nextflow clean: Can't perform I/O on pseudo-directories

[nick-youngblut]

Bug report

nextflow clean $RUN_NAME -force -quiet

Error:

ERROR ~ Can't perform I/O on pseudo-directories (trailing slash): /BUCKET_NAME/RUN_NAME/24/0b221c571de08d4b5dcb7f9fcca4e1

Notes:

• I'm running nextflow clean directory after running nextflow run with the same run name.
• I'm running the nextflow clean on a GCP Cloud Run job

The working directory in the GCP bucket is not "cleaned".

Expected behavior and actual behavior

See above

Steps to reproduce the problem

See above

Program output

See above

Environment

• Nextflow version: 24.10.2
• Java version: 21.0.0
• Operating system: Linux
• Bash version: 5.1.16

[ynsoysa]

I have seen the exact same error after cleaning up few work directories on GCP using Nextflow version: 24.10.1 , was there any resolution?

Thank you

[bentsherman]

Can you try with 24.04? I'm wondering if it's a regression.

If not that, it may be that "directories" in GCS don't need to be deleted because they are just prefixes:

nextflow/modules/nextflow/src/main/groovy/nextflow/cli/CmdClean.groovy

Lines 266 to 279 in eae3411

	private static delete0(Path path, boolean dir) {
	try {
	log.trace "Deleting path [dir=$dir]: ${path.toUriString()}"
	Files.delete(path)
	return true
	}
	catch( IOException e ) {
	// kind of hack: directory deletion
	if( dir && path.scheme=='gs' && e instanceof NoSuchFileException )
	return true
	log.debug("Failed to remove path: ${path.toUriString()}", e)
	return false
	}
	}