feat: Varscan2 - SnpEff Meta wrapper

[tdayris]

I have been contacted about issue #275 . Varscan2 and SnpEff are compatible while calling somatic variants. No error is produced, and SNP are correctly annotated in the end.

QC

• [X] I confirm that I have followed the documentation for contributing to snakemake-wrappers.

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

  • Introduced a structured meta-wrapper configuration for a bioinformatics pipeline detailing variant calling and annotation steps.
  • Added a new Snakefile that outlines a comprehensive workflow for genomic variant analysis, integrating multiple tools.
  • Updated the used wrappers file to include new bioinformatics tools for enhanced functionality.

• Tests

  • Added a new test function to verify the integration of VarScan2 with SnpEff for variant annotation.

[coderabbitai[bot]]

📝 Walkthrough

📝 Walkthrough

## Walkthrough The changes introduce a new meta-wrapper configuration for a bioinformatics pipeline in the `meta.yaml` file, detailing five steps for variant calling and annotation. A new `Snakefile` establishes rules for genome analysis workflows, integrating tools like Samtools and SnpEff. The `used_wrappers.yaml` file is updated to include a section listing relevant bioinformatics tools. Additionally, a new test function is added to `test_wrappers.py` to validate the integration of VarScan2 with SnpEff. These updates enhance the structure and testing of the bioinformatics pipeline. ## Changes | File | Change Summary | |-------------------------------------------|-------------------------------------------------------------------------------------------------| | `meta/bio/varscan2_snpeff/meta.yaml` | Added `description` and `authors` fields; outlined five key steps for variant calling/annotation. | | `meta/bio/varscan2_snpeff/test/Snakefile`| Introduced five rules: `get_genome_fasta`, `samtools_mpileup`, `varscan2_somatic`, `snpeff_download`, and `snpeff_annotate`. | | `meta/bio/varscan2_snpeff/used_wrappers.yaml` | Added a new `wrappers` section listing five bioinformatics tools. | | `test_wrappers.py` | Added a new test function `test_varscan2_snpeff_meta(run)` for testing the Snakemake command. | ## Possibly related PRs - **#3122**: Relates to the overall structure and organization of wrapper files, similar to updates in the meta-wrapper configuration. - **#3125**: Focuses on wrapper functionality, potentially connecting with the structured approach in the main PR's `meta.yaml`. - **#3135**: Introduces a feature related to Snakemake workflows, which may connect with workflow enhancements in the main PR. - **#3171**: Focuses on quality control in bioinformatics workflows, which could relate to the overall structure of the pipeline. - **#3305**: Relates to improvements in bioinformatics tools and workflows, similar to the changes made in the main PR. - **#3367**: Fixes to the gffread wrapper may connect with handling genomic annotations in the main PR. - **#3453**: Connects with the structured approach to bioinformatics tools in the main PR. - **#3496**: Directly related to the main PR's focus on improving the configuration and usability of bioinformatics tools. ## Suggested reviewers - fgvieira

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