Description

The listFiles() method on Path objects does not follow symbolic links, causing it to fail to locate files when:

1. The directory itself is a symlink
2. Files within the directory are symlinks

Root Cause

In modules/nf-commons/src/main/nextflow/extension/FilesEx.groovy, the listFiles0 method uses Files.walkFileTree() without specifying FileVisitOption.FOLLOW_LINKS:

private static Collection<Path> listFiles0(Path self, Closure<Boolean> filter=null) {
    if( !self.isDirectory() )
        return null

    final result = []
    Files.walkFileTree(self, new SimpleFileVisitor<Path>() {
        // ...
    })
    return result
}

By default, walkFileTree does not follow symbolic links. This is inconsistent with isDirectory() which does follow symlinks by default.

Workaround Limitation

A suggested workaround is to use toRealPath() to resolve symlinks before calling listFiles():

dir.toRealPath().listFiles()

However, this does not work for cloud storage (S3, Azure, GCS) because:

• S3: toRealPath() throws UnsupportedOperationException
• Azure: toRealPath() just returns toAbsolutePath() (no symlink resolution)
• GCS: Depends on Google's library implementation

Proposed Fix

Add FileVisitOption.FOLLOW_LINKS to the walkFileTree call:

import java.nio.file.FileVisitOption

private static Collection<Path> listFiles0(Path self, Closure<Boolean> filter=null) {
    if( !self.isDirectory() )
        return null

    final result = []
    final walkOptions = EnumSet.of(FileVisitOption.FOLLOW_LINKS)
    
    Files.walkFileTree(self, walkOptions, 1, new SimpleFileVisitor<Path>() {
        // ... same visitor code
    })

    return result
}

This should be safe for cloud filesystems since:

1. Cloud storage doesn't have symlinks, so FOLLOW_LINKS is effectively a no-op
2. The S3 client already uses EnumSet.of(FileVisitOption.FOLLOW_LINKS) internally for downloads (S3Client.java:405)

Environment

• Nextflow version: master branch
• Affects both local and cloud file systems (local due to symlink issue, cloud due to workaround not being viable)