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@nvnieuwk nvnieuwk commented Sep 1, 2025

New features

  1. Added a new option to the samplesheet (msi). This option takes a boolean to indicate whether or not the MSI status of the sample should be checked. A baseline should be provided using the --msi_baseline parameter to run MSI calling.
  2. The Multiqc module now generates branded reports.

Fixes

  1. Fixed PED file writing on cloud platforms.
  2. Fixed publishing of the MultiQC data directory throwing a NullPointerException.
  3. QUAL scores of 256 are no longer converted to . (due to a VCFanno bug).

@nvnieuwk nvnieuwk merged commit 7c074c4 into main Sep 1, 2025
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3 participants