Profiles

nf-gwas provides different execution profiles which can be specified with the -profile parameter.

nextflow run genepi/nf-gwas -r v1.X.X -profile test, <docker,singularity,development, slurm,slurm_with_scratch>.

Docker

For local runs, Docker is the easiest way to run the pipeline.

Singularity

For HPC clusters, we recommend to use Singularity. Singularity is also required for the Slurm profiles below.

Slurm

Nextflow supports Slurm as an execution engine. The profile slurm_with-scratch includes a directive to execute the process in a temporary folder that is local to the execution node (/tmp by default). You can change the default location by setting export NXF_TEMP=/your/path on the command line before executing the pipeline.

Development

The profile development can be used to e.g. test/adapt the code and e.g. create pull requests. This profile requires that the image must be available locally.

git clone https://github.com/genepi/nf-gwas
cd nf-gwas
docker build -t genepi/nf-gwas . # don't ignore the dot
nextflow run main.nf -profile test,development