All nf-core pipelines have been successfully configured for use on the Yale University McCleary cluster. To use, run the pipeline with -profile mccleary.
NB: You will need an account to use the HPC cluster on the McCleary cluster in order to run the pipeline. If in doubt contact IT. To use nf-core pipelines on McCleary:
- Install Nextflow for your user. Move the Nextflow executable to a folder in your
$PATHvariable (e.g.~/bin).
module load Java/17.0.4
curl -s https://get.nextflow.io | bash
- Submit your pipeline script via
sbatch script.sh. With the following script. Update--job-name,--time, and--partition` as needed for your head job. 2 CPUs and 5GB of memory is usually sufficient for the Nextflow head job but you can also update as needed.
#! /bin/bash
#SBATCH --job-name=nf-core
#SBATCH --out="slurm-%j.out"
#SBATCH --time=07-00:00:00
#SBATCH --cpus-per-task=2
#SBATCH --mem=5G
#SBATCH --mail-type=ALL
#SBATCH --partition=week
module load Java/17.0.4
export NXF_WRAPPER_STAGE_FILE_THRESHOLD='40000'
nextflow pull nf-core/<pipeline> -r <release>
nextflow run nf-core/<pipeline> -r <release> \
-profile mccleary \
--outdir "results" \
...
There are no specific profiles added for now