JAX Configuration

All nf-core pipelines have been successfully configured for use on the JAX Sumner cluster at The Jackson Laboratory.

To use, run the pipeline with -profile jax. This will download and launch the jax.config which has been pre-configured with a setup suitable for JAX Sumner cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline and slurm will be used as well.

NB: You will need an account to use the HPC cluster JAX in order to run the pipeline. If in doubt contact IT.
NB: Nextflow should not be executed on the login nodes. If in doubt contact IT.

Config file

See config file on GitHub

params {  
      config_profile_description = 'The Jackson Laboratory Sumner HPC profile provided by nf-core/configs.'  
      config_profile_contact = 'Bill Flynn (@flynnb)'  
      config_profile_url = 'https://jacksonlaboratory.sharepoint.com/sites/ResearchIT/SitePages/Welcome-to-Sumner.aspx'  
      singularity_cache_dir = '/fastscratch/singularity_cache_nfcore'  
executor.$slurm.queueSize = 250  
process {  
    executor = "slurm"  
    queue = "compute"  
    clusterOptions = {task.time < 72.h ? '-q batch' : '-q long'}  
    module = "slurm"  
    beforeScript = 'module load singularity'  
    enabled = true  
    autoMounts = true  
    cacheDir = params.singularity_cache_dir  
params {  
      max_memory = 320.GB  
      max_cpus = 32  
      max_time = 336.h