wustl_htcf.md

nf-core/configs: WUSTL High Throughput Computing Facility Configuration

Forked from the prince configuration.

nf-core pipelines that use this repo

All nf-core pipelines that use this config repo (which is most), can be run on the HTCF. Before running a pipeline for the first time, go into an interactive slurm session on a compute node (srun --pty --time=02:00:00 -c 2), as the docker images for the pipeline will need to be pulled and converted.

Now, run the pipeline of your choice with -profile wustl_htcf. This will download and launch wustl_htcf.config which has been pre-configured with a setup suitable for the HTCF 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. This step takes time!! An example commandline:

nextflow run nf-core/<pipeline name> -profile wustl_htcf <additional flags>

nf-core pipelines that do not use this repo

If the pipeline has not yet been configured to use the nf-core/configs repository, then you will have to do it manually. Add the following lines to the end of the pipeline's nextflow.config

// Allow the use of nf-core/configs configuration files
includeConfig "https://raw.githubusercontent.com/nf-core/configs/master/nfcore_custom.config"