Directories fail to publish via `>>` operator in cloud environments

Environment

Nextflow version: 26.04.6 (build 12646)
Java version: openjdk version "21.0.7" 2025-04-15 LTS
Operating system: Tested with macOS and Debian

Description

Publishing directories (e.g. path('somedir/')) via the >> operator (e.g. path { dir -> dir >> "somewhere_else/${dir.name}/" }) silently fails when running on cloud environments (in my case Google Cloud).

Individual files publish fine, e.g. path('*.txt').

The below sections are vibe-coded/tested. I made some manual edits to reduce slop.

Minimal reproduction

main.nf:

nextflow.enable.dsl=2

process MAKE_DIR {
    output:
    path('outdir/'), topic: my_dir

    script:
    """
    mkdir -p outdir
    echo hello > outdir/hello.txt
    echo world > outdir/world.txt
    """
}

workflow {
    main:
    MAKE_DIR()

    publish:
    results = channel.topic('my_dir')
}

output {
    results {
        path { dir -> dir >> "published/${dir.name}/" }
    }
}


// Note, this works:
// output {
//     results {
//         path 'published'
//     }
// }

Run with below example command. -work-dir should be cloud storage bucket. -output-dir can be a cloud storage bucket or local path.

nextflow run main.nf -work-dir gs://<bucket>/work -output-dir ./out

Expected outcome: ./out/published/outdir/hello.txt and ./out/published/outdir/world.txt exist
Actual outcome: ./out/published/ doesn't even get created. No error/warning in .nextflow.log or console

Workaround

The temporary solution I'm using is to publish the directory contents as individual files:

publish:
results = channel.topic('my_dir').flatMap { dir -> dir.listFiles() }

Suspected root cause

• file >> filepath builds a saveAs lookup map keyed by the file's path relative to its task dir (PublishDsl.publish0).
• For a directory, that key keeps its trailing slash: "outdir/".
• Before copying, PublishDir dedups all paths by round-tripping them through PathTrie (tokenize on /, rebuild).
• That round-trip silently drops trailing empty segments, so the directory path comes back as "outdir" — no slash.
• PublishDir looks up "outdir" in a map keyed "outdir/" → no match → null → silently skips publishing. No error, no warning, no directory created.
• Confirmed not a filesystem-provider issue: reproduces identically for gs:// workDir → local --outdir and gs:// workDir → gs:// --outdir.
• Only directory-shaped values are affected — individual files never carry a trailing slash.
• Confirmed scoped to the >> operator form only: plain path 'somedir' string directive has no saveAs map, no lookup, no bug — same directory publishes fine with it.

Reproduce the issue with the provided main.nf, a gs:// work directory, and local or cloud output. Read PublishDsl.publish0 in modules/nextflow/src/main/groovy/nextflow/extension/PublishOp.groovy and the PathTrie implementation, then trace the PublishDir lookup; done means the directory and both files appear under published/outdir without warnings.