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28 lines
1.9 KiB
Markdown
28 lines
1.9 KiB
Markdown
# nf-core/configs: Academic Leiden Interdisciplinary Cluster Environment (ALICE), Leiden University Configuration
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> **NB:** You will need an [account](https://wiki.alice.universiteitleiden.nl/index.php?title=Getting_an_account) to use the HPC cluster to run the pipeline.
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The profile is configured to run with Singularity version 3.6.1-Go-1.14 and needs to be loaded as a module.
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Before running the pipeline you will need to load Java 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 load Singularity/3.6.1-Go-1.14
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module load Nextflow/21.03.0
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module load Java/11.0.2
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```
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We also highly recommend specifying a location of a cache directory to store singularity images (so you re-use them across runs, and not pull each time), by specifying the location with the `$NXF_SINGULARITY_CACHE_DIR` bash environment variable in your `.bash_profile` or `.bashrc`.
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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.
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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.
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This configuration will automatically choose the correct SLURM queue (short,medium,long) depending on the time required by each process. If there are
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high memory requirements (>240GB), e.g. using MALT, use the 'mem' profile:
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```bash
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run nextflow nf-core/eager -p alice,mem
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```
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> **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.
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