nf-configs/docs/mjolnir_globe.md

# 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 running the pipeline for the first time with the `mjolnir_globe.config` (../conf/mjolnir_globe.config), users **must** create a hidden directory called `.tmp_eager` in their data/project directory on Mjolnir where the temp files from `nf-core/eager` will be re-directed by the `NXF_TEMP` command (see below).

The contents of the `.tmp_eager` directory should be periodically deleted manually to save on space. 
If the `NXF_TEMP` command is not used to properly re-direct temp files the `/tmp` directory on the compute nodes will be used and quickly filled up, which blocks anyone from working on these nodes until the offending user removes their files.

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'
```

Once you have created the `.tmp_eager` directory and added the above lines of code to your `.bash_profile` you can run the pipeline.

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 output 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 `mjolnir_globe` 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.