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Fix Azure startTask command concatenation #6305

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Merged
merged 2 commits into from
Aug 14, 2025
Merged

Fix Azure startTask command concatenation #6305

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03b0501
Fix Azure Batch startTask concatenation issue (#6300)
adamrtalbot Jul 23, 2025
1083648
Merge branch 'master' into fix-azure-starttask-concatenation
pditommaso Aug 14, 2025
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2 changes: 1 addition & 1 deletion plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -835,7 +835,7 @@ class AzBatchService implements Closeable {
}

// otherwise return a StartTask object with the start task command and resource files
return new BatchStartTask(startCmd.join('; '))
return new BatchStartTask(startCmd.join(' && '))
.setResourceFiles(resourceFiles)
.setUserIdentity(userIdentity(opts.privileged, null, AutoUserScope.POOL))
}
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2 changes: 1 addition & 1 deletion plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchServiceTest.groovy
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Expand Up @@ -308,7 +308,7 @@ class AzBatchServiceTest extends Specification {
when:
def configuredStartTask = svc.createStartTask( new AzStartTaskOpts(script: 'echo hello-world') )
then:
configuredStartTask.commandLine == 'bash -c "chmod +x azcopy && mkdir $AZ_BATCH_NODE_SHARED_DIR/bin/ && cp azcopy $AZ_BATCH_NODE_SHARED_DIR/bin/"; bash -c \'echo hello-world\''
configuredStartTask.commandLine == 'bash -c "chmod +x azcopy && mkdir $AZ_BATCH_NODE_SHARED_DIR/bin/ && cp azcopy $AZ_BATCH_NODE_SHARED_DIR/bin/" && bash -c \'echo hello-world\''
and:
configuredStartTask.resourceFiles.size()==1
configuredStartTask.resourceFiles.first().filePath == 'azcopy'
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