Add facets-suite somatic variant caller

[iamh2o]

Summary

• add new Snakemake rule for running facets-suite on tumor-normal pairs
• wire rule into main workflow and configuration templates
• register facets as a somatic SNV caller

Testing

• pytest

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https://chatgpt.com/codex/tasks/task_e_68bf7aeb89f48331849ef7e083db44cf

[Copilot]

Pull Request Overview

This PR integrates the facets-suite somatic variant caller into the Snakemake workflow by adding a new rule and wiring it into the existing pipeline configuration.

• Adds a new Snakemake rule facets_suite to run the facets-suite variant caller on tumor-normal pairs
• Registers facets as a somatic SNV caller in the global configuration
• Provides resource configuration templates for both SLURM and local execution environments

Reviewed Changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
workflow/rules/facets_suite.smk	Implements the main facets-suite rule and target gathering rule
workflow/Snakefile	Includes the new facets-suite rule file
config/global.yaml	Registers facets as a somatic SNV caller
config/day_profiles/slurm/templates/rule_config.yaml	Adds SLURM-specific resource configuration for facets
config/day_profiles/local/templates/rule_config.yaml	Adds local execution resource configuration for facets

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[Copilot]

The os module is imported but never used in this file. This unused import should be removed to keep the code clean.

Suggested change

import os