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nf-configs/docs/wcm.md
Ashley S Doane 6343a7f87c
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2021-03-11 14:01:07 -05:00

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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.

  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