From 2988e33576695923f7ecf832b705789441610e4d 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, 2 Jun 2022 15:38:07 +0200
Subject: [PATCH] Create mjolnir_globe.md

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+# nf-core/configs: Section for Hologenomics at GLOBE, Univeristy of Copenhagen (Mjolnir server) Configuration
+
+> **NB:** You will need an account on Mjolnir to run the pipeline. If in doubt contact IT.
+
+Prior to runing the pipeline for the first time, users must create a hidden directory called .tmp_eager in their user/work directory where the tmp files from nf-core/eager will be re-directed by the NXF_TEMP command (see below).
+
+```bash
+#navigate into correct directory
+cd /maps/projects/mjolnir1/people/$USER
+
+#create .tmp_eager directory. This is a hidden directory.
+mkdir .tmp_eager
+```
+
+The contents of the .tmp_eager directory should be periodically deleted to save on space. 
+If the NXF_TEMP command is not used to properly re-direct tmp files the /tmp directory on the compute nodes will be used and quickly filled up, which will make it so that noone can work on these nodes until the files are removed.
+
+The following lines **must** be added by users to their .bash_profile:
+
+```bash
+#re-direct tmp files away from /tmp directories on compute nodes or the headnode
+export NXF_TEMP=/maps/projects/mjolnir1/people/$USER/.tmp_eager
+
+# nextflow - limiting memory of virtual java machine
+NXF_OPTS='-Xms1g -Xmx4g'
+```
+
+
+The profile is configured to run with Singularity
+
+Before running the pipeline you will need to load Java, Miniconda, Singularity and Nextflow. You can do this by including the commands below in your SLURM/sbatch script:
+
+```bash
+## Load Java and Nextflow environment modules
+module purge
+module load jdk/1.8.0_291 miniconda/4.9.2 singularity/3.8.0 nextflow/21.04.1.5556
+```
+
+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.