Add GATK ValidateVariants

[G-kodes]

Description

An implementation of the GATK ValidateVariants tool

QC

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,
• 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.

Lord have mercy on my code. PR's are stressful lol

[johanneskoester]

I cannot find this to be used in the wrapper. On the other hand, extra is missing. Maybe you meant to write

Suggested change

	R="genome.fasta",
	extra="", # optional extra arguments

[johanneskoester]

I think the output should just have a .txt suffix or so, since this tool will not create a vcf file, right?

[fgvieira]

Maybe it would also be nice to set tmpdir with tempfile.

[github-actions]

This PR was marked as stale because it has been open for 6 months with no activity.