Snakemake

Changed

- Fixed a bug in script and wrapper directives. Tried to decode a str.

Changed

- Fixed an issue with the parameter linting code, that could cause an
index out of bounds exception.

Added

- The multiext function now allows arbitrary file extensions (no
longer required to start with a "." (thanks to jafors)
- The include directive can now also take a Pathlib Path object
(thanks to mbhall88).

Changed

- Jupyter notebook integration no longer automatically starts a
browser.
- Empty directories are cleaned up after workflow execution.
- Fixed directory handling: no longer fail if the same job writes both
a dir and a contained file.
- Linter now recommends using spaces only for indentation.
- Persistence dir "aux" has been renamed to "auxiliary" in order to
make windows happy.
- Linter now distinguishes awk syntax from regular variable usage.
- Various bug fixes for Windows (thanks to melund).

Added

- Native Google Cloud support via the (despite the name generic)
lifesciences API.
- Ability to optionally exchange the conda frontend to mamba (faster
and sometimes more correct) instead of conda.

Changed

- Improved notebook integration experience, with various removed bugs and
pitfalls.
- Auto-retry google storage API calls on transient or checksum errors.

Added

- --envvars flag for passing secrets to cloud executors

Changed

- Wider thumbnail dialogs in report.
- Updated installation instructions.
- Various small kubernetes bug fixes.
- Bug fix for iRods remote files.

Added

- Interactive jupyter notebook editing. Notebooks defined by rules can
be interactively drafted and updated using snakemake --edit-notebook
(see docs).

Changed

- Fixed group resource usage to occupy one cluster/cloud node.
- Minor bug fixes.