feat: Mutect2 additional parameters

[tdayris]

Description

This PR handles bed intervals, germline vcf, panel of normals input files and f1r2 output file.

I also introduced how to enable multi threading in some special cases, since I have witnessed issues on several computing clusters last year.

QC

For all wrappers added by this PR, I made sure that

• [x] there is a test case which covers any introduced changes,
• [x] input: and output: file paths in the resulting rule can be changed arbitrarily,
• [x] either the wrapper can only use a single core, or the example rule contains a threads: x statement with x being a reasonable default,
• [x] 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),
• [x] all environment.yaml specifications follow the respective best practices,
• [x] wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in input: or output:),
• [x] all fields of the example rules in the Snakefiles and their entries are explained via comments (input:/output:/params: etc.),
• [x] stderr and/or stdout are logged correctly (log:), depending on the wrapped tool,
• [x] 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),
• [x] the meta.yaml contains a link to the documentation of the respective tool or command,
• [x] Snakefiles pass the linting (snakemake --lint),
• [x] Snakefiles are formatted with snakefmt,
• [x] Python wrapper scripts are formatted with black.