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snakemake / snakemake-wrappers

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feat: NGS-bits SampleSimilarity #3500

Open tdayris opened 1 day ago

tdayris commented 1 day ago

Adds a wrapper for ngs-bits SampleSimilarity. There are a lot of subcommands for ngs-bits. Many of them requires a connection to a mysql database (NGSD), which I don't know how to deploy smoothly through a snakemake wrapper.

I'll wrap some other subcommands soon.

QC

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Summary by CodeRabbit

Release Notes

coderabbitai[bot] commented 1 day ago
📝 Walkthrough
📝 Walkthrough ## Walkthrough This pull request introduces several new files related to the `bio/ngsbits/samplesimilarity` tool, including environment configuration files for Conda and a metadata file. Specifically, it adds `environment.linux-64.pin.txt` and `environment.yaml` for package management, `meta.yaml` for tool metadata, and a `wrapper.py` for Snakemake integration. Additionally, it includes test files in VCF format and a new test function in `test_wrappers.py` to validate the wrapper's functionality. ## Changes | File Path | Change Summary | |---------------------------------------------------|---------------------------------------------------------------------------------------------------| | bio/ngsbits/samplesimilarity/environment.linux-64.pin.txt | New file created for Conda environment specification, listing package URLs and versions. | | bio/ngsbits/samplesimilarity/environment.yaml | New file created specifying channels and dependencies for the Conda environment. | | bio/ngsbits/samplesimilarity/meta.yaml | New metadata file created with tool name, authors, URL, input/output specifications, and parameters. | | bio/ngsbits/samplesimilarity/test/Snakefile | New rule `test_ngsbits_samplesimilarity` added to define input and output for testing. | | bio/ngsbits/samplesimilarity/test/a.vcf | New VCF file added containing genomic variant data. | | bio/ngsbits/samplesimilarity/test/b.vcf | New VCF file added containing genomic variant data. | | bio/ngsbits/samplesimilarity/wrapper.py | New Snakemake wrapper script created for the `SampleSimilarity` tool, handling input and execution. | | test_wrappers.py | New test function `test_ngsbits_samplesimilarity(run)` added to execute the wrapper in tests. | ## Possibly related PRs - **#3135**: Introduces a new `environment.linux-64.pin.txt` file for Conda, similar to this PR's focus on environment setup. - **#3139**: Creates a new `environment.linux-64.pin.txt` file for the Rseqc tool, highlighting a shared emphasis on establishing reproducible environments. - **#3162**: This PR also introduces an `environment.linux-64.pin.txt` file for the Bwameth tool, indicating a consistent approach to managing dependencies. - **#3165**: Introduces an `environment.linux-64.pin.txt` file for the Nanosim tool, aligning with the main PR's changes. - **#3302**: The introduction of a new `environment.linux-64.pin.txt` for the vg giraffe tool in this PR is consistent with the main PR's changes. - **#3452**: This PR also introduces a new `environment.linux-64.pin.txt` for the vg autoindex tool, further emphasizing the trend of creating environment files for bioinformatics applications. - **#3496**: The addition of a new `environment.linux-64.pin.txt` for the MTNucRatioCalculator in this PR mirrors the main PR's focus on environment setup, indicating a shared objective in managing dependencies for bioinformatics tools. ## Suggested reviewers - fgvieira

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