Feature request: Make bqsr_bams.smk Output Paths Dynamic

[berntpopp]

Feature request: Make bqsr_bams.smk Output Paths Dynamic

Description:
The bqsr_bams.smk script currently has hardcoded output paths. Modify the script to make output paths dynamic based on input or the previous command's output.

Acceptance Criteria:

• Modify bqsr_bams.smk to generate dynamic output paths.
• Ensure compatibility with input paths and the output of previous commands.
• Update the documentation to reflect the changes.

Implementation Steps:

1. Modify bqsr_bams.smk to create dynamic output paths.
2. Ensure the output paths are correctly generated based on the input or previous command's output.
3. Test the updated script to ensure it works with dynamic paths.
4. Update the documentation with the new usage instructions.