feat: deeptools plotcoverage

[tdayris]

Description

Add Deeptools plotcoverage to the list of available wrappers

QC

• I confirm that:

For all wrappers added by this PR,

• 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.
• Conda environments use a minimal amount of channels, in recommended ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as conda-forge should have highest priority and defaults channels are usually not needed because most packages are in conda-forge nowadays).

[fgvieira]

It would be nice if the wrapper could infer the output plot file format and set --plotFileFormat.

[tdayris]

Hi, thank you for your review.

The file format is automatically inferred from output file with deepTools. The documentation reads:

--outFileName, -out, -o
  | File name to save the image to. The file ending will  be used to determine the image format. The available options are: “png”,  “eps”, “pdf” and “svg”, e.g., MyHeatmap.png.

Let me make the changes anyway. This will avoid all ambiguity and will let the wrapper raise the format error (if any) instead of deepTools.

[fgvieira]

If --coverageThresholds is needed with --outCoverageMetrics, why not just add it also to the command line?

[tdayris]

Because --coverageThresholds requires a value set by user. I do not check the value, just the fact that user provided a threshold through the extra parameters. Thus, multiple coverage thresholds can be provided when multiple alignment files are provided.