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24 lines
1.1 KiB
Markdown
24 lines
1.1 KiB
Markdown
# nf-core/configs: Weill Cornell Medicine Configuration
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All nf-core pipelines have been successfully configured for use on the panda cluster at the WCM.
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To use, run the pipeline with `-profile wcm`. This will download and launch the [`wcm.config`](../conf/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.
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## Running the workflow on the Pasteur cluster
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Nextflow is not installed by default on the WCM cluster.
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- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)
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Nextflow manages each process as a separate job that is submitted to the cluster by using the `sbatch` command.
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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.
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1. Run nextflow on a compute node or interactive server with submit host capability:
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```bash
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# Run nextflow workflow
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nextflow run \\
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nf-core/chipseq \\
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-resume \\
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-profile test,wcm
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```
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