fix: Gatk filter mutect call typo

[tdayris]

Thanks to @ypradat , this PR fixes a typo leading to contamination tables being ignored in GATK FilterMutectCall. There also was a non-finished sentence in the documentation.

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

  • Updated input parameter description for the contamination table in the GATK FilterMutectCalls tool.

• Bug Fixes

  • Corrected a typo in the variable name for the contamination table input, ensuring accurate parameter access.

[coderabbitai]

Walkthrough

The changes in this pull request involve modifications to two files related to the gatk FilterMutectCalls tool. The meta.yaml file has been updated to clarify the description of the contamination input parameter, specifically indicating it as an "Optional path to contamination table." In the wrapper.py file, a variable name typo was corrected from contemination_table to contamination_table, ensuring proper access to the input parameter from the snakemake.input dictionary. No other structural changes were made.

Changes

File	Change Summary
bio/gatk/filtermutectcalls/meta.yaml	Updated description of contamination parameter from "Optional path to" to "Optional path to contamination table."
bio/gatk/filtermutectcalls/wrapper.py	Corrected variable name from contemination_table to contamination_table for input parameter access.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant Snakemake
    participant GATK

    User->>Snakemake: Provide input parameters
    Snakemake->>GATK: Execute FilterMutectCalls with contamination_table
    GATK-->>Snakemake: Return results
    Snakemake-->>User: Output results

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📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between fb512aa and d937829.

📒 Files selected for processing (2)

• bio/gatk/filtermutectcalls/meta.yaml (1 hunks)
• bio/gatk/filtermutectcalls/wrapper.py (1 hunks)

🧰 Additional context used

📓 Path-based instructions (1)

bio/gatk/filtermutectcalls/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.

🪛 yamllint

bio/gatk/filtermutectcalls/meta.yaml

[error] 13-13: trailing spaces

(trailing-spaces)

🪛 Ruff

bio/gatk/filtermutectcalls/wrapper.py

20-20: Undefined name snakemake

(F821)

🔇 Additional comments (2)

bio/gatk/filtermutectcalls/wrapper.py (2)

20-20: LGTM! Typo correction addresses the reported issue.

The change from contemination_table to contamination_table correctly fixes the typo that was causing contamination tables to be ignored. This aligns with the PR objective and ensures that the GATK FilterMutectCalls process will now properly consider the contamination table input when provided.

🧰 Tools

🪛 Ruff

20-20: Undefined name snakemake

(F821)

---

20-23: Verify the impact on FilterMutectCalls functionality.

While the typo correction is straightforward, it's important to ensure that this change results in the expected behavior for the GATK FilterMutectCalls process.

To verify the impact, please run the following script:

This script will help confirm that:

1. The contamination_table is correctly retrieved from the input.
2. The --contamination-table argument is properly included in the GATK command when a contamination table is provided.

✅ Verification successful

FilterMutectCalls functionality verified.

The contamination table is correctly retrieved and included in the GATK FilterMutectCalls command as expected.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify the usage of contamination_table in the GATK command

# Test: Check if the contamination table is correctly passed to the GATK command
# Expect: The contamination table should be included in the command when provided
rg --type python -A 10 'contamination_table' bio/gatk/filtermutectcalls/wrapper.py
rg --type python -A 20 'FilterMutectCalls' bio/gatk/filtermutectcalls/wrapper.py

Length of output: 225

---

Script:

#!/bin/bash
# Description: Retry verification of contamination_table usage in the GATK command without specifying file type

# Test 1: Check if the contamination table is correctly passed to the GATK command using file extension
rg -A 10 'contamination_table' bio/gatk/filtermutectcalls/wrapper.py

# Test 2: Check the inclusion of FilterMutectCalls in the command using file extension
rg -A 20 'FilterMutectCalls' bio/gatk/filtermutectcalls/wrapper.py

Length of output: 1112

🧰 Tools

🪛 Ruff

20-20: Undefined name snakemake

(F821)

---

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