feat: gatk modelsegments wrapper

[Smeds]

Description

gatk ModelSegments 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,
• 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]

Not sure if this would do the same:

prefix = os.path.commonprefix(output)
output_prefix = os.path.basename(prefix)

It only works with, at least, 2 files; and does not check the extensions, but this would be done by the rule when it finishes.

[Smeds]

Your solution is much nicer. But it could be that the user only wants one output. I could handle that by making a check for at least 2 files and if only one is listed throw an exception saying that prefix needs to be specified when only one file is request.

[fgvieira]

It was really just a suggestion to make the code more readable, so completely up to you! 😄

But looking into it again, maybe the files don't even need to have the same prefix. Since you are copying them from the temp folder at the end, you can use any prefix you want, no? You just need to have a dict with the correspondence between output names and extensions.
And it would make it compatible with the second item of PR best-practices (input: and output: file paths in the resulting rule can be changed arbitrarily).

[Smeds]

I have updated the code doing the copy. The user can now:

• have different prefix for each file, generated output will be matched with listed output
• the wrapper will not assume that specif filed are generate, i.e gatk can update output from the function and this should not break the wrapper
• prefix has been removed from params since the output list will set name of files