Dundee Configuration
The nf-core pipelines rnaseq and sarek have been successfully tested on the University of Dundee compute cluster.
To use, run the pipeline with -profile uod_hpc. This will download and launch the uod_hpc.config which has been pre-configured with a setup suitable for the Dundee cluster.
Using Nextflow on Dundee Cluster
Installation
Before running the pipeline you will need to install and configure Nextflow. You can do this by issuing the commands below:
# Create a Bioconda environment and install Nextflow
setup-miniconda-env /cluster/<group_name>/<your_directory>/nextflow-env
source "/cluster/<group_name>/<your_directory>/nextflow-env/bin/activate"
conda install -c bioconda nextflow
# Specify a cache directory in your /cluster space for Singularity containers
export NXF_SINGULARITY_CACHEDIR="/cluster/<group_name>/<your_directory>/nxf-singularity-cache"For convenience, append the export NXF_SINGULARITY_CACHEDIR and conda activation commands to your .bashrc file to avoid having to run both on each log-in or include both in every job script:
echo export NXF_SINGULARITY_CACHEDIR='"/cluster/<group_name>/<your_directory>/nxf-singularity-cache"' >> ~/.bashrc
echo source '"/cluster/<group_name>/<your_directory>/nextflow-env/bin/activate"' >> ~/.bashrcUsage
Create a job script containing your desired Nextflow command, always including -profile uod_hpc to ensure the correct cluster configuration is applied. For example:
nano myjobscript.shwith contents:
# NOTE: The following two lines should be omitted if they are already appended to your .bashrc
export NXF_SINGULARITY_CACHEDIR="/cluster/<group_name>/<your_directory>/nxf-singularity-cache"
source "/cluster/<group_name>/<your_directory>/nextflow-env/bin/activate"
nextflow run nf-core/sarek -profile uod_hpc -r 3.3.2 --input ./samplesheet.csv --outdir ./results ...<further parameters as required>...Submit the script using qsub:
qsub -cwd myjobscript.shStandard and error output for the job will be produced in .o and .e files, such as myjobscript.sh.o1400340 and myjobscript.sh.e1400340, as it runs.
You will need an account to use the HPC cluster in order to run the pipeline. If in doubt raise a support request with University of Dundee service desk.
Nextflow will need to submit the jobs via the job 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 raise a support request with University of Dundee service desk.
Config file
params {
config_profile_description = 'University of Dundee Compute Cluster'
config_profile_contact = 'Dominic Sloan-Murphy (dsloanmurphy001@dundee.ac.uk)'
config_profile_url = 'https://uod-hpc.readthedocs.io/en/latest/software/nextflow/'
}
process {
executor = 'sge'
penv = 'smp'
queue = 'all.q'
clusterOptions = '-jc nextflow'
}
executor {
max_memory = 128.GB
max_cpus = 24
max_time = 72.h
}
singularity {
enabled = true
autoMounts = true
}
executor
contact
