Update wrapper documentation

[tdayris]

Description

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

• [X] there is a test case which covers any introduced changes, (no wrapper changes)
• [X] input: and output: file paths in the resulting rule can be changed arbitrarily, (no wrapper changes)
• [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), (no Snakefile changes)
• [X] all environment.yaml specifications follow the respective best practices, (no environment changes)
• [X] wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in input: or output:), (no wrapper changes)
• [ ] 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, (no wrapper changes)
• [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), (no wrapper changes)
• [ ] the meta.yaml contains a link to the documentation of the respective tool or command,
• [X] Snakefiles pass the linting (snakemake --lint), (no wrapper changes)
• [X] Snakefiles are formatted with snakefmt, (no wrapper changes)
• [X] Python wrapper scripts are formatted with black. (no wrapper changes)

[johanneskoester]

Awesome, this is a great effort!! Thanks a lot! We can also merge this in chunks if you prefer.

[johanneskoester]

Sphinx seems to have a problem with the pbhmm meta.yaml

[tdayris]

pbmm2 meta syntax error was fixed, thank you for your vigilance

You may merge this by chunks if you think it is better/easier. Just tell me how to proceed (one PR per tool ? Per meta ? Per chunk of size X ?) You are right, this PR touches a lot of files and is quite long to review.

[johanneskoester]

Chunks of some reasonable size, like 10 or 20 are fine.

[johanneskoester]

@tdayris do you plan to generate more chunks from this?

[github-actions[bot]]

This PR was marked as stale because it has been open for 6 months with no activity.