feat: MtNucRatioCalculator

[tdayris]

Add a wrapper for MtNucRatioCalculator.

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

Release Notes

• New Features

  • Introduced environment.linux-64.pin.txt for easy environment setup on Linux 64-bit.
  • Added a new YAML configuration file for managing project dependencies.
  • Launched the MTNucRatioCalculator with clear input/output specifications and parameters.
  • Implemented a Snakemake wrapper for seamless integration with workflows.

• Tests

  • Added a new test function to validate the functionality of the MTNucRatioCalculator wrapper.

[coderabbitai]

📝 Walkthrough

Walkthrough

This pull request introduces several new files and modifications related to the MTNucRatioCalculator project. It creates an environment configuration file (environment.linux-64.pin.txt), a YAML file for managing dependencies (environment.yaml), and a metadata file (meta.yaml). Additionally, a new Snakemake wrapper (wrapper.py) is added to facilitate tool execution, along with a test function for validation in test_wrappers.py. These changes collectively enhance the project's structure for environment management, metadata documentation, and workflow integration.

Changes

File Path	Change Summary
bio/mtnucratio/environment.linux-64.pin.txt	New file created for Conda environment with specific package URLs and versions.
bio/mtnucratio/environment.yaml	New YAML file created specifying channels and dependencies for the environment.
bio/mtnucratio/meta.yaml	New metadata file created detailing the calculator's name, URL, authors, input/output, and parameters.
bio/mtnucratio/test/Snakefile	New rule test_mtnucratio added for processing BAM files and generating output files.
bio/mtnucratio/wrapper.py	New Snakemake wrapper created for executing the MTNucRatioCalculator.
test_wrappers.py	New test function test_mtnucratiocalculator added to validate the wrapper functionality.

Possibly related PRs

• feat: Deeptools multibigwig summary #3135: Introduces a new file environment.linux-64.pin.txt for Conda, similar to the changes made here.
• feat: Rseqc bamstat #3139: Addition of environment.yaml aligns with a similar file for Rseqc, defining Conda environments.
• feat: Rseqc inner distance #3140: Creation of meta.yaml relates to a similar file for Rseqc, providing essential metadata.
• chore: remove wrapper for unmaintained nanosim-h in favor of new nanosim wrapper (#3165) #3143: Addition of wrapper.py corresponds with a wrapper for Rseqc, facilitating tool execution in Snakemake.
• feat: Bwameth index #3162: Changes in environment.linux-64.pin.txt relate to a similar file for Bwameth, focusing on Conda environments.
• feat: create nanosim wrapper for all three modes of simulator.py #3165: Introduction of environment.yaml is akin to changes for Nanosim, establishing environment configurations.
• feat: add toulligqc wrapper #3171: Addition of meta.yaml is related to a similar file for ToulligQC, providing metadata.
• feat: add vg autoindex giraffe #3452: Creation of environment.linux-64.pin.txt is similar to changes for VG, aimed at defining Conda environments.
• feat: add prinseq++ wrapper #3453: Addition of wrapper.py aligns with changes for Prinseq++, facilitating tool execution in Snakemake.

Suggested reviewers

• fgvieira

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[coderabbitai]

Actionable comments posted: 4

🧹 Outside diff range and nitpick comments (5)

bio/mtnucratio/test/Snakefile (1)

10-13: Consider improvements for parameters and wrapper versioning

A few suggestions to enhance maintainability and reliability:

1. Move the chromosome parameter to a config file for better configurability
2. Use a specific version tag instead of "master" for the wrapper to ensure stability

Consider these improvements:

     params:
-        chrom="ref2",
+        chrom=lambda wildcards, config: config["mtnucratio"].get("chromosome", "ref2"),
     wrapper:
-        "master/bio/mtnucratio"
+        "v3.3.3/bio/mtnucratio"

Add to your config.yaml:

mtnucratio:
    chromosome: "ref2"  # default value, can be overridden

bio/mtnucratio/wrapper.py (3)

10-11: Document the significance of the 'MT' default value.

Consider adding a comment explaining why 'MT' is chosen as the default chromosome name (e.g., if it's a standard convention for mitochondrial DNA).

-# Default mito chromosome name is set to 'MT'
+# Default mitochondrial chromosome name is set to 'MT' as per human genome convention

🧰 Tools

🪛 Ruff (0.7.0)

11-11: Undefined name snakemake

(F821)

---

17-17: Validate input BAM file existence.

The input BAM file path is used without validation. Consider adding a check to ensure the file exists and is accessible.

 bam = str(snakemake.input)
+if not os.path.isfile(bam):
+    raise FileNotFoundError(f"Input BAM file not found: {bam}")

🧰 Tools

🪛 Ruff (0.7.0)

17-17: Undefined name snakemake

(F821)

---

1-37: Consider enhancing logging for better debugging.

The wrapper could benefit from additional logging to help users track the process flow and debug issues.

Consider adding log messages for key steps:

1. Input file validation
2. Temporary directory creation
3. Symlink creation
4. Command execution
5. Output file movement

This can be achieved by using Snakemake's logging functionality or Python's logging module.

🧰 Tools

🪛 Ruff (0.7.0)

11-11: Undefined name snakemake

(F821)

---

12-12: Undefined name snakemake

(F821)

---

17-17: Undefined name snakemake

(F821)

---

31-31: Undefined name snakemake

(F821)

---

35-35: Undefined name snakemake

(F821)

test_wrappers.py (1)

3420-3425: Consider adding more test cases

The current test only verifies basic functionality with a single output file. Consider adding test cases for:

• Different input file formats/types
• Multiple output files if supported
• Various parameter combinations
• Edge cases and error conditions

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 50980f1 and 85e5a2b.

📒 Files selected for processing (6)

• bio/mtnucratio/environment.linux-64.pin.txt (1 hunks)
• bio/mtnucratio/environment.yaml (1 hunks)
• bio/mtnucratio/meta.yaml (1 hunks)
• bio/mtnucratio/test/Snakefile (1 hunks)
• bio/mtnucratio/wrapper.py (1 hunks)
• test_wrappers.py (1 hunks)

✅ Files skipped from review due to trivial changes (3)

• bio/mtnucratio/environment.linux-64.pin.txt
• bio/mtnucratio/environment.yaml
• bio/mtnucratio/meta.yaml

🧰 Additional context used

📓 Path-based instructions (2)

bio/mtnucratio/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_wrappers.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 (0.7.0)

bio/mtnucratio/wrapper.py

11-11: Undefined name snakemake

(F821)

---

12-12: Undefined name snakemake

(F821)

---

17-17: Undefined name snakemake

(F821)

---

31-31: Undefined name snakemake

(F821)

---

35-35: Undefined name snakemake

(F821)

🔇 Additional comments (2)

bio/mtnucratio/wrapper.py (1)

1-9: LGTM! Imports and docstring are appropriate.

The imports cover all necessary functionality for file operations and Snakemake integration.

test_wrappers.py (1)

3420-3425: LGTM: Test function follows established patterns

The test function follows the standard pattern used throughout the test suite, with proper use of the run fixture and standard snakemake parameters.