Added experimental gpu directive for k8s runs, updated README.md

Author: bentsherman

README.md

@@ -29,3 +29,10 @@ To use Docker or Singularity, run nextflow with the `-with-docker` or `-with-sin
 ## Kubernetes
 
 You can run this pipeline, as well as any other nextflow pipeline, on a [Kubernetes](https://kubernetes.io/) cluster with minimal effort. Consult the [kube-runner](https://github.com/SystemsGenetics/kube-runner) repo for instructions.
+
+### Experimental GPU Support
+
+Nextflow provides experimental support for using GPUs on a Kubernetes cluster with the `gpu` directive. To use this feature, you must specify the appropriate version of Nextflow version when you run it:
+```bash
+NXF_VER=19.04.0-edge nextflow kuberun [...]
+```

nextflow.config

@@ -119,6 +119,8 @@ profiles {
 			withName:similarity_chunk {
 				cpus = { params.similarity.gpu ? "${params.similarity.threads}" : 1 }
 				memory = "8 GB"
+
+				gpu = { params.similarity.gpu ? 1 : 0 }
 			}
 			withName:similarity_mpi {
 				cpus = { params.similarity.gpu ? "${params.similarity.chunks * params.similarity.threads}" : "${params.similarity.chunks}" }