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Allow to skip PublishDir #11

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Merged
Lehmann-Fabian merged 1 commit into from
Jun 2, 2025
Merged

Allow to skip PublishDir #11

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7 changes: 7 additions & 0 deletions plugins/nf-cws/src/main/nextflow/cws/processor/CWSTaskPollingMonitor.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -66,6 +66,12 @@ class CWSTaskPollingMonitor extends TaskPollingMonitor {
return pendingTasks
}

private static removePublishDirIfSkipEnabled( TaskHandler handler ) {
if( handler.task.config.get('skipPublishDir') ) {
handler.task.config.put('publishDir', null)
}
}

private static void checkPublishDirMode(TaskHandler handler ) {
def publishDirs = handler.task.config.get('publishDir')
if ( publishDirs && publishDirs instanceof List ) {
Expand Down Expand Up @@ -95,6 +101,7 @@ class CWSTaskPollingMonitor extends TaskPollingMonitor {
OfflineLocalPath path = new WorkdirPath( workDir, attributes, workDir, helper )
handler.task.workDir = path
}
removePublishDirIfSkipEnabled(handler)
checkPublishDirMode(handler)
super.finalizeTask(handler)
helper?.validate()
Expand Down