Add .command.log redirection in K8s container command (#6455) [ci fast]

Signed-off-by: jorgee <[email protected]>

Author: jorgee

plugins/nf-k8s/src/main/nextflow/k8s/K8sTaskHandler.groovy

@@ -148,8 +148,11 @@ class K8sTaskHandler extends TaskHandler implements FusionAwareTask {
     }
 
     protected List<String> classicSubmitCli(TaskRun task) {
+        final workDir = Escape.path(task.workDir)
+
         final result = new ArrayList(BashWrapperBuilder.BASH)
-        result.add("${Escape.path(task.workDir)}/${TaskRun.CMD_RUN}".toString())
+        result.add('-c')
+        result.add("bash ${workDir}/${TaskRun.CMD_RUN} 2>&1 | tee ${workDir}/${TaskRun.CMD_LOG}")
         return result
     }
 

plugins/nf-k8s/src/test/nextflow/k8s/K8sTaskHandlerTest.groovy

@@ -96,7 +96,7 @@ class K8sTaskHandlerTest extends Specification {
                 containers: [[
                     name:'nf-123',
                     image:'debian:latest',
-                    args:['/bin/bash', '-ue','/some/work/dir/.command.run']
+                    args:['/bin/bash', '-ue','-c','bash /some/work/dir/.command.run 2>&1 | tee /some/work/dir/.command.log']
                 ]]
             ]
         ]
@@ -123,7 +123,7 @@ class K8sTaskHandlerTest extends Specification {
         and:
         result.metadata.labels == [sessionId: 'xxx']
         result.metadata.annotations == [evict: 'false']
-        result.spec.containers[0].command == ['/bin/bash', '-ue', '/some/work/dir/.command.run']
+        result.spec.containers[0].command == ['/bin/bash', '-ue', '-c','bash /some/work/dir/.command.run 2>&1 | tee /some/work/dir/.command.log']
         result.spec.containers[0].resources == [ requests: [cpu:1] ]
         result.spec.containers[0].env == [ [name:'NXF_OWNER', value:'501:502'] ]
 
@@ -148,7 +148,7 @@ class K8sTaskHandlerTest extends Specification {
         and:
         result.metadata.namespace == 'namespace-x'
         result.spec.containers[0].image == 'user/alpine:1.0'
-        result.spec.containers[0].command == ['/bin/bash', '-ue', '/some/work/dir/.command.run']
+        result.spec.containers[0].command == ['/bin/bash', '-ue', '-c','bash /some/work/dir/.command.run 2>&1 | tee /some/work/dir/.command.log']
         result.spec.containers[0].resources == [ requests: [cpu:4, memory:'16384Mi'], limits: [memory:'16384Mi'] ]
 
     }
@@ -428,7 +428,7 @@ class K8sTaskHandlerTest extends Specification {
                         containers: [[
                             name: 'nf-123',
                             image: 'debian:latest',
-                            command: ['/bin/bash', '-ue','/some/work/dir/.command.run']
+                            command: ['/bin/bash', '-ue','-c','bash /some/work/dir/.command.run 2>&1 | tee /some/work/dir/.command.log']
                         ]]
                     ]
                 ]