nf-gwas provides different execution profiles which can be specified with the
nextflow run genepi/nf-gwas -r v0.3.4 -profile test, <docker,singularity,development, slurm,slurm_with_scratch>.
For local runs, Docker is the easiest way to run the pipeline.
For HPC clusters, we recommend to use Singularity. Singularity is also required for the Slurm profiles below.
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 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