nf-core/configs: wcm
Weill Cornell Medicine, Scientific Computing Unit Slurm cluster profile
nf-core/configs: 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.
- 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
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 envWhitelist = 'SINGULARITY_BINDPATH' cacheDir = "/athena/elementolab/scratch/reference/.singularity/singularity_images_nextflow" autoMounts = true}
process { resourceLimits = [ memory: 32.GB, cpus: 8, time: 24.h ] executor = 'slurm' queue = 'panda_physbio' scratch = true scratch = '/scratchLocal/`whoami`_${SLURM_JOBID}'}
params { max_memory = 32.GB max_cpus = 8 max_time = 24.h}