feat: add mehari wrappers

[tedil]

This PR adds wrappers for mehari:

• annotate-seqvars for annotating VCF/VCF.gz/BCF (sequence variants, SNVs, indels, excluding structural variants)
• download-transcript-db for downloading transcript databases required for annotation of SO terms / consequences
• download-clinvar-db for downloading clinvar databases required for annotation of clinvar VCVs

Right now there's no corresponding download-frequencies-db for gnomAD, as there's no publicly hosted version of those available yet. There is also no annotate-strucvars variant yet, this will likely be added later in a different PR.

TODO:

• [x] Test for download-clinvar-db
• [x] Subset transcript db and reference fasta for proper but small enough annotate-seqvars test

Btw: Does this repository make use of git lfs yet?

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
  • Added tools and workflows for downloading and managing Mehari transcript and ClinVar databases.
  • Introduced a workflow for annotating sequence variants using Mehari, including sample data and configuration files.
• Tests
  • Added tests to verify the correct operation of Mehari database downloads and variant annotation workflows.
• Documentation
  • Included metadata files describing tool inputs, outputs, parameters, and authorship for workflow integration.
• Chores
  • Added Conda environment files for reproducible setup of all new tools and workflows.

[coderabbitai[bot]]

📝 Walkthrough

Walkthrough

This change adds new Snakemake wrappers, environment specifications, metadata files, test data, and test cases for the Mehari bioinformatics toolkit. It introduces tools for downloading transcript and ClinVar databases and for annotating sequence variants, enabling reproducible workflows and automated testing of Mehari-based processes.

Changes

File(s)	Change Summary
bio/mehari/annotate-seqvars/environment.linux-64.pin.txt bio/mehari/annotate-seqvars/environment.yaml	Added Conda environment specification and configuration files for Mehari annotate-seqvars, listing exact package versions and channels.
bio/mehari/annotate-seqvars/meta.yaml	Added metadata file describing the Mehari annotate-seqvars tool with inputs, outputs, parameters, and author.
bio/mehari/annotate-seqvars/wrapper.py	Added wrapper script that builds and executes the Mehari annotation command based on Snakemake inputs and parameters, including validation and conditional options.
bio/mehari/annotate-seqvars/test/Snakefile	Added Snakemake rule for running Mehari annotate-seqvars on test data, specifying inputs, outputs, parameters, logging, and wrapper usage.
bio/mehari/annotate-seqvars/test/resources/MT-ND2.vcf bio/mehari/annotate-seqvars/test/resources/MT.fasta bio/mehari/annotate-seqvars/test/resources/MT.fasta.fai	Added test resource files: mitochondrial variant VCF, corresponding FASTA reference, and its index.
bio/mehari/download-clinvar-db/environment.linux-64.pin.txt bio/mehari/download-clinvar-db/environment.yaml	Added Conda environment specification and configuration files for Mehari ClinVar DB download process.
bio/mehari/download-clinvar-db/meta.yaml	Added metadata file for the Mehari ClinVar DB download process with parameters and outputs.
bio/mehari/download-clinvar-db/wrapper.py	Added wrapper script to download and extract a ClinVar database release based on parameters, including validation and logging.
bio/mehari/download-clinvar-db/test/Snakefile	Added Snakemake rule for downloading the Mehari ClinVar DB (SV flavour) with parameters, output directory, logging, and wrapper reference.
bio/mehari/download-transcript-db/environment.linux-64.pin.txt bio/mehari/download-transcript-db/environment.yaml	Added Conda environment specification and configuration files for Mehari transcript DB download process.
bio/mehari/download-transcript-db/meta.yaml	Added metadata file for the Mehari transcript DB download tool with parameters and outputs.
bio/mehari/download-transcript-db/wrapper.py	Added wrapper script to download a transcript database binary file from a GitHub release based on parameters, with validation and logging.
bio/mehari/download-transcript-db/test/Snakefile	Added Snakemake rule for downloading the Mehari transcript DB with parameters, output file, logging, caching, and wrapper usage.
test_wrappers.py	Added three test functions to run and verify the Mehari transcript DB download, ClinVar DB download, and annotate-seqvars wrappers using Snakemake with specified targets and options.

Sequence Diagram(s)

Mehari Annotate Seqvars Workflow

sequenceDiagram
    participant Snakemake
    participant Wrapper (annotate-seqvars)
    participant Mehari CLI

    Snakemake->>Wrapper (annotate-seqvars): Provide input files, parameters, and output path
    Wrapper (annotate-seqvars)->>Wrapper (annotate-seqvars): Build Mehari command with inputs and options
    Wrapper (annotate-seqvars)->>Mehari CLI: Execute command for annotation
    Mehari CLI-->>Wrapper (annotate-seqvars): Annotated VCF/BCF file
    Wrapper (annotate-seqvars)-->>Snakemake: Output file and logs

Mehari Download Transcript DB Workflow

sequenceDiagram
    participant Snakemake
    participant Wrapper (download-transcript-db)
    participant GitHub Releases

    Snakemake->>Wrapper (download-transcript-db): Provide version, build, source parameters, and output path
    Wrapper (download-transcript-db)->>GitHub Releases: Download transcript DB binary (.bin.zst)
    GitHub Releases-->>Wrapper (download-transcript-db): Transcript DB file
    Wrapper (download-transcript-db)-->>Snakemake: Output file and logs

Mehari Download ClinVar DB Workflow

sequenceDiagram
    participant Snakemake
    participant Wrapper (download-clinvar-db)
    participant GitHub Releases

    Snakemake->>Wrapper (download-clinvar-db): Provide version, build, flavour parameters, and output directory
    Wrapper (download-clinvar-db)->>GitHub Releases: Download ClinVar DB tarball
    GitHub Releases-->>Wrapper (download-clinvar-db): ClinVar DB tarball
    Wrapper (download-clinvar-db)->>Wrapper (download-clinvar-db): Extract tarball to output directory
    Wrapper (download-clinvar-db)-->>Snakemake: Output directory and logs

Suggested reviewers

• fgvieira

✨ Finishing Touches

• [ ] 📝 Generate Docstrings

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[tedil]

~TODO: update conda pin once mehari 0.36.1 is available from bioconda~ done

[fgvieira]

Thanks for your contributions! :+1: