feat: add ragtag wrapper

[currocam]

Description

Add RagTag wrappers.
https://github.com/malonge/RagTag/tree/master

Some test files are not small, but the tool requires alignments of a certain length not to fail. It seems more reasonable to me not to change the test case to use unrealistic parameters and add some test files as small as possible.

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).

[fgvieira]

It seems that ragtag outputs files to the same output folder. However, as stated in the PR QC, "file paths in the resulting rule can be changed arbitrarily".

One way to do it is to output everything to a temp folder, and then copy the relevant files to their final destinations (e.g. see STAR wrapper).

[fgvieira]

Thanks for your work on this!
I think it is fine now and have approved it but won't merge it now, just in case @johanneskoester has some more comments.

[currocam]

Thanks for your work on this! I think it is fine now and have approved it but won't merge it now, just in case @johanneskoester has some more comments.

Thx to you! I look forward to contributing more. I constantly use the wrappers when available :) Thanks for the thorough review :)

[johanneskoester]

I trust your judgement, @fgvieira! :-)