feat: make it possible to set input as files or dirs to multiqc

[Smeds]

make it possible to use the actual input from the rule as input to multiqc, instead of converting it to dirs that are then searched.

Description

If multiqc search directories it's possible that unwanted files are included to the reports. This will make it possible to only use the provided files, when wanted.

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

• 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.

[fgvieira]

I find the variable name convert_file_input_to_dirs a bit confusing. Could we have something a bit simpler, like (e.g.) use_input_files_only, use_input_dirs, scan_input_dirs?

[Smeds]

I find the variable name convert_file_input_to_dirs a bit confusing. Could we have something a bit simpler, like (e.g.) use_input_files_only, use_input_dirs, scan_input_dirs?

good suggestion! I have updated the pull-request with variable name use_input_files_only instead of convert_file_input_to_dirs

[fgvieira]

I think it looks goos, but could you also describe this new parameter in the meta.yaml file?
Just so it is explained in the documentation.