OIST Configuration

The nf-core pipelines rnaseq and eager have been successfully tested on the Deigo cluster at the Okinawa Institute of Science and Technology Graduate University (OIST). We have no reason to expect that other pipelines would not work.

To use, run the pipeline with -profile oist. This will download and launch the oist.config which has been pre-configured with a setup suitable for Deigo. 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.

Below are non-mandatory information e.g. on modules to load etc

Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on Deigo. You can do this by issuing the commands below:

## Load the latest Nextflow and Singularity environment modules
ml purge
ml bioinfo-ugrp-modules Nextflow2

If you run a nf-core pipeline via the nf-core tool, the following command will load all the modules you need.

ml bioinfo-ugrp-modules nf-core

NB: You will need an account to use the Deigo cluster in order to run the pipeline. If in doubt contact SCDA.

NB: Nextflow submits the jobs via the SLURM scheduler to the compute nodes. You can run the nextflow or nf-core commands on the login nodes, but pay attention that the Nextflow work directory must be on the /flash file system.

Config file

See config file on GitHub

//Profile config names for nf-core/configs
params {
    config_profile_description = 'The Okinawa Institute of Science and Technology Graduate University (OIST) HPC cluster profile provided by nf-core/configs.'
    config_profile_contact = 'OISTs Bioinformatics User Group <BioinfoUgrp@oist.jp>'
    config_profile_url = 'https://github.com/nf-core/configs/blob/master/docs/oist.md'
singularity {
    enabled = true
process {
    executor = 'slurm'
    queue = 'compute'
    clusterOptions = '-C zen2'
params {
    max_memory = 500.GB
    max_cpus = 128
    max_time = 90.h