nf-core/configs: palmetto
nf-core config for the Clemson University Palmetto HPC cluster
nf-core/configs: Palmetto HPC Configuration
Configuration profile for the Clemson University Palmetto HPC cluster.
This profile is maintained by the Research Computing and Data Engagment team at Clemson University. Contact us at ithelp@clemson.edu for questions or issues.
Using the profile
To use this profile, specify it when running any nf-core pipeline:
## Load Nextflow module
module load nextflow
nextflow run nf-core/<pipeline-name> -profile palmetto
This will automatically apply all cluster-specific settings including executor, resource limits, and container configurations.
Sub-profiles
The following sub-profiles are available for specialized resources:
palmetto,cleanup: Removes your pipeline’sworkdirectory after a successful run
Example:
nextflow run nf-core/<pipeline-name> -profile palmetto,cleanup
Prerequisites
Before running pipelines with this profile:
- Ensure you have access to the Clemson University HPC cluster
- Load the Nextflow module:
module load nextflow - Verify Singularity is available:
singularity --version
First-time setup
At least the first time you run a piepline, it may take several minutes
to download container images. If you would like to reuse these images,
please set $NXF_SINGULARITY_CACHEDIR in your ~/.bashrc to a folder
in your /home or /project folder.
Cluster details
- Scheduler: SLURM
- Default queue:
work1 - Container engine: Singularity
- Resource limits:
- Maximum CPUs: 192 cores
- Maximum memory: 750GB
- Maximum walltime: 72 hours
Reference genomes
This profile includes paths to local iGenomes reference genomes at
/datasets/igenomes/. Pipelines will automatically use local copies
instead of downloading references, saving time and bandwidth.
Known issues
- Jobs requesting more than 24 hours may experience longer queue times
- The
/homefilesystem has a 250GB quota. Use/scratchfor large datasets - Container builds are not supported. Contact support if you need custom containers
Troubleshooting
Quota exceeded errors
Move your work directory to /scratch if you exceed /home quota:
cd /scratch/$USER
nextflow run nf-core/<pipeline-name> -profile palmetto
Support
For issues related to this profile or the Clemson University HPC cluster:
- Email: ithelp@clemson.edu
- Documentation: https://docs.rcd.clemson.edu
- Submit tickets: https://docs.rcd.clemson.edu/support/category/submit-a-ticket/
For issues with nf-core pipelines, see the nf-core website.
Config file
// Clemson University - Palmetto HPC cluster// nf-core institutional config// Scheduler: SLURM | Containers: Apptainer/Singularity//// To activate: nextflow run <pipeline> -profile palmetto//
params { config_profile_name = 'PALMETTO' config_profile_description = 'nf-core config for the Clemson University Palmetto HPC cluster' config_profile_contact = 'Research Computing and Data Engagement (ithelp@clemson.edu)' config_profile_url = 'https://docs.rcd.clemson.edu'
// Use local igenomes database igenomes_ignore = true igenomes_base = '/datasets/igenomes/'
max_memory = 750.GB max_cpus = 192 max_time = 72.h partition = 'work1'}
validation.ignoreParams = ["work1"]
env.TMPDIR = "/local_scratch/slurm.${System.getenv('SLURM_JOBID')}"
cleanup = false
executor { queueSize = 256 pollInterval = '1 min' queueStatInterval = '5 min' submitRateLimit = '10 sec'}
// Set $NXF_SINGULARITY_CACHEDIR in your ~/.bashrc// to stop downloading the same image for every runsingularity { enabled = true autoMounts = true}
apptainer { autoMounts = true}
process { resourceLimits = [ cpus: params.max_cpus, memory: params.max_memory, time: params.max_time ] executor = 'slurm' queue = { params.partition }
scratch = true
maxRetries = 3 }
//// This profile will clean up your work directory after a// successful run, intermediate files will not consume storage space//// To activate: nextflow run <pipeline> -profile palmetto,cleanup//
profiles { cleanup { cleanup = true }}