Feature request: Generalize Run Script to Take Snakemake File as Parameter

[berntpopp]

Generalize Run Script to Take Snakemake File as Parameter

Description:
The current run scripts are specific to individual Snakemake files. This issue aims to generalize the run script to accept the Snakemake file as a parameter, along with other parameters such as the number of jobs.

Acceptance Criteria:

• Modify the run script to take the Snakemake file as a parameter.
• Ensure the script can handle additional parameters such as the number of jobs.
• Update the documentation to reflect the changes.

Implementation Steps:

1. Modify the run script to accept the Snakemake file as a parameter.
2. Ensure the script can handle additional parameters such as the number of jobs and log output.
3. Test the generalized run script to ensure it works with different Snakemake files.
4. Update the documentation with instructions for using the generalized run script.