v2.8.0

What's Changed

• chore: post-release cleanup for v2.7.6 by @github-actions[bot] in #236
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #238
• fix: pre-commit codespell and Ruff failures by @Copilot in #239
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #240
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #242
• release: CARLISLE v2.8.0 by @kopardev in #243

New Contributors

• @Copilot made their first contribution in #239

Full Changelog: v2.7.6...v2.8.0

CARLISLE 2.7.6

• Scheduler-safe Snakemake defaults: Replaced hardcoded -j 500 with safer defaults (-j 100, --max-jobs-per-second 1, --max-status-checks-per-second 0.1) for cluster-friendly submission and status polling behavior. (#223, @kopardev)

v2.7.5

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)

v2.7.3

What's Changed

• chore: 🤖 prepare release v2.7.2 by @github-actions[bot] in #199
• v2.7.3 by @kopardev in #206

Full Changelog: v2.7.2...v2.7.3

CARLISLE 2.7.2

• Fix how singularity bind paths are set. (#187, @kelly-sovacool)
• Fix the DESeq rule when using the hs1 T2T genome. (#187, @kelly-sovacool, @wong-nw)
• Fix incorrect jobby version (needs v0.4). (#194, @kelly-sovacool)
• Fix jobby usage to output stdout/stderr to log file. (#196, @kopardev)
• Fix numpy error. (#198, @kelly-sovacool)
• Fix logic error with scaling factor calcutions. (#195, @kopardev)
• Run MACS2 with control by default. (#195, @kopardev)
• Make sure submit_slurm.sbatch is not overwritten. (#195, @kopardev)
• Handle case when sample names are subsets of each other. (#195, @kopardev)

CARLISLE 2.7.1

• Remove deprecated 'ccr' partition. (#176, @kopardev)

CARLISLE 2.7.0

• Now depends on ccbr_tools v0.4 for updated jobby & spooker utilities. (#168, @kelly-sovacool)

CARLISLE 2.6.4

• Fix driver script: do not try to load the shared conda environment. (#166, @kelly-sovacool)

CARLISLE 2.6.3

• Minor documentation update to use readthedocs theme. (#162, @kelly-sovacool)
• Fix deprecation warning during initialization. (#163, @kelly-sovacool)

CARLISLE 2.6.2

• Documentation improvements. (#154, @kelly-sovacool)
• If jobby & spooker are not available, try adding them to the path on workflow completion. (#155, @kelly-sovacool)
• Fix bug that flipped library normalization scaling factor (#157, @epehrsson)