Use a remote config in kuberun (#2781) [ci fast]

Signed-off-by: Lehmann-Fabian <fabian.lehmann@informatik.hu-berlin.de> Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
nextflow-io · Apr 14, 2022 · 5485b69 · 5485b69
1 parent 78f5c10
commit 5485b69
Show file tree

Hide file tree

Showing 3 changed files with 17 additions and 1 deletion.
diff --git a/docs/cli.rst b/docs/cli.rst
@@ -847,6 +847,10 @@ the :ref:`k8s-page` section.
 +---------------------------+-------------+--------------------------------------------------------------------------------+
 | -qs, -queue-size          |             | Max number of processes that can be executed in parallel by each executor.     |
 +---------------------------+-------------+--------------------------------------------------------------------------------+
+| -remoteConfig             |             | Add the specified file from the K8s cluster to configuration set.              |
++---------------------------+-------------+--------------------------------------------------------------------------------+
+| -remoteProfile            |             | Choose a configuration profile in the remoteConfig.                            |
++---------------------------+-------------+--------------------------------------------------------------------------------+
 | -resume                   |             | Execute the script using the cached results, useful to continue executions that|
 |                           |             | was stopped by an error.                                                       |
 +---------------------------+-------------+--------------------------------------------------------------------------------+

diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdKubeRun.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdKubeRun.groovy
@@ -53,6 +53,12 @@ class CmdKubeRun extends CmdRun {
     @Parameter(names = '-head-memory', description = 'Specify amount of memory requested for the Nextflow pod')
     String headMemory
 
+    @Parameter(names= '-remoteConfig', description = 'Add the specified file from the K8s cluster to configuration set', hidden = true )
+    List<String> runRemoteConfig
+
+    @Parameter(names=['-remoteProfile'], description = 'Choose a configuration profile in the remoteConfig')
+    String remoteProfile
+
 
     @Override
     String getName() { 'kuberun' }

diff --git a/modules/nextflow/src/main/groovy/nextflow/k8s/K8sDriverLauncher.groovy b/modules/nextflow/src/main/groovy/nextflow/k8s/K8sDriverLauncher.groovy
@@ -248,7 +248,7 @@ class K8sDriverLauncher {
                 .setProfile(cmd.profile)
                 .setCmdRun(cmd)
 
-        if( !interactive && !pipelineName.startsWith('/') ) {
+        if( !interactive && !pipelineName.startsWith('/') && !cmd.remoteProfile && !cmd.runRemoteConfig ) {
             // -- check and parse project remote config
             final pipelineConfig = new AssetManager(pipelineName, cmd) .getConfigFile()
             builder.setUserConfigFiles(pipelineConfig)
@@ -463,6 +463,12 @@ class K8sDriverLauncher {
             result << "-params-file $paramsFile"
         }
 
+        if ( cmd.runRemoteConfig )
+            cmd.runRemoteConfig.forEach { result << "-config $it" }
+
+        if ( cmd.remoteProfile )
+            result << "-profile ${cmd.remoteProfile}"
+
         if( cmd.process?.executor )
             abort('process.executor')