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nf-core/configs: BlueBEAR HPC Configuration

Configuration for the BlueBEAR high performance computing (HPC) cluster at the University of Birmingham.

Setup

To run a Nextflow pipeline, load the following modules,

module load bear-apps/2022b
module load Nextflow/24.04.2

Apptainer/Singularity

BlueBEAR comes with Apptainer installed for running processes inside containers. Our configuration makes use of this when executing processes.

We advise you create a directory in which to cache images using the NXF_SINGULARITY_CACHEDIR environment variable. For example,

export NXF_SINGULARITY_CACHEDIR="/rds/projects/_initial_/_project_/.apptainer"

where _project_ is your project code and _initial_ is its initial letter. Edit and add the above line to the .bashrc file in your home directory. If this variable is not defined, Nextflow will store images in the pipeline working directory which is cleaned after each successful run.

You may notice that our nf-core configuration file enables Singularity, not Apptainer, for use with Nextflow. Due to their similarities (see this announcement), Apptainer creates the alias singularity for apptainer allowing both commands to be used. Nextflow's Singularity engine makes use of pre-built Singularity images, whereas its Apptainer engine does not.

Run

Do not run Nextflow pipelines on a login node. Instead, create a submission script or start an interactive job.

To run a Nextflow pipeline, specify the BlueBEAR profile option. For example,

nextflow run nf-core/_pipeline_ -profile bluebear --outdir results

where _pipeline_ is the name of the pipeline.

Make sure the job time requested is sufficient for running the full pipeline. If the job ends before the pipeline is complete, rerun it from a checkpoint using the -resume option. For example, run

nextflow run nf-core/_pipeline_ -profile bluebear --outdir results -resume

in a new job with more time requested.

Nextflow creates a working directory to store files while the pipeline is running. We have configured Nextflow to clean the contents of this directory after a successful run. The -resume option will only work after an unsuccessful run. If you want to keep the working directory contents, add the debug profile to your run command (e.g. -profile bluebear,debug).

Example

Here is an example job submission script. This job runs the nf-core/rnaseq pipeline tests with the BlueBEAR config file. We request 1 hour to run the pipeline on 1 node with 2 tasks.

#!/bin/bash
#SBATCH --account _project_
#SBATCH --qos bbdefault
#SBATCH --time 1:0:0
#SBATCH --nodes 1
#SBATCH --ntasks 2

set -e

module purge; module load bluebear
module load bear-apps/2022b
module load Nextflow/24.04.2

nextflow run nf-core/rnaseq -profile bluebear,test --outdir test_results

Troubleshooting

Failed while making image from oci registry

You may get an error which looks like the following,

FATAL: While making image from oci registry: error fetching image to cache: while building SIF from
layers: conveyor failed to get: while getting config: no descriptor found for reference
"139610e0c1955f333b61f10e6681e6c70c94357105e2ec6f486659dc61152a21"

This may be caused by an issue with parallel image downloads (see e.g. this issue). You can fix this by downloading all images required by the pipeline using nf-core tools to download the pipeline either interactively with

nf-core download _pipeline_ -o /path/to/outdir --container-system singularity --container-cache-utilisation amend

or in a Slurm job.

Note: nf-core tools is a Python package which needs to be installed first.

Here is an example Slurm job script which downloads version 3.14.0 of the nf-core/rnaseq pipeline.

#!/bin/bash
#SBATCH --account _project_
#SBATCH --qos bbdefault
#SBATCH --time 30
#SBATCH --nodes 1
#SBATCH --ntasks 2

set -e  # exit on first error

module purge; module load bluebear
module load bear-apps/2022b
module load Nextflow/24.04.2
module load Python/3.10.8-GCCcore-12.2.0

# Path to Python virtual environment with nf-core tools
VENV_DIR="/path/to/virtual/environments"
VENV_PATH="${VENV_DIR}/nf-core-${BB_CPU}"

# Check if base virtual environment directory exists and create it if not
if [[ ! -d ${VENV_DIR} ]]; then
    mkdir -p ${VENV_DIR}
fi

# Check if virtual environment exists and create it if not
if [[ ! -d ${VENV_PATH} ]]; then
    python3 -m venv ${VENV_PATH}
    ${VENV_PATH}/bin/python3 -m pip install --upgrade pip
    ${VENV_PATH}/bin/python3 -m pip install nf-core
fi

# Activate virtual environment
source ${VENV_PATH}/bin/activate

# Run nf-core download tool to fetch pipeline and pull apptainer/singularity images
# You must specify the pipeline revision/branch
nf-core download rnaseq -r 3.14.0 -o /path/to/outdir -d -x none \
--container-system singularity --container-cache-utilisation amend

Then, you can update the final line in the example script with the path to the locally downloaded pipeline.

nextflow run /path/to/outdir/3_14_0 -profile bluebear,test --outdir test_results

Note: Make sure that the NXF_SINGULARITY_CACHEDIR environment variable defined (e.g. in your .bashrc file) and takes the same value when downloading and running the pipeline.