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.
Older scripts can be kept in the archive directory for future reference.
Files with the prefix batch are used to run jobs on a workstation or other computer where the user runs jobs directly (interactively) via the command line.
These scripts should be run from the command line as ./[file]
Files with the prefix sbatch are used to run jobs on a cluster where the user submits jobs to a queueing system (e.g. SLURM).
These scripts should be run from the command line as sbatch [file]
Files with the prefix submit are used to run jobs on a cluster where the user submits jobs to a queueing system as well.
However, these scripts will submit multiple jobs to sbatch at once using the GNU parallel tool.
These scripts should be run from the command line as ./[file]
Slurm helper submit files that take in global variables are placed in the slurm directory.
Slurm output logs are placed in the logs directory.
The log files are often large and commonly deleted, so they are ignored by git.