CLC Main Workbench

This 4-week fully functional demo of CLC Combined Workbench aggregates all DNA sequence analyses of CLC Gene Workbench and all protein sequence analyses of CLC Protein Workbench. All analyses are fully integrated in one single, user-friendly, and intuitive software application.

What is new in this release:

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
• Various minor bugfixes.

What is new in version 7.7.2:

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}.

What is new in version 7.7.1:

• 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.

What is new in version 7.7:

Import Metadata - basic and easy metadata import. This tool supplements the tools available in the Metadata Table Editor.

What is new in version 7.6.4:

Bug fixes

• Fixed a bug when the Search for sequences at NCB 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 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.

What is new in version 7.6.3:

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.

What is new in version 7.6.2:

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.

What is new in version 7.6.1:

New features and improvements

• 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).

Bug fixes

• 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).

What is new in version 7.6:

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.

What is new in version 7.5.1:

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