Import Metadata – basic and easy metadata import. This tool supplements the tools available in the Metadata Table Editor.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- The ChIP-Seq Analysis (legacy) tool has been retired.
- 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 QIAGEN 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.
- This release can be used with QIAGEN CLC Genomics Server 8.0.
From the autumn 2016 release, only 64 bit versions of the QIAGEN CLC Genomics Server, QIAGEN CLC Genomics Workbench, Biomedical Genomics Workbench, CLC Bioinformatics Database and QIAGEN CLC Assembly Cell will be made available. 32 bit versions of these will be discontinued from that time.