Snakemake

Added

- Script directives now also support Julia.

Changed

- Various small bug fixes.

Changed

- Fixed a bug with pipe output.
- Cleaned up error output.

Changed

- Vastly improved performance of HTML reports generated with --report,
via a more efficient encoding of dara-uri based download links.
- Tighter layout, plus thumbnails and a lightbox for graphical results
in HTML reports.
- Bug fix for pipe groups.
- Updated docs.
- Better error handling in DRMAA executor.

Changed

- More robust handling of conda environment activation that should
work with all setups where the conda is available when starting
snakemake.
- Fixed bugs on windows.

Changed

- Fixed a bug where git module cannot be imported from wrapper.

Added

- Warning when R script is used in combination with conda and R_LIBS
environment variable is set. This can cause unexpected results and
should be avoided.

Changed

- Improved quoting of paths in conda commands.
- Fixed various issues with checkpoints.
- Improved error messages when combining groups with cluster config.
- Fixed bugs in group implementation.
- Fixed singularity in combination with shadow.