Add configurable rules for additional variant callers

[iamh2o]

Summary

• add configurable Snakemake rules for ASCAT, CNVkit, Control-FREEC, FreeBayes, GATK HaplotypeCaller, GATK Mutect2, indexcov, mpileup, MSIsensor2, MSIsensor-pro, MuSE, and Strelka
• expose template configuration blocks for each new caller in the local and Slurm rule profiles
• include the new rule module from the main Snakefile

Testing

• not run (not requested)

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https://chatgpt.com/codex/tasks/task_e_68ef656c4824833182192f22d307bdca

[Copilot]

Pull Request Overview

This PR adds configurable Snakemake rules for 12 additional variant callers to expand the workflow's analytical capabilities. Each caller is implemented with flexible configuration options and can fall back to placeholder commands when not fully configured.

• Adds support for somatic variant callers (ASCAT, CNVkit, Control-FREEC, Mutect2, MuSE, Strelka), germline callers (FreeBayes, HaplotypeCaller), MSI detection tools (MSIsensor2, MSIsensor-pro), and utility tools (indexcov, mpileup)
• Implements a shared helper framework for command building, input preparation, and configuration management
• Provides template configurations for both local and Slurm execution profiles with appropriate resource allocations

Reviewed Changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 4 comments.

File	Description
workflow/rules/additional_variant_callers.smk	Implements 12 new variant caller rules with shared utilities and flexible command templating
workflow/Snakefile	Includes the new rule module in the main workflow
config/day_profiles/slurm/templates/rule_config.yaml	Adds Slurm-optimized configuration templates for all new callers
config/day_profiles/local/templates/rule_config.yaml	Adds local execution configuration templates for all new callers

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[Copilot]

Corrected spelling of 'tumour' to 'tumor' for consistency with American English used elsewhere in the codebase.

Suggested change

	"""Run CNVkit on tumour/normal pairs."""
	"""Run CNVkit on tumor/normal pairs."""