Issues

• Update test config and test manifests to point to testing directories

  SINCLAIR
  CCBR/SINCLAIR#246 · Filter by author wong-nw opened on Jun 4, 2026
  

• Move workflow directory contents to subworkflows

  SINCLAIR
  CCBR/SINCLAIR#245 · Filter by author wong-nw opened on Jun 4, 2026
  

• docs website version selector

  documentationSINCLAIR
  CCBR/SINCLAIR#244 · Filter by author kelly-sovacool opened on Jun 1, 2026

• Inclusion of .loupe outputs

  SINCLAIR
  CCBR/SINCLAIR#240 · Filter by author wong-nw opened on May 12, 2026
  5

  

• Flexible entry points and granular selection of processes to run

  refactorSINCLAIR
  CCBR/SINCLAIR#238 · Filter by author wong-nw opened on May 11, 2026
  

• Delete fullWorkflow_202304/

  SINCLAIR
  CCBR/SINCLAIR#237 · Filter by author kelly-sovacool opened on May 11, 2026

• add test profiles for multiple large datasets

  SINCLAIR
  CCBR/SINCLAIR#235 · Filter by author kelly-sovacool opened on May 8, 2026

• Add fastMNN integration to batch correction

  SINCLAIR
  CCBR/SINCLAIR#220 · Filter by author wong-nw opened on Apr 1, 2026
  

• refactor: use output directive instead of publish dir mode

  refactorSINCLAIR
  CCBR/SINCLAIR#215 · Filter by author kelly-sovacool opened on Mar 27, 2026 · 2026-09
  

• docs: recommend deleting work dir after project completion

  documentationSINCLAIR
  CCBR/SINCLAIR#214 · Filter by author kelly-sovacool opened on Mar 27, 2026

• Bug: Test run produces both output and results directory

  SINCLAIR
  CCBR/SINCLAIR#207 · Filter by author wong-nw opened on Mar 9, 2026
  1

• refactor with improved modular design

  refactorSINCLAIR
  CCBR/SINCLAIR#202 · Filter by author kelly-sovacool opened on Nov 7, 2025
  3

  

• Use RDS files as input files for Filtering/Preprocess

  refactorSINCLAIR
  CCBR/SINCLAIR#200 · Filter by author wong-nw opened on Oct 10, 2025

• small sample sizes failing at batch correction

  low prioritySINCLAIR
  CCBR/SINCLAIR#194 · Filter by author kcgfarb opened on Sep 12, 2025

• document the execution timeline report

  documentationSINCLAIR
  CCBR/SINCLAIR#192 · Filter by author kelly-sovacool opened on Sep 9, 2025

• seurat_preprocess - break up into separate filtering steps

  bugrefactorSINCLAIR
  CCBR/SINCLAIR#191 · Filter by author kelly-sovacool opened on Sep 9, 2025

• Output tool versions

  enhancementSINCLAIR
  CCBR/SINCLAIR#188 · Filter by author wong-nw opened on Aug 22, 2025
  2

  

• Samplesheet_check will fail if CellRanger is run manually and has all default outputs in directory

  SINCLAIR
  CCBR/SINCLAIR#185 · Filter by author wong-nw opened on Aug 22, 2025

• Update samplesheet check process

  SINCLAIR
  CCBR/SINCLAIR#184 · Filter by author wong-nw opened on Aug 22, 2025
  1

• Feature: Generate multiple flowcell config.csv and run CellRanger multi

  enhancementSINCLAIR
  CCBR/SINCLAIR#179 · Filter by author wong-nw opened on Aug 15, 2025
  1

• Feature: Break point switches (control flow options)

  enhancementSINCLAIR
  CCBR/SINCLAIR#178 · Filter by author wong-nw opened on Aug 15, 2025
  1

• percent.mt vs nFeature_RNA plots different at high MT/low nFeature when comparing with old bones

  SINCLAIR
  CCBR/SINCLAIR#173 · Filter by author kcgfarb opened on Jul 28, 2025

• Remove average silhouette score plot from Integration report for datasets > 90k cells

  bugSINCLAIR
  Bug

  CCBR/SINCLAIR#172 · Filter by author kcgfarb opened on Jul 28, 2025
  

• Bug: Clustering missing in Integration report

  bugSINCLAIR
  Bug

  CCBR/SINCLAIR#171 · Filter by author kcgfarb opened on Jul 28, 2025
  1

• UMAPs not displayed in integration report for >100k cells

  bugSINCLAIR
  Bug

  CCBR/SINCLAIR#170 · Filter by author kcgfarb opened on Jul 28, 2025