Snakemake

Added

- Flag --max-inventory-time for setting maximum time spend on creating
file inventory.
- Flag --scheduler-ilp-solver for defining which solver to use for the
ILP scheduler.

Changed

- Fixed various bugs with the new scheduler (FelixMoelder).
- Fixed bug causing certain parameters not to be passed to the cluster
(--set-scatter, --scheduler, --set-threads).
- Updated docs and fixed of google backend (vsoch).
- Display jupyter notebook code in reports.
- Improved scheduler behavior in order to directly remove temporary
files if possible.

Added

- Simplified and more configurable support for scatter-gather
processes (see docs).
- Fully configurable DAG partitioning by grouping jobs at the command
line. This should provide a vast additional improvement to
scalability in cluster and cloud settings.

Changed

- Depend on latest pulp, thereby enable Python >=3.8 compatibility
again.
- Fixes for snakefile handling in google life sciences backend
(vsoch).

Changed

- Fixed a bug in the linter that caused a false warning when using
resources in shell commands.

Changed

- Depend on pulp \< 2.0, which includes the default coin cbc solver
for all platforms.

Added

- Preemtion support for google cloud backend (vsoch).

Changed

- Fixed compatibility issues in new scheduler code (dtrodrigues and
johanneskoester).
- Improved error messages (Sam-Tygier, terrycojones)
- Various small bug fixes.
- Improved profile documentation (johanneskoester).

Added

- Support for workflow configuration via portable encapsulated
projects (PEPs, <https://pep.databio.org>).
- A new ILP based default scheduler now ensures that temporary files
are deleted as fast as possible (FelixMoelder, johanneskoester).

Changed

- Fixed bug in modification date comparison for files in google
storage (vsoch).
- Various small documentation improvements (dcroote, erjel,
dlaehnemann, goi42).