From b5916c4bff9e3ab009bf57ff66873770b344cf0d Mon Sep 17 00:00:00 2001 From: Raphael Coimbra <48868934+rtfcoimbra@users.noreply.github.com> Date: Sat, 31 Aug 2024 14:42:19 +0200 Subject: [PATCH] feat: adds GRCm39 to `default_effective_genome_size` in deepTools bamCoverage (#3164) 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 * [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:` * [x] conda environments use a minimal amount of channels and packages, in recommended ordering ## 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. --- bio/deeptools/bamcoverage/meta.yaml | 6 +++--- bio/deeptools/bamcoverage/wrapper.py | 8 ++++++++ 2 files changed, 11 insertions(+), 3 deletions(-) diff --git a/bio/deeptools/bamcoverage/meta.yaml b/bio/deeptools/bamcoverage/meta.yaml index 96576727be7..512022f13c3 100644 --- a/bio/deeptools/bamcoverage/meta.yaml +++ b/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 \ No newline at end of file + - 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 diff --git a/bio/deeptools/bamcoverage/wrapper.py b/bio/deeptools/bamcoverage/wrapper.py index e5d607e2cd8..d6b281ebe57 100644 --- a/bio/deeptools/bamcoverage/wrapper.py +++ b/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,