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snakemake / snakemake-wrappers

This is the development home of the Snakemake wrapper repository, see
https://snakemake-wrappers.readthedocs.io
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feat: Sex.DetERRmine #3497

Open tdayris opened 2 days ago

tdayris commented 2 days ago

Add a wrapper for Sex.detERRmine.

QC

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Summary by CodeRabbit

coderabbitai[bot] commented 2 days ago
📝 Walkthrough
📝 Walkthrough ## Walkthrough This pull request introduces several new files and configurations for the `sexdeterrmine` bioinformatics tool. It includes a Conda environment file (`environment.linux-64.pin.txt`) and a YAML configuration file (`environment.yaml`) to specify dependencies and channels. A metadata file (`meta.yaml`) provides essential information about the tool's functionality and requirements. Additionally, a Snakemake wrapper (`wrapper.py`) is added to facilitate execution, along with a test function (`test_sexdeterrmine`) in `test_wrappers.py` to validate the workflow. ## Changes | File | Change Summary | |------------------------------------------------|-------------------------------------------------------------------------------------------------------------| | `bio/sexdeterrmine/environment.linux-64.pin.txt` | New file created for Conda environment with specific package URLs. | | `bio/sexdeterrmine/environment.yaml` | New YAML file added specifying channels and a dependency on `sexdeterrmine=1.1.2`. | | `bio/sexdeterrmine/meta.yaml` | New metadata file created with details about the tool, including name, description, authorship, input/output specifications, and notes. | | `bio/sexdeterrmine/test/Snakefile` | New rule `test_sexdeterrmine` added to define inputs and outputs for testing the tool. | | `bio/sexdeterrmine/wrapper.py` | New Snakemake wrapper introduced to manage execution of the `sexdeterrmine` tool with specified parameters. | | `test_wrappers.py` | New test function `test_sexdeterrmine(run)` added to execute the Snakemake command for the workflow. | ## Possibly related PRs - **#3135**: Introduces a new Conda environment file for the Deeptools project, which is similar to the main PR's introduction of `environment.linux-64.pin.txt` for the `sexdeterrmine` package. - **#3139**: The introduction of `environment.yaml` for the Rseqc package parallels the main PR's addition of `environment.yaml` for `sexdeterrmine`. - **#3140**: Similar to the main PR, this PR introduces a new `environment.yaml` file for the Rseqc inner distance tool. - **#3162**: This PR adds a new `environment.linux-64.pin.txt` file for the Bwameth project, akin to the main PR's addition for `sexdeterrmine`. - **#3165**: The introduction of `environment.linux-64.pin.txt` for the Nanosim tool mirrors the main PR's creation of the same type of file for `sexdeterrmine`. - **#3372**: This PR addresses issues related to input files in subfolders and updates the `meta.yaml` file, which is relevant to the main PR's focus on environment management for the `sexdeterrmine` package. - **#3452**: The addition of a wrapper for the `vg autoindex` command in this PR is related to the main PR's focus on creating a structured environment for the `sexdeterrmine` package. - **#3453**: This PR introduces a wrapper for the `prinseq++` tool, which is similar to the main PR's introduction of the `sexdeterrmine` package. - **#3496**: The introduction of the `MTNucRatioCalculator` wrapper in this PR aligns with the main PR's focus on establishing a new environment for the `sexdeterrmine` package.

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