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Bug: "containerize" branch does not complete batch correction

bugSomething isn't workingSomething isn't working

high priority

SINCLAIR

Status: Open.

#211 In CCBR/SINCLAIR;

· wong-nw opened on Mar 16, 2026

Bug: Test run produces both output and results directory

SINCLAIR

Status: Open.

#207 In CCBR/SINCLAIR;

· wong-nw opened on Mar 9, 2026

refactor with improved modular design

SINCLAIR

Status: Open.

#202 In CCBR/SINCLAIR;

· kelly-sovacool opened on Nov 7, 2025

Upgrade to liger >= v2

low priority

SINCLAIR

Status: Open.

#201 In CCBR/SINCLAIR;

· kelly-sovacool opened on Oct 16, 2025

Use RDS files as input files for Filtering/Preprocess

SINCLAIR

Status: Open.

#200 In CCBR/SINCLAIR;

· wong-nw opened on Oct 10, 2025

celldex expects access to a lock file in the user's home dir

bugSomething isn't workingSomething isn't working

SINCLAIR

Status: Open.

#199 In CCBR/SINCLAIR;

· kelly-sovacool opened on Sep 22, 2025

small sample sizes failing at batch correction

low priority

SINCLAIR

Status: Open.

#194 In CCBR/SINCLAIR;

· kcgfarb opened on Sep 12, 2025

document the execution timeline report

documentationImprovements or additions to documentationImprovements or additions to documentation

SINCLAIR

Status: Open.

#192 In CCBR/SINCLAIR;

· kelly-sovacool opened on Sep 9, 2025

seurat_preprocess - break up into separate filtering steps

bugSomething isn't workingSomething isn't working

SINCLAIR

Status: Open.

#191 In CCBR/SINCLAIR;

· kelly-sovacool opened on Sep 9, 2025

Output tool versions

enhancementNew feature or requestNew feature or request

SINCLAIR

Status: Open.

#188 In CCBR/SINCLAIR;

· wong-nw opened on Aug 22, 2025

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

SINCLAIR

Status: Open.

#185 In CCBR/SINCLAIR;

· wong-nw opened on Aug 22, 2025

Update samplesheet check process

SINCLAIR

Status: Open.

#184 In CCBR/SINCLAIR;

· wong-nw opened on Aug 22, 2025