Nextflow config update (autoMounts, envWhitelist)

doc/source/configuration.rst

@@ -125,9 +125,12 @@ The Nextflow configuration file is used to configure various settings for the *k
     singularity {
         enabled = true
         cacheDir = ''
+        autoMounts = true
+        envWhitelist = '' 
     }
     docker {
         enabled = false
+        envWhitelist = '' 
     }
 
     executor.name = ''
@@ -149,7 +152,9 @@ The Nextflow configuration file is used to configure various settings for the *k
 * The **singularity** and **docker** scopes configure container type usage and execution:
 
     * **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.
+    * **cacheDir** (only for Singularity) 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** (only for Singularity) automatically mounts host paths in the executed container and allows the user to run the pipeline from any directory in a cluster [Default: true]. It requires the `user bind control <https://sylabs.io/guides/3.7/admin-guide/configfiles.html?highlight=user%20bind%20control#bind-mount-management>`__ feature in Singularity installation, which is active by default.
+    * **envWhitelist** accepts a comma separated list of environment variable names to be included in the container environment. If working on a SGE cluster, please include the ``NSLOTS`` variable (defining the number of cores/processes/slots), since it is used in the Nextflow pipeline.
 
 * 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/installation.rst

@@ -36,6 +36,9 @@ The machine where *ksrates* will be executed (either local computer or remote co
 For Linux installation we suggest to follow the *Install from Source* `section <https://sylabs.io/guides/3.7/admin-guide/installation.html#before-you-begin>`__ (*Install Dependencies*, *Install Go*, *Download Singularity from a release* and *Compile Singularity*).
 For up-to-date and version-specific instructions, please refer to this `page <https://sylabs.io/docs/>`__.
 
+.. note::
+   To allow users to run the pipeline from any directory in a cluster (i.e. not necessarily from their home directory), the `user bind control <https://sylabs.io/guides/3.7/admin-guide/configfiles.html?highlight=user%20bind%20control#bind-mount-management>`__ feature needs to be left active during Singularity installation [Default: "YES"].
+
 When using the *ksrates* Nextflow pipeline, the only other dependency that must be installed is Nextflow (for more information see its official installation `page <https://www.nextflow.io/docs/latest/getstarted.html#requirements>`__).
 
 *   First install Java 8 or later. ``default-djk`` works as well::

doc/source/template_docker_nextflow.config

@@ -3,8 +3,10 @@
 
 
 // CONTAINER SETTINGS:
-docker.enabled = true
-
+docker {
+    enabled = true
+    // envWhitelist = 'NSLOTS'  // to define the number of cores when running the container on a SGE cluster
+}
 
 // CLUSTER SETTINGS:
 executor.name = ''  // set cluster type, e.g. sge
@@ -16,23 +18,23 @@ process {
     // Specify memory and number of threads for processes submitted to the cluster 
     // It is advised to provide higher computational power to wgdParalogs and wgdOrthologs 
     withName: 'wgdParalogs' {
-        clusterOptions =  ''  // e.g. '-pe serial 10 -l h_vmem=2G'
+        clusterOptions = ''  // e.g. '-pe serial 10 -l h_vmem=2G'
     }
 
     withName: 'wgdOrthologs' {
-        clusterOptions = ''   // e.g. '-pe serial 10 -l h_vmem=2G'
+        clusterOptions = ''  // e.g. '-pe serial 10 -l h_vmem=2G'
     }
 
     withName: 'estimatePeak' {
-        clusterOptions =  ''  // e.g. '-pe serial 5 -l h_vmem=2G'
+        clusterOptions = ''  // e.g. '-l h_vmem=2G'
     }
 
     withName: 'paralogsAnalyses' {
-        clusterOptions =  ''  // e.g. '-pe serial 5 -l h_vmem=2G'
+        clusterOptions = ''  // e.g. '-l h_vmem=2G'
     }
 
     withName: 'plotOrthologDistrib' {
-        clusterOptions =  ''  // e.g. '-pe serial 5 -l h_vmem=2G'
+        clusterOptions = ''  // e.g. '-l h_vmem=2G'
     }
 }
 

doc/source/template_nocontainer_nextflow.config

@@ -22,17 +22,17 @@ process {
     }
 
     withName: 'estimatePeak' {
-        clusterOptions = ''  // e.g. '-pe serial 5 -l h_vmem=2G'
+        clusterOptions = ''  // e.g. '-l h_vmem=2G'
         beforeScript = ''    // e.g. 'module load python'
     }
 
     withName: 'paralogsAnalyses' {
-        clusterOptions = ''  // e.g. '-pe serial 5 -l h_vmem=2G'
+        clusterOptions = ''  // e.g. '-l h_vmem=2G'
         beforeScript = ''    // e.g. 'module load python'
     }
 
     withName: 'plotOrthologDistrib' {
-        clusterOptions = ''  // e.g. '-pe serial 5 -l h_vmem=2G'
+        clusterOptions = ''  // e.g. '-l h_vmem=2G'
         beforeScript = ''    // e.g. 'module load python'
     }
 }

doc/source/template_singularity_nextflow.config

@@ -6,7 +6,8 @@
 singularity {
     enabled = true
     cacheDir = ''               // set a directory where to download the container file
-    // envWhitelist = 'NSLOTS'  // to be used when running the Singularity container on a SGE cluster
+    autoMounts = true           // to automatically mount host paths in the executed container
+    // envWhitelist = 'NSLOTS'  // to define the number of cores when running the container on a SGE cluster
 }
 
 // CLUSTER SETTINGS:
@@ -26,15 +27,15 @@ process {
     }
 
     withName: 'estimatePeak' {
-        clusterOptions = ''  // e.g. '-pe serial 5 -l h_vmem=2G'
+        clusterOptions = ''  // e.g. '-l h_vmem=2G'
     }
 
     withName: 'paralogsAnalyses' {
-        clusterOptions = ''  // e.g. '-pe serial 5 -l h_vmem=2G'
+        clusterOptions = ''  // e.g. '-l h_vmem=2G'
     }
 
     withName: 'plotOrthologDistrib' {
-        clusterOptions = ''  // e.g. '-pe serial 5 -l h_vmem=2G'
+        clusterOptions = ''  // e.g. '-l h_vmem=2G'
     }
 }
 

example/custom_nextflow.config

@@ -5,11 +5,14 @@
 // 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 define the number of cores when running the container on a SGE cluster
 }
-// docker.enabled = true
-
+//docker {
+//    enabled = true
+//    // envWhitelist = 'NSLOTS'  // to define the number of cores when running the container on a SGE cluster
+//}
 
 // CLUSTER SETTINGS:
 executor.name = ''  // e.g. sge
@@ -30,15 +33,15 @@ process {
     }
 
     withName: 'estimatePeak' {
-        clusterOptions = ''  // e.g. '-pe serial 5 -l h_vmem=2G'
+        clusterOptions = ''  // e.g. '-l h_vmem=2G'
     }
 
     withName: 'paralogsAnalyses' {
-        clusterOptions = ''  // e.g. '-pe serial 5 -l h_vmem=2G'
+        clusterOptions = ''  // e.g. '-l h_vmem=2G'
     }
 
     withName: 'plotOrthologDistrib' {
-        clusterOptions = ''  // e.g. '-pe serial 5 -l h_vmem=2G'
+        clusterOptions = ''  // e.g. '-l h_vmem=2G'
     }
 }
 

test/custom_nextflow.config

@@ -5,11 +5,14 @@
 // 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 define the number of cores when running the container on a SGE cluster
 }
-// docker.enabled = true
-
+//docker {
+//    enabled = true
+//    // envWhitelist = 'NSLOTS'  // to define the number of cores when running the container on a SGE cluster
+//}
 
 // CLUSTER SETTINGS:
 executor.name = ''  // e.g. sge
@@ -22,23 +25,23 @@ process {
     // Specify memory and number of threads for processes submitted to the cluster 
     // It is advised to provide higher computational power to wgdParalogs and wgdOrthologs 
     withName: 'wgdParalogs' {
-        clusterOptions =   // e.g. '-pe serial 10 -l h_vmem=2G'
+        clusterOptions = ''  // e.g. '-pe serial 10 -l h_vmem=2G'
     }
 
     withName: 'wgdOrthologs' {
-        clusterOptions =   // e.g. '-pe serial 10 -l h_vmem=2G'
+        clusterOptions = ''  // e.g. '-pe serial 10 -l h_vmem=2G'
     }
 
     withName: 'estimatePeak' {
-        clusterOptions =   // e.g. '-pe serial 5 -l h_vmem=2G'
+        clusterOptions = ''  // e.g. '-l h_vmem=2G'
     }
 
     withName: 'paralogsAnalyses' {
-        clusterOptions =   // e.g. '-pe serial 5 -l h_vmem=2G'
+        clusterOptions = ''  // e.g. '-l h_vmem=2G'
     }
 
     withName: 'plotOrthologDistrib' {
-        clusterOptions =   // e.g. '-pe serial 5 -l h_vmem=2G'
+        clusterOptions = ''  // e.g. '-l h_vmem=2G'
     }
 }