feat: Add wrapper for defining columns in TTree in ROOT

[laf070810]

Adds a wrapper for defining columns in TTree in the ROOT software package. The ntuple ROOT files in the test are from the test of the hadd wrapper.

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).

[laf070810]

Thanks for the reviews!

[laf070810]

The linting test should be ok now.

[fgvieira]

From what I can see, the wrapper takes several input files and each will generate an output file.
If so, wouldn't make more sense to have the wrapper process a single file, and let snakemake take care of the several files?

[laf070810]

From what I can see, the wrapper takes several input files and each will generate an output file. If so, wouldn't make more sense to have the wrapper process a single file, and let snakemake take care of the several files?

Do you mean using wildcards to take care of several files? Yes, this should be the most common case, and this wrapper already supports single file processing. As I imagined, the codes for dealing with multiple files are added as some kind of "sugar", in case someone doesn't want to add a wildcard because of inconvenience or something.

[fgvieira]

Unless there is a specific need for such behavior, I think it is better to keep the wrappers as simple as possible and not try to do things that snakemake is more suitable to.

[laf070810]

OK, I removed the corresponding parts.