Kubernetes process

conf/docker.config

@@ -0,0 +1,9 @@
+process {
+    if ( params.medaka || params.nanopolish ){
+        container = 'location of artic-ncov2019-artic container'
+    }
+
+    if ( params.illumina ){
+        container = 'location of artic-ncov2019-illumina container'
+    }   
+}

nextflow.config

@@ -38,11 +38,40 @@ profiles {
      }
      includeConfig 'conf/conda.config'
   }
+
   docker {
     docker.enabled = true
     fixOwnership = true
     runOptions = "-u \$(id -u):\$(id -g)"
+    docker.runOptions = '-u $(id -u):$(id -g)'
+    process.stageInMode = 'copy'
+    includeConfig 'conf/docker.config'
+    process.containerOptions = '--user root'
   }
+
+
+  k8s {
+
+    process {
+      executor = 'k8s'
+    }
+
+    k8s {
+      storageClaimName = ''
+      storageMountPath = ''
+    }
+
+    docker.enabled = true
+    fixOwnership = true
+    runOptions = "-u \$(id -u):\$(id -g)"
+    docker.runOptions = '-u $(id -u):$(id -g)'
+    //process.container = 'path to docker image'
+    process.stageInMode = 'copy'
+    includeConfig 'conf/docker.config'
+    process.containerOptions = '--user root'
+
+  }
+
   singularity {
     singularity.enabled = true 
     singularity.autoMounts = true