Added wrapper for verifybamid2.

[brcopeland]

Description

This provides a wrapper for the tool verifybamid2 which can be used to estimate intra-species contamination in a BAM file.

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.

[johanneskoester]

This should be an optional input file then, not a parameter.

[brcopeland]

So the svd_prefix that is passed in to verifybamid2 is not actually a file that exists, so that's why I didn't make it an input file. I could change it to have as an input one of the files that do exist, strip off the file suffix, and pass that to verifybamid2 if you would prefer.

[johanneskoester]

Mhm, would it be possible to specify all needed files under that prefix explicitly? E.g. using multiext?

[brcopeland]

I changed params.svd_prefix to input.svd_mu. This file name would be the same as the other with the suffix .mu appended. verifybamid2 requires other files with suffixes .bed, .UD, and .V to exist so the wrapper checks that.

Please note that the wrapper looks explicitly for input.svd_mu and not for the others as far as specified arguments go. I just thought that approach would be simpler to work with.

[johanneskoester]

Thanks a lot, nice work! Just one comment above.