Drop transient object tags when publishing files to S3

[pditommaso]

Problem

When Nextflow copies an S3 object from one bucket to another (e.g. publishDir), it was propagating the source object's tags to the destination.

By default Fusion tags all task outputs with nextflow.io/temporary=true (via fusion.tags) so intermediates can be reaped by a retention policy. Because these tags were carried over on publish, a retention policy on the output directory would also delete "permanent" published outputs.

Root cause

S3Client.copyFile() only set the REPLACE tagging directive when the publish target had explicit tags:

if( tags != null && !tags.isEmpty()) {
    reqBuilder.taggingDirective(TaggingDirective.REPLACE);
    reqBuilder.tagging(...);
}

With no tags the directive was left unset, so the S3 CopyObject API defaulted to COPY — inheriting the source object's tags on the destination.

Fix

Always set the REPLACE tagging directive so the destination gets exactly the requested tag set (empty = no tags) rather than inheriting source tags. Extracted into a testable applyTagging helper.

Test

Added a unit test in S3ClientTest verifying REPLACE is always used and tags are set only when provided.

Closes #7339

🤖 Generated with Claude Code

[netlify]

✅ Deploy Preview for nextflow-docs canceled.

Name	Link
🔨 Latest commit	cf1fdc8
🔍 Latest deploy log	https://app.netlify.com/projects/nextflow-docs/deploys/6a58878208720f0008f2b875

[jorgee]

I think it is the simplest case to solve the issue, and it is the correct behaviour for PublishDir. What I don't like about the solution is that it will apply to all s3-to-s3 copies done by Nextflow. Basically, it will only affect nextflow fs cp/mv commands because the file porter will not perform any s3-to-s3 copy because they are not considered foreign files.

So I see two options: we can keep the current code that removes tags infscommand and document this change; or add a new field in TagAwareFile to set the tagging directive (replace or not) and set it just in the PublishDir case.