Snakemake

Changed

- Fixed the ability to supply functions for the thread directive.
- Improved error messages for caching.

Added

- A new "cache: true" directive that allows to annotate between
workflow caching eligibility for rules in the workflow.

Changed

- Fixed a spurious error message complaining about missing singularity
image if --use-singularity is not activated.

Changed

- Fixed a KeyError bug when executing a workflow that defines
containers without --use-singularity.

Changed

- Fixes for environment modules and tibanna-based AWS execution.
- Fixes for --default-resources defaults.
- --cores is now a mandatory argument!
- Automatic checksum validation for google storage.

Added

- Azure storage authentication via SAS
- A generic container directive that will in the future allow for
other backends than just singularity. This deprecates the
singularity directive, which will however stay functional at least
until the next major release.
- envvars directive for asserting environment variable existence. See
docs.
- support for AWS spot instances via --tibanna-config spot=true.
- Automatic code quality linting via --lint.

Added

- Jupyter notebook integration, see docs. This enables interactive
development of certain data analysis parts (e.g. for plotting).
- Ability to overwrite thread definitions at the command line
(`--threads rulename=3`), thereby improving scalability.
- Requester pays configuration for google storage remote files.
- Add keyword `allow_missing` to expand function, thereby allowing
partial expansion by skipping wildcards for which no keywords are
defined.

Changed

- Various bug fixes, e.g. for between workflow caching and script
execution.

Changed

- Added a missing module.