feat: for bwa, auto infer block size, extra tests, code cleanup and add docs

[fgvieira]

Description

• Automated infer of block size
• extra tests
• improve docs
• code clean up

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).

[fgvieira]

Tried doing:

block_size = snakemake.input.size_mb / 10

but kept getting an error:

Traceback (most recent call last):
[...]
    block_size = snakemake.input.size_mb / 10
                 ^^^^^^^^^^^^^^^^^^^^^^^
[...]
    return self.size / 1024 / 1024
           ^^^^^^^^^
[...]
    return sum(f.size for f in self)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
[...]
    return sum(f.size for f in self)
               ^^^^^^
AttributeError: 'str' object has no attribute 'size'

It seems to be a snakemake error.