Feature request: Make Scripts Take Config Values and Input Parameters

[berntpopp]

Make Scripts Take Config Values and Input Parameters

Description:
Scripts like alignment_v2.smk and merge_bams_v2.smk currently have hardcoded values, such as the metadata.tsv file. This issue aims to make these scripts more flexible by allowing these values to be specified in the configuration file or through input parameters.

Acceptance Criteria:

• Modify alignment_v2.smk and merge_bams_v2.smk to take values from the configuration file.
• Allow specifying input parameters for values currently hardcoded.
• Update the documentation to reflect the changes.

Implementation Steps:

1. Modify alignment_v2.smk to take values from the configuration file and input parameters.
2. Modify merge_bams_v2.smk to take values from the configuration file and input parameters.
3. Test the updated scripts to ensure they work with configurable values.
4. Update the documentation with the new usage instructions.