9.13.1 (2025-10-11)

Bug Fixes

• config: restore $ref resolution for schemas (#3777) (a3e0939)
• fix iofile formatting to always display the storage query if it is set, also in case of missing input exceptions (#3786) (b1c29fa)

9.13.0 (2025-10-10)

Features

• expect meta-wrapper snakefile in meta_wrapper.smk (#3785) (843948d)

Bug Fixes

• re-evaluate until and omit-from after checkpoint updates (#3773) (2eb9079)

9.12.0 (2025-10-04)

Features

• introduce pathvars, allowing to configure parts of input/output/log/benchmark paths for the entire workflow, per module, or per rule (#3760) (e376a25)

9.11.9 (2025-10-03)

Bug Fixes

• Raise WorkflowError on empty file path in _IOFile.check (#3769) (4249ff7)
• remove id field in notebook cells created by nbformat, thereby increasing compatibility with different jupyter versions (#3767) (46cf3ed)
• show failed logs in generated unit tests (#3771) (61f4e9b)

9.11.8 (2025-10-02)

Bug Fixes

• use proper callable when accessing rule proxy with associated path modifier (#3763) (b5d12c8)

Documentation

• add snakemake logo to automatic mastodon release posts (#3764) (7b66250)

9.11.7 (2025-10-01)

Bug Fixes

• Add type annotations in logging module (#3757) (63404b2)
• source_path not mounted (#3738) (86e30b3)

Documentation

• mastodon announcements (#3723) (7da1b18)

9.11.6 (2025-09-25)

Bug Fixes

• select specific rule from module will raise "rule not defined" that cause #3751 failed (#3753) (d6fa3ca)

9.11.5 (2025-09-23)

Bug Fixes

• fail if single-file report is generated with output directories marked for inclusion (#3748) (e2ca738)

9.11.4 (2025-09-19)

Bug Fixes

• Confusion with Overriding input After Snakemake Modularization (#3714) (bd94dc1)
• properly handle temp files in group jobs that are not needed outside of the group (do not upload them to storage and delete them early) (#3730) (3ffd8e1)

9.11.3 (2025-09-16)

Bug Fixes

• logging refinements (#3571) (47ae16e)
• use proper default and fallback LP solver in scheduler settings (thanks @raffienficiaud) (#3736) (e00e5aa)

Documentation

• mention nodefaults for installation (a6db049)