fix: use new java memory overhead utils

[dlaehnemann]

Description

This updates all uses of snakemake-wrapper-utils to the latest version 0.5.2. Mostly, to automatically have all the wrappers that use the get_java_opts() function reserve 20% of the reserved memory for overhead of the JVM. In some cases, I have increased that default, where the documentation indicated that the overhead is usually larger. And in some cases, I switched the specification in the example Snakefile from mem_gb to the canonical mem_mb, which is sure to be interpreted correctly for job submissions on cluster systems.

QC

• 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.
• Conda environments use a minimal amount of channels, in recommended ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as conda-forge should have highest priority and defaults channels are usually not needed because most packages are in conda-forge nowadays).

[dlaehnemann]

When merged, this finally closes snakemake/snakemake-wrapper-utils#9.

[dlaehnemann]

This will close snakemake/snakemake-wrapper-utils#9, which I kept open for tracking.

[johanneskoester]

Awesome work!