From 65831b73ef4c7e1257350810777f98ef46000d82 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?=
 <60298098+ashildv@users.noreply.github.com>
Date: Thu, 21 Jan 2021 00:17:08 +0100
Subject: [PATCH] Create ceh.md

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+# nf-core/configs: Centre for Evolutionary Hologenomics / EvoGenomics (hologenomics partition on HPC) Configuration
+
+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, Miniconda and Nextflow. You can do this by including the commands below in your SLURM/sbatch script:
+
+```bash
+## Load Java, Miniconda and Nextflow environment modules
+module purge
+module load lib
+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.
+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: You will need an account to use the HPC cluster to run the pipeline. If in doubt contact IT.
+
+>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.