Fixed K8s launcher fails to set pod work directory

The workflow execution work directory may be created by the pod itself by the init script. Therefore it should not be set as pod work directory otherwise the pod creation fails if it does not exist.
nextflow-io · Nov 14, 2018 · dc8bfea · dc8bfea
1 parent 697efff
commit dc8bfea
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/src/main/groovy/nextflow/k8s/K8sDriverLauncher.groovy b/src/main/groovy/nextflow/k8s/K8sDriverLauncher.groovy
@@ -386,11 +386,11 @@ class K8sDriverLauncher {
         // -- setup config file
         String cmd = "source /etc/nextflow/init.sh; ${getLaunchCli()}"
 
+        // create the launcher pod
         new PodSpecBuilder()
             .withPodName(runName)
             .withImageName(k8sConfig.getNextflowImageName())
             .withCommand(['/bin/bash', '-c', cmd])
-            .withWorkDir(k8sConfig.getLaunchDir())
             .withLabels([ app: 'nextflow', runName: runName ])
             .withNamespace(k8sClient.config.namespace)
             .withServiceAccount(k8sClient.config.serviceAccount)
@@ -399,6 +399,8 @@ class K8sDriverLauncher {
             .withEnv( PodEnv.value('NXF_ASSETS', k8sConfig.getProjectDir()) )
             .withEnv( PodEnv.value('NXF_EXECUTOR', 'k8s'))
             .build()
+
+        // note: do *not* set the work directory because it may need to be created  by the init script
     }
 
     /**

diff --git a/src/test/groovy/nextflow/k8s/K8sDriverLauncherTest.groovy b/src/test/groovy/nextflow/k8s/K8sDriverLauncherTest.groovy
@@ -163,7 +163,6 @@ class K8sDriverLauncherTest extends Specification {
                                 [name:'foo-boo',
                                  image:'the-image',
                                  command:['/bin/bash', '-c', "source /etc/nextflow/init.sh; nextflow run foo"],
-                                 workingDir: '/the/user/dir',
                                  env:[
                                          [name:'NXF_WORK', value:'/the/work/dir'],
                                          [name:'NXF_ASSETS', value:'/the/project/dir'],