- Introduced a new module system, see
<https://snakemake.readthedocs.io/en/stable/snakefiles/modularization.html#modules>
(johanneskoester).
- Introduced a rule inheritance mechanism, see
<https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#rule-inheritance>
(johanneskoester).
- Automatically containerize a conda-based pipeline with
`--containerize`, see
<https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#containerization-of-conda-based-workflows>
(johanneskoester).
- Use temporary files for long shell commands (epruesse).
- Various fixes in the documentation (ctb, SilasK, EthanHolleman).
- Fixed a bug in job grouping that led to non-deterministic behavior
(johanneskoester).