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21 lines
1.5 KiB
Markdown
21 lines
1.5 KiB
Markdown
# nf-core/configs: Centre for Evolutionary Hologenomics / EvoGenomics (hologenomics partition on HPC) Configuration
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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.
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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:
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```bash
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## Load Java, Miniconda and Nextflow environment modules
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module purge
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module load lib
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module load java/v1.8.0_202-jdk miniconda nextflow/v20.07.1.5412
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```
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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.
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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.
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This configuration will automatically choose the correct SLURM queue (short,medium,long) depending on the time and memory required by each process.
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>NB: You will need an account to use the HPC cluster to run the pipeline. If in doubt contact IT.
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>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.
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