"cleanup" option does not remove staged files from S3

[stevekm]

Bug report

When using Nextflow with the cleanup = true option, input files staged from S3 are left in the work dir.

Expected behavior and actual behavior

In order to automatically clean up the work directory after a successful pipeline run, I was hoping that the cleanup option described here might also remove the S3 input files that were staged during pipeline execution. This does not seem to be the case and the files remain in the work dir under a path such as work/stage-xyz

You can reproduce this by running a pipeline with input files on S3, and include the option cleanup = true in your nextflow.config file. The contents of the task work dirs are removed but the staged files remain.

Environment

• Nextflow version: 24.04.2
• Java version: openjdk version "17.0.10" 2024-01-16 LTS
• Operating system: Ubuntu 22.04

Additional context

Not sure if this is intentional?