Fix unstage controls in command.run when using storeDir#6364
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pditommaso merged 6 commits intomasterfrom Sep 24, 2025
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Fix unstage controls in command.run when using storeDir#6364pditommaso merged 6 commits intomasterfrom
pditommaso merged 6 commits intomasterfrom
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Signed-off-by: jorgee <jorge.ejarque@seqera.io>
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Signed-off-by: jorgee <jorge.ejarque@seqera.io>
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modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
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plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchScriptLauncher.groovy
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Signed-off-by: jorgee <jorge.ejarque@seqera.io>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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…6364) Signed-off-by: jorgee <jorge.ejarque@seqera.io> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Signed-off-by: Emma Rogge <emmarogge@verily.health>
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close #6311
unstage_controlswas set in .command.runusing the same condition as inunstage_outputs. It was producing an "are the same file" error message in.command.logwhen using thestoreDir.By default
targetDiris set to the working directory, but when user defines astoreDir, thetargetDiris set tostoreDir. The conditionshouldUnstageOutputschecks iftargetDiris different from the working directory, and the fucntion to generate theunstage_outputscreate the commands to copy the outputs totargetDir. However, control logs (.command.err, .command.out, .command.trace and .command.env) are always copied to the working directory using the functioncopyFileToWorkDir. For this reason, the same condition cannot be applied.This PR changes the condition when the
unstage_controlsis set. A new methodshouldUnstageControlsis created to differentiate the condition when checking the outputs or controls. By default, it is set to false, the unstage controls will be applied if scratch is defined. There is a special case for Azure, where both controls and outputs are forced to be unstaged