Templating for multiple envs/containers

nextflow.config

@@ -9,13 +9,6 @@
 //
 // for further help editing this file.
 
-
-process {
-    withLabel:containerCPU {
-        container = 'workflow-template:latest'
-    }
-}
-
 profiles {
     // the "standard" profile is used implicitely by nextflow
     // if no other profile is given on the CLI
@@ -26,6 +19,11 @@ profiles {
             //    also adds host user to the within-container group
             runOptions = "--user \$(id -u):\$(id -g) --group-add 100"
         }
+        process {
+            withLabel:default {
+                container = 'workflow-template:latest'
+            }
+        }
     }
 
     // profile using conda environments rather than docker
@@ -35,7 +33,9 @@ profiles {
             enabled = false
         }
         process {
-            conda = "environment.yaml"
+            withLabel:default {
+                conda = "environment.yaml"
+            }
         }
         conda {
              cacheDir = ""

workflow.nf

@@ -32,7 +32,7 @@ if(params.help) {
 
 process readSeqs {
     // Just write a file with sequence lengths
-    label "containerCPU"
+    label "default"
     input:
         file reads
     output: