feat: update to snakemake 8

[Smeds]

This PR:

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Added: for new features.
Changed: for changes in existing functionality.
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Removed: for now removed features.
Fixed: for any bug fixes.
Security: in case of vulnerabilities.

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[maehler]

Something seems to go wrong with the copy rules when running the integration test. I get the following traceback:

Traceback (most recent call last):
  File "/adhome/nima18/.pyenv/versions/hydra-reports-dev/lib/python3.11/site-packages/snakemake/executors/local.py", line 259, in _callback
    raise ex
  File "/adhome/nima18/.pyenv/versions/3.11.6/lib/python3.11/concurrent/futures/thread.py", line 58, in run
    result = self.fn(*self.args, **self.kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/adhome/nima18/.pyenv/versions/hydra-reports-dev/lib/python3.11/site-packages/snakemake/executors/local.py", line 245, in cached_or_run
    run_func(*args)
  File "/adhome/nima18/.pyenv/versions/hydra-reports-dev/lib/python3.11/site-packages/snakemake/executors/local.py", line 463, in run_wrapper
    raise ex
  File "/adhome/nima18/.pyenv/versions/hydra-reports-dev/lib/python3.11/site-packages/snakemake/executors/local.py", line 420, in run_wrapper
    run(
  File "copy_result_files", line 11, in __rule__copy_cnv_html_report
    import sys
  File "/adhome/nima18/.pyenv/versions/hydra-reports-dev/lib/python3.11/site-packages/snakemake/shell.py", line 281, in __new__
    with benchmarked(proc.pid, bench_record):
  File "/adhome/nima18/.pyenv/versions/3.11.6/lib/python3.11/contextlib.py", line 144, in __exit__
    next(self.gen)
  File "/adhome/nima18/.pyenv/versions/hydra-reports-dev/lib/python3.11/site-packages/snakemake/benchmark.py", line 376, in benchmarked
    result.running_time = time.time() - start_time
    ^^^^^^^^^^^^^^^^^^^
AttributeError: 'int' object has no attribute 'running_time'

My guess is that something about the rule function signature has changed in snakemake 8 and that the corresponding update needs to be made to generate_copy_rules. I don't have time to dig deeper at the moment though.

[maehler]

Found a post on stackoverflow that claims that you can use a different syntax for generating dynamic rules, and I imagine that this would make things much more portable. Really cool if that works!

Example:

config = {'person1': 'Amy', 'person2': 'Bruce'}

def create_rule(thiskey, thisperson):
    rule:
        name: f"{thisperson}s_rule"
        output: f"{thiskey}.txt"
        run:
            print(f'\n{thiskey} is called {thisperson}!\n')

# Generate rules
for thiskey, thisperson in config.items():
    create_rule(thiskey, thisperson)

rule people:
    input: [this + '.txt' for this in config.keys()]