feat: Sex.DetERRmine

[tdayris]

Add a wrapper for Sex.detERRmine.

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 a new Conda environment configuration for the sexdeterrmine package, enabling easy setup on Linux 64-bit systems.
  • Added a metadata file detailing the functionality of the Sex.detERRmine tool for calculating chromosome coverage.
  • Implemented a new Snakemake rule for testing the sexdeterrmine workflow.

• Bug Fixes

  • Enhanced error handling and logging in the Snakemake wrapper for improved execution feedback.

• Tests

  • Added a test function to validate the sexdeterrmine workflow execution within a Conda environment.

[coderabbitai]

📝 Walkthrough

📝 Walkthrough

Walkthrough

This pull request introduces several new files and configurations for the sexdeterrmine bioinformatics tool. It includes a Conda environment file (environment.linux-64.pin.txt) and a YAML configuration file (environment.yaml) to specify dependencies and channels. A metadata file (meta.yaml) provides essential information about the tool's functionality and requirements. Additionally, a Snakemake wrapper (wrapper.py) is added to facilitate execution, along with a test function (test_sexdeterrmine) in test_wrappers.py to validate the workflow.

Changes

File	Change Summary
bio/sexdeterrmine/environment.linux-64.pin.txt	New file created for Conda environment with specific package URLs.
bio/sexdeterrmine/environment.yaml	New YAML file added specifying channels and a dependency on sexdeterrmine=1.1.2.
bio/sexdeterrmine/meta.yaml	New metadata file created with details about the tool, including name, description, authorship, input/output specifications, and notes.
bio/sexdeterrmine/test/Snakefile	New rule test_sexdeterrmine added to define inputs and outputs for testing the tool.
bio/sexdeterrmine/wrapper.py	New Snakemake wrapper introduced to manage execution of the sexdeterrmine tool with specified parameters.
test_wrappers.py	New test function test_sexdeterrmine(run) added to execute the Snakemake command for the workflow.

Possibly related PRs

• feat: Deeptools multibigwig summary #3135: Introduces a new Conda environment file for the Deeptools project, which is similar to the main PR's introduction of environment.linux-64.pin.txt for the sexdeterrmine package.
• feat: Rseqc bamstat #3139: The introduction of environment.yaml for the Rseqc package parallels the main PR's addition of environment.yaml for sexdeterrmine.
• feat: Rseqc inner distance #3140: Similar to the main PR, this PR introduces a new environment.yaml file for the Rseqc inner distance tool.
• feat: Bwameth index #3162: This PR adds a new environment.linux-64.pin.txt file for the Bwameth project, akin to the main PR's addition for sexdeterrmine.
• feat: create nanosim wrapper for all three modes of simulator.py #3165: The introduction of environment.linux-64.pin.txt for the Nanosim tool mirrors the main PR's creation of the same type of file for sexdeterrmine.
• fix: issue when input files are in subfolders #3372: This PR addresses issues related to input files in subfolders and updates the meta.yaml file, which is relevant to the main PR's focus on environment management for the sexdeterrmine package.
• feat: add vg autoindex giraffe #3452: The addition of a wrapper for the vg autoindex command in this PR is related to the main PR's focus on creating a structured environment for the sexdeterrmine package.
• feat: add prinseq++ wrapper #3453: This PR introduces a wrapper for the prinseq++ tool, which is similar to the main PR's introduction of the sexdeterrmine package.
• feat: MtNucRatioCalculator #3496: The introduction of the MTNucRatioCalculator wrapper in this PR aligns with the main PR's focus on establishing a new environment for the sexdeterrmine package.

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📥 Commits

Reviewing files that changed from the base of the PR and between 0e3e017 and a00cdcd.

---

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 0e3e017 and a00cdcd.

📒 Files selected for processing (1)

• test_wrappers.py (1 hunks)

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

• test_wrappers.py

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[coderabbitai]

Actionable comments posted: 3

🧹 Outside diff range and nitpick comments (2)

bio/sexdeterrmine/test/Snakefile (1)

1-11: Add example usage and description

Consider adding comments to document:

1. Expected input file format
2. Example command usage
3. Description of output files

Add this documentation at the start of the rule:

+# Rule: test_sexdeterrmine
+# Purpose: Determines biological sex from sequencing depth data
+# Input: Tab-separated depth file with format: <chr> <pos> <depth>
+# Output: 
+#   - TSV file with sex determination statistics
+#   - JSON file with detailed results
+# Example usage:
+#   snakemake --cores 1 sample1.sexdeterrmine.tsv
rule test_sexdeterrmine:

bio/sexdeterrmine/wrapper.py (1)

16-21: Document the supported extra parameters.

Consider adding a comment or docstring explaining what extra parameters are supported by the Sex.DetERRmine tool and how they should be provided in the Snakefile.

🧰 Tools

🪛 Ruff (0.7.0)

16-16: Undefined name snakemake

(F821)

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21-21: Undefined name snakemake

(F821)

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 50980f1 and 99d8cb4.

⛔ Files ignored due to path filters (1)

• bio/sexdeterrmine/test/samples.depth.tsv is excluded by !**/*.tsv

📒 Files selected for processing (6)

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

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

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

🧰 Additional context used

📓 Path-based instructions (2)

bio/sexdeterrmine/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/sexdeterrmine/wrapper.py

16-16: Undefined name snakemake

(F821)

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21-21: Undefined name snakemake

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🔇 Additional comments (5)

bio/sexdeterrmine/test/Snakefile (1)

10-11: Verify the wrapper path exists

Let's ensure the wrapper path is valid and the wrapper is properly implemented.

✅ Verification successful

Wrapper implementation is valid and complete

The wrapper is properly implemented with all required components:

• Correct wrapper.py with proper imports, error handling, and snakemake shell execution
• Valid meta.yaml with clear description, inputs, and outputs
• Proper environment.yaml specifying the required dependency (sexdeterrmine=1.1.2)

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify wrapper path and implementation

# Check if wrapper.py exists at the specified path
if [ -f "bio/sexdeterrmine/wrapper.py" ]; then
    echo "Wrapper exists"
    # Check for essential wrapper components
    rg -l "snakemake" "bio/sexdeterrmine/wrapper.py"
    # Check for proper error handling
    rg -l "raise|except" "bio/sexdeterrmine/wrapper.py"
else
    echo "Wrapper not found at bio/sexdeterrmine/wrapper.py"
fi

Length of output: 208

---

Script:

#!/bin/bash
# Let's examine the actual content of the wrapper file
cat bio/sexdeterrmine/wrapper.py

# Also check if there's a meta.yaml file which is typically required for wrappers
if [ -f "bio/sexdeterrmine/meta.yaml" ]; then
    echo -e "\nFound meta.yaml:"
    cat bio/sexdeterrmine/meta.yaml
else
    echo -e "\nmeta.yaml not found"
fi

# Check the environment setup
if [ -f "bio/sexdeterrmine/environment.yaml" ]; then
    echo -e "\nFound environment.yaml:"
    cat bio/sexdeterrmine/environment.yaml
else
    echo -e "\nenvironment.yaml not found"
fi

Length of output: 2029

bio/sexdeterrmine/wrapper.py (3)

1-15: LGTM! Well-structured file header with appropriate imports.

The file header includes all necessary metadata and imports are minimal and focused.

---

29-34: 🛠️ Refactor suggestion

Remove redundant log configuration and verify tree command availability.

The log configuration is unnecessarily redefined, and the tree command might not be available in all environments.

-    log = snakemake.log_fmt_shell(
-        stdout=False,
-        stderr=True,
-        append=True,
-    )
-    shell("tree -shrf {tempdir} {log}")
+    shell("ls -R {tempdir} {log}")

Likely invalid or redundant comment.

🧰 Tools

🪛 Ruff (0.7.0)

29-29: Undefined name snakemake

(F821)

---

1-44: Verify wrapper behavior with different input scenarios.

Please ensure the wrapper handles various input scenarios correctly:

1. Missing input files
2. Empty input files
3. Large input files
4. Input files with special characters in paths

✅ Verification successful

Let me try another search strategy to verify the wrapper behavior.

---

Let me try another search strategy to verify the wrapper behavior.

---

Let me try one final search to check the wrapper implementation.

---

Based on the wrapper implementation and test files, I can now provide a final response:

The wrapper handles input scenarios appropriately

The wrapper already implements robust handling of different scenarios:

1. Uses realpath to handle special characters in paths
2. Uses a temporary directory to avoid file conflicts
3. Properly handles optional outputs (tsv/json)
4. Captures and redirects all error messages to the log file
5. Uses shell's verbose mode for file operations

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Check for test files and example inputs
fd -t f "test.*" -X cat
rg -A 5 "input.*depth.*="

Length of output: 131155

---

Script:

#!/bin/bash
# Check for test files and example inputs
fd -t f "Snakefile" -X cat

Length of output: 110576

---

Script:

#!/bin/bash
# Check for test files and test directory
fd -t f "test.*" bio/sexdeterrmine/

Length of output: 37

---

Script:

#!/bin/bash
# Check wrapper implementation and test files
cat bio/sexdeterrmine/wrapper.py
cat bio/sexdeterrmine/test/Snakefile

Length of output: 1448

🧰 Tools

🪛 Ruff (0.7.0)

16-16: Undefined name snakemake

(F821)

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21-21: Undefined name snakemake

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42-42: Undefined name snakemake

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test_wrappers.py (1)

4611-4616: LGTM! Test function follows established patterns.

The test function for Sex.detERRmine follows the standard test implementation pattern used throughout the file, with appropriate command line arguments and expected output file.

[coderabbitai]

Actionable comments posted: 3

🧹 Outside diff range and nitpick comments (1)

bio/sexdeterrmine/wrapper.py (1)

34-34: Replace tree command with portable directory listing.

The tree command might not be available in all environments. Consider using Python's built-in functions for directory listing.

-    shell("tree -shrf {tempdir} {log}")
+    shell("python -c 'import os; print(\"\n\".join(os.listdir(\"{tempdir}\")))' {log}")

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 99d8cb4 and 580e5e2.

📒 Files selected for processing (1)

• bio/sexdeterrmine/wrapper.py (1 hunks)

🧰 Additional context used

📓 Path-based instructions (1)

bio/sexdeterrmine/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.

🪛 Ruff (0.7.0)

bio/sexdeterrmine/wrapper.py

16-16: Undefined name snakemake

(F821)

---

21-21: Undefined name snakemake

(F821)

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25-25: Undefined name snakemake

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38-38: Undefined name snakemake

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42-42: Undefined name snakemake

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🔇 Additional comments (2)

bio/sexdeterrmine/wrapper.py (2)

1-15: LGTM! Well-documented header with proper imports.

The file header is well-structured with clear documentation and all necessary imports.

---

16-20: LGTM! Appropriate log configuration.

The logging setup is properly configured to capture errors while appending to maintain history.

🧰 Tools

🪛 Ruff (0.7.0)

16-16: Undefined name snakemake

(F821)

[coderabbitai]

Actionable comments posted: 2

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 580e5e2 and 54eea00.

📒 Files selected for processing (1)

• bio/sexdeterrmine/wrapper.py (1 hunks)

🧰 Additional context used

📓 Path-based instructions (1)

bio/sexdeterrmine/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.

🪛 Ruff (0.7.0)

bio/sexdeterrmine/wrapper.py

16-16: Undefined name snakemake

(F821)

---

21-21: Undefined name snakemake

(F821)

---

25-25: Undefined name snakemake

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29-29: Undefined name snakemake

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36-36: Undefined name snakemake

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38-38: Undefined name snakemake

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---

42-42: Undefined name snakemake

(F821)

🔇 Additional comments (1)

bio/sexdeterrmine/wrapper.py (1)

1-15: LGTM! Well-structured file header with clear documentation.

The imports and metadata are appropriate for the wrapper's functionality.

[coderabbitai]

Actionable comments posted: 3

🧹 Outside diff range and nitpick comments (1)

bio/sexdeterrmine/wrapper.py (1)

1-44: Consider adding comprehensive error reporting and cleanup.

While the wrapper follows Snakemake conventions, consider enhancing it with:

1. A dedicated error reporting function to standardize error messages
2. A cleanup function to handle temporary files in case of failures
3. Logging of command execution time and resource usage
4. Documentation of expected input formats and output structures

This would improve maintainability and user experience.

🧰 Tools

🪛 Ruff (0.7.0)

16-16: Undefined name snakemake

(F821)

---

21-21: Undefined name snakemake

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25-25: Undefined name snakemake

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29-29: Undefined name snakemake

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36-36: Undefined name snakemake

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38-38: Undefined name snakemake

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---

42-42: Undefined name snakemake

(F821)

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 54eea00 and 4af7254.

📒 Files selected for processing (1)

• bio/sexdeterrmine/wrapper.py (1 hunks)

🧰 Additional context used

📓 Path-based instructions (1)

bio/sexdeterrmine/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.

🪛 Ruff (0.7.0)

bio/sexdeterrmine/wrapper.py

16-16: Undefined name snakemake

(F821)

---

21-21: Undefined name snakemake

(F821)

---

25-25: Undefined name snakemake

(F821)

---

29-29: Undefined name snakemake

(F821)

---

36-36: Undefined name snakemake

(F821)

---

38-38: Undefined name snakemake

(F821)

---

42-42: Undefined name snakemake

(F821)

🔇 Additional comments (1)

bio/sexdeterrmine/wrapper.py (1)

1-15: LGTM! Well-structured file header with complete metadata.

The imports and metadata are appropriate and follow best practices.

[coderabbitai]

Actionable comments posted: 2

🧹 Outside diff range and nitpick comments (1)

bio/sexdeterrmine/wrapper.py (1)

29-33: Consider consolidating log format configuration

The log format is configured twice with different settings. This could be simplified to avoid potential inconsistencies.

Consider setting the append flag to true from the start:

-log = snakemake.log_fmt_shell(
-    stdout=False,
-    stderr=True,
-    append=False,
-)
+log = snakemake.log_fmt_shell(
+    stdout=True,
+    stderr=True,
+    append=True,
+)

This would eliminate the need for the second log format configuration while maintaining the same functionality.

🧰 Tools

🪛 Ruff (0.7.0)

29-29: Undefined name snakemake

(F821)

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 4af7254 and 31f18d8.

📒 Files selected for processing (2)

• bio/sexdeterrmine/test/Snakefile (1 hunks)
• bio/sexdeterrmine/wrapper.py (1 hunks)

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

• bio/sexdeterrmine/test/Snakefile

🧰 Additional context used

📓 Path-based instructions (1)

bio/sexdeterrmine/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.

🪛 Ruff (0.7.0)

bio/sexdeterrmine/wrapper.py

16-16: Undefined name snakemake

(F821)

---

21-21: Undefined name snakemake

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25-25: Undefined name snakemake

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29-29: Undefined name snakemake

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36-36: Undefined name snakemake

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38-38: Undefined name snakemake

(F821)

---

42-42: Undefined name snakemake

(F821)

🔇 Additional comments (1)

bio/sexdeterrmine/wrapper.py (1)

1-15: LGTM: Metadata and imports are well-structured

The file header contains all necessary metadata and appropriate imports for the wrapper's functionality.

[johanneskoester]

@tdayris something seems wrong with your fork. You always carry theses massive commit lists in your PRs. Maybe once we have merged your open PRs you could delete your fork and fork again, in order to have a fresh start?