feat: MultiQC automatically detects configuration from input file(s)

[tdayris]

This PR lets MultiQC automatically detect configuration file, when user provides them in input, as described in official documentation.

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,
• the environment.yaml pinning has been updated by running snakedeploy pin-conda-envs environment.yaml on a linux machine,
• 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]

Is the new test being triggered in test.py?

[tdayris]

Is the new test being triggered in test.py?

It was unstashed, my fault. It's in now. Thanks !

[fgvieira]

Can it be a problem that the config will also be included as input?

snakemake-wrappers/bio/multiqc/wrapper.py

Lines 22 to 26 in 7611d30

	use_input_files_only = snakemake.params.get("use_input_files_only", False)
	if not use_input_files_only:
	input_data = set(Path(fp).parent for fp in snakemake.input)
	else:
	input_data = set(snakemake.input)

[tdayris]

Having config in input does not raise any error. However not having them will speed-up the process.