feat: automate inference of index name

[fgvieira]

Description

Added automated inference of index name and to call MarkDuplicatesWithMateCigar instead of the default, since both tools are quite similar.
These changes render the wrapper bio/picard/markduplicateswithmatecigar redundant,

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]

Nice work!

Some questions/suggestions are in the code, and additionally these two:

1. Users might not want the index, and maybe we can simply leave one of the example rules without an idx= specified, to showcase that it is not necessary to specify it.
2. If the wrapper MarkDuplicatesWithMateCigar becomes obsolete with these changes, I'd simply remove it with the same pull request. Or do you see any unforeseen side-effects of this?

[fgvieira]

1. Done!
2. Sure, for me we can remove the MarkDuplicatesWithMateCigar wrapper.

[dlaehnemann]

Another little suggestion, but otherwise this looks really good to me!