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Add .command.log redirection in K8s container command when Fusion is not enabled #6455

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Merged
merged 2 commits into from
Oct 21, 2025
Merged

Add .command.log redirection in K8s container command when Fusion is not enabled #6455

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2765d4a
redirect .command.run output to .command.log when fusion is not enabled
jorgee Oct 7, 2025
1fed07f
revert savePodLogOnError remove
jorgee Oct 14, 2025
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5 changes: 4 additions & 1 deletion plugins/nf-k8s/src/main/nextflow/k8s/K8sTaskHandler.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -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
}

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8 changes: 4 additions & 4 deletions plugins/nf-k8s/src/test/nextflow/k8s/K8sTaskHandlerTest.groovy
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Expand Up @@ -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']
]]
]
]
Expand All @@ -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'] ]

Expand All @@ -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'] ]

}
Expand Down Expand Up @@ -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']
]]
]
]
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