Snakemake

Changed

- Fixed various corner case bugs. Many thanks to the community for
pull requests and reporting!
- Container execution adapted to latest singularity.

Added

- First class support for Amazon cloud execution via a new
[Tibanna backend](https://snakemake.readthedocs.io/en/v5.7.0/executable.html#executing-a-snakemake-workflow-via-tibanna-on-amazon-web-services).
Thanks to Soo Lee from Harvard Biomedical Informatics!
- Allow multiple config files to be passed via the command line.
- A new, more detailed way to visualize the DAG (--filegraph). Thanks
to Henning Timm!
- Pathlib compatibility added. Input and output files can now also be
Path objects. Thanks to Frederik Boulund!
- New azure storage remote provider. Transparently access input and
output files on Microsoft Azure. Thanks to Sebastian Kurscheid!

Changed

- Fix compatibility with latest singularity versions.
- Various bug fixes (e.g. in cluster error handling, remote providers,
kubernetes backend).

Added

- Add --default-resources flag, that
allows to define default resources for jobs (e.g. mem_mb, disk_mb), see
[docs](https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#resources).
- Accept `--dry-run` as a synonym of `--dryrun`. Other Snakemake options
are similarly hyphenated, so other documentation now refers to
`--dry-run` but both (and also `-n`) will always be accepted
equivalently.

Changed

- Reports now automatically include workflow code and configuration
for improved transparency.

Changed

- Various bug fixes.
- Polished reports.

Changed

- Various minor bug fixes in reports.
- Speed improvements when using checkpoints.

Changed

- Improved report interface. In particular for large files.
- Small TSV tables are automatically rendered as HTML with datatables.
- Be more permissive with Snakefile choices: allow "Snakefile",
"snakefile", "workflow/Snakefile", "workflow/snakefile".