Before running the pipeline you will need to load Java, miniconda and Nextflow. You can do this by including the commands below in your SLURM/sbatch script:
All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway.
The config contains a `cleanup` command that removes the `work/` directory automatically once the pipeline has completeed successfully. If the run does not complete successfully then the `work/` dir should be removed manually to save storage space.
This configuration will automatically choose the correct SLURM queue (short,medium,long) depending on the time and memory required by each process.
> **NB:** Nextflow will need to submit the jobs via SLURM to the HPC cluster and as such the commands above will have to be submitted from one of the login nodes.
