feat: Mashmap

[tdayris]

Description

This PR adds MashMap, a long read aligner.

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]

It seems that MashMap has its own output format, "space-delimited with each line consisting of query name, length, 0-based start, end, strand, target name, length, start, end and mapping nucleotide identity".
Just for the sake com consistency with other read mappers, is there a way to convert this output to a SAM/BAM/CRAM?

Also, does MasMap uses any temp folder?

[tdayris]

Just for the sake com consistency with other read mappers, is there a way to convert this output to a SAM/BAM/CRAM?

Mashmap format to SAM/BAM/CRAM is not supported by MashMap. There is an open issue about that on their git. I'm wrapping this tool to follow Salmon guideline to create a gentrome file with decoy sequences.

Also, does MasMap uses any temp folder?

There is no official variable or command line argument to overload any default temporary directory.