Feature request: Add Run Script for merge_bams_v2.smk

[berntpopp]

Add Run Script for merge_bams_v2.smk

Description:
There is currently no run script for merge_bams_v2.smk. This issue aims to add a run script similar to the existing ones for other Snakemake workflows.

Acceptance Criteria:

• Create a run script for merge_bams_v2.smk.
• Ensure the script handles necessary parameters and logging.
• Update the documentation to include the new run script.

Implementation Steps:

1. Create a run script for merge_bams_v2.smk.
2. Ensure the script handles parameters such as the number of jobs and log output.
3. Test the run script to ensure it works correctly.
4. Update the documentation with instructions for using the new run script.