1
0
Fork 0
mirror of https://github.com/MillironX/nf-configs.git synced 2024-11-24 17:19:54 +00:00

Create wcm.md

This commit is contained in:
Ashley S Doane 2021-03-11 13:59:55 -05:00 committed by GitHub
parent e7f8189dfc
commit d630bcfb6c
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23

24
docs/wcm.md Normal file
View file

@ -0,0 +1,24 @@
# 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 Pasteur 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
```