feat: added tmpdir to all GATK wrappers, plus some doc changes

[fgvieira]

Description

Added tmpdir (with tempfile) to all GATK wrappers, plus some doc changes

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,
• 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.

[fgvieira]

Getting the same error as in #448 and #446.

[fgvieira]

Previous error was fixed with snakemake version 6.15.2, but now I get an error in the linting step about missing google dependencies, even though it passes all tests. Any idea of what it might be?

[johanneskoester]

No idea what's wrong there. The google sdk should be a dependency of the full snakemake.

[fgvieira]

And why an error on the linting check? If it was a missing dependency, shouldn't it give an error on the test?

[fgvieira]

@johanneskoester it seems it was because of an old Snakefile, so I just deleted it. But no idea why.. 😄