feat: Implemented handling of memory constraints in fasterq-dump wrapper

[fgvieira]

Description

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]

Would it make sense to have the get_mem function in snakemake-wrapper-utils (snakemake/snakemake-wrapper-utils#10 (comment))?

[johanneskoester]

Yes that would be awesome, thanks!

[fgvieira]

Done, but feel free to change whatever you see fit.
Not quite sure how you prefer the functions named/organized.

PS - could you also take a look at the other PRs?

thanks,

[johanneskoester]

Thanks a lot, all merged and released as 0.3.0!

[fgvieira]

Cool! I might make a new PR of this wrapper soon with the new wrapper-utils get_mem function. :)

[fgvieira]

@johanneskoester could you update snakemake-wrapper-utils on bioconda?