Feature request: Adapt merge_bams_v2.smk for Flexible Input File Location

[berntpopp]

Adapt merge_bams_v2.smk for Flexible Input File Location

Description:
The current merge_bams_v2.smk script has hardcoded input file paths. This issue aims to make the script more flexible by allowing input file locations to be specified through configuration parameters or aligned with the output from alignment_v2.smk.

Acceptance Criteria:

• Modify merge_bams_v2.smk to accept input file paths from the configuration file.
• Ensure compatibility with the output paths from alignment_v2.smk.
• Update the documentation to reflect the changes.

Implementation Steps:

1. Modify merge_bams_v2.smk to read input file paths from the configuration file.
2. Align input paths with the output from alignment_v2.smk.
3. Test the updated script to ensure it works with flexible input paths.
4. Update the documentation with the new usage instructions.