Nextflow config update (autoMounts, envWhitelist)

doc/source/configuration.rst

@@ -125,6 +125,8 @@ The Nextflow configuration file is used to configure various settings for the *k
     singularity {
         enabled = true
         cacheDir = ''
+        autoMounts = true
+        envWhitelist = '' 
     }
     docker {
         enabled = false
@@ -150,6 +152,8 @@ The Nextflow configuration file is used to configure various settings for the *k
 
     * **enable** enables or disables the use of the respective container
     * **cacheDir** the directory where remote the Singularity image from Docker Hub is stored. When using a computing cluster it must be a shared folder accessible to all computing nodes.
+    * **autoMounts** automatically mounts host paths in the executed container
+    * **envWhitelist** accepts a comma separated list of environment variable names to be included in the container environment. Include 'NSLOTS' if working on a SGE cluster
 
 * The **executor.name** setting defines the system type or HPC scheduler to be used (e.g. ``sge``, ``local``)
 * The **process** scope defines the configuration for the processes of the *ksrates* pipeline:

doc/source/template_singularity_nextflow.config

@@ -6,6 +6,7 @@
 singularity {
     enabled = true
     cacheDir = ''               // set a directory where to download the container file
+    autoMounts = true           // to automatically mount host paths in the executed container
     // envWhitelist = 'NSLOTS'  // to be used when running the Singularity container on a SGE cluster
 }
 

example/custom_nextflow.config

@@ -5,8 +5,9 @@
 // CONTAINER SETTINGS:
 singularity {
     enabled = true
-    // envWhitelist = 'NSLOTS'  // to be used when running the Singularity container on a SGE cluster  
     // cacheDir = ''            // to set a directory where to download the container file 
+    autoMounts = true           // to automatically mount host paths in the executed container
+    // envWhitelist = 'NSLOTS'  // to be used when running the Singularity container on a SGE cluster  
 }
 // docker.enabled = true
 

test/custom_nextflow.config

@@ -5,8 +5,9 @@
 // CONTAINER SETTINGS:
 singularity {
     enabled = true
-    // envWhitelist = 'NSLOTS'  // to be used when running the Singularity container on a SGE cluster  
     // cacheDir = ''            // to set a directory where to download the container file 
+    autoMounts = true           // to automatically mount host paths in the executed container
+    // envWhitelist = 'NSLOTS'  // to be used when running the Singularity container on a SGE cluster  
 }
 // docker.enabled = true