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added JAX conf

This commit is contained in:
Asaf Peer 2021-03-21 06:49:11 -04:00
parent 93bde78faa
commit 30c864e112
2 changed files with 29 additions and 0 deletions

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conf/jax.config Normal file
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params {
config_profile_description = 'The Jackson Laboratory Sumner HPC profile provided by nf-core/configs.'
config_profile_contact = 'Asaf Peer (@peera)'
config_profile_url = 'https://jacksonlaboratory.sharepoint.com/sites/ResearchIT/SitePages/Welcome-to-Sumner.aspx'
}
executor.$slurm.queueSize = 250
process {
executor = "slurm"
queue = "compute"
clusterOptions = {task.time < 72.h ? '-q batch' : '-q long'}
module = "slurm"
beforeScript = 'module load singularity'
}
singularity.enabled = true
singularity.autoMounts = true
params {
max_memory = 768.GB
max_cpus = 70
max_time = 336.h
}

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docs/jax.md Normal file
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# nf-core/configs: 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`](../conf/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.