QIAGEN CLC Genomics Workbench Improvements

• A link to the Modify a Workflow tutorial, which steps through creation of a customized analysis pipeline by editing an existing workflow, has been added to the Workbench background canvas.
• The minimum coverage of target region positions from QC for Targeted Sequencing reports can be selected for inclusion in reports generated by Create Sample Report and Combine Reports.
• Detect Fusion Genes from DNA adds "Fusion pair" information for fusions reported when "Include all fusions in the track output" is checked but where there is no fusion crossing reads supporting the fusion. This addition provides better support for downstream filtering.
• Iterate workflow elements can now be connected downstream of Differential Expression for RNA-Seq, enabling downstream filtering when multiple statistical comparisons are produced.
• Using left or right arrow navigation buttons in a variant track jumps the focus to the next visible variant. Previously, focus was moved to the next variant, even if it was hidden due to view settings in the Side Panel.
• Exporting PDFs of reports that contain plots with many points is faster than previously.
• Various minor improvements Bug fixes
• Fixed an issue where Detect and Refine Fusion Genes sometimes output fusions with duplicated "Fusion pair" values when "Include all fusions in the WT track output" was checked. This could cause VCF export to fail and filtering tools to keep or remove too many fusions. See the public notification about this issue.
• Fixed an issue in Create Sequence Constructs where, when a saved Sequence List was used as input and at least three sequences in that list were deselected, roughly half of the deselected sequences would be included in the construct set generated.
• Fixed an issue causing the "Pairwise % identity" value in the Positional stats palette in the Side Panel of alignments to be incorrectly calculated.
• Fixed an issue where the "Read Mapping" output channel from Merge Read Mappings could not be connected to all workflow elements that accept a read mapping as input, e.g. QC for Read Mapping.
• Fixed an issue where the processing order defined for a tool in a workflow was not respected if one or more inputs to that tool originated from a Fork element that had at least one unconnected output channel. This is not expected to affect the substance of results, but could affect ordering within an output, for example, the order of sections in a sample report or the order of tracks in a Track List.
• Fixes relating workflow history information:
  • Fixed an issue affecting the history information in outputs generated using installed or template workflows that contained at least one Fork element with all its output channels connected to downstream steps, where the workflow version was reported as 0.0 and no build-id was included. Note that for template workflows, the version of the software delivering that workflow can act as a proxy for the build-id.
  • Fixed an issue affecting the history of workflow log elements generated by running a workflow on a CLC Workbench, where the details of the workflow run (name, version, and where relevant, build id) were not present. This problem did not affect log elements generated by analyses run on a CLC Server or on the cloud.
  • The following fixes affecting history information in outputs generated by workflows run on the cloud:
    • Details of the workflow run (name, version, and where relevant, build id) were not present in the history of Workflow Result Metadata elements.
    • History information in outputs generated using installed workflows did not contain the correct workflow build-id.
    • History information in outputs from workflows launched from the workflow editor contained a workflow build-id when there should not have been one.
• Various minor bug fixes
• CVEs fixed in this release include:
  • CVE-2025-67735
  • CVE-2025-12183
  • CVE-2025-66566 Plugin notes Upgrading to CLC Genomics Workbench 26.03 fixes an issue where no sequences were imported from IMGT files using Import Immune Reference Segments, provided by the Biomedical Genomics Analysis plugin and CLC Single Cell Analysis Module. Advanced notice The AGP export (legacy) tool will be retired in a future version of the software.