Snakemake

Added

- Snakemake now allows for data-dependent conditional re-evaluation of
the job DAG via checkpoints. This feature also deprecates the
`dynamic` flag. See [the
docs](https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#data-dependent-conditional-execution).

Changed

- Various fixed bugs and papercuts, e.g., in group handling,
kubernetes execution, singularity support, wrapper and script usage,
benchmarking, schema validation.

Added

- Snakemake workflows can now be exported to CWL via the flag
--export-cwl, see [the
docs](https://snakemake.readthedocs.io/en/stable/executing/interoperability.html).

Changed

- Fixed bug in script and wrapper execution when using
`--use-singularity --use-conda`.
- Add host argument to S3RemoteProvider.
- Various minor bug fixes.

Added

- New command line flag --shadow-prefix

Changed

- Fixed permission issue when using the script directive. This is a
breaking change for scripts referring to files relative to the
script directory (see the
[docs](https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#external-scripts)).
- Fixed various minor bugs and papercuts.
- Allow URL to local git repo with wrapper directive
(`git+file:///path/to/your/repo/path_to_fileversion`)

Changed

- Always print timestamps, removed the --timestamps CLI option.
- more robust detection of conda command
- Fixed bug in RMarkdown script execution.
- Fixed a bug in detection of group jobs.

Changed

- Directory outputs have to marked with `directory`. This ensures
proper handling of timestamps and cleanup. This is a breaking
change. Implemented by Rasmus Ågren.
- Fixed kubernetes tests, fixed kubernetes volume handling.
Implemented by Andrew Schriefer.
- jinja2 and networkx are not optional dependencies when installing
via pip.
- When conda or singularity directives are used and the corresponding
CLI flags are not specified, the user is notified at the beginning
of the log output.
- Fixed numerous small bugs and papercuts and extended documentation.