Snakemake

Changed

- The resource directive can now take strings, e.g. for defining a GPU
model (see docs). This will e.g. be used for upcoming updates to
cloud executors.
- More extensive conda cleanup with --conda-cleanup-packages, meant
for CI usage.
- Further polish for reports.

Changed

- Redesigned HTML reports, with improved interface and performance.
- For big data, HTML reports can now be stored as ZIP, where files are
not anymore embedded but rather are stored in an auxiliary folder,
such that they don't have to be in memory during report rendering.
- Added subcategories to report (see docs).
- Fixed a bug linter, leading to only one rule or snakefile to be
linted.
- Breaking change in CLI: added flags --conda-cleanup-envs and
--conda-cleanup-pkgs, removed flag --cleanup-conda.
- Fixed scheduling of pipe jobs, they are now always scheduled, fixing
a hangup.
- Corrected quoting of shell command for cluster submission.

Added

- Allow to flag directories for inclusion in the report.

Changed

- Fixed hash computation for --cache in case of positional params
arguments.
- Automatically restrict thread usage of linear algebra libraries to whatever
is specified in the rule/job.

Changed

- Various minor bug fixes.

Changed

- Further improved linter output.

Changed

- Linter fixes