LSF Cluster

To run the pipeline on a compute cluster, Singularity must be installed on all the cluster nodes you are using. Singularity is a popular HPC containerization tool, so many institutional clusters already support it. If not, ask your system administrator to install it.

To run on an IBM Platform LSF cluster, simply specify the lsf profile:

./ -profile lsf

You can also set arbitrary bsub flags with the lsf_opts parameter, for example:

./ -profile lsf --lsf_opts "-P project_code" [arguments]

The lsf profile is optimized for Janelia’s compute cluster and may need modifications to run elsewhere. You can find it in the nextflow.config file.

Usage examples are available in the examples directory.