Weill Cornell Medicine Configuration

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.

Running the workflow on the Pasteur cluster

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.

  1. 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

Config file

See config file on GitHub

singularityDir = "/athena/elementolab/scratch/reference/.singularity/singularity_images_nextflow"
params {
    config_profile_description = 'Weill Cornell Medicine, Scientific Computing Unit Slurm cluster profile provided by nf-core/configs'
    config_profile_contact = 'Ashley Stephen Doane, PhD (@DoaneAS)'
    igenomes_base = '/athena/elementolab/scratch/reference/igenomes'
singularity {
    enabled = true
    cacheDir =  "/athena/elementolab/scratch/reference/.singularity/singularity_images_nextflow"
    autoMounts = true
process {
    executor = 'slurm'
    queue = 'panda_physbio'
    scratch = true
    scratch = '/scratchLocal/`whoami`_${SLURM_JOBID}'
params {
    max_memory = 32.GB
    max_cpus = 8
    max_time = 24.h