue that could cause GenBank export to fail.
• Fixed an issue with the Realign Selection tool where clicking on the ? button to see the manual information resulted in an error. This tool is launched from the right-click context menu for selections in sequence alignments.
• Fixed an issue where workflows run in batch mode would fail in the case where no results are saved to the Navigation Area and only one file is exported per batch unit.
• Fixed an issue introduced in CLC Main Workbench 7.8.1 where the Download Sequences from NCBI tool would continue to indicate it was searching when in fact the search had finished and no items were found.

Bug fixes

• Fixed an issue where the Search for Sequences at NCBI tool did not display the first and last search result in each page of results returned.

BLAST

• Added “RefSeq representative genomes” database.
• Removed “New or revised GenBank sequences (month)”. This is no longer supported by the NCBI.
• Changed “References mRNA sequences”name to “References RNA sequences”. The database that is searched remains the same as before.
• Changed “16S ribosomal RNA sequences” database to now search the  “rRNA_typestrains/prokaryotic_16S_ribosomal_RNA” database, as listed on the NCBI website. It previously queried “TL/16S_ribosomal_RNA_Bacteria_and_Archaea”.
• Fixed “Human genomic plus transcripts” and “Mouse genomic plus transcripts” databases configuration to reflect their new location. Searching these previously returned an error.

Metadata

• Usability aspects of data association using the Import Metadata tool have been improved, including adding a preview of data items to be associated with particular metadata rows.
• The speed of searches for data elements with associations to specified metadata, from within a Metadata Table, has been greatly improved. To enable metadata related searches to work after upgrading to the CLC Main Workbench 7.8, indices for the locations containing the relevant data will need to be rebuilt.
• A preview of data items that will be associated with particular metadata rows has been added to the Import Metadata tool.
• Various small usability improvements have been made to the Import Metadata tool.

New features and improvements

• Tutorial windows are no longer blocked when a wizard is open.
• An exporter has been added to export annotations on sequences or tracks to Generic Feature Format Version 3 (GFF3) format.
• When working with Gene Sets that refer to Gene Ontology terms, gene annotations are now automatically propagated to parent Gene Ontology terms. This improvement affects the tools Hypergeometric Tests on Annotations and Gene Set Enrichment Analysis (GSEA).
• It is now possible to right-click on a table cell and filter table rows based on the value of that cell by choosing options under the new context menu section called  "Table filters". This change applies to all tables where advanced filtering is available.
• Support has been added for 'negative lookahead' when using Java regular expressions when using the Motif Search Tool.
• In cases where tools within a workflow have been renamed, it is now possible to filter for original tool names within the workflow configuration view of the workflow editing tool.
• Various minor improvements

Bug fixes

• Fixed an issue with GenBank and EMBL exports where quoting specifications were not being conformed to.
• Fixed an issue where a workflow containing an export step that failed did not provide any indication that a problem had occurred.
• Fixed an issue with the Annotation Table view of a sequence where it was possible to change the types of annotations displayed at the same time as an annotation was being edited, which could lead to an error being thrown or the wrong annotation being changed.
• Fixed an issue with Primer Tables where an error resulted if either the option "Save Primer(s) Fwd, Rev" or "Save Fragment" was chosen and then the save operation was stopped by clicking on the Cancel button.
• Fixed an issue where in some cases filtering tables for empty values would not produce any results.
• Fixed an issue where advanced filtering did not work when looking for rows with cells containing multiple values using the filtering term "=" (equals).
• A sporadic java issue that led to errors including the text "java.lang.ClassCastException: sun.awt.image.BufImgSurfaceData cannot be cast to sun.java2d.xr.XRSurfaceData", has been addressed through an upgrade to java. This issue was primarily seen when using the Workbench remotely on Linux systems.
• Fixed a problem with the identification of the correct sequence types from MLST schemes in cases where the schemes contained blank characters. This issue affected workbenches with CLC MLST installed.
• Various minor bugfixes.

Retirement

• The GFF exporter has been retired and is no longer available. The new GFF3 exporter should be used instead.

Other notifications

• An option to opt out of providing anonymous usage information to QIAGEN has been added to the Workbench Preferences. We are not yet collecting any usage information so opting in or out does not have any effect at this time.

Bug fixes

• Fixed a problem with the identification of the correct sequence types from MLST schemes in cases where the schemes contained blank characters. This issue affected Workbenches with the CLC MLST Module installed.

Improvements

• Updated the restriction enzyme list from REBASE.

Bug fixes

• Fixed an issue with running BLAST on macOS Sierra.
• Updated PFAM links reported by the Pfam Domain Search tool.
• Fixed an issue introduced in CLC Main Workbench 7.7.2 where enzymes listed alphabetically after RdeGBI were missing methylation information.
• Fixed a problem where launching a tool from the Quick Launch window after sorting led to the wrong tool being started.
• Various minor bugfixes.

Advanced Notice

• Windows: Windows Vista and Windows Server 2008
• Mac: Mac OS X 10.7 and 10.8
• Linux:  Red Hat Enterprise Linux 5, SUSE Linux Enterprise Server 10 and 11 and Fedora 6 through 21

Workflows

• Workflow outputs can now be configured so that subfolders to contain the outputs are created.
• New placeholders are available when defining the names of workflow outputs: {user}, {host}, and for elements of the timestamp of the output object, {year}, {month}, {day}, {hour}, {minute}, {second}.
• Placeholders within workflow output names that were previously available only as digits can now be specified using written names: {name} is a synonym for {1} and {input} is a synonyms for {2}.

• When using the {2} placeholder for custom naming in workflow output elements, only unlocked inputs will be included in the generated name.

• In the generated pdf showing all the configured parameters of a workflow, entries for parameters connected to a tool or an input element now list the names of the defining elements. Previously the parameter listings for such elements were left blank.

• Where a tool name has been altered in a workflow, the original name is now included alongside the changed name when exporting workflow parameters.

• The History view of data elements created using a workflow now includes information about the workflow that created them.

• The order of the tools in the workflow "Add Element" menu now matches the order in the Workbench Toolbox menu.
• Improved workflow validation to aid the user in identifying inputs that will be ignored due to the configuration of the workflow elements.

Launch

• The Quick Launch tool is now found under the Toolbox menu instead of the View menu and a button called Launch that brings up this tool has been added to the toolbar.
• Analyses can now be launched on data elements listed in the results table of a Local Search by selecting the elements of interest, right clicking with the mouse and navigating through the context menu that appears.

Metadata

•  A "Remove Association(s)" option for removing metadata associations from selected data elements has been added sin the Metadata Elements view in a right click context menu.
• In the Metadata Find Associated Data view it is now also possible to use Find in Navigation Area when multiple rows are selected.
• When importing metadata from a spreadsheet with formulas in it, the result of the evaluation of the formula (as displayed in Excel) is now imported rather than the formula itself.

General

• All NCBI server communication is now encrypted. (NCBI will be moving all web services to the HTTPS protocol on September 30, 2016).
• The list of enzymes pre-installed in the workbench has been updated from REBASE.
• The option "is not in list" has been introduced as a new table filtering option.
• Read group details are now shown on the Element Info view of sequence lists.
• GenBank import now also allows for file names with 'GBFF' extension.
• The "Sort folder" tool now uses numerical sorting for filenames prefixed with a number.
• New placeholders are available when defining the names of exporter outputs:  {user}, {host}, and for elements of the timestamp of the output object, {year}, {month}, {day}, {hour, {minute}, {second}.
• Placeholders within export output names that were previously available only as digits can now be specified using written names: {input} is a synonym for {1}, {extension} is a synonym for {2} and {counter} is a synonym for {3}.

Bug fixes

• Fixed an issue that caused characters in sequence names to be rendered incorrectly when a report was exported to Excel.
• Fixed an issue where the Motif Search tool was incorrectly reporting all match accuracies as either 0% or 100%.
• The Create New Sequence List button in a broken pair table now works when multiple read groups are involved.
• Fixed a bug that made graphics export of some plots from reports fail.
• The Find Binding Sites and Create Fragments tools now properly display mismatches when the primer input is in lower-case.
• Tables with more than 126 million entries now show a warning that they contain too much data to display instead of leaving the table empty.
• Fixed an issue where sequences of length zero would cause the Create BLAST Database tool to throw an error. Such sequences are now skipped and will not included in the final database.
• Fixed an issue in the wizard for the tool Create Entry Clone where a previously used data located on an unmounted location would result in an error message being shown.
• Fixed a rare issue where some annotations could, but did not necessarily, go missing on  sequences with greater than 1000 annotations of a given type on that sequence before the deletion and where the right-click context menu option "Delete selection" was used.
• Fixed a bug in the "Manage Enzymes" wizard that prevented a user from cancelling the action if "Save as new enzyme list" was enabled.
• Fixed an issue with the Import Metadata tool where, if a spreadsheet had already been loaded, then selecting the same spreadsheet again did not reload the spreadsheet content.
• Fixed an issue where it took a long time to open a workbench it it was previouslyclosed when displaying an open table editor that had been sorted.
• Fixed an issue where right-clicking on a graph in a report and choosing to show "Report", "History" or "Element Info" triggered an error.
• Fixed an issue with links in tables to the PDB and dbEST databases.
• Fixed an issue where the save wizard dialog did not pre-select "Save in input folder" when that option was the most recently used one.
• Fixed an issue where the save wizard dialog did not pre-select "Save in input folder" when that option was the most recently used one.
• Fixed an issue where, when the Processes tab was hidden and then shown again, any processes listed before the tab was hidden were no longer shown.
• Fixed an issue that made "Download and save" fail when invoked on a Blast editor.
• Updated the URL to use for links to UniProt databases.
• Various minor bugfixes.

Bug fixes

• Fixed an issue that arose when executing workflows with multiple inputs in batch, where changes to pre-defined, fixed inputs specified during the launch process were not applied.
• Fixed an issue where the Motif Search tool incorrectly reported all match accuracies as either 0% or 100%.
• Fixed an issue where sorting a folder while saving into it could trigger an error.
• Fixed a bug in the batch mode dialog that would lead to an error when problems related to the underlying file or data location were encountered.

Advanced notice

New tools

Improvements

Metadata

• The use of partial or exact matching schemes can be chosen when associating data with metadata using the Associate Data Automatically option.
• It is now possible to change the type of a metadata column, even if it already contains values. Conversion is only possible when all existing values in the given column can be converted to the new data type.
• Usability enhancements in the Metadata Table Editor.

Workflow

• Workflow inputs  can now be ordered via the Workflow Editor, affecting the order that input information is requested when setting up a Workflow run.
  • Workflows with multiple input elements, where all input elements will be changed per batch, can now launched in batch by right-clicking on the installed workflow name and choosing the option "Run in Batch Mode...".
• Tools in a Worfklow that have been renamed will have both the new tool name and the original tool name displayed in the Workflow Configuration Editor.

General

• Performance optimization for sizing phylogenetic trees by metadata
• The Download Pfam Database tool has been updated to download version 29.
• Improvements to the way Ensembl IDs are parsed to links in tables: stable Ensembl IDs are now correctly parsed to links for all Ensembl-supported organisms (Ensembl release 83).
• The options for saving the output from "batch jobs" have been improved. Outputs can now be saved into a specified single folder in addition to the other established save options.
• All Excel sheets in a document are now imported and each sheet has a table created for its contents.
• The CSV, HTML and Excel table/tabular exporter now use "Inf" and "NaN" values to replace the ambiguous "?".
• In the wizard for exporting a table in CSV format, when not exporting all columns, it is now possible to cancel or go back to the previous step while selected columns are loading.
• An option has been added to allow the same print settings to be applied to all reports being exported to pdf format in a given export run.
• The "Manage Resources" tab has been removed from the the Plugin Manager.

Changes

Workflow

• The Create Scatter Plot tool is now Workflow enabled.
• The Create MA Plot tool is now Workflow enabled.

General

• Versions of individual tools are now reported in the history of output objects.
• Export to clc format now truncates very long filenames.
• Plots without any data points will now be skipped when rendering reports.
• RPM package installers for Linux are no longer available.
• Associate Data Automatically accepts data elements (not folders) as input.
• The 'Database Fields' label shown in the 'Show Element Info' view has been renamed to ' Local Attribute Fields'.
• The "Metadata Role Override" parameter that was visible when creating Workflows has been removed.
• The user can no longer uncheck "export all columns" for input objects that do not support this option. This applies to command line functionality as well, where the user will now receive an error if this is attempted.

Bug fixes

• Fixed a bug when the download buttons on BLAST result table view failed for nucleotide sequences.
• Fixed a frame offset bug that occurred when translating reverse complemented CDS regions into protein sequences.
• In heat maps it is now possible again to show colors legend to the left and right of the heat map.
• Fixed a bug that caused the Excel importer to use column names as cell values of the first row.
• Fixed an issue where open tabs were not correctly ordered after splitting view horizontally or vertically using the View menu or keyboard shortcuts.
• Fixed an issue where an error was reported if the local realignment tool detected an insertion followed by a deletion in the original mapping. Such positions are now ignored.
• Fixed an issue where Workflows were not able to remove intermediate data from permission enabled locations unless the top folder was writable.
• Fixed an issue where the "Show results"option in the Processes tab would lead to an error if the results dataset was very large.
• Fixed an issue so that double clicking on clc:// urls on Mac OS X now opens the data element in a view in an installed CLC Workbench.
• Fixed an issue where an error arose when renewing a borrowed network license.
• Fixed a bug that led to the creation of an empty folder for each excluded batch unit.
• Fixed a bug that  led to the inclusion of the number of excluded batch units in the count of the total number of batch units to be processed.
• Added missing percentage signs for identities and gaps in Blast text exports.
• A Workbench Data Location pointing at a file on the system instead of a folder will now appear as unavailable in the Workbench Navigation area instead of throwing an error.
• Fixed a bug where it was possible to type non-number characters into a number field when starting up a job in the Workbench.
• An error was previously thrown when encountering blank annotation-values. Blank values are now ignored.
• Fixed an error that could appear when moving the mouse over annotations in a sequence annotation table.
• Fixed an issue with Open Copy of Workflow so it now works on all workspaces rather than just the first workspace.
• Fix an issue that could lead to an error when a job status description changed while a full description was being generated.
• Fixed an issue with handling dates when importing metadata from Excel format files using the Metadata Table Editor.
• Fixed a bug that was causing missing report text lines.
• Fixed an issue where, when the option to "Skip these updates" was checked in the plugin update information window, this information was not saved. This led to the same plugin update information being presented after each Workbench restart if the plugins were not updated.
• Fixed an error that occurred when pressing the Print button in the Help dialog (Mac OS X only).
• Fixed an issue where the text area in error dialogs did not expand vertically when the dialog was expanded.
• Fixed an issue where sub-jobs were not resumed after pausing and resuming a batch process.
• Fixed an issue where the workflow installer creation keyboard shortcut could be used when it should have been disabled.
• Fixed a rare issue that could be triggered by switching editor view with a double click.
• Fixed an issue that caused the 'Use random codon' parameter in the tool "Reverse Translate" to report a null-error.

Plugin updates and fixes

Changes to freely available plugins

• Annotate with GFF: Now supports spaces in annotation names.
• Batch rename: Fixed an issue where a warning was displayed for entries not modified.

Improvements

• All NCBI server communication is now encrypted (uses HTTPS).
• Updated the URL to use for links to UniProt databases.
• Updated BLAST executables to be compatible with macOS Sierra. This change only affects Mac users.

Bug fixes.

• Fixed a rare issue where some annotations could, but did not necessarily, go missing on sequences with greater than 1000 annotations of a given type on that sequence before the deletion and where the right-click context menu option "Delete selection" was used.
• Fixed a bug in the Manage Enzymes wizard that prevented a user from cancelling the action if "Save as new enzyme list" was enabled.
• Fixed a problem with the identification of the correct sequence types from MLST schemes in cases where the schemes contained blank characters. This issue affected workbenches with CLC MLST Module installed.*

Bug fixes

• Fixed an issue where the Motif Search tool incorrectly reported all match accuracies as either 0% or 100%.
• Fixed a bug that made the help for tree side panel settings inaccessible when the workbench was run in limited (evaluation) mode.

Advanced notice

Improvement

• Performance optimization for sizing phylogenetic trees by metadata.

Bug fixes

• Fixed an issue with handling dates when importing metadata from Excel format files using the Metadata Table Editor.
• Bug fixed causing missing report text lines.
• The Download Pfam Database tool has been updated to download version 29.
• Fixed an issue where Workflows were not able to remove intermediate data from permission enabled locations unless the top folder was writable.
• The "Metadata Role Override" parameter that was visible when creating Workflows has been removed.
• Fixed a frame offset bug that occurred when translating reverse complemented CDS regions into protein sequences.
• Fixed an issue that caused the 'Use random codon' parameter in the Reverse Translate tool to report a null-error.
• Fixed bug when download buttons on BLAST result table view failed for nucleotide sequences.
• Fixed an issue with renewing a borrowed license.

Bug fixes

• Fixed a bug when the "Search for sequences at NCBI" tool would fail to download nucleotide sequences with the error message "The following sequences were not downloaded correctly: ...".
• Fixed a problem with the BLAST at NCBI step of the Create Protein Report tool.
• Fixed an issue leading to an error during VCF export where the data involved had originally been imported from VCF files and the values in the QUAL field were integers.
• Export of floating-point (decimal) numbers to VCF format were previously dependent on the specified locale. This has been fixed so that the decimal separator now always is a point.
• When doing automatic association of metadata, the log now shows which metadata rows were not associated with any data.
• Fixed a bug that prevented metadata manual information to be accessed from within the Workbench.
• Fixed a bug where doing automatic association using a metadata table stored on a CLC Server would fail.
• Automatic association of metadata now handles association based on the a prefix of data names rather and exact matching to the whole data name.
• A metadata table no longer needs a key column for its rows to be manually associated with data elements.
• An option to override metadata roles previously visible in the configuration of Workflow outputs was removed.
• Fixed issue that caused locked parameters to be overwritten by a previously entered value, during workflow execution.
• Fixed an error happening when a Workbench Data Location was pointing at a file on the system instead of a folder. It will now appear as unavailable in the Workbench Navigation area.
• Enabled tooltips for all parameters when configuring and executing workflows.
• The login process from a Workbench to a CLC Server must now complete before opening a clc url will begin.
• Fix a problem on Macs where the Workbench was not recognized as a custom protocol handler for clc:// urls.
• Resolved a rare occurring exception that could be triggered by switching editor view with a double click.
• Fixed an error that occurred when pressing the Print button in the Help dialog (Mac OS X only).

New features and improvements

• Batching on selected elements is now possible: it used to be restricted to selected folders.
• One can now select "EST" as database when using the Search for Sequences at NCBI tool.
• The Hierarchical Clustering of Samples tool can now be executed as part of workflows and on the server.
• Improved memory management when handling large report elements.
• Tooltips on leaves of phylogenetic trees now display a description of the attached sequence.
• Numbers are no longer appended to the names of Workflow elements when creating a copy of a Workflow using "Open Copy of Workflow".
• Metadata Management. Keep track of input files and import meta information for your samples.

Bug fixes

• Fixed a rare occurring issue where the Workbench would display an error message when installing a 3rd party licensed plugin.
• Fixed an issue where selecting an entry in a Blast results table could highlight the wrong alignment in the Blast editor if the table had been filtered or sorted.
• Fixed an issue where clicking on an annotation in the Design Primers editor could give rise to an error message.
• Fixed an issue where annotations that spanned the ends of a circular sequence would be incorrectly placed in the Circular Sequence View.
• Fixed a bug that caused the workbench to freeze if certain sequences were displayed in circular view with radial rendering of labels.
• Fixed exported reports having the wrong author in certain situations.
• Fixed an issue whereby Create Box Plot and Principal Component Analysis could sometimes be run with illegal arguments, leading to an error message.
• The output of the Reverse Complement Sequence tool now gets the suffix -RC attached to the name of the input instead of -1 before.
• Fixed a bug in the Predict Secondary Structure tool when the option to calculate the partition function was selected  for long molecules (>1000 nucleotides).
• Fixed an issue where one could not zoom in after zooming out fully on very large workflows.
• Fixed an issue that prevented a root folder on Windows drives from being used as a File Location.
• Fixed an issue where updating an existing installation on Windows would result in the .vmoptions file being deleted, which makes the Workbench run with the default Java configuration.

Bug fixes

• Added a work around to a java issue that occasionally resulted in the Workbench displaying an uninformative error and requiring a restart to continue working.
• Fixed an issue with running BLAST at NCBI where an NCBI-generated error about their CPU usage limit being exceeded was not being reported transparently and a result of "no hits" was being reported instead.
• A fix was applied to avoid an exception in circumstances when the cleanup of downloaded files from BLAST failed.
• The Reverse Translate tool ignored any genetic code specified in the codon frequency tables. All reverse translation would thus default to the standard genetic code.
• When installing a workflow with bundled data, it is no longer possible to select a read-only folder for storing the data.
• Fixed wrong display of "Supported format" when exporting elements from either the Folder Editor or the Local Search Editor.
• Fix of potential wrong file being saved when editing a file found via the Local Search Editor.
• Plots inside reports are now shown with their saved side panel settings.
• Fixed saving different line colors in plots through the side panel.
• Side panel option to show legends for a plot with more than 10 samples is now enabled.
• Fixed an issue that led to an error when rendering plots for empty data sets.
• Fixed an issue where the "Empty Recycle Bin” option was sometimes incorrectly unavailable.

New features and improvements

• BLAST has been upgraded to BLAST+ 2.2.30 that includes a number of improvements and bug fixes. A full list of BLAST+ 2.2.30 changes can be viewed at http://www.ncbi.nlm.nih.gov/books/NBK131777
• The GTF exporter is now available for the Main Workbench.
• Transcriptomics experiment and sample tables can now be sorted, even with large numbers of rows.
• Improved Excel, HTML and tab delimited export of variants (choose only the annotations/columns you need).
• The results of BLAST searches now include a new view, the Blast Hit Table.

Bug fixes

• Fixed an issue with running blast searches at the NCBI where an NCBI-generated error about their CPU usage limit being exceeded was not being reported transparently and a result of "no hits" was being reported instead.
• Fixed an error affecting the "Cut Sequence Before/After Selection" tool in the Cloning editor.
• Fixed bug where a left-click quickly followed by right-click was interpreted as double-click on OS X (in the persistence search result list, in the toolbox tree, and in the workflow editor).

New features and improvements

• Tracks:
  • Consistent output when enriching variant tracks and annotation tracks with extra table columns. Output tracks from these tools now have the same number of added table columns and the columns will always be in the same order. Previously, if an added column had empty values for all variant rows, it would have been removed from the final table, resulting in varying number and relative order of additional columns when multiple samples were processed with the same tools/workflows. All columns are retained now, facilitating downstream processing of exported tables, and providing immediate visual reference as to which enrichment/annotation tools have been applied, even if they did not produce any results for a particular sample.
  • Tables for variant tracks and annotation tracks can now sort and filter columns with cells containing multiple numbers.
  • Improved the track viewer for variant tracks to show the sequence alteration on the rendered variant.
  • Graph tracks now show negative values filled upwards to y=0 (as expected).
  • Increased decimals for numbers when exporting table to CSV, tab delimited text, and Excel.
  • Improved reporting of errors related to low disk space.
• Workflows:
  • When installing a workflow in the workflow manager, the newly installed workflow is automatically selected.
  • The "Run" button in the workflow editor does not require a saved workflow anymore to be enabled.
  • In the execution wizard of a workflow the "Reset to default" button is now active.
  • All icons in the workflow editor are now on the left side.
  • Introduction of snippets: Parts of workflows can now be saved as a snippet and reused in other workflows.
  • Installed workflows: It is now possible to create a copy of an installed workflow and open the copy in the view area by clicking once and then right-clicking on the installed workflow in the toolbox. This brings up the option "Open Copy of Workflow".
• New features for the 3D molecule viewer:
  • Align to Existing Sequence makes it possible to connect a 3D protein chain to a sequence, sequence list, or an existing alignment.
  • Transfer Annotations makes it possible to create atom groups from sequence annotations (and vice versa) for connected sequences.
  • Improved layout of the property viewer.
  • Improved PDB import of water molecules, DNA/RNA, and saccharides.
  • When importing PDB files, the resulting Molecule Project now contains citation information (PDB ID and primary reference), which can be found in the 'Show History' view.
• MA plots, scatter plots and histograms can now accept expression tracks as input.
• Batching: Processes tab and analysis execution logs now display batch names in addition to analysis names for enhanced clarity.
• The External Application Client Plugin is now available directly from the Workbench Plugin Manager.

Bug fixes

• Fixed display problem in read mappings showing too many hidden insertions (as vertical black lines) in certain overlapping paired reads.
• Fixed problem with links and text in tables that were being cut off when succeeding a link.
• Restriction site analysis: The values "Cut position(s)" column of the restriction site analysis table now behaves like numbers instead of text, meaning sorting and filtering works.
• Workflows:
  • In the workflow editor the "Reset to default" now always reverts to the right names.
  • In the workflow editor the validation is now correctly triggered when changing the configuration of an input element.
  • The workflow editor can now open workflows in which the graphical view of the workflow is corrupt.
  • Fixed an exception which could occur during workflow migration.
  • Data with the same name can now be bundled multiple times in a workflow installer.
  • Previously when a plugin contained custom actions and a workflow, the workflow could not be installed. This has been fixed.
  • Fixed problem with unlocked output names that previously could not be configured during execution of a workflow.
  • A workflow with configured data from a server is now automatically validated when connected to the server (when opened in the editor). Previously the workflow had to be closed and reopened first.
  • The original workflow file included in a workflow installer can now be exported directly without having to restart the workbench in advance.”

• A problem with saved table settings that sometimes did not work has been fixed. The bug fix includes a more robust/generic way of saving table settings with different columns. To fix this problem, existing saved table settings should first be loaded on an object where it works (i.e. has the same columns as when it was saved); and then the table settings should be saved with the old name to overwrite the settings.

•  Fixed an error that could cause batch processing to open all results rather than saving them.

• Fixed problem going back in the wizard for the "Find Binding Site and Create Fragments" tool.
• Fixed error occurring when removing an unsaved reads track from a track list.
• Metadata for phylogenetic trees: A bug has been fixed with import of metadata containing column names with colons.
• Fixed error when showing protein translations of annotations shorter than 3 bases.
• Search for PDB Structures at NCBI has been fixed to correctly show PDB deposit date and organism type.
•  Fixed a bug that in some cases caused an error when annotating read sequence lists with the GFF/GTF/GVF annotation tool.
• Hypergeometric test on annotations: Fixed a rare error that occurred for some datasets containing annotations of the form: '1234 // abc'.
• The alignment editor view and alignment primer design view now have independent settings.

Plugin updates and bug fixes

• TRANSFAC Plugin updated and now has two modes of operation: "Classic" and "Genomic". Classic mode is the legacy mode taking sequences as input and annotating these sequences. The new Genomic mode takes regions on a genome (an annotations track) as input. In addition, in both modes it is now possible to specify global thresholds of similarity score which can be used to filter the annotations included in the output.
• A bug has been fixed with import of metadata containing column names with colons in the Metadata Import plugin.

Bug fixes

• Fixed an issue that caused the Reverse Translate tool to ignore the genetic code specified in the codon frequency tables such that the reverse translation used the standard genetic code.
• Fixed saving different line colors in plots through the side panel.
• Plots inside reports are now shown with their saved side panel settings.
• Side panel option to show legends for a plot with more than 10 samples is now enabled.
• Fixed an error that occurred when hovering the mouse cursor over the edge of a read mapping.
• Read-only folders are no longer offered as potential locations to save data bundled with a Workflow.

Bug fixes

• Fixed an error affecting the "Cut Sequence Before/After Selection" tool in the Cloning editor.
• Fixed an issue with running blast searches at the NCBI where an NCBI-generated error about their CPU usage limit being exceeded was not being reported transparently and a result of "no hits" was being reported instead.

New features and improvements

• It is now possible to run a workflow without an optional input.

Bug fixes

• The AAC tool did not annotate variants in 3' UTR with their DNA-level change using the HGVS c.xxx format. This affects any analysis done with Gx 7.5 or earlier based on ENSEMBL CDS tracks from older versons. The AAC analysis should be redone using Gx 7.5.1 for correct annotation.
• Pfam filtering bug fixed. Previously, Pfam only reported the first domain of each type in a query and as a consequence many domains were missed. We recommend that users whose research depends on Pfam annotations re-run the tool on their data.
• Fixed a bug in the 'Maximum Likelihood Phylogeny' tool that failed when generating bootstrap values for certain input alignments.
• Fixed problem with scrolling to the relevant files when selecting objects as parameters in tool wizards.
• The Blast text results have been improved so they show the correct query and subject positions regardless of strand.
• Fixed a problem that prevented BLAST operations when choosing to run these on the CLC Server.
• It is now possible to run a workflow without an optional input.

New features and improvements

• Workflows:
  • The input information is now shown in the preview dialog and also exported to all formats.
  • It is now possible to edit the workflow input name by right-clicking on the input name in the workflow.
  • Workflows as such can have multiple inputs (though this will disable the batch functionality).
  • Data can now be directly bundled with a workflow installation. This means that reference data can be packed and shared together with a workflow (only recommended for small data).
  • A workflow input can be pre-configured. If kept unlocked, it can be used to give a default when executing the workflow.
  • A text field has been added to the side panel, where you can search for elements in the workflow. A found element will be centered and highlighted.
  • A new editor was added to the workflow to make it easier to check the configuration. The new editor can be accessed from the lower left corner of the View Area and lists all configuration parameters.
  • Workflows can be packaged with a plugin and will get installed with the plugin simultaneously.
  • Workflows installed on the server now have an overlay icon in the workbench, to make them easily distinguishable from workflows installed in the workbench.
  • The execution of a workflow in the workbench and on the server have been unified to have the same behavior regarding logs, intermediate results and output naming.
  • Locked settings in the workflow wizard are now again hidden per default when executing the workflow, to give a cleaner, simpler look to the configuration. When expanding, all parameters are displayed.
• Protein Analysis, Pfam domain search:
  • Pfam Domain Search now uses HMMER3 and the latest Pfam database that can be downloaded with the new tool "Download Pfam Database".
  • Searching multiple sequences is significantly faster.
  • New filters are available in the improved Pfam Domain Search tool to enable generation of the same results as the online tool.
• 3D Molecule Viewer:
  • Protein Structure Alignment - high quality structural alignment of whole protein chains or selected regions of a protein, available from the Side Panel of Molecule Projects.
  • Project Tree improvements - new ways of selecting nearby atoms. Improved visualization of intermolecular bonds. Atom groups are now stored on the Molecule Project and can be renamed. Labels on custom atom groups now show residue names if applicable.
  • New molecule color scheme where only the carbon atom color is varied.
  • 3D view state - all 3D visualization settings (including custom atom groups) can now be stored on a molecule project and shared with others.
  • Molecule Preparation. Many improvements, including better handling of partial charges and more recognized chemical groups.

• Local Search enabled from the menu bar now includes filtering on "Path".
• Advanced filtering on tables now includes the option to filter for a space, comma or semi-colon delimited lists of terms.
• Zoom tools redesign: The “Zoom to selection” feature is now also available for sequences, sequence lists, alignments and read mappings.
• The tracks info panel, with track names in the left side of the track, now wraps information instead of showing a scroll bar.
• Saving/applying side-panel settings for tables now works for different tables that share some columns.
• Copy operations can now be stopped.
• Output from "Reverse Translate" can now be a Sequence List.
• Import of Example Data and imports done through dragging files into the workbench and dropping them in the Navigation Area will no longer block the user interface while executing. Instead, the import happens as a background process that can be monitored and controlled via the Processes tab in the lower left corner.
• CLC workbenches now support high resolution displays such as Apple retina displays of all data shown in the View Area (including tooltips).
• Improved error message in the Empirical Analysis of DGE tool in case of invalid expression values in experiments (occurs rarely).
• More informative naming of coding region translations produced by the tool Translate to Protein. The name for a coding region translation consists of the name of the input sequence followed by the annotation type and finally the annotation name.
• Genetic codes: The list of NCBI translation tables has been expanded to include  translation table 25 "Candidate Division SR1 and Gracilibacteria" (See: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c).
• Improved error messages due to low disk space.

Bug fixes

• Translation of CDS annotations to protein sequences was wrong in cases where the reading frame was not +1 or -1 in CDS annotations imported from ENSEMBL. This error affected the Translate to Protein tool, translation functionality in sequence viewers and their context menus, as well as the Amino Acid Consequences (AAC) variant annotation tool. We highly recommend redoing the AAC analysis for correct variant annotation, as CDS tracks typically are created from ENSEMBL data.
• The right-click menu on certain annotations in tracks was not working when viewing a single track. This has been fixed.
• Icons in the workflow editor are now scaled consistently when zooming in or out.
• Several issues with the validation display in the workflow editor have been fixed.
• A bug has been fixed in the workflow configuration wizard. Previously the input was not taken into account when deciding which parameters were enabled.
• Fixed problem where the "space" key did not trigger "Find Conflict" in the stand-alone read mapping editor.
• Fixed stand-alone read mappings not showing mismatches and insertions in the overflow graph.
• 'Replace input sequences with result' in Cloning Editor no longer fails.
• Multi-sequence BLAST search results (BLAST tables) are now exportable as plain text.

Changes

• Due to upgrade to Java 7,  Windows Server 2003 and OSX 10.5.8, 10.6 are no longer supported by Oracle. Hence, the system requirements are now: Linux, Windows Vista, Windows 7, Windows 8 or Windows Server 2008, or Mac OS X 10.7 or later.

Bug fixes

• Fixed error that caused selections in views not to be centered in the middle of the view.
• Fixed bug that caused a crash in the Reassemble Contigs tool
• Fixed bug that made the Workbench crash when viewing tables under certain circumstances
• Fixed problem with "Find" on stand-alone read mappings with a circular reference and sequence lists containing circular sequences.
• Fixed problem with some parts of workflow not being executed if there was multiple branches in workflow.

Bug fixes

• Fixed problems causing an error when trying to uninstall plugins.
• Fixed issue with pausing and resuming running processes

Improvements

• Fasta export:
  • Fasta export with trimming is now much faster and consumes less memory
  • Fasta export now reports progress while executing
  • When the "Remove trimmed regions" option is set, the Fasta export will ignore sequences in which all nucleotides are covered by a Trim annotation
• Translate to Protein (Batch Process):
  • The wizard now has options for specifying whether to translate the coding regions or extract translations from the annotations
  • The log has been made more detailed and informative
  • If the result is just a single protein sequence, the output will be just that, otherwise all sequences are output as a list
  • If the tool estimates that the number of protein sequences to be produced is greater than 1.000.000, it will create protein sequences without history, and it will not copy the common name, latin name, and taxonomy fields
• The PDB importer has improved support for custom residues

Bug fixes

• Fixed missing icon for "Metadata Import" in the phylogenetic tree table
• Multi BLAST results table: the missing "Description (E-value)" field is displayed again in the table output
• Fixed a bug that made PDB import fail on workstations with Turkish Locale settings
• The tool "Restriction Site Analysis" ignored the selected number of cut sites in GWB 7.0. This has been fixed

New features and improvements

• New functionality for phylogenetic trees (was previously part of a beta plugin)
  • Greatly enhanced viewer for visualizing and working with phylogenetic trees. The viewer allows the user to rapidly create high-quality, publication-ready figures of the trees.
  • Large trees are made easy to explore using different zoom functionalities and a small minimap of the entire tree. The viewer also comes with two alternative tree layouts, namely circular layouts and radial layouts, which are great for visualizing very large trees.
  • Supports importing, editing and visualization of metadata associated with nodes in phylogenetic trees.
  • Tool to reconstruct phylogenetic trees based on k-mers. This approach avoids the computationally intensive step of constructing a multiple alignment of the input sequences. The k-mer based reconstruction tool is especially useful for whole genome phylogenetic reconstruction where the genomes are closely related.
  • Tool performing a statistic evaluation of different substitution models to be used with maximum likelihood tree construction. The output of this tool is a report that lists the recommended settings to be used when constructing phylogenetic trees based on maximum likelihood.
  • Added an option for using the Kimura 80 substitution model when creating trees with distance based methods.
  • Distance-based tree reconstruction methods can now reconstruct trees from protein alignments using the Jukes-Cantor substitution model or the Kimura protein ML distance estimate.
  • A user defined start tree can now be supplied to the ML inference tool.
• Complete redesign of the graphical user interface including:
  • New tool bar graphics
  • New product logos and colors, including splash screen
  • New background graphics on canvas and in dialogs
  • Tool bar has been re-organized
  • New tab design. Aligning the look and feel across platforms, which is particularly important to mac-users as split screen used to take up a lot of screen space.
• New concept for Side Panels and Views:
  • Support for multiple screens: views can be moved to a different screen by dragging the tab of the view
  • Side Panels now consist of palettes that can be organized in group and the order can be customized
  • Palettes can be detached and placed anywhere on the screen
  • Navigation Area and Toolbox can be minimized to allow more pixels for displaying data
• Zoom tools redesign:
  • The zoom tools have been re-organized and placed closer to the data
  • A zoom slidershows the present zoom level and can be used to adjust zoom
    • Detailed zoom is a new feature that allows zooming in and out in very small increments by dragging the zoom slider and moving the cursor above it. An expert feature for e.g. large tracks.
  • New zoom tools. Easy adjustment of zoom speed for improved zooming of huge sequences.
  • Detachable Side Panel editors. A Side Panel editor can be dragged from the main workbench window and dropped outside the workbench, making a separate window e.g. on a second screen, if available.
• Copying data in the Navigation Area runs much faster and uses less memory than before. This is a great improvement which also kicks in when moving data between a CLC Genomics Server and a Workbench.
• Workflows:
  • Possibility to have bulk configuration of elements. This enables to set the same reference data for multiple elements at once.
  • Workflows can be added inside a workflow. The inner workflow is "unfolded" into the single elements.
  • Parameters can now be renamed in the editor by the creator during configuration of the elements.
  • Workflows with invalid/unknown elements are laid out nicer and more consistent.
  • The sidepanel has now an option to display rulers in the editor to indicate better the size of a workflow (particularly when exporting)
  • Fit Width now fits the entire workflow in the editor by zooming out.
  • The sidepanel has a new section "Minimap" which shows an outline of the whole workflow. It allows to navigate the workflow in the view and also supports zooming
  • One can change the design of the workflow editor via the sidepanel (removed the old designs in the preferences)
  • Better validation when configuring parameters in workflows
  • If a tool receives inputs from at least two tools, the inputs can now be ordered via the context menu on the connections or the input part of the target element.
  • The name of an output in the workflow can be set by configuring the output element
  • Parameters of a workflow run can now be exported to various formats via the wizard
  • It is now possible to reset a reference parameter. Before it was only possible by removing the whole element and add it again.
  • In the workbench the installed workflows are now sorted alphabetically.
  • The graphics export of a workflow now knows about the scale and one can now export the whole workflow or only the current view.
  • A cpw file can now be dragged into the workflow manager and will be installed.
  • Further speed improvements on working with larger workflows in the editor
  • New tools that are now workflow-enabled:
    • All tools in Statistical Tests
• 3D structure viewer:
  • Property viewer - a new tab in the Side Panel. Shows detailed information about the atom under the mouse pointer. If multiple atoms are selected (Ctrl-click), the distance (two atoms selected), angle (three atoms selected), dihedral angle (four atoms selected) formed by the selected atoms, is shown in the Property viewer. If a molecule is selected in the Project Tree, meta-data relating to the molecule is shown in the Property viewer.
  • Issues List. Issues related to the molecule structures and their chemistry representation is listed in the Issues List view on Molecule Projects. If seen in split-view with the 3D viewer, a selected issue will zoom to the atoms involved in the issue and select them in the 3D view.
  • General improvements to the PDB importer
  • Double-clicking an entry in the Project Tree will zoom-to-fit on the molecule or atom group.
  • When selecting atoms (by mouse clicking or from sequence), the atom context (whole residue or molecule) will also be shown in the 3D view. From context menu on 'Current' selection, an atom group can be generated either from the exact selection or from the selection plus the context (whole residues or molecules).
• Extract consensus sequence is now able to copy annotations from both existing consensus sequence and the reference sequence.
• When extracting consensus sequence from a mapping, conflict and low coverage annotations now include the position on the reference.
• Trim annotations can be used to trim off sequences when exporting to fasta.
• Secondary peak calling has been improved: it now only detects peaks that have a distinct peak shape, only peaks that fall within the same interval as the top peak are called. In addition, trim annotations are taken into account so that no peaks are called within trimmed regions. This greatly reduced false positive calls. Finally, the annotations now include information about the secondary peak's fraction of the maximum peak height.
• Advanced table filter now includes an option to search for "starts with" in addition to just "contains"
• Limitations on export of Excel 2010 files (xlsx) are removed:
  • Multiple tables can be exported to one xlsx file
  • Reports can be exported to xlsx
  • Hyperlinks are preserved in xlsx files
• SignalP prediction has been updated to be server-, batch- and workflow enabled.
• Folder contents view: subfolders will display how many items they have
• Assemble Sequences tools now accept sequence lists as input.
• REBASE restriction enzyme list updated to version 310.

Bug fixes

• Workflow:
  • In the editor the "Fit Width" zooming was active, but behaved as "100%" zooming. Therefore the "100%" zooming is now active instead of the "FitWidth"
  • Added or connected elements are now placed near where you connect or add them, even when zoomed near or far.
  • It was possible to Undo the action of adding a workflow output, but it was not possible to Redo afterwards.
  • The right-hand icons in an element now scale with zooming.
  • The log of a workflow run on the server contains now the same information as when run in the workbench.
  • When configuring elements in the editor, the "Reset to CLC Standards" button is now functional and will reset the parameters to their default values. When configuring during installation or execution the button is disabled.
  • The log of a server executed workflow now states when the workflow has been cancelled.
  • A workflow with elements which provide additional inputs could not be batched.
• Crash when adding data to experiments (e.g. by running any of the statistical analysis tools) has been fixed.
• Various bugs in the extract consensus sequence tool have been fixed.
• When translating to protein, ambiguous nucleotides potentially resulting in stop codons were not translated properly, and only the codons resulting in an amino acid were represented in the protein. Now the stop codons are also represented by an X in the protein sequence.
• A problem with filtering and sorting the BLAST output table has been solved. Some of the columns were treated as text instead of numeric.
• Restriction maps, histogram data, and primer tables could not be exported to csv or similar. This has been fixed.
• When using the “Find Open Reading Frame” tool, the input sequence was reported incorrectly in the ORF table. This has been fixed.
• Fixed problems with Excel export that failed when special characters were used in the name.

Changes

• The two tools in the "Multiplexing" folder in the toolbox category have been changed:
  • "Process Tagged Sequences" has been removed..
  • "Sort Sequences by Name" has been moved directly into the Sequencing Data Analysis folder.
• Motif search: annotations created by the motif search are of type "Motif" instead of "Region"