Mana (at University of Hawaii at Manoa) Configuration

To use, run the pipeline with -profile mana. It will use the following parameters for Mana (UHM HPCC):

  • Load singularity and use it as default container technology
  • Setup a container cache directory in your home (~/.singularity_images_cache)
  • Select appropriate queues (currently: shared,exclusive,kill-shared,kill-exclusive)
  • Set the maximum available resources (available in 09/02/2022):
    • CPUs: 96
    • Memory: 400.GB
    • Time: 72.h


In order to run a nf-core pipeline on Mana, you will need to setup nextflow in your environment.
At the moment, nextflow is not available as a module (but might be in the future).

Install nextflow in a conda environment

Before we start, we will need to work on an interactive node (currently, mana doesn't let you execute any program in the login node):

# Request an interactive sandbox node for 30 min  
srun --pty -t 30 -p sandbox /bin/bash  

To setup nextflow on your account, follow these steps.

# Load the latest anaconda3 module  
module load lang/Anaconda3/2022.05  
# Initialize environment  
. $(conda info --base)/etc/profile.d/  
# Install nextflow (here in base environment, but you can create a new one if you'd like)  
conda install -c bioconda nextflow  

If you want these settings to be persistent, you can add the first 2 commands in your .bash_profile file like this:

echo "module load lang/Anaconda3/2022.05" >> ~/.bash_profile  
echo "$(conda info --base)/etc/profile.d/" >> ~/.bash_profile  

Config file

See config file on GitHub

params {  
  config_profile_description = 'University of Hawaii at Manoa'  
  config_profile_url = ''  
  config_profile_contact = 'Cedric Arisdakessian'  
  max_memory = 400.GB  
  max_cpus = 96  
  max_time = 72.h  
process {  
  executor = 'slurm'  
  queue = 'shared,exclusive,kill-shared,kill-exclusive'  
  module = 'tools/Singularity'  
singularity {  
  enabled = true  
  cacheDir = "$HOME/.singularity_images_cache"  
  autoMounts = true