Myriad Configuration

All nf-core pipelines have been successfully configured for use on UCL's myriad cluster University College London.

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

Using Nextflow on Myriad

Before running the pipeline you will need to install and configure Nextflow and Singularity.


This can be done with the following commands:

## Load Singularity environment modules - these commands can be placed in your ~/.bashrc also  
module add java/openjdk-11/11.0.1  
module add singularity-env/1.0.0  

Then set the correct configuration of the cache directories, where <YOUR_ID> is replaced with you credentials which you can find by entering whoami into the terminal once you are logged into myriad. Once you have added your credentials save these lines into your .bashrc file in the base directory (e.g. /home/<YOUR_ID>/.bashrc):

# Set all the Singularity cache dirs to Scratch  
export SINGULARITY_CACHEDIR=/home/<YOUR_ID>/Scratch/.singularity/  
export SINGULARITY_TMPDIR=/home/<YOUR_ID>/Scratch/.singularity/tmp  
export SINGULARITY_LOCALCACHEDIR=/home/<YOUR_ID>/Scratch/.singularity/localcache  
export SINGULARITY_PULLFOLDER=/home/<YOUR_ID>/Scratch/.singularity/pull  
# Bind your Scratch directory so it is accessible from inside the container  
export SINGULARITY_BINDPATH=/scratch/scratch/<YOUR_ID>  


Download the latest release of nextflow. Warning: the self-update line should update to the latest version, but sometimes not, so please check which is the latest release (, you can then manually set this by entering (NXF_VER=XX.XX.X).

## Download Nextflow-all  
curl -s | bash  
nextflow -self-update  
chmod a+x nextflow  
mv nextflow ~/bin/nextflow  

Then make sure that your bin PATH is executable, by placing the following line in your .bashrc:

export PATH=$PATH:/home/<YOUR_ID>/bin  

Config file

See config file on GitHub

params {  
  config_profile_description = 'University College London Myriad cluster'  
  config_profile_contact = 'Chris Wyatt ('  
  config_profile_url = ''  
process {  
  penv = 'smp'  
params {  
  // Defaults only, expecting to be overwritten  
  max_memory = 128.GB  
  max_cpus = 36  
  max_time = 72.h  
  // igenomes_base = 's3://ngi-igenomes/igenomes/'  
// optional executor settings  
executor {  
  queueSize = 10  
  submitRateLimit = '1 sec'  
singularity {  
    enabled = true  
    autoMounts = true