Snakemake

Added

- Allow URLs for the conda directive. Changed
- Various minor updates in the docs.
- Several bug fixes with remote file handling.
- Fix ImportError occurring with script directive.
- Use latest singularity.
- Improved caching for file existence checks. We first check existence
of parent directories and cache these results. By this, large parts
of the generated FS tree can be pruned if files are not yet present.
If files are present, the overhead is minimal, since the checks for
the parents are cached.
- Various minor bug fixes.

Added

- Integration with CWL: the `cwl` directive allows to use CWL tool
definitions in addition to shell commands or Snakemake wrappers.
- A global `singularity` directive allows to define a global
singularity container to be used for all rules that don't specify
their own.
- Singularity and Conda can now be combined. This can be used to
specify the operating system (via singularity), and the software
stack (via conda), without the overhead of creating specialized
container images for workflows or tasks.

Changed

- Speedups when calculating dry-runs.
- Speedups for workflows with many rules when calculating the DAG.
- Accept SIGTERM to gracefully finish all running jobs and exit.
- Various minor bug fixes.

Changed

- Log files can now be used as input files for other rules.
- Adapted to changes in Kubernetes client API.
- Fixed minor issues in --archive option.
- Search path order in scripts was changed to fix a bug with leaked
packages from root env when using script directive together with
conda.

Added

- Input and output files can now tag pathlib objects. Changed
- Various minor bug fixes.

Added

- iRODS remote provider Changed
- Bug fix in shell usage of scripts and wrappers.
- Bug fixes for cluster execution, --immediate-submit and
subworkflows.