fix: fixed GATK3 conda channel priorities and code reformat

[fgvieira]

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Description

Fixed conda channel priorities, plus some code clean-up

QC

• [x] I confirm that:

For all wrappers added by this PR,

• there is a test case which covers any introduced changes,
• input: and output: file paths in the resulting rule can be changed arbitrarily,
• either the wrapper can only use a single core, or the example rule contains a threads: x statement with x being a reasonable default,
• rule names in the test case are in snake_case and somehow tell what the rule is about or match the tools purpose or name (e.g., map_reads for a step that maps reads),
• all environment.yaml specifications follow the respective best practices,
• wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in input: or output:),
• all fields of the example rules in the Snakefiles and their entries are explained via comments (input:/output:/params: etc.),
• stderr and/or stdout are logged correctly (log:), depending on the wrapped tool,
• temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function tempfile.gettempdir() points to (see here; this also means that using any Python tempfile default behavior works),
• the meta.yaml contains a link to the documentation of the respective tool or command,
• Snakefiles pass the linting (snakemake --lint),
• Snakefiles are formatted with snakefmt,
• Python wrapper scripts are formatted with black.

[johanneskoester]

Closing in favor of #508. Thanks anyway!

[fgvieira]

I'll re-open it (and convert to draft), since I am planning to add some proper testing for GATK3.

[johanneskoester]

Oh sure, sorry!

[fgvieira]

When I test these changes locally, all works without any error or warning but, on GitHub I am getting a warning and an error:

Environment defines Python version < 3.7. Using Python of the main process to execute script. Note that this cannot be avoided, because the script uses data structures from Snakemake which are Python >=3.7 only.

/usr/share/miniconda/envs/snakemake/bin/python3.10 /tmp/tmpx7gcjxc0/test/.snakemake/scripts/tmpqx1der4s.wrapper.py
Activating conda environment: .snakemake/conda/81a69fc1574731cf5b92c4d702182e2c
Traceback (most recent call last):
  File "/tmp/tmpx7gcjxc0/test/.snakemake/scripts/tmpqx1der4s.wrapper.py", line 13, in <module>
    from snakemake_wrapper_utils.java import get_java_opts
ModuleNotFoundError: No module named 'snakemake_wrapper_utils'

It seems it cannot find snakemake_wrapper_utils, but it is in the environment.yaml file. Could it be because of the Python 3.7 warning? Why does environment on GitHub defines Python version < 3.7 while locally it uses 3.10.5?

[fgvieira]

Finally managed to get it to work! Had to add python >= 3.10 in the environment, otherwise it would install a python lower than 3.7 (no idea why).