oist.md

nf-core/configs: 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
ml Other/Nextflow

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

NB: Nextflow will submit the jobs via the SLURM scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT.