feat: Bwameth index

[tdayris]

QC

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

While the contributions guidelines are more extensive, please particularly ensure that:

• test.py was updated to call any added or updated example rules in a Snakefile
• input: and output: file paths in the rules can be chosen arbitrarily
• wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in input: or output:)
• 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
• the meta.yaml contains a link to the documentation of the respective tool or command under url:
• conda environments use a minimal amount of channels and packages, in recommended ordering

Summary by CodeRabbit

• New Features

  • Introduced environment.linux-64.pin.txt and environment.yaml files for simplified conda environment setup tailored for bioinformatics applications.
  • Added meta.yaml file containing essential metadata for the bwa-meth index functionality, enhancing user guidance.
  • Implemented a new Snakefile for testing bwameth indexing functionality, ensuring reliable performance.
  • Created a new genomic FASTA file for sample data storage and analysis.
  • Developed a wrapper script to automate the BWA-Meth indexing process, improving user experience.

• Tests

  • Added a new test function to validate the bwameth indexing command, ensuring reliability in processing.

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Commits

Files that changed from the base of the PR and between 2aefa9e and b0a25cb.

Walkthrough

The changes introduce several new files and configurations for the bwameth bioinformatics tool, including environment specifications for Conda, metadata for the indexing functionality, a Snakefile for testing, a genomic FASTA file, and a Python wrapper for executing indexing commands. These additions facilitate the setup, testing, and execution of the BWA-Meth indexing process within bioinformatics workflows.

Changes

File Path	Change Summary
bio/bwameth/index/environment.linux-64.pin.txt, bio/bwameth/index/environment.yaml	New files created for Conda environment setup with specified package dependencies and channels.
bio/bwameth/index/meta.yaml	New file created defining metadata for the bwa-meth index functionality, including input/output requirements.
bio/bwameth/index/test/Snakefile	New Snakefile introduced with rules for testing bwameth indexing functionality.
bio/bwameth/index/test/genome.fasta	New FASTA file added containing a genomic sequence entry for testing purposes.
bio/bwameth/index/wrapper.py	New Python wrapper script created to automate the BWA-Meth indexing process.
test.py	New test function added to validate the bwameth indexing command functionality.

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Actionable comments posted: 0

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between f79e634 and 2aefa9e.

Files selected for processing (7)

• bio/bwameth/index/environment.linux-64.pin.txt (1 hunks)
• bio/bwameth/index/environment.yaml (1 hunks)
• bio/bwameth/index/meta.yaml (1 hunks)
• bio/bwameth/index/test/Snakefile (1 hunks)
• bio/bwameth/index/test/genome.fasta (1 hunks)
• bio/bwameth/index/wrapper.py (1 hunks)
• test.py (1 hunks)

Files skipped from review due to trivial changes (4)

• bio/bwameth/index/environment.linux-64.pin.txt
• bio/bwameth/index/environment.yaml
• bio/bwameth/index/meta.yaml
• bio/bwameth/index/test/genome.fasta

Additional context used

Path-based instructions (2)

bio/bwameth/index/wrapper.py (2)

Pattern **/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.

---

Pattern **/wrapper.py: Do not complain about use of undefined variable called snakemake.

test.py (1)

Pattern **/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.

Ruff

bio/bwameth/index/wrapper.py

16-16: Undefined name snakemake

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20-20: Undefined name snakemake

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25-25: Undefined name snakemake

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27-27: Undefined name snakemake

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30-30: Undefined name snakemake

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Additional comments not posted (4)

bio/bwameth/index/test/Snakefile (2)

1-20: Well-structured Snakemake rule for Bwameth indexing.

The rule test_bwameth_index_mem is well-structured and makes good use of Snakemake features like caching and logging. The output file extensions are consistent with the Bwameth tool's expected outputs.

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22-40: Well-structured Snakemake rule for Bwameth indexing with extended output.

The rule test_bwameth_index_mem2 is similar to the first rule but includes additional output file extensions, which are consistent with an extended version of the Bwameth tool's indexing functionality.

bio/bwameth/index/wrapper.py (1)

1-38: Well-implemented Snakemake wrapper for Bwameth indexing.

The wrapper script is well-structured and follows good practices for managing temporary files and executing the Bwameth index command. The use of snakemake as an undefined variable is expected in this context and should not be flagged as an error.

Tools

Ruff

16-16: Undefined name snakemake

(F821)

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20-20: Undefined name snakemake

(F821)

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25-25: Undefined name snakemake

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27-27: Undefined name snakemake

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30-30: Undefined name snakemake

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test.py (1)

461-484: Review of the new test function test_bwameth_index

The function test_bwameth_index is well-structured and follows the existing pattern of test functions in the file. It uses the run method to execute the bio/bwameth/index command with specific parameters for two different input files. The use of the @skip_if_not_modified decorator is appropriate, ensuring the test is only run when necessary.

However, there are a few points to consider:

1. Parameter Validation: Ensure that the parameters passed to the run method, such as "--cores", "1", "--use-conda", "-F", are consistent with the requirements of the bio/bwameth/index command. It's crucial that these parameters are validated against the command's expected inputs to avoid runtime errors.
2. Decorator Usage: The @skip_if_not_modified decorator is used correctly here. However, it's important to ensure that the underlying logic for determining modifications is robust and accurately reflects changes that would affect this test's relevance.
3. Error Handling: Consider adding error handling within the test to manage potential exceptions from the run method. This could improve the test's robustness and provide clearer debugging information in case of failures.
4. Test Coverage: Verify that the test adequately covers all significant pathways and potential edge cases in the bio/bwameth/index command. This may involve reviewing the command's documentation or source code to understand its behavior thoroughly.

Overall, the addition of this test function enhances the test suite's coverage and helps maintain the reliability of the bio/bwameth/index functionality.

The code changes are approved.