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32 lines
2.2 KiB
Markdown
# nf-core/configs: Section for Hologenomics at GLOBE, University of Copenhagen (Mjolnir server) Configuration
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> **NB:** You will need an account on Mjolnir to run the pipeline. If in doubt contact IT.
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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_nfcore` in their data/project directory on Mjolnir where the temp files from nf-core pipelines will be re-directed by the `NXF_TEMP` command (see below).
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The contents of the `.tmp_nfcore` directory should be periodically deleted manually to save on space.
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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.
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The following lines **must** be added by users to their `~/.bash_profile`:
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```bash
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#re-direct tmp files away from /tmp directories on compute nodes or the headnode
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export NXF_TEMP=/maps/projects/mjolnir1/people/$USER/.tmp_nfcore
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# nextflow - limiting memory of virtual java machine
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NXF_OPTS='-Xms1g -Xmx4g'
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```
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Once you have created the `.tmp_nfcore` directory and added the above lines of code to your `.bash_profile` you can run an nf-core pipeline.
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Before running a 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:
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```bash
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## Load Java and Nextflow environment modules
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module purge
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module load jdk/1.8.0_291 miniconda singularity/3.8.0 nextflow/21.04.1.5556
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```
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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.
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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.
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