1
0
Fork 0
mirror of https://github.com/MillironX/nf-configs.git synced 2024-11-22 16:29:55 +00:00
nf-configs/docs/mjolnir_globe.md

32 lines
2.2 KiB
Markdown
Raw Normal View History

2022-06-03 14:42:08 +00:00
# nf-core/configs: Section for Hologenomics at GLOBE, University of Copenhagen (Mjolnir server) Configuration
2022-06-02 13:38:07 +00:00
> **NB:** You will need an account on Mjolnir to run the pipeline. If in doubt contact IT.
2022-06-02 14:40:29 +00:00
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).
2022-06-02 13:38:07 +00:00
2022-06-03 15:08:15 +00:00
The contents of the `.tmp_nfcore` directory should be periodically deleted manually to save on space.
2022-06-02 14:00:22 +00:00
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.
2022-06-02 13:38:07 +00:00
2022-06-02 13:59:11 +00:00
The following lines **must** be added by users to their `~/.bash_profile`:
2022-06-02 13:38:07 +00:00
```bash
#re-direct tmp files away from /tmp directories on compute nodes or the headnode
2022-06-02 14:40:29 +00:00
export NXF_TEMP=/maps/projects/mjolnir1/people/$USER/.tmp_nfcore
2022-06-02 13:38:07 +00:00
# nextflow - limiting memory of virtual java machine
NXF_OPTS='-Xms1g -Xmx4g'
```
2022-06-02 14:40:29 +00:00
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.
2022-06-02 13:38:07 +00:00
2022-06-02 14:40:29 +00:00
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:
2022-06-02 13:38:07 +00:00
```bash
## Load Java and Nextflow environment modules
module purge
2022-06-03 13:36:19 +00:00
module load jdk/1.8.0_291 miniconda singularity/3.8.0 nextflow/21.04.1.5556
2022-06-02 13:38:07 +00:00
```
2022-06-02 13:59:11 +00:00
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.