Workflow publish directive for channels can not take empty relative path

[siddharthab]

Bug report

Expected behavior and actual behavior

When using the new output feature, the root output directory is specified separately, and then each channel takes a relative path. There is currently no way to specify that the files should be written to the output directory directly. One could use '.', but that is a POSIX specific syntax and not valid syntax for cloud storage URLs like Google Cloud Storage.

I think this is just a side-effect of using the truthy-ness of the values to check whether to publish or not.

Steps to reproduce the problem

workflow {
  ch = Channel.fromPath('*')
  publish:
  ch >> ''
}

output {
  directory 'gs://my-cloud-path'
}

Program output

Program completes execution without the files being copied.

Environment

• Nextflow version: 24.04.4 build 5917
• Java version: OpenJDK Runtime Environment Zulu21.28+85-CA (build 21+35)
• Operating system: macOS
• Bash version: zsh 5.9 (arm64-apple-darwin24.0)

Additional context

[bentsherman]

You can configure the relative path in the output block:

workflow {
  ch = Channel.fromPath('*')
  publish:
  ch >> 'foo'
}

output {
  directory 'gs://my-cloud-path'

  'foo' {
    path '.'
  }
}

It works for both local and remote paths

[siddharthab]

It's the same issue. I think paths with . will need to be normalized in Nextflow for cloud storage paths. This is what I get with your suggestion:

java.lang.IllegalArgumentException: I/O not allowed on dot-dirs or extra slashes when !permitEmptyPathComponents: /sidb/workflow-test/sample/./sample.bam
        at com.google.common.base.Preconditions.checkArgument(Preconditions.java:218)
        at com.google.cloud.storage.contrib.nio.CloudStoragePath.toRealPathInternal(CloudStoragePath.java:195)
        at com.google.cloud.storage.contrib.nio.CloudStoragePath.toRealPath(CloudStoragePath.java:189)
        at com.google.cloud.storage.contrib.nio.CloudStoragePath.getBlobId(CloudStoragePath.java:84)
        at com.google.cloud.storage.contrib.nio.CloudStorageFileSystemProvider.copy(CloudStorageFileSystemProvider.java:561)
        at nextflow.file.FileHelper.copyPath(FileHelper.groovy:990)
        at nextflow.processor.PublishDir.processFileImpl(PublishDir.groovy:507)

[bentsherman]

Good catch, I thought these paths were being normalized but I guess not. I'll make a note to address this in #5185

[siddharthab]

Thank you! I will leave this issue open, but please feel free to close if you are tracking somewhere else.