feat: Deeptools plot correlation

[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 for consistent Conda environment setup on Linux 64-bit.
  • Added environment.yaml for configuring Conda environment with DeepTools dependencies.
  • Launched meta.yaml providing essential metadata for the Deeptools Plot Correlation tool.
  • Created a Snakemake rule for testing correlation plot generation.
  • Developed wrapper.py to facilitate plotting with customizable parameters.
  • Implemented a new test function for validating plot correlation functionality.

• Documentation

  • Enhanced documentation within new files to support user setup and usage instructions.

[coderabbitai]

Walkthrough

The changes introduce several new files related to the DeepTools Plot Correlation tool, including configuration files for Conda environments (environment.linux-64.pin.txt, environment.yaml), a metadata file (meta.yaml), a Snakemake workflow definition (Snakefile), and a wrapper script (wrapper.py). Additionally, a test function for validating the plotcorrelation functionality is added to test.py. These files collectively enhance the setup, configuration, and testing of the correlation plotting capabilities.

Changes

Files	Change Summary
bio/deeptools/plotcorrelation/environment.linux-64.pin.txt, bio/deeptools/plotcorrelation/environment.yaml	New files specifying Conda environment configurations, including package dependencies and channels for bioinformatics tools.
bio/deeptools/plotcorrelation/meta.yaml	New file providing metadata and configuration details for the DeepTools Plot Correlation tool, including input/output specifications.
bio/deeptools/plotcorrelation/test/Snakefile, bio/deeptools/plotcorrelation/wrapper.py	New files implementing a Snakemake rule for correlation plotting and a wrapper for the plotCorrelation command, respectively.
test.py	New test function added to validate the execution of the plotcorrelation functionality within the DeepTools suite.

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[coderabbitai]

Actionable comments posted: 3

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between df7e2bf and 48c6c8d.

Files selected for processing (6)

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

Files skipped from review due to trivial changes (2)

• bio/deeptools/plotcorrelation/environment.linux-64.pin.txt
• bio/deeptools/plotcorrelation/environment.yaml

Additional context used

Path-based instructions (2)

bio/deeptools/plotcorrelation/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.

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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/deeptools/plotcorrelation/wrapper.py

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Additional comments not posted (4)

bio/deeptools/plotcorrelation/test/Snakefile (1)

1-15: LGTM!

The rule is well-defined and follows Snakemake conventions.

The code changes are approved.

bio/deeptools/plotcorrelation/meta.yaml (1)

1-17: LGTM!

The metadata is well-defined and follows the conventions for Snakemake wrappers.

The code changes are approved.

bio/deeptools/plotcorrelation/wrapper.py (1)

1-34: LGTM!

The wrapper script is well-defined and follows the conventions for Snakemake wrappers. The static analysis tool's warnings about undefined snakemake references can be ignored as snakemake is assumed to be defined in this context.

The code changes are approved.

Tools

Ruff

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test.py (1)

2844-2855: LGTM!

The function test_deeptools_plotcorrelation is correctly implemented. Ensure that it is properly integrated into the test suite.

The code changes are approved.

Run the following script to verify the integration of the test function into the test suite:

[coderabbitai]

Actionable comments posted: 1

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 48c6c8d and c432fed.

Files selected for processing (4)

• bio/deeptools/plotcorrelation/meta.yaml (1 hunks)
• bio/deeptools/plotcorrelation/test/Snakefile (1 hunks)
• bio/deeptools/plotcorrelation/wrapper.py (1 hunks)
• test.py (1 hunks)

Files skipped from review due to trivial changes (2)

• bio/deeptools/plotcorrelation/meta.yaml
• test.py

Files skipped from review as they are similar to previous changes (1)

• bio/deeptools/plotcorrelation/test/Snakefile

Additional context used

Path-based instructions (1)

bio/deeptools/plotcorrelation/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.

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

Ruff

bio/deeptools/plotcorrelation/wrapper.py

12-12: Undefined name snakemake

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Additional comments not posted (5)

bio/deeptools/plotcorrelation/wrapper.py (5)

1-7: LGTM!

The metadata is correctly formatted and provides useful information.

The code changes are approved.

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9-10: LGTM!

The import statement is correct and necessary for the subsequent code.

The code changes are approved.

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11-14: LGTM!

The code correctly sets up optional parameters for logging and extra arguments.

The code changes are approved.

Tools

Ruff

12-12: Undefined name snakemake

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15-18: LGTM!

The code correctly retrieves required arguments for correlation method and plot type.

The code changes are approved.

Tools

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19-25: LGTM!

The code correctly handles the plot file format and optional output matrix.

The code changes are approved.

Tools

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