feat: adds GRCm39 to default_effective_genome_size in deepTools bam…

…Coverage (#3164)

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The deepTools
[documentation](https://deeptools.readthedocs.io/en/develop/content/feature/effectiveGenomeSize.html)
provides the effective genome size by read length for GRCm39, so I added
it to the `default_effective_genome_size` dictionary in the deepTools
bamCoverage wrapper. I've also made minor adjustments to the `params` in
the "meta.yaml" file - i.e., added GRCm39 to `genome`, and 250 to
`read_length` (which was already allowed in the code but missing from
the docs).

### QC
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* [x] I confirm that I have followed the [documentation for contributing
to
`snakemake-wrappers`](https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html).

While the contributions guidelines are more extensive, please
particularly ensure that:
* [x] `test.py` was updated to call any added or updated example rules
in a `Snakefile`
* [x] `input:` and `output:` file paths in the rules can be chosen
arbitrarily
* [x] wherever possible, command line arguments are inferred and set
automatically (e.g. based on file extensions in `input:` or `output:`)
* [x] 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
* [x] the `meta.yaml` contains a link to the documentation of the
respective tool or command under `url:`
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in recommended ordering


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

- **New Features**
- Added support for the `GRCm39` genome assembly in the configuration
options.
- Expanded the `read_length` parameter to include a new option of `250`.
  
These updates enhance flexibility and functionality for users working
with genomic data.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

bio/deeptools/bamcoverage/meta.yaml

@@ -12,6 +12,6 @@ output:
   - Path to coverage file
 params:
   - effective_genome_size: Optional effective genome size value
-  - genome: Optional parameter used to fill effective genome size with pre-computed parameters. Can only be one of `GRCm37`, `GRCm38`, `GRCh37`, `GRCh38`, `dm3`, `dm6`, `WBcel235`, or `GRCz10`.
-  - read_length: Optional parameter used to fill effective genome size with pre-computed parameters. Can only be one of `50`, `75`, `100`, `150`, or `200`.
-  - extra: Optional parameters to be given to deepTools bamcoverage
+  - genome: Optional parameter used to fill effective genome size with pre-computed parameters. Can only be one of `GRCm37`, `GRCm38`, `GRCm39`, `GRCh37`, `GRCh38`, `dm3`, `dm6`, `WBcel235`, or `GRCz10`.
+  - read_length: Optional parameter used to fill effective genome size with pre-computed parameters. Can only be one of `50`, `75`, `100`, `150`, `200`, or `250`.
+  - extra: Optional parameters to be given to deepTools bamcoverage

bio/deeptools/bamcoverage/wrapper.py

@@ -42,6 +42,14 @@
         "200": 2520868989,
         "250": 2538590322,
     },
+    "GRCm39": {
+        "50": 2309746861,
+        "75": 2410055689,
+        "100": 2468088461,
+        "150": 2495461690,
+        "200": 2521902382,
+        "250": 2538633971,
+    },
     "GRCz10": {
         "50": 1195445541,
         "75": 1251132611,