Containerize all processes

workflow/configs/biohpc.config

@@ -7,6 +7,9 @@ singularity {
 
 process {
     executor = 'local'
+    withName:parameters {
+        container = 'docker://ubuntu:latest'
+    }
     withName:uppercase {
         container = 'docker://ubuntu:latest'
     }

workflow/configs/biohpc_singularity_gitlab.config

 singularity {
   enabled = true
-  runOptions = '--bind /vagrant:/vagrant'
+  runOptions = '--disable-cache'                                // use this one for production
+  // runOptions = '--disable-cache --bind /vagrant:/vagrant'    // use this one for vagrant development env only
   cacheDir = "$baseDir/images/singularity"
 }