UCD Sonic Configuration

The nf-core pipeline sarek has been successfully tested on [Sonic HPC] (https://www.ucd.ie/itservices/ourservices/researchit/researchcomputing/sonichpc) using this config.

This Sonic config offers very minimal options to users but should allow the use of all nf-core pipelines.


To run a pipeline, you can optionally use the sbatch_nxf_creator method.

This allows you to write a YAML file including all of your sample names that you want to process individually, as well as your basic Nextflow command and where the output should be written.

There are some additional requirements on Sonic based on its use of SLURM which are resolved using this write this method.

The sbatch_nxf_creator.sh parses your YAML and makes an sbatch file that can be submitted to the scheduler via a simple sbatch my_file.sbatch command.

Practically, it means appending srun to the command and appending -with-mpi, as well as a few other vaguaries like specifying output and loading Nextflow and Singularity.

Config file

See config file on GitHub

params {
    config_profile_name = 'UCD_SONIC'
    config_profile_description = 'University College Dublin Sonic HPC profile provided by nf-core/configs.'
    config_profile_contact = 'Bruce Moran (@brucemoran)'
    config_profile_url = 'https://www.ucd.ie/itservices/ourservices/researchit/researchcomputing/sonichpc/'
    max_cpus = 40
    max_time = 12.h
process {
    executor = 'slurm'
    queue = 'shared'
    queueSize = 50
    submitRateLimit = '10 sec'
    maxRetries = 2
    beforeScript = 'export NXF_OPTS="-Xms2G -Xmx40G"; module load nextflow/ singularity/3.5.2'
    clusterOptions = { "--mem 1M" }
    cache = 'lenient'
    memory = 1.MB
cleanup = true