Snakemake

Changed

- fixed missing version info in docker image.
- several minor fixes to EGA support.

Added

- Allow `category` to be set.

Changed

- Various cosmetic changes to reports.
- Fixed encoding issues in reports.

Changed

- Fixed various bugs in job groups, shadow directive, singularity
directive, and more.

Changed

- Fixed a bug in the report stylesheet.

Added

- A new framework for self-contained HTML reports, including results,
statistics and topology information. In future releases this will be
further extended.
- A new utility snakemake.utils.validate() which allows to validate
config and pandas data frames using JSON schemas.
- Two new flags --cleanup-shadow and --cleanup-conda to clean up old
unused conda and shadow data.

Changed

- Benchmark repeats are now specified inside the workflow via a new
flag repeat().
- Command line interface help has been refactored into groups for
better readability.

Added

- Group jobs for reduced queuing and network overhead, in particular
with short running jobs.
- Output files can be marked as pipes, such that producing and
consuming job are executed simultaneously and interfomation is
transferred directly without using disk.
- Command line flags to clean output files.
- Command line flag to list files in working directory that are not
tracked by Snakemake.

Changed

- Fix of --default-remote-prefix in case of input functions returning
lists or dicts.
- Scheduler no longer prefers jobs with many downstream jobs.