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Latest improvements for QIAGEN CLC Main Workbench early access

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QIAGEN CLC Main Workbench early access 21.0

Release date: 2020-10-14

New features

Protein structures
  • PDB exporter. It is now possible to export the molecule structures in a Molecule Project to a PDB file.
  • Biomolecule Generator. A new tool making it possible to generate or extract biomolecules based on symmetry
    information in PDB files.
  • Homology Modeling. A new tool makes it possible to go from amino acid sequence to structure in two steps. The
    Find and Model Structure tool will identify suitable protein templates from the PDB and automatically build a
    structure model for a given input sequence. (For MWB only: The tool requires a database to run, which is
    downloaded by the new Download 3D Protein Structure Database tool.)
  • Download | Search for PDB Structures at NCBI is now available in Viewing Mode
Exports
  • A new tool has been added to allow exporting reports in JSON format: Export -> JSON reports
  • The “Export to PDF” tool can now be used in workflows to export reports in PDF format.
  • The “Export to PDF” tool now includes an option to export the history of the report as well.
Workflows
  • This feature is probably completely useless for the WB customers as
    effectively only the NGS importers are supported…) It is now possible to run a workflow design or an
    installed workflow from the Toolbox, directly using raw data (such as .fastq files), without having to import
    the data first.
  • Functionality has been added for advanced batching in workflows:
    • It is now possible to batch workflows with multiple inputs, such that the inputs are matched up with
      each other using metadata. <link to manual>
    • It is now possible to batch only parts of a workflow, and split outputs in batches to different workflow
      paths based on metadata. For this, two new workflow elements have been added to control the flow of data
      in the workflow: “Iterate” and “Collect and Distribute”. Using these elements, it is possible to execute
      complex analyses in a single step. <link to manual>
  • Workflows optionally produce a Workflow Result Metadata table, where the outputs are organized into batches,
    with the relevant metadata. <link to manual>
Other new tools
  • A new tool has been added to allow exporting reports in JSON format: Export -> JSON reports
  • The “Export to PDF” tool can now be used in workflows to export reports in PDF format.
  • The “Export to PDF” tool now includes an option to export the history of the report as well.

 

Improvements

Nexus import
  • When importing trees from a Nexus file that also contains information about the sequences, the trees now include
    the sequence information.
  • The import of Nexus files has been updated:
    1. The tree labels are translated if the command TRANSLATE is used or the labels are integers
    2. Warning messages are displayed when an unsupported block / command is encountered, but when this does not
    break the parsing of the file
    3. Default missing character is “?”
    4. Polymophic and uncertain sites are not supported. Sequences that are not DNA, RNA or protein are not
    supported. When one of these unsupported features is encountered, the import ends with an exception detailing
    the reason.
  • The import of Nexus files has been updated to more closely match the format specifications:
    1. In DATA and CHARACTERS blocks, NCHAR is a mandatory entry in DIMENSIONS
    2. In DATA and CHARACTERS blocks, sequences can span multiple lines unless interleaved. If data is interleaved,
    this has to be specified in the FORMAT. Previously, the interleaved format was assumed by default.
    3. In UNALIGNED, sequences can span multiple lines and should end with “,” unless interleaved.
    4. Taxa labels specified in TAXLABELS can span multiple lines
Create Box Plot
  • In the “Create Box Plot” tool, the calculation of the median and percentile values has been improved, to match
    the definitions used by the default implementation of the “quantile” method in R, which is also the definition
    used elsewhere in the workbench.
  • The whiskers in boxplots have been changed. The whiskers now show the most extreme data points, which are by
    default in the range [lower quartile – 1.5*IQR, upper quartile + 1.5*IQR]. Previously, the whiskers extended 1.5
    times the height of the box (IQR).
CSV import
Might not need a separate category for WB
  • The .csv importer has been improved:
    1) Data values starting with a numeric character, but also containing non-numeric characters, were previously
    converted to numbers, so data values of this type were only imported up to the first non-numeric character. Now,
    such values will be interpreted as text, preserving all data.
    2) The .csv importer can now also import .csv files where the values are not enclosed in quotation marks. It is
    enough if the values are separated by commas or semicolons.
Performance improvements:
  • Saving results to an SSD is now considerably faster.
  • The import of ZIP files has been improved: temporary objects are cleaned up during the import process, reducing
    the required disk space.
  • Moving and deleting many elements at once is now faster.
  • The performance of the Navigation Area has been improved.
  • The performance has been improved for large sequence lists when using the following tools: BLAST, Add attB Sites
  • The performance has been improved when opening large protein sequences.
  • Improved performance of making a BLAST database of <=100k sequences where most
    sequences have the same name.
  • Emptying the Recycle bin now takes place in the background.
  • Messages from tools are no longer presented in the form of black bubbles in the
    Processes area. Any messages will still be present in the log.
Metadata and search
  • It is now possible to move a metadata table to a new file location, without losing the metadata associations.
    For more details about this, see <manual link>
  • It is now also possible to search for values contained in metadata tables. See <manual link> for more
    information.
  • It is now possible to search for elements in the CLC_References locations.
  • It is now possible to find elements that have been moved to the Recycle Bin when searching in the Navigation
    Area.
Workflows
  • It is now possible to update all installed workflows in one operation, using the “Update workflows” button in
    the “Manage Workflows” dialog.
  • The placeholder-based naming of outputs in workflows has changed: by default, the {input} or {2} placeholder
    will only expand to use the name of the workflow input, and not any parameters. Previously, a workflow output
    configured as {2} would be named using a concatenation of the names of all inputs. To use the names of other
    inputs, include the comma-separated numbers of the inputs in the placeholder – for example: {2:1,3} will use the
    names of inputs 1 and 3 in the output name.
  • The “Add Element” dialog in the workflow editor has been made more specific, so it no longer lists installed
    workflows in the , and no longer matches texts in the tooltips of the tools.
  • When running a workflow configured to use reference data, the Reference Data Set selection step has been updated
    to show the list of preconfigured elements in the tooltip.
Tracks and track lists
  • When hovering over a position in a Reads track that is shown in non-aggregated view, a tooltip appears, which
    shows the read counts for each observed nucleotide in that position, together with the directions of the reads
    with that nucleotide.
  • When opening a track list, the first track is no longer opened if it was already open in an editor.
  • In a track view or track list view, the “Location” field in the side panel now accepts ranges including spaces.
    For example, “X: 70,832,863 – 70,842,697” will now correctly find the location. Previously, the same range had
    to be specified without spaces as “X:70,832,863-70,842,697”.
Other improvements
  • Outputs of tools provided by plugins now include the plugin name and version in the element history.
  • A new option when right-clicking on a table , Edit | Copy , allows individual cells to be copied to the
    clipboard. Previously only whole rows could be copied.
  • Tool and workflow logs now display an “Elapsed time” column.
  • The “Excel 2010” and “Excel 97-2007” exporters now export NaN and +/-Infinity values to #N/A.
  • The BLAST binaries have been updated to version 2.9.0. An option to filter out redundant results has been added.
    The option “Choose filter to mask low complexity regions” has been renamed to “Mask low complexity regions”.
  • In the tree view of phylogenetic trees, the “Reset Tree Toplogy” button will now also uncollapse any collapsed
    nodes.
  • When importing multiple files using the Standard Import, the process ends with an error if at least one of the
    files failed to import. The details of which file failed and why can be seen in the log.
  • The name of a non-default workspace is now shown in the title bar.
  • The table view (“Show Table”) of plots has been improved in the cases where multiple data series are shown in
    the plot. The table now includes all of the x values from all data series, instead of the x values from just the
    first data series. If a data series is missing a y value for a specific x value, than the entry in the table
    will be empty.
  • In the Batch Rename tool, the option ‘Replace part of the name’ fields have changed from ‘From’ and ‘To’ to
    ‘Replace’ and ‘With’ for clarification.
  • The maximum size of a plot in a report displayed in the has been increased too 800 pixels, and the width/height
    ratio has been changed from 2/3 to 1/2.
  • The ranking of search results in Quick Launch has been improved.
  • URL’s have been made more compact, therefore will appear shorter.
  • The icon for the sequence view has been changed for protein sequences, so it is possible to distinguish protein
    sequence views from nucleotide sequence views based on the icon.
  • The “Trimming” folder has been removed from the Example Data provided via Help | Import Example Data because the
    included data was outdated. maybe not worth mentioning

Bug fixes

  • (should this be in the release notes?) Fixed an issue where moving a folder
    within a location occasionally caused the contents of the folder to become corrupt, until the persistence was
    reindexed.
  • Fixed an issue affecting mac OS X setups with accessibility settings enabled, where the “Replace Selection with
    Sequence” functionality available from within the Cloning editor could fail with an error.
  • Fixed a bug where workflow installer files did not include the specified icon.
  • Fixed an issue causing the file chooser dialog on Windows systems to freeze when selecting bzip2 format files
    for import. (Maybe this does not need an explicit mention for the WB, it mostly affects
    the Illumina importer.)

Changes

  • The Java version bundled with the <product name> has been updated to the
    Java 11, where we now use the JRE from AdoptOpenJDK.
  • Merge Overlapping Pairs is no longer scheduled for retirement and has therefore
    been moved from the Legacy Tools folder to the Utility Tools folder.
  • The Reverse Sequence tool has been moved to the Legacy folder of the Workbench
    Toolbox and “(legacy”) appended to its name. It will be removed in a future version of the software.

Plugin notes

New plugins
  • Navigation Tools Provides the functionality formerly provided by the Bookmark Navigator and Recent Items Navigator plugins.
  • SignalP and TMHMM Provides the
    functionality formerly provided by the SignalP and TMHMM plugins
Plugin retirements

The following plugins have been retired, with their functionality being provided by a new plugin:

  • Bookmark Navigator
  • Recent Items Navigator
  • SignalP
  • TMHMM

The following plugins have been retired and their functionality is no longer available through the QIAGEN CLC Main
Workbench:

  • PPfold
  • TRANSFAC

Advanced notice

The Reverse Sequence (legacy) will be removed in a future version of the software.

The “Run in Batch Mode…” functionality for installed workflows with multiple inputs will
be retired in a future release. Workflows with multiple inputs can now be launched in batch mode by checking the
“Batch” checkbox when selecting input data.

If you are concerned about these proposed changes, please contact our Support team by emailing ts-bioinformatics@.com.