Release 2.5.1

What's Changed

Full Changelog: v2.5.0...v2.5.1

Container Images 🐳

All images available on GitHub Container Registry:

# Base image (all conda environments, no BSgenome)
ghcr.io/friendsofstrandseq/mosaicatcher-pipeline:base-2.5.1
ghcr.io/friendsofstrandseq/mosaicatcher-pipeline:base-latest

# Assembly-specific images (base + BSgenome)
ghcr.io/friendsofstrandseq/mosaicatcher-pipeline:hg38-2.5.1
ghcr.io/friendsofstrandseq/mosaicatcher-pipeline:hg19-2.5.1
ghcr.io/friendsofstrandseq/mosaicatcher-pipeline:T2T-2.5.1
ghcr.io/friendsofstrandseq/mosaicatcher-pipeline:mm10-2.5.1
ghcr.io/friendsofstrandseq/mosaicatcher-pipeline:mm39-2.5.1

# Latest tags (updated on stable releases)
ghcr.io/friendsofstrandseq/mosaicatcher-pipeline:hg38-latest
ghcr.io/friendsofstrandseq/mosaicatcher-pipeline:hg19-latest
ghcr.io/friendsofstrandseq/mosaicatcher-pipeline:T2T-latest
ghcr.io/friendsofstrandseq/mosaicatcher-pipeline:mm10-latest
ghcr.io/friendsofstrandseq/mosaicatcher-pipeline:mm39-latest

Changes 📜

Chores 🧹

• chore: bump version from 2.5.0 to 2.5.1 [2289f7c]

Other Changes 📝

• chore(config): leave reference_base_dir unset by default [01bfcf8]
• feat(config): default arbigent mapability track to T2T [a1ea519]
• feat(arbigent): skip SV plot and stats outputs in arbigent mode [6fff499]
• chore(profile): raise local-cores to 128 in the EMBL apptainer profile [8465953]
• refactor(rules): disable job groups, mark lightweight rules local [091c4f8]
• ... and 26 more

📝 Full Commit History (click to expand)

• 2289f7c - chore: bump version from 2.5.0 to 2.5.1
• 01bfcf8 - chore(config): leave reference_base_dir unset by default
• a1ea519 - feat(config): default arbigent mapability track to T2T
• 6fff499 - feat(arbigent): skip SV plot and stats outputs in arbigent mode
• 8465953 - chore(profile): raise local-cores to 128 in the EMBL apptainer profile
• 091c4f8 - refactor(rules): disable job groups, mark lightweight rules local
• 09fc8cd - perf(rules): scale runtime with retry attempt
• f5b4931 - perf(arbigent): scale regenotype memory by input size
• ad21a27 - perf(resources): retune memory from job accounting data
• 57f6ea7 - fix(haplotagging): stamp prepare_haplotag_input_bam outputs
• bbd7213 - feat(toolbox): add apptainer container pull and validation script
• 976a860 - fix(utils): make BSgenome tarball installs idempotent
• 9c87aca - fix(reorganise): use the last index match when splitting sample names
• 0b02b51 - fix(watcher): pass real booleans in config overrides
• 1939095 - feat(watcher): add heartbeat file and staleness monitor
• d1e521b - chore(utils): run check_sm_tag outside the container
• 2f2d2c4 - feat(haplotagging): normalise @rg SM tag for pooled libraries
• bd2ae71 - fix(arbigent): coerce confidence column to numeric
• 444dd9f - fix(strandphaser): write header-only VCF when nothing phases
• 68be151 - fix(strandphaser): allow empty phasing behind a config flag
• 149776f - fix(strandphaser): tolerate chromosomes with too few informative SNPs
• af542ec - chore(deps): bump prefix-dev/setup-pixi from 0.10.0 to 0.10.1
• 1b6fd46 - fix(docs): restore MosaiCatcher logo
• fe52a3f - fix(scNOVA): keep scNOVA conda envs out of the containerized image
• 9188b08 - feat(scNOVA): re-enable module with container-excluded conda envs
• c4d1c93 - fix(envs): put conda-forge before bioconda in rtools.yaml
• 6943153 - chore(deps): bump prefix-dev/setup-pixi from 0.9.4 to 0.10.0
• ee01153 - chore(deps): bump actions/cache from 4 to 6
• 1316266 - chore(deps): bump actions/checkout from 4 to 7
• 3aa2a44 - chore(deps): bump softprops/action-gh-release from 2 to 3
• d8f934a - chore(deps): bump mamba-org/setup-micromamba from 2 to 3
• f3f13d7 - chore(deps): bump docker/build-push-action from 6 to 7

Documentation 📖

For more details, please refer to:

• MosaiCatcher Documentation
• Version Management Guide
• Release Workflow
• Container Usage