Snakemake

- Fixed a bug occurring when using --resources in the command line
interface (johanneskoester).
- Minor improvements in the docs (johanneskoester).

- Create directory pointed to by tmpdir resource if it does not yet
exist (johanneskoester).
- Use a single core again in dryrun if --cores is not specified
(johanneskoester).
- Bugfix for FTP remote provider (jmeppley).
- Improved documentation (corneliusroemer).

- Extended best practices document (johanneskoester)
- Restore `-j all` behavior for local execution as a (deprecated) way
of running Snakemake on all cores. Recommended now: `--cores all`
(johanneskoester).
- Improved handling and better error messages for checkpoints
(johanneskoester).

- Allow to set the default profile via the environment variable
$SNAKEMAKE_PROFILE.
- There is a new default resource tmpdir (by default reflects the
system setting), which is automatically used for temporary files by
shell commands and scripts which properly consider the usual
environment variables like $TMP, $TEMP, $TMPDIR (johanneskoester).
- The CLI flags --jobs and --cores are now separated, with --cores
being responsible for local cores and global cores in the cluster
case, and --jobs being responsible for number of jobs. Still -j and
--jobs works as a fallback for local execution (johanneskoester).
- Added the ability to overwrite resources via --set-resources
(johanneskoester).
- Various fixes for Windows execution (melund).
- Fixed a bug with fractional resources (johanneskoester).
- Fixed timeouts and other issues in google life science backend
(johanneskoester).
- Fixed a bug with missing conda frontend definitions in subworkflows
(johanneskoester).
- Skip envvar checking during linting (johanneskoester).
- Fixed a bug causing container images in modules to be ignored
(johanneskoester).

- Fixed bug in `workflow.source_path()` that occurred with modules
included from remote locations (johanneskoester).
- Inform cluster jobs about conda/mamba/activate path such that they
don't need to determine this themselves (johanneskoester).

- Improvements in the docs (resource usage, best practices, remote
files) (johanneskoester, admorris).
- functions given to params can now safely open input files generated
by previous rules. If they are not present, TBD will be displayed
and function will be reevaluated immediately before the job is
executed (i.e. when files are present) (ASLeonard).
- Connection pool for SFTP and FTP remote files, increasing download
performance (jmeppley).
- Require correct minimum version of smart_open
(Redmar-van-den-Berg).
- Added workflow.source_path(path), allowing to get the correct path
relative to the current Snakefile, even when Snakefile is included
via URL (johanneskoester).
- Fixed bugs in module system (johanneskoester, dlaehnemann).
- Fixed issue with checkpoints and ruleorder where phantom
dependencies are not properly removed from the DAG (jmeppley,
johanneskoester).
- Disable tibanna behavior that opens a browser window for each job
(nigiord).
- Allow `Paramspace(..., filename_params="*")`, meaning that all
columns of the paramspace will be encoded into the filename (kpj).
- Avoid PATH modification in cluster jobs (johanneskoester).
- For large sets of input files, pass files to wait for (FS latency)
as a file instead of command line args (kpj, epruesse).