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The profile is configured to run with Singularity version 3.6.3-1.el7 which is part of the OS installtion and does not need to be loaded as a module. The profile is configured to run with Singularity version 3.6.3-1.el7 which is part of the OS installtion and does not need to be loaded as a module.
Before running the pipeline you will need to load Java and Nextflow. You can do this by including the commands below in your SLURM/sbatch script: 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:
```bash ```bash
## Load Java and Nextflow environment modules ## Load Java and Nextflow environment modules
module purge module purge
module load lib module load lib
module load java/v1.8.0_202-jdk nextflow/v20.07.1.5412 module load java/v1.8.0_202-jdk miniconda nextflow/v20.07.1.5412
``` ```
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. 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.