feat: BWA mem2 index - remove prefix parameter and determine prefix from output

[christopher-schroeder]

Description

Remove the param prefix and detect prefix by output

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.

[tedil]

LGTM!

[fgvieira]

Wouldn't it be cleaner to infer the prefix with os.path.commonprefix()?

Btw, since you are fixing the bwa-mem2 wrapper, do you think you could look into issue #522? It seems a straightforward fix...
Thanks!

[fgvieira]

Like mentioned on issue #494, maybe we can define a function to infer the prefixes and add it to snakemake-wrapper-utils. Someting like:

def infer_prefix(files, suffixes, strict = True):
    prefixes = []
    suffixes = set(suffixes)
    
    for file in files:
        for suffix in suffixes:
            if file.endswith(suffix):
                prefixes.append(file[:-len(suffix)])

    if len(prefixes) != len(files) and strict:
        raise ValueError("All files must have a valid suffix.")
    if len(set(prefixes)) != 1:
        raise ValueError("All files must share common prefix.")

    return prefixes[0]

[johanneskoester]

Nice work, some suggestions below. In general, I like the idea of @fgvieira to move the suffix handling code into snakemake-wrapper-utils, but to get things going I am fine with committing it here for now and moving it there later.