CARLISLE: Cut And Run anaLysIS pipeLinE

CARLISLE 2.7.5

New Features

• ROSE containerization: Containerized the ROSE workflow, added a dedicated prep script, and simplified dependencies by removing annotation-folder/refseq coupling for supported genomes (hg19, hg38, mm10). (@kopardev)
• GO enrichment workflow split: Separated GO enrichment table generation from dotplot generation to improve rerun behavior and failure isolation. (@kopardev)

Improvements

• ROSE output streamlining: Reduced ROSE outputs to only required deliverables and adjusted cluster resource requests accordingly. (@kopardev)
• GO enrichment execution hardening: Improved GO enrichment and dotplot logging and scheduling defaults for cluster execution. (#210, #211, #212, #213, @kopardev)

Bug Fixes

• GO enrichment robustness: Handle empty BED/TSV inputs without hard failure and improve fallback checks in dotplot generation. (#212, @kopardev)
• Dotplot label handling: Fix duplicate wrapped enrichment labels in GO dotplot output. (@kopardev)
• ROSE empty-input handling: Prevent hard failures when ROSE prep receives empty peak inputs. (@kopardev)