The submission directory contains files that are used to submit jobs to a cluster or workstation.
These files are essentially wrappers on the pipeline run script.
The files gather previous data from the data directory, pipeline global variables from the parameters directory, and call the pipeline script.
Files in this directory can be added/deleted/modified as needed.
Slurm output logs are placed in the logs directory.
The log files are often large and commonly deleted, so they are ignored by git.