Latest improvements for CLC Genomics Workbench

  Current line         Previous line          Archive

CLC Genomics Workbench 9.5.5

Release date: 2017-06-08

Improvements

  • When importing tracks, the history of the track now contains the full path name of the imported file.

Bug fixes

  • Fixed an issue with the Basic Variant Detection, Low Frequency Variant Detection and Fixed Ploidy Variant Detection tools that could cause the count and frequency values to be too low for a small subset of those variants that are contained within a larger variant region (e.g., an MNV or deletion). For a variant to be affected by this problem, there needed to be at least two other potential variants nearby that were disregarded during the variant calling process. This circumstance and our testing suggest this is a rare issue.

  • Fixed a bug that in some cases would result in incorrect BaseQRankSum values being reported in the outputs of the  Basic Variant Detection Low Frequency Variant Detection  and Fixed Ploidy Variant Detection  tools.

  • Fixed an issue that could cause the SRA search view to display an error when trying to show results.

  • 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 or CLC Microbial Genomics Module installed.



CLC Genomics Workbench 9.5.4

Release date: 2017-02-14

Improvements

  • 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.

Bug fixes

  • A timeout value that would lead a job to fail after 24 hours, which was introduced as part of optimizations to run on multiple threads in the CLC Genomics Workbench 9.5 has been extended to 7 weeks. The tools affected by this change are Annotate from Known Variants, Filter against Known Variants, Filter against Control Reads, Annotate with Exon Number, Annotate with Flanking Sequences, Filter Marginal Variant Calls, Compare Sample Variant Tracks, Trio Analysis, GO enrichment Analysis, Amino Acid Changes, Annotate with Conservation Score, Predict Splice Site Effect, Link Variants to 3D Protein Structure, Merge Annotation Tracks, Create Statistics for Target Regions, Fisher Exact Test, Annotate with Overlap Information, Filter Based on Overlap, Filter Reference Variants, Identify Candidate Variants, Coverage Analysis, and InDels and Structural Variants.
  • Fixed an issue in the RNA-Seq Analysis tool where running in EM mode, with a "Strand specific" setting of "Forward" or "Reverse" would result in the second read of a pair mapped as a broken pair being counted incorrectly if that read was mapped outside a region annotated as a transcript.
  • Fixed an issue where an error arose when using the RNA-Seq Analysis tool with the EM option and a strand specific setting of "Forward" or "Reverse" in cases where the second read of mapped broken pair mapped to the opposite strand of the strand specific setting.
  • Fixed an issue with the Basic Variant Detection, Low Frequency Variant Detection and Fixed Ploidy Variant Detection tools where the forward and/or reverse count for a longer variant, supported by paired reads with both children having the same direction, could be too low. The forward count and reverse count is now reported correctly.
  • Fixed an issue with the InDels and Structural Variants tool where an incorrect insertion could be called when the optimal alignment of a read's unaligned end around the breakpoint included a gap in the insertion sequence.
  • Fixed an issue in the InDels and Structural Variants tool that would terminate analysis of large read mappings prematurely a fraction of the times.
  • Fixed an issue with the Basic Variant Detection, Low Frequency Variant Detection and Fixed Ploidy Variant Detection tools where the count and read count could be reported as marginally higher than they actually were in a small minority of cases. For the affected variants, this could then also result in variant frequencies being reported that were slightly higher than they should have been, in some cases above 100%. Variants affected by this issue are a small subset of variants where the variant affected overlapped another potential variant and where only the affected variant was then reported. This change could lead to a small decrease in the number variants reported compared to earlier versions of the CLC software, due to a variant no longer passing the count or read count filtering constraints. The impact of this change is expected to be low. For example, in our tests, for a particular analysis that reported 250,000 variants, 30 fewer were reported with the same parameters and filters applied after this fix was implemented.
  • Fixed an issue where the Basic Variant Detection, Fixed Ploidy Variant Detection, Low Frequent Variant Detection and Local Realignment tools could fail if a deletion was encountered at the end of a match between a read and the reference in the mapping used as input.
  •  Fixed an issue in the Basic Variant Detection, Fixed Ploidy Variant Detection and Low Frequent Variant Detection tools where the tools could stop with an error. The problem arose when a read split up within a mapping (e.g. to map to separate exons) was split into 4 or more parts, and at least 4 of those parts would map within a region of adjacent variants being considered as a possible multiple nucleotide variant (MNV). This infrequent problem was most likely to occur when using high coverage RNA-Seq mappings and looking for variants occurring at low frequency. It was introduced in the previous bugfix release of the CLC Genomics Workbench, version 9.5.3.

Advanced notice

  • The Probabilistic Variant Detection (legacy) and Quality-based Variant Detection (legacy) tools will be removed from the Server and Workbenches in March 2017.
  • Support for some older operating systems (OS), listed below, will be discontinued in March 2017. Software released at that time and later may still run without issue, but problems experienced due to using an unsupported OS will not be addressed. If you are concerned about the proposed change, please contact our Support team ([email protected]), letting them know the OS being used and the products you are running on that OS.
    • 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


CLC Genomics Workbench 9.5.3

Release date: 2016-12-14

Improvements

  • Server import and export locations shown in Workbench wizards now have tooltips giving the path to those locations.
  • Various other minor improvements (e.g. improved tooltips)

Bugfixes

For the Basic Variant Detection, Fixed Ploidy Variant Detection and Low Frequency Variant Detection tools, the following have been addressed:
  • Fixed an issue where the coverage of a longer variant that contained another variant was reported for both the longer variant and the contained variant. The coverage for the contained variant is now reported correctly.
  • Fixed an issue affecting coverage calculation for SNVs without immediately adjacent variants when using paired read data: if the second read of a pair containing the variant did not meet the requirements of the quality filter, neither the first nor second read of that pair contributed to the coverage calculated for the variant.
  • Fixed an issue where, for an SNV without immediately adjacent variants, overlapping reads of a pair that had conflicting base calls for that variant position contributed to the values calculated for coverage, read coverage, and read count of that variant.
  • Fixed a bug where count, read count, and forward- and reverse read count could be incorrect for variants found in overlapping regions of a pair of reads and where the variant was originally identified as being adjacent to one or more other variants.

The above issues, including information on the products affected, are described on the public notification page: Coverage and count reporting for variants in certain circumstances are incorrect

For the Identify Known Mutations from Sample Mappings tool, the following issues have been addressed:
  • Fixed an issue with the Identify Known Mutations from Sample Mappings tool where reads in a sample mapping were not identified as supporting the presence of a known variant in cases where the first position of the variant region in the mapped read contained a gap.
  • Fixed an issue with the Identify Known Mutations from Sample Mappings tool where a read containing a variant longer than a known variant being tested for was counted as supporting the known variant in cases where the first part of the read’s variant sequence is identical to that of the known variant.
  • Fixed an issue in the Identify Known Mutations from Sample Mappings tool where overlapping reads of a pair having conflicting base calls for a variant position could contribute to the coverage calculated for that variant.

Advanced notice

  • The Probabilistic Variant Detection (legacy) and Quality-based Variant Detection (legacy) tools will be removed from the Server and Workbenches in early 2017.
  • The Expression Profiling by Tags tools (Extract and Count Tags, Create Virtual Tag List, and Annotate Tag Experiment) are scheduled to be removed from the Server and Workbench in spring, 2017.
  • Support for some older operating systems (OS), listed below, will be discontinued in early 2017. Software released at that time and later may still run without issue, but problems experienced due to using an unsupported OS will not be addressed. If you are concerned about the proposed change, please contact our Support team ([email protected]), letting them know the OS being used and the products you are running on that OS.
    • 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
 


CLC Genomics Workbench 9.5.2

Release date: 2016-10-25

Improvements

  • SRA download functionality has been updated to support the upcoming NCBI transition to HTTPS.
  • Updated the restriction enzyme list from REBASE.

Bug fixes

  • Fixed a bug where running two or more concurrent instances of RNA-Seq Analysis with EM quantification could in some cases lead to incorrect results or error messages.
  • 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 Genomics Workbench 9.5 where enzymes listed alphabetically after RdeGBI were missing methylation information.
  • Various minor bugfixes.

Advanced Notice

  • The Probabilistic Variant Detection (legacy) and Quality-based Variant Detection (legacy) tools will be removed from the Server and Workbenches in early 2017.
  • The Expression Profiling by Tags tools (Extract and Count Tags, Create Virtual Tag List, and Annotate Tag Experiment) are scheduled to be removed from the Server and Workbench in spring, 2017.
  • Support for some older operating systems (OS), listed below, will be discontinued in early 2017. Software released at that time and later may still run without issue, but problems experienced due to using an unsupported OS will not be addressed. If you are concerned about the proposed change, please contact our Support team ([email protected]), letting them know the OS being used and the products you are running on that OS.
    • 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


CLC Genomics Workbench 9.5.1

Release date: 2016-09-28

Bug fixes



CLC Genomics Workbench 9.5

Release date: 2016-09-15

New features and improvements

New tools

  • "Search for Reads in SRA..." allows search and download of reads from the SRA database. Its is available from the Download button.
  • A new GFF3 importer is available as an option in the Import -> Tracks tool.
  • "Identify Known Mutations from Sample Mapping" can be used to look up known genomic variants in read mappings. Available from the "Resequencing Analysis" tool folder.
  • "Identify Candidate Variants" can be used to identify and extract variants that fulfill certain criteria. Available from the "Annotate and Filter Variants" tool folder.
  • A new option "Use EM estimation (recommended)" was added to the RNA-Seq Analysis tool. This enables the use of an expectation-maximization algorithm to distribute ambiguous reads between isoform/genes.

Improvements

Resequencing

  • The Local Realignment tool has a new option that can allow the use of guidance variants longer than 100bp.
  • The InDels and Structural Variants tool now offers the option to include reads mapped as broken pairs in the analysis.
  • The InDels and Structural Variants tool offers now the option for consensus calculation to ignore reads if their relative coverage or quality scores are too low.
  • The COSMIC importer has been updated to support the latest version of the COSMIC database, release v77.
  • Improved performance of a number of tools when run on systems with multiple cores: Annotate from Known Variants, Filter against Known Variants, Filter against Control Reads, Annotate with Exon Number, Annotate with Flanking Sequences, Filter Marginal Variant Calls, Compare Sample Variant Tracks, Trio Analysis, GO enrichment Analysis, Amino Acid Changes, Annotate with Conservation Score, Predict Splice Site Effect, Link Variants to 3D Protein Structure, Merge Annotation Tracks, Create Statistics for Target Regions, Fisher Exact Test, Annotate with Overlap Information, Filter Based on Overlap, Identify Candidate Variants, and Filter Reference Variants.

RNA-Seq

  • The tools "Filter Based On Overlap" and "Annotate with Overlap Information" now work with the Statistical Comparison Tracks produced by the Advanced RNA-Seq plugin.
  • It is now possible to export expression tracks in BED format. The expression value will be exported as the score.
  • Expression tracks are now colored according to a log-scale to ease visual interpretation of expression data.
  • The track view of expression tracks dynamically rescales to make best use of the screen real estate. This change brings expression tracks in line with other track types.

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.

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.
  • The History view of data elements created using a workflow now includes information about the workflow that created them.
  • 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 order of the tools in the workflow "Add Element" menu now matches the order in the Workbench Toolbox menu.

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.
  • Improved workflow validation to aid the user in identifying inputs that will be ignored due to the configuration of the workflow elements.

General

  • The Trim Sequences tool under Toolbox | NGS Core Tools now handles ambiguity codes in the adapter/primer sequences.
  •  The upper limit for the "discard reads above length" option of the Trim Sequences tool under Toolbox | NGS Core Tools has been raised from 8000 to 99,999.
  • The Identify Graph Thresholds tool can now be configured to work on specified regions only.
  • A new option in the Sample Reads tool makes it possible to choose whether sampling should be deterministic or random.
  • 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}.
  • The Identify Graph Thresholds tool can now be run using only a lower or upper threshold limit, rather than having to specify both.
  • The Extract Consensus Sequence tool now outputs a sequence list for all results. Previously, when running this tool directly, if the result was a single sequence, it would output a sequence, not a sequence list. (Nothing has changed when this tool is run as part of a workflow, where sequence lists were always generated).
  • The Extract Consensus Sequence tool no longer displays a message bubble after each contig has been processed.
  • The Download Reference Genome Data manager now shows version numbers for several genome annotations.
  • The list of enzymes pre-installed in the workbench has been updated from REBASE.
  • Read group details are now shown on the Element Info view of sequence lists.
  • The "Unknown" feature category can now be hidden in tree editors.
  • The option "is not in list" has been introduced as a new table filtering option.
  • All NCBI server communication is now encrypted. (NCBI will be moving all web services to the HTTPS protocol on September 30, 2016).
  • GenBank import now also allows for file names with 'GBFF' extension.
  • Standard deviations in reports are now being calculated with a different algorithm than previously. This will have no noticeable effect in the overwhelming majority of cases.
  • The History view of variant, feature and expression tracks that are created by pressing the "Create Track from Selection" button on the table view of an existing track will now include details of any advanced filtering that was applied to the table at the time the new track was made.
  • Three prime UTR and five prime UTR tracks from the "Download Reference Genome Data" tool are now named with distinct suffices. Previously the track names ended with ""_utr" and ""_utr-1".
  • Improved the progress reporting for the import of large, gzip compressed Illumina and Ion-Torrent files.
  • General speed and usability improvements.

Changes

Retirements

  • The Expression Profiling by Tags folder has been moved to the Legacy Tools section of the toolbox

Bug fixes

  • Fixed an issue with the tools "Extract from Selection" and "Extract Reads Based on Overlap" so that they now correctly extract mapped reads that extend over the (arbitrarily chosen) ends of the 1D representation of a circular genome.
  • Fixed an issue where the Motif Search tool was incorrectly reporting all match accuracies as either 0% or 100%.
  • Fixed an issue that caused characters in sequence names to be rendered incorrectly when a report was exported to Excel.
  • The Download Reference Genome Data manager will now always refer to the latest version of the Ensembl GRCh38 Genome. It was previously locked to Ensembl version 82.
  • Fixed an issue where, when searching for both read1 and read2 in a broken pair, the "Find Broken Pair Mates" tool reported that the mate of read1 was itself. The tool now correctly shows that the mate of read1 is read2.
  • The Create New Sequence List button in a broken pair table now works when multiple read groups are involved.
  • Fixed an issue that would make the wizard for the Demultiplex Reads tool fail if an invalid bar code was entered.
  • Fixed a bug that made graphics export of some plots from reports fail.
  • Fixed a rarely occurring bug where rendering of a Read Mapping in a Track List would fail.
  • The Find Binding Sites and Create Fragments tools now properly display mismatches when the primer input is in lower-case.
  • Fixed an issue where, when viewing statistical comparison tracks together with read mapping tracks, the statistical comparison track annotations could sometimes be rendered as offset from their true genomic positions.
  • Fixed a memory leak in the Extract Consensus Sequence tool.
  • 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.
  • The Illumina High-Throughput Sequencing Import tool now correctly warns that zip files with multiple entries are not supported.
  • 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 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 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 where it took a long time to open a workbench it it was previously closed when displaying an open table editor that had been sorted.
  • 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 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 an issue with links in tables to the PDB and dbEST databases.
  • Fixed a rare issue that caused the "Extract from selection" right-click option not to work for a reads track in a track list.
  • Fixed a bug where exporting to Wiggle on systems with specific system locales would produce files that could not be re-imported.
  • 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 affecting the launching of workflows with multiple inputs in batch, where the workflow execution wizard did not update correctly when another metadata spreadsheet was selected.
  • 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 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 that could arise when migrating a workflow containing Create Sequencing QC Report where the workflow was originally created using the CLC Genomics Workbench 6.5 or older.
  • 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.

Notice

From now on, only 64 bit versions of the CLC Genomics Server, CLC Genomics Workbench, Biomedical Genomics Workbench, CLC Bioinformatics Database and CLC Assembly Cell will be made available. 32 bit versions of these are discontinued.

Advance Notice

  • The Probabilistic Variant Detection (legacy) and Quality-based Variant Detection (legacy) tools are scheduled to be removed from the Server and Workbench in spring, 2017.
  • The Expression Profiling by Tags tools (Extract and Count Tags, Create Virtual Tag List, and Annotate Tag Experiment) are scheduled to be removed from the Server and Workbench in spring, 2017.


CLC Genomics Workbench 9.0.1

Release date: 2016-06-07

Bug fixes

  • Fixed an issue with the RNA-Seq Analysis tool that could arise when the "Genomes annotated with genes and transcripts" option was chosen: If two or more genes had the same name, and a transcript could be assigned to each from the mRNA track, then the value in the "Transcripts annotated" column in the GE track and in the TE track was 0. Furthermore, all counts for such genes were reported as zero, even when there were reads mapping to them.
  • 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 exception in the Read Mapping Editor that could arise when working with mappings to circular references.
  • 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.
  • Fixed broken help link in Ion Torrent importer.

Advanced notice

  • From the autumn 2016 release, only 64 bit versions of the CLC Genomics Server, CLC Genomics Workbench, Biomedical Genomics Workbench, CLC Bioinformatics Database and CLC Assembly Cell will be made available. 32 bit versions of these will be discontinued from that time.
  • The Probabilistic Variant Detection (legacy) and Quality-based Variant Detection (legacy) tools will be removed from the Server and Workbenches in early 2017.
 


CLC Genomics Workbench 9.0

Release date: 2016-03-31

New tools

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

Improvements

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.
  • Made it possible to select files located on a CLC Server when using exporters in the workflow configuration editor of a CLC Workbench.

RNA-seq

  • The RNA-Seq Analysis tool now computes Transcripts Per Million (TPM) values, which appear as an additional column in expression tracks.
  • Faster analysis of multiple samples in the RNA-Seq Analysis tool due to caching of reference index files.
  • Performance improvements for Expression Tracks in RNA-Seq.
  • Expression track table views now have two new buttons for selecting or copying genes/transcripts names.
  • Expression tracks now contain links to external databases when available.
  • Transcript level expression tracks now contain the gene name for each transcript.

Mapping

Track

  • The tool Create Mapping Graph can now create a coverage graph over the start positions of reads in a read mapping.
  • Improved error messaging when trying to import malformed fasta files into tracks.

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.

General

  • Fixed an issue with the VCF-exporter resulting in inconsistent information being output to the exported VCF. The metadata field "##reference" field now contains a human readable string-representation identifying the reference genome the exported variants are based on. The metadata field "##fileOrigin" was added to contain a human readable string-representation identifing the exported variant track.
  • Performance optimization for sizing phylogenetic trees by metadata.
  • The 3D Protein Structure Database has been updated. Please use the Download 3D Protein Structure Database tool to work with the latest version.
  • 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).
  • Substantial speed improvements to BAM export.
  • 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.
  • SAM records with CIGAR strings with no aligned residues can now be handled when importing SAM/BAM files.
  • 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.
  • GFF Track Import now supports spaces in annotation names
  • The "Manage Resources" tab has been removed from the the Plugin Manager.

Changes

Workflow related

General

  • The naming rules for the outputs of several tools have been changed to align with those applied by most other tools. The tools affected by these changes are: Local Realignment,Low Frequency Variant Detection, Fixed Ploidy Variant Detection, Basic Variant Detection as well as the legacy variant detection tools: Probabilistic Variant Detection and Quality-based Variant Detection.
  • The BaseQRankSum value for variants is now negative to indicate that the qualities for the variant is below those for the reference allele. The BaseQRankSum is now calculated as a positive value when the qualities for the variant are above those for the reference allele.
  • Export to clc format now truncates very long filenames.
  • Versions of individual tools are now reported in the history of output objects.
  • The default view of the expression tracks has been changed: the table view opens first by default, and some columns are hidden, to simplify the view.
  • For the NGS importers, the paired reads minimum and maximum default interval has been updated to 1 - 1000.
  • Plots without any data points will now be skipped when rendering reports.
  • The annotations "Known variation", "Validated by other experiment", "Ancestral allele", and "Phenotype related", created by variant track import are not used and have therefore been removed from variant tracks.
  • The Detailed Mapping Report statistics table now shows previously missing values for regions with partial coverage. For fully covered regions these values cannot be calculated, and empty strings are replaced with coverage minimum, average and standard deviation. Numeric sorting is retained by inserting NaN values instead of empty strings, where calculations cannot be made.
  • 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.

Retirements

  • The ChIP-Seq Analysis (legacy) tool has been retired.

Bug fixes

  • Fixed a bug when the download buttons on BLAST result table view failed for nucleotide sequences.
  • Fixed an error when running merge overlapping pairs on extremely short reads.
  • BED Export: when exporting block list entries (such as connected exons from mRNA tracks), positions were absolute, but are now relative to the 'chromStart' position.
  • 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 an off-by-one error for read start positions in the 'Find Broken Pair Mates...' output table.
  • 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 a bug that prevented the output from certain tools to be used as input in the "References" channel of the Map Reads to Reference tool when used in workflows.
  • 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 a bug, where the Reference Data Manager fails to open, when the CLC_References folder is located on a resource (e.g. an external disk), which is currently not available (e.g. the disk might be unplugged/disconnected).
  • 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.
  • When the InDels and Structural Variants tool is added to the workflow the "P-value Threshold" parameter did not show up in the Select settings wizard step under "Significance of unaligned ends breakpoints". This has been fixed.
  • 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.
  • The "Extract and Count" tool in Small RNA analysis now only accepts sequences and sequence lists. Previously, it incorrectly accepted standalone read mappings or small RNA samples as well.
  • 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.
  •  A bug was fixed where no BaseQRankSum was calculated for insertions of length 1.

Plugin updates and fixes

All plugins need to be installed in the new Workbench for compatibility reasons. Changes to freely available plugins
  • A new RNA-Seq analysis plugin is now available: Advanced RNA-Seq
  • Ingenuity Pathway Analysis: Expanded with a new tool supporting Statistical Comparisons and a Ready-to-Use Workflow for statistical analysis, visualization, and upload to IPA.
  • Annotate with GFF: Now supports spaces in annotation names.
  • Batch rename: Fixed an issue where a warning was displayed for entries not modified.
  • The RNA-Seq Legacy plugin has been retired.

Compatibility

  • This release can be used with CLC Genomics Server 8.0.

Advanced notice

From the autumn 2016 release, only 64 bit versions of the CLC Genomics Server, CLC Genomics Workbench, Biomedical Genomics Workbench, CLC Bioinformatics Database and CLC Assembly Cell will be made available. 32 bit versions of these will be discontinued from that time.


© QIAGEN 2017. All rights reserved - Trademarks & Disclaimers