publishDir enabled: false creates empty directory

[gsainsbury86]

Bug report

Creating a process with a publishDir enabled set to false will create the output directory anyway.

Expected behavior and actual behavior

• Expected behaviour would be that enabled: false would not create any files or directories.
• Actual behaviour is that an empty directory of that name is created.

Steps to reproduce the problem

process publishDirBug {
	publishDir 'out', enabled: false
	
	output:
	file("a.txt")
	
	script:
	"""
	touch a.txt
	"""

}

Program output

Execution does not fail.

Environment

• Nextflow version: nextflow version 19.10.0.5170
• Java version: java version "10.0.2" 2018-07-17
• Operating system: macOS 10.15.1 (19B88)

Additional context

It's possible this is a design choice, rather than a bug. My use case is in image processing. I have an optional output of intermediary images that I sometimes would like to produce. If I have one directory per image, there are potentially thousands of empty directories created.

[haqle314]

From what I can gather, the enabled param is checked too late. Simply checking
enabled earlier like this should do the trick. Is there anything that I
missed, @pditommaso?

// PublishDir.groovy:181
void apply( List<Path> files, Path sourceDir ) {
    // Check here instead of inside void apply(Path source, boolean inProcess)
    if( !files || !enabled )
        return
    this.sourceDir = sourceDir
    this.sourceFileSystem = sourceDir ? sourceDir.fileSystem : null
    apply0(files)
}

[pditommaso]

Well spotted, yes the patch suggested should do the trick.