Merge 25.11 to develop #401
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* Update view sort * Add wrapper for IdentifyAndStoreActiveClonotypes * Error checking for CommonFilters * Update defaults * Set baseUrl in script * Do not storeStimLevelData for TRA * Do not force seurat object name to match readset * Do not force seurat object name to match readset * Drop CS-Core and Tricycle * Expand data cleanup * Minor code cleanup * Add subadapter + reflection pattern to ExtendedVariantAdapter in order to delete VCFTabixAdapter (#353) * Add subadapter + reflection pattern to ExtendedVariantAdapter in order to delete VCFTabixAdapter * Add API wrapper for getMetadata and getHeader --------- Co-authored-by: Sebastian Benjamin <sebastiancbenjamin@gmail.com> * Correct HTML syntax * Expand study triggers and update cohort fields * Expose getter for StudiesTriggerFactory * Clean up trigger/customizer layer code * Create fields to coalesce name/label for studies * Add null check * Switch default * Bugfix to StudiesTriggerFactory * Update default * Improve SnpEff index check * Switch sequence init tasks to use webserver-high-priority * Build short delay into github triggers to aid cross-repo commits * Switch ETLs to log row count discrepancies * Update dependencies * Support sawfish --sample-csv arg * Option to create readsets from SRA (#355) * Option to create readsets from SRA * Test fix * Error check * Add nimble/bulk step * Allow nimble step to use cached barcodes * Bugfix to NimbleAlignmentStep * Bugfix to NimbleAlignmentStep * Bugfix to NimbleAlignmentStep * Bugfix to NimbleAlignmentStep * Add CD4_Activation_Axis * Better support readsets created directly from SRA * Expand BAM header * Bugfix to RestoreSraDataHandler * Bugfix to RestoreSraDataHandler for new SRA datasets * Bugfix to RestoreSraDataHandler for new SRA datasets * Bugfix to RestoreSraDataHandler for new SRA datasets * Bugfix to RestoreSraDataHandler for new SRA datasets * Reduce logging * Update sawfish install * Better error handling * Updates to Save10xBarcodes * Expand StudyMetadata cohorts * Throw exception when existing file present * Improve resume for ReadsetInitTask * Improve resume for ReadsetInitTask * Bugfix to Save10xBarcodes * Bugfix to handling of 10x barcodes * Switch nimble/CR barcodes to CB alone * Omit writing to 10x barcodes * Add another coalesce() term in case name and label are blank * Bugfix to study import * Fix typo * Add manage freezer button and expand TagPcrSummaryStep * Change the pattern of nimble fastq-to-bam * Add check for integers * Expand ETL/presentation of SIV data * Expand ETL/presentation of SIV data * Int -> long * npm dependency updates * Build fix --------- Co-authored-by: hextraza <hex@hextraza.moe> Co-authored-by: Sebastian Benjamin <sebastiancbenjamin@gmail.com>
hextraza
approved these changes
Nov 25, 2025
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