All nf-core pipelines have been successfully configured for use on the Brain Image Libraryy (BIL) cluster at the Pittsburgh Supercomputing Center.
To use, run the pipeline with -profile brain. This will download and launch the brain.config which has been pre-configured with a setup suitable for the Brain Image Library (BIL) Analysis Ecosystem. 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.
Nextflow is not installed by default on the Brain Image Library Analysis Ecosystem.
- Install Nextflow : here
Nextflow manages each process as a separate job that is submitted to the cluster by using the sbatch command.
Nextflow shouldin't run directly on a login node but on a compute node.
- Run nextflow on a compute node with submit host capability:
# Run nextflow workflow
nextflow run \\
nf-core/chipseq \\
-resume \\
-profile test,brain