nf-configs/docs/wcm.md

# 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`](../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.

## Running the workflow on the Pasteur cluster

Nextflow is not installed by default on the WCM cluster.

- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)

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:

```bash
# Run nextflow workflow
nextflow run \\
nf-core/chipseq \\
-resume \\
-profile test,wcm
```
Create wcm.md 2021-03-11 18:59:55 +00:00			`# nf-core/configs: Weill Cornell Medicine Configuration`

			`All nf-core pipelines have been successfully configured for use on the panda cluster at the WCM.`

Update wcm.md 2021-03-11 19:01:07 +00:00			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.
Create wcm.md 2021-03-11 18:59:55 +00:00
			`## Running the workflow on the Pasteur cluster`

			`Nextflow is not installed by default on the WCM cluster.`

			`- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)`

			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:`

			```bash
			`# Run nextflow workflow`
			`nextflow run \\`
			`nf-core/chipseq \\`
			`-resume \\`
			`-profile test,wcm`
			```