Global Parameters

The GLOBAL_PARAMETERS module allows you to set default values for all modules in the pipeline file.

If an option is defined in both GLOBAL_PARAMETERS and a specific module, the value specified in that specific module will take precedence during execution.

Typically, GLOBAL_PARAMETERS can be used to:

• Enable or disable verbose mode with the verbose option.

• Enable or disable the timer to log the execution time of each module using the timer option.

• Select the job scheduler (either SGE, SLURM or NONE) with the job_scheduler option.

• Enable or disable multiprocessing and specify the number of cores to use with the multiprocessing option.

Warning

When enabling multiprocessing in the pipeline file, it does not automatically request the specified number of cores when submitting a job. You need to configure this setting in the qsub (for SGE) or sbatch (for SLURM) script.

Example usage of the GLOBAL_PARAMETERS module:

GLOBAL_PARAMETERS:
{
    timer: True
    verbose: True
    job_scheduler: SLURM
    multiprocessing: 1  # No multiprocessing
    new_log_file: True #Create a new log file: if a log file with the same name already exists, it will be overwritten.
}