docs: Documentation update

[tdayris]

Description

Last year, I opened #392. We agreed on splitting these documentation updates into chunks of size 10 to 20.

General meta.yaml updates:

no information lost : it has been moved to correct section
no wrapper update: Only meta.yaml were updated
key-word arguments provided in input, output, and params sections when missing
url to source/documentation added when missing (it has been moved from notes/descriptions
Some meta.yaml include a section called citations. Their content were moved to notes sections

This is a work in progress, i'm currently at the letter "q".

Why ? I have been told it was difficult to read Python/Snakemake codes to search for exact parameters list, nomenclature and expected results.

QC

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

• there is a test case which covers any introduced changes. Does not apply.
• input: and output: file paths in the resulting rule can be changed arbitrarily. Does not apply.
• either the wrapper can only use a single core, or the example rule contains a threads: x statement with x being a reasonable default. Does not apply.
• 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). Does not apply.
• all environment.yaml specifications follow the respective best practices. Does not apply.
• wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in input: or output:). Does not apply.
• all fields of the example rules in the Snakefiles and their entries are explained via comments (input:/output:/params: etc.). Does not apply.
• stderr and/or stdout are logged correctly (log:), depending on the wrapped tool. Does not apply.
• 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). Does not apply.
• the meta.yaml contains a link to the documentation of the respective tool or command
• Snakefiles pass the linting (snakemake --lint). Does not apply.
• Snakefiles are formatted with snakefmt. Does not apply
• Python wrapper scripts are formatted with black. Does not apply.