All nf-core pipelines have been successfully configured for use on the panda cluster at the WCM.
To use, run the pipeline with -profile wcm. This will download and launch the wcm.config which has been pre-configured with a setup suitable for the WCM slurm 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.
Nextflow is not installed by default on the WCM cluster.
- Install Nextflow : here
Nextflow manages each process as a separate job that is submitted to the cluster by using the sbatch command.
Nextflow shouldn't run directly on a login node but on a compute node or lab-specific interactive server when configured as a submit host.
- Run nextflow on a compute node or interactive server with submit host capability:
# Run nextflow workflow
nextflow run \\
nf-core/chipseq \\
-resume \\
-profile test,wcm